1
|
Heimeier D, Garland EC, Eichenberger F, Garrigue C, Vella A, Baker CS, Carroll EL. A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Mol Ecol Resour 2024; 24:e13955. [PMID: 38520161 DOI: 10.1111/1755-0998.13955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 03/25/2024]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
Collapse
Affiliation(s)
- Dorothea Heimeier
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
| | - Ellen C Garland
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Franca Eichenberger
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Claire Garrigue
- UMR ENTROPIE, (IRD, Université de La Réunion, Université de la Nouvelle-Calédonie, IFREMER, CNRS, Laboratoire d'Excellence-CORAIL), Nouméa, New Caledonia
- Opération Cétacés, Nouméa, New Caledonia
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Corvallis, Oregon, USA
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
| |
Collapse
|
2
|
Abedin I, Mukherjee T, Kang HE, Yoon TH, Kim HW, Kundu S. Unraveling the unknown: Adaptive spatial planning to enhance climate resilience for the endangered Swamp Grass-babbler ( Laticilla cinerascens) with habitat connectivity and complexity approach. Heliyon 2024; 10:e30273. [PMID: 38694028 PMCID: PMC11061760 DOI: 10.1016/j.heliyon.2024.e30273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024] Open
Abstract
The endangered and poorly known Swamp Grass-babbler, Laticilla cinerascens (Passeriformes: Pellorneidae), confronts critical threats and vulnerability due to its specific habitat requirements and restricted populations in the northeastern region of the Indian Subcontinent. This study investigates the distribution of the species, habitat quality, geometry and shape complexity of connectivity among the protected areas (PAs), and responses to climate change in Northeast India under different climate change pathways by utilizing ensemble distribution models, and ecological metrics. From the total distribution extent (1,42,000 km2), approximately 9366 km2 (6.59 %) is identified as the suitable habitat for this threatened species. Historically centered around Dibru Saikhowa National Park (DSNP), the species faced a drastic decline due to anthropogenic activities and alteration in land use and lover cover. The study also reveals a significant decline in suitable habitat for L. cinerascens in future climate scenarios, with alarming reductions under SSP126 (>10 % in the timeframe 2041-2060 and > 30 % from 2061 to 2080), SSP245 (>90 % in both time periods), and SSP585 (>90 % in both timeframes) from the present scenario. At present, DSNP has the most suitable habitat within the distribution range but is projected to decline (>90 %) under more severe climate change scenarios, as observed in other PAs. Landscape fragmentation analysis indicates a shift in habitat geometry, highlighting the intricate impact of climate change. It predicts a substantial 343 % increase (in the SSP126) in small habitat patches in the future. Connectivity analysis among PAs shows a significant shift, with a decline exceeding 20 %. The analysis of shape complexity and connectivity geometry reveals a significant increase of over 220 % in the fragmentation of connectivity among PAs between 2061 and 2080 under the SSP585 climate change scenario compared to the present conditions. The study underscores the urgent need for conservation actions, emphasizing the complex interplay of climate change, habitat suitability, and fragmentation. Prioritizing PAs with suitable habitats and assessing their connectivity is crucial. Adaptive management strategies are essential to address ongoing environmental changes and safeguard biodiversity. Future research in critical areas is needed to establish long-term monitoring programs to lead/extend effective conservation strategies.
Collapse
Affiliation(s)
- Imon Abedin
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata, 700108, India
| | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata, 700108, India
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan, 48513, Republic of Korea
| | - Tae-Ho Yoon
- KNU LAMP Research Center, College of Natural Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Shantanu Kundu
- Institute of Fisheries Science, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| |
Collapse
|
3
|
Huang JP, Wu SP, Chen WY, Pham GJ, Kuan YH. Genomic data revealed inbreeding despite a geographically connected stable effective population size since the Holocene in the protected Formosan Long-Arm Scarab beetle, Cheirotonus formosanus. J Hered 2024; 115:292-301. [PMID: 38364316 DOI: 10.1093/jhered/esae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies.
Collapse
Affiliation(s)
- Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Ping Wu
- Department of Earth and Life Science, University of Taipei, Taipei, Taiwan
| | - Wei-Yun Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Guan Jie Pham
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
4
|
Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Cox-Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii). Mol Ecol 2024:e17362. [PMID: 38682494 DOI: 10.1111/mec.17362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
Collapse
Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Karah Cox-Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| |
Collapse
|
5
|
Dogantzis KA, Raffiudin R, Putra RE, Shaleh I, Conflitti IM, Pepinelli M, Roberts J, Holmes M, Oldroyd BP, Zayed A, Gloag R. Post-invasion selection acts on standing genetic variation despite a severe founding bottleneck. Curr Biol 2024; 34:1349-1356.e4. [PMID: 38428415 DOI: 10.1016/j.cub.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/12/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Invasive populations often have lower genetic diversity relative to the native-range populations from which they derive.1,2 Despite this, many biological invaders succeed in their new environments, in part due to rapid adaptation.3,4,5,6 Therefore, the role of genetic bottlenecks in constraining the adaptation of invaders is debated.7,8,9,10 Here, we use whole-genome resequencing of samples from a 10-year time-series dataset, representing the natural invasion of the Asian honey bee (Apis cerana) in Australia, to investigate natural selection occurring in the aftermath of a founding event. We find that Australia's A. cerana population was founded by as few as one colony, whose arrival was followed by a period of rapid population expansion associated with an increase of rare variants.11 The bottleneck resulted in a steep loss of overall genetic diversity, yet we nevertheless detected loci with signatures of positive selection during the first years post-invasion. When we investigated the origin of alleles under selection, we found that selection acted primarily on the variation introduced by founders and not on the variants that arose post-invasion by mutation. In all, our data highlight that selection on standing genetic variation can occur in the early years post-invasion, even where founding bottlenecks are severe.
Collapse
Affiliation(s)
- Kathleen A Dogantzis
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Rika Raffiudin
- IPB University, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor 16680, Indonesia
| | - Ramadhani Eka Putra
- Bandung Institute of Technology, School of Life Sciences and Technology, Bandung 40132, West Java, Indonesia
| | - Ismail Shaleh
- IPB University, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor 16680, Indonesia
| | - Ida M Conflitti
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Mateus Pepinelli
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - John Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Michael Holmes
- University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Benjamin P Oldroyd
- University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Amro Zayed
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Rosalyn Gloag
- University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia.
| |
Collapse
|
6
|
Taylor RS, Manseau M, Keobouasone S, Liu P, Mastromonaco G, Solmundson K, Kelly A, Larter NC, Gamberg M, Schwantje H, Thacker C, Polfus J, Andrew L, Hervieux D, Simmons D, Wilson PJ. High genetic load without purging in caribou, a diverse species at risk. Curr Biol 2024; 34:1234-1246.e7. [PMID: 38417444 DOI: 10.1016/j.cub.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/17/2023] [Accepted: 02/01/2024] [Indexed: 03/01/2024]
Abstract
High intra-specific genetic diversity is associated with adaptive potential, which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging of deleterious variation has been demonstrated in some threatened species. However, less is known about the costs of declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that are expected to undergo population declines. Caribou is a species of ecological and cultural significance in North America with a wide distribution supporting extensive phenotypic variation but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole-genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We found highly divergent levels of inbreeding across individuals, including the loss of alleles by drift but not increased purging in inbred individuals, which had more homozygous deleterious alleles. We also found comparable frequencies of homozygous deleterious alleles between lineages regardless of nucleotide diversity. Thus, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the "double-edged sword" of genetic diversity that may be representative of other species atrisk affected by anthropogenic activities.
Collapse
Affiliation(s)
- Rebecca S Taylor
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Micheline Manseau
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Sonesinh Keobouasone
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Peng Liu
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | | | - Kirsten Solmundson
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, ON K9L 1Z8, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Mary Gamberg
- Gamberg Consulting, Jarvis Street, Whitehorse, YK Y1A 2J2, Canada
| | - Helen Schwantje
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Caeley Thacker
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Jean Polfus
- Canadian Wildlife Service - Pacific Region, Environment and Climate Change Canada, 1238 Discovery Avenue, Kelowna, BC V1V 1V9, Canada
| | - Leon Andrew
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Dave Hervieux
- Alberta Ministry of Environment and Protected Areas, Government of Alberta, 10320-99 Street, Grande Prairie, AB T8V 6J4, Canada
| | - Deborah Simmons
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Paul J Wilson
- Biology Department, Trent University, East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| |
Collapse
|
7
|
Zhang W, Lin K, Fu W, Xie J, Fan X, Zhang M, Luo H, Yin Y, Guo Q, Huang H, Chen T, Lin X, Yuan Y, Huang C, Du S. Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey. Genes (Basel) 2024; 15:398. [PMID: 38674333 PMCID: PMC11049310 DOI: 10.3390/genes15040398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.
Collapse
Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - Kaixiong Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Wenyuan Fu
- Longyan Geopark Protection and Development Center, Longyan 364201, China
| | - Junjin Xie
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xueyang Fan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu 611830, China;
| | - Hongxing Luo
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Qiang Guo
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Tengteng Chen
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Xipan Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Cheng Huang
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| |
Collapse
|
8
|
Dickel L, Arcese P, Keller LF, Nietlisbach P, Goedert D, Jensen H, Reid JM. Multigenerational Fitness Effects of Natural Immigration Indicate Strong Heterosis and Epistatic Breakdown in a Wild Bird Population. Am Nat 2024; 203:411-431. [PMID: 38358807 DOI: 10.1086/728669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractThe fitness of immigrants and their descendants produced within recipient populations fundamentally underpins the genetic and population dynamic consequences of immigration. Immigrants can in principle induce contrasting genetic effects on fitness across generations, reflecting multifaceted additive, dominance, and epistatic effects. Yet full multigenerational and sex-specific fitness effects of regular immigration have not been quantified within naturally structured systems, precluding inference on underlying genetic architectures and population outcomes. We used four decades of song sparrow (Melospiza melodia) life history and pedigree data to quantify fitness of natural immigrants, natives, and their F1, F2, and backcross descendants and test for evidence of nonadditive genetic effects. Values of key fitness components (including adult lifetime reproductive success and zygote survival) of F1 offspring of immigrant-native matings substantially exceeded their parent mean, indicating strong heterosis. Meanwhile, F2 offspring of F1-F1 matings had notably low values, indicating surprisingly strong epistatic breakdown. Furthermore, magnitudes of effects varied among fitness components and differed between female and male descendants. These results demonstrate that strong nonadditive genetic effects on fitness can arise within weakly structured and fragmented populations experiencing frequent natural immigration. Such effects will substantially affect the net degree of effective gene flow and resulting local genetic introgression and adaptation.
Collapse
|
9
|
Zarzyczny KM, Rius M, Williams ST, Fenberg PB. The ecological and evolutionary consequences of tropicalisation. Trends Ecol Evol 2024; 39:267-279. [PMID: 38030539 DOI: 10.1016/j.tree.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Tropicalisation is a marine phenomenon arising from contemporary climate change, and is characterised by the range expansion of tropical/subtropical species and the retraction of temperate species. Tropicalisation occurs globally and can be detected in both tropical/temperate transition zones and temperate regions. The ecological consequences of tropicalisation range from single-species impacts (e.g., altered behaviour) to whole ecosystem changes (e.g., phase shifts in intertidal and subtidal habitats). Our understanding of the evolutionary consequences of tropicalisation is limited, but emerging evidence suggests that tropicalisation could induce phenotypic change as well as shifts in the genotypic composition of both expanding and retracting species. Given the rapid rate of contemporary climate change, research on tropicalisation focusing on shifts in ecosystem functioning, biodiversity change, and socioeconomic impacts is urgently needed.
Collapse
Affiliation(s)
- Karolina M Zarzyczny
- School of Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, UK; Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Marc Rius
- Centre for Advanced Studies of Blanes (CEAB), Consejo Superior de Investigaciones Científicas (CSIC), Accés a la Cala Sant Francesc 14, Blanes 17300, Spain; Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | | | - Phillip B Fenberg
- School of Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, UK; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| |
Collapse
|
10
|
Zhou Z, Liu F, Xu Y, Hu W. Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu. PLANTS (BASEL, SWITZERLAND) 2024; 13:618. [PMID: 38475465 DOI: 10.3390/plants13050618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024]
Abstract
Rubus chingii Hu is the only species that is used for both edible and medicinal purposes among the 194 species of the genus Rubus in China. It is well known for its sweet and sour fresh fruits that are rich in vitamins and for its dried immature fruits that are used to treat kidney-related ailments. This study aims to evaluate genetic diversity and population structure and build a core germplasm repository of 132 R. chingii accessions from the provinces of Jiangxi and Fujian, using Hyper-seq-derived single-nucleotide polymorphism (SNP) markers. This is the first genetic study of R. chingii based on SNP molecular markers, and a total of 1,303,850 SNPs and 433,159 insertions/deletions (InDels) were identified. Low values for observed heterozygosity, nucleotide diversity (Pi) and fixation indexes (Fis) indicated low genetic diversity within populations, and an analysis of molecular variance (AMOVA) showed that 37.4% and 62.6% of the variations were found between populations and within samples, respectively. Four main clusters were identified by means of neighbor-joining (NJ) trees, the ADMIXTURE program and principal component analysis (PCA). Based on the genetic diversity, we finally constructed 38 representative core collections, representing 50% of the total core germplasm samples and 95.3% of the genotypes. In summary, the results of our study can provide valuable information on the genetic structure of R. chingii germplasm resources, which is helpful for further explorations of potential high-quality genes and for formulating future breeding and conservation strategies.
Collapse
Affiliation(s)
- Ziwei Zhou
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China
| | - Yanqin Xu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Weiming Hu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| |
Collapse
|
11
|
Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
Collapse
Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| |
Collapse
|
12
|
Wolf M, Greve C, Schell T, Janke A, Schmitt T, Pauls SU, Aspöck H, Aspöck U. The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils. J Hered 2024; 115:112-119. [PMID: 37988623 PMCID: PMC10838129 DOI: 10.1093/jhered/esad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.
Collapse
Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Carola Greve
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tilman Schell
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, Müncheberg, Germany
- Entomology and Biogeography, Faculty of Science, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Steffen U Pauls
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Insects Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- Department of Entomology, Natural History Museum Vienna, Vienna, Austria
| |
Collapse
|
13
|
de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
Collapse
Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
| |
Collapse
|
14
|
Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone ( Haliotis cracherodii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577275. [PMID: 38352393 PMCID: PMC10862700 DOI: 10.1101/2024.01.26.577275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species' designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
Collapse
Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Karah Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| |
Collapse
|
15
|
Pegueroles C, Pascual M, Carreras C. Going beyond a reference genome in conservation genomics. Trends Ecol Evol 2024; 39:13-15. [PMID: 38040545 DOI: 10.1016/j.tree.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
The current biodiversity crisis demands scientifically based management. The generation of reference genomes is crucial in conservation, but is not enough to capture species diversity. By incorporating whole-genome sequencing (WGS) at the population level, Nigenda-Morales et al. provide key genomic information for the conservation of fin whale populations in the Pacific.
Collapse
Affiliation(s)
- Cinta Pegueroles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain.
| |
Collapse
|
16
|
Kardos M. Genomes of an endangered rattlesnake show that neutral genetic variation predicts adaptive genetic variation and genetic load. Proc Natl Acad Sci U S A 2023; 120:e2316880120. [PMID: 38011578 PMCID: PMC10710039 DOI: 10.1073/pnas.2316880120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
- Marty Kardos
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA98112
| |
Collapse
|
17
|
Pinsky ML, Clark RD, Bos JT. Coral Reef Population Genomics in an Age of Global Change. Annu Rev Genet 2023; 57:87-115. [PMID: 37384733 DOI: 10.1146/annurev-genet-022123-102748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.
Collapse
Affiliation(s)
- Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA;
| | - René D Clark
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| | - Jaelyn T Bos
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| |
Collapse
|
18
|
Trieu LN, Bich TT, Van Ket N, Van Long N. Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d'Orbigny) in Con Dao and Phu Quoc islands, Vietnam. J Genet Eng Biotechnol 2023; 21:116. [PMID: 37955754 PMCID: PMC10643773 DOI: 10.1186/s43141-023-00573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Bigfin squid is one of the economically important seafood resources in Vietnam's fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box-derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. RESULTS Con Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. CONCLUSIONS For the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.
Collapse
Affiliation(s)
- Le Ngoc Trieu
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam.
| | - Thai Thach Bich
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam
| | - Nguyen Van Ket
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam
| | - Nguyen Van Long
- Institute of Oceanography, Vietnam Academy of Science and Technology (VAST), Khanh Hoa, Vietnam
- Graduated University of Science and Technology (GUST), VAST, Ha Noi, Vietnam
| |
Collapse
|
19
|
Choquet M, Lenner F, Cocco A, Toullec G, Corre E, Toullec JY, Wallberg A. Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill. Mol Biol Evol 2023; 40:msad225. [PMID: 37816123 PMCID: PMC10642690 DOI: 10.1093/molbev/msad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.
Collapse
Affiliation(s)
- Marvin Choquet
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Felix Lenner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Arianna Cocco
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erwan Corre
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Yves Toullec
- CNRS, UMR 7144, AD2M, Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
20
|
Bazzicalupo E, Ratkiewicz M, Seryodkin IV, Okhlopkov I, Galsandorj N, Yarovenko YA, Ozolins J, Saveljev AP, Melovski D, Gavashelishvili A, Schmidt K, Godoy JA. Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivore Lynx lynx (Linnaeus, 1758). Evol Appl 2023; 16:1773-1788. [PMID: 38029067 PMCID: PMC10681490 DOI: 10.1111/eva.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 12/01/2023] Open
Abstract
Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north-western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre-adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate.
Collapse
Affiliation(s)
- Enrico Bazzicalupo
- Department of Ecology and EvolutionEstación Biológica de Doñana (CSIC)SevilleSpain
| | | | - Ivan V. Seryodkin
- Laboratory of Ecology and Conservation of AnimalsPacific Institute of Geography of Far East Branch of Russian Academy of SciencesVladivostokRussia
| | - Innokentiy Okhlopkov
- Institute for Biological Problems of CryolithozoneSiberian Branch of the Russian Academy of SciencesYakutskRussia
| | | | - Yuriy A. Yarovenko
- Pre‐Caspian Institute of Biological ResourcesDagestan Federal Scientific Centre of RASMakhachkalaRussia
| | - Janis Ozolins
- Department of Hunting and Wildlife ManagementLatvijas Valsts mežzinātnes institūts "Silava"SalaspilsLatvia
| | - Alexander P. Saveljev
- Department of Animal EcologyRussian Research Institute of Game Management and Fur FarmingKirovRussia
| | - Dime Melovski
- Macedonian Ecological Society (MES)SkopjeNorth Macedonia
| | | | | | - José A. Godoy
- Department of Ecology and EvolutionEstación Biológica de Doñana (CSIC)SevilleSpain
| |
Collapse
|
21
|
Chambers EA, Bishop AP, Wang IJ. Individual-based landscape genomics for conservation: An analysis pipeline. Mol Ecol Resour 2023. [PMID: 37883295 DOI: 10.1111/1755-0998.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/18/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.
Collapse
Affiliation(s)
- E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Anusha P Bishop
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| |
Collapse
|
22
|
Mathur S, Mason AJ, Bradburd GS, Gibbs HL. Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. Proc Natl Acad Sci U S A 2023; 120:e2303043120. [PMID: 37844221 PMCID: PMC10614936 DOI: 10.1073/pnas.2303043120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future.
Collapse
Affiliation(s)
- Samarth Mathur
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
| | - Andrew J. Mason
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
| | - Gideon S. Bradburd
- Evolution and Behavior Program, Department of Integrative Biology, Ecology, Michigan State University, East Lansing, MI48824
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI48109
| | - H. Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
| |
Collapse
|
23
|
Martchenko D, Shafer ABA. Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study. Heredity (Edinb) 2023; 131:273-281. [PMID: 37532838 PMCID: PMC10539292 DOI: 10.1038/s41437-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023] Open
Abstract
Genomes capture the adaptive and demographic history of a species, but the choice of sequencing strategy and sample size can impact such inferences. We compared whole genome and reduced representation sequencing approaches to study the population demographic and adaptive signals of the North American mountain goat (Oreamnos americanus). We applied the restriction site-associated DNA sequencing (RADseq) approach to 254 individuals and whole genome resequencing (WGS) approach to 35 individuals across the species range at mid-level coverage (9X) and to 5 individuals at high coverage (30X). We used ANGSD to estimate the genotype likelihoods and estimated the effective population size (Ne), population structure, and explicitly modelled the demographic history with δaδi and MSMC2. The data sets were overall concordant in supporting a glacial induced vicariance and extremely low Ne in mountain goats. We evaluated a set of climatic variables and geographic location as predictors of genetic diversity using redundancy analysis. A moderate proportion of total variance (36% for WGS and 21% for RADseq data sets) was explained by geography and climate variables; both data sets support a large impact of drift and some degree of local adaptation. The empirical similarities of WGS and RADseq presented herein reassuringly suggest that both approaches will recover large demographic and adaptive signals in a population; however, WGS offers several advantages over RADseq, such as inferring adaptive processes and calculating runs-of-homozygosity estimates. Considering the predicted climate-induced changes in alpine environments and the genetically depauperate mountain goat, the long-term adaptive capabilities of this enigmatic species are questionable.
Collapse
Affiliation(s)
- Daria Martchenko
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics & Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| |
Collapse
|
24
|
Kundu S, Mukherjee T, Kamalakannan M, Barhadiya G, Ghosh C, Kim HW. Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle ( Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences. PeerJ 2023; 11:e15975. [PMID: 37692114 PMCID: PMC10492536 DOI: 10.7717/peerj.15975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021-2040 and 2061-2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins.
Collapse
Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan, South Korea
| | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata, West Bengal, India
| | | | - Gaurav Barhadiya
- Department of Environmental Studies, University of Delhi, New Delhi, New Delhi, India
| | - Chirashree Ghosh
- Department of Environmental Studies, University of Delhi, New Delhi, New Delhi, India
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan, South Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, South Korea
| |
Collapse
|
25
|
Li Y, Cui M, Le X, Gong J, Jiang K, Tong X, Zhang Q, Li J, Li H, Lu L, Zou J, Wang R, Chen X. Genetic structure shows the presence of small-scale management units in a relict tree species. Ecol Evol 2023; 13:e10500. [PMID: 37706160 PMCID: PMC10495812 DOI: 10.1002/ece3.10500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Identifying conservation units is crucial for the effective conservation of threatened species. Previous cases are almost exclusively based on large-scale but coarse sampling for genetic structure analyses. Significant genetic structure can occur within a small range, and thus multiple conservation units may exist in narrowly distributed plants. However, small-scale genetic structure is often overlooked in conservation planning especially for wind-pollinated and wind-dispersed trees, largely due to the absence of dense and elaborate sampling. In this study, we focused on a representative endangered relict plant, Metasequoia glyptostroboides. Using both nuclear microsatellites (nSSRs) and chloroplast DNA (cpDNA) fragments, we sampled across the narrow distribution range of this species and determined its conservation units by exploring its genetic structure and historical demography. cpDNA haplotypes were classified into two groups, but mixed in space, suggesting that the existent wild trees of M. glyptostroboides cannot be divided into different evolutionarily significant units. However, using nSSRs, we detected strong spatial genetic structure, with significant genetic differentiation and weak gene flow between the samples in the east of the species' distribution range and other samples. The divergence between the two nSSR groups was dated to the Last Glacial Maximum (c. 19.6 kya), suggesting that such spatial genetic structure has been maintained for a long term. Therefore, these two nSSR groups should be considered as different conservation units, that is, management units, to protect intergroup genetic variations, which is likely to be the outputs of local adaptation. Our findings highlight the necessity to reveal small-scale genetic structure and population demography to improve the conservation strategies of evolutionary potential of endangered plants.
Collapse
Affiliation(s)
- Yuan‐Yuan Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Institute of Eco‐Chongming (IEC)ShanghaiChina
| | - Min‐Yan Cui
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Xiao‐Wei Le
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Jun Gong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Kai Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
| | - Xin Tong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
| | - Qian Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Jia‐Hui Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Hong‐Yue Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Ling Lu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Jie Zou
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Shanghai Engineering Research Center of Sustainable Plant InnovationShanghaiChina
- Shanghai Institute of Pollution Control and Ecological SecurityShanghaiChina
| | - Xiao‐Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco‐Restoration, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Shanghai Engineering Research Center of Sustainable Plant InnovationShanghaiChina
- Shanghai Institute of Pollution Control and Ecological SecurityShanghaiChina
| |
Collapse
|
26
|
Rougemont Q, Leroy T, Rondeau EB, Koop B, Bernatchez L. Allele surfing causes maladaptation in a Pacific salmon of conservation concern. PLoS Genet 2023; 19:e1010918. [PMID: 37683018 PMCID: PMC10545117 DOI: 10.1371/journal.pgen.1010918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 10/02/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations, is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.
Collapse
Affiliation(s)
- Quentin Rougemont
- Centre d’Ecologie Fonctionnelle et Evolutive, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Auzeville- Tolosane, France
| | - Eric B. Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, Canada
| | - Ben Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| |
Collapse
|
27
|
Zhang J, Wang S, Xu C, Wang S, Du J, Niu M, Yang J, Li Y. Pathogenic selection promotes adaptive immune variations against serious bottlenecks in early invasions of bullfrogs. iScience 2023; 26:107316. [PMID: 37539025 PMCID: PMC10393753 DOI: 10.1016/j.isci.2023.107316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/22/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Adaptive genetic variations are key for understanding evolutionary processes influencing invasions. However, we have limited knowledge on how adaptive genetic diversity in invasive species responds to new pathogenic environments. Here, we compared variations in immune major histocompatibility complex (MHC) class-II β gene and neutral loci in relation to pathogenic chytrid fungus (Batrachochytrium dendrobatidis, Bd) infection across invasive and native populations of American bullfrog between China and United States (US). Chinese invasive populations show a 60% reduction in neutral cytb variations relative to US native populations, and there were similar MHC variation and functional diversity between them. One MHC allele private to China was under recent positive selection and associated with decreased Bd infection, partly explaining the lower Bd prevalence for Chinese populations than for native US populations. These results suggest that pathogen-mediated selection favors adaptive MHC variations and functional diversity maintenance against serious bottlenecks during the early invasions (within 15 generations) of bullfrogs.
Collapse
Affiliation(s)
- Jiaqi Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
| | - Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
| | - Siqi Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
| | - Jiacong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Meiling Niu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Jiaxue Yang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| |
Collapse
|
28
|
Tan HZ, Jansen JJFJ, Allport GA, Garg KM, Chattopadhyay B, Irestedt M, Pang SEH, Chilton G, Gwee CY, Rheindt FE. Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds. eLife 2023; 12:e85422. [PMID: 37549057 PMCID: PMC10406428 DOI: 10.7554/elife.85422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/27/2023] [Indexed: 08/09/2023] Open
Abstract
Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.
Collapse
Affiliation(s)
- Hui Zhen Tan
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | | | | | - Kritika M Garg
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Sean EH Pang
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Glen Chilton
- Department of Biology, St. Mary's UniversityCalgaryCanada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| |
Collapse
|
29
|
Aliaga-Samanez GG, Bulhões Javarotti N, Orecife G, Chávez-Congrains K, Pissinatti A, Monticelli C, Cristina Marques M, Galbusera P, Galetti PM, Domingues de Freitas P. Genetic diversity in ex situ populations of the endangered Leontopithecus chrysomelas and implications for its conservation. PLoS One 2023; 18:e0288097. [PMID: 37531319 PMCID: PMC10395972 DOI: 10.1371/journal.pone.0288097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Leontopithecus chrysomelas, the Golden-headed Lion Tamarin (GHLT), is an endangered and endemic Neotropical primate from the Atlantic Forest of Brazil that has suffered a reduction of its habitat and population size in the wild. Ex situ populations have been established as a relevant alternative to safeguard the species and retain its genetic diversity and evolutionary potential. This study evaluated the genetic diversity and structure of the two main Brazilian captive populations of GHLT, which have been under human care at the Primatology Center of Rio de Janeiro (CPRJ) and the Zoological Park Foundation of São Paulo (FPZSP). Our results revealed levels of genetic diversity overall comparable to those observed for other Leontopithecus species and for ex situ and in situ populations of GHLT previously studied. Bayesian and principal coordinate analyses showed a moderate differentiation between CPRJ and FPZSP populations. Both populations presented observed heterozygosity values higher than expected heterozygosity values for most of the microsatellites used in this study, suggesting that the management has been efficient in avoiding an increase in homozygosity. However, simulations point to a significant loss of genetic diversity in the next 100 years, mainly in the FPZSP population. Such data are relevant for further decision-making on the metapopulation management of L. chrysomelas in captive conditions and for integrating in situ and ex situ conservation plans.
Collapse
Affiliation(s)
| | | | - Gisele Orecife
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Karla Chávez-Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Guapimirim, Rio de Janeiro, Brazil
| | - Cauê Monticelli
- Departamento de Conservação e Pesquisas Aplicadas, Coordenadoria de Fauna Silvestre, Secretaria de Meio Ambiente, Infraestrutura e Logística do Estado de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Peter Galbusera
- Antwerp Zoo Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | |
Collapse
|
30
|
Li Y, Xia M, Zhao X, Hou H. Water temperature and chlorophyll a density drive the genetic and epigenetic variation of Vallisneria natans across a subtropical freshwater lake. Ecol Evol 2023; 13:e10434. [PMID: 37589037 PMCID: PMC10425707 DOI: 10.1002/ece3.10434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/08/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023] Open
Abstract
Plant genetic diversity differs in habitat's oscillations, especially species distributed under heterogeneous environmental conditions. Freshwater ecosystems are vulnerable to biotic and abiotic impacts, which affect the genetic and epigenetic variations in aquatic plants. The extent of environmental heterogeneous attributes can be examined based on genetic and epigenetic variations. Such variations under environmental gradient can provide evidence for understanding the correlations between rapid environmental changes and species evolution. In this study, we performed amplified fragment polymorphism length and methylated-sensitive amplified polymorphism analysis to depict the genetic and epigenetic variations of Vallisneria natans in a subtropical lake. Results showed that this species maintained a relatively high genetic diversity (mean H E = 0.320, I = 0.474, PPL = 85.93%) and epigenetic variation (mean eH E = 0.282, eI = 0.428, ePPL = 83.91%). Water body temperature and chlorophyll a density were positively correlated to the genetic and epigenetic variations. The clonal generates of V. natans depicted a relative high methylation level and shew ancestral scenario between the genet and the second clonal generation. These findings revealed that species diversity is unevenly distributed under environmental heterogeneity, even at a fine geographic scale. Environmental characteristics in relation to temperature and chlorophyll a should be considered in the analysis of the genetic and epigenetic variations. Additionally, epigenetic variations between genets and ramets should be considered with caution when applied to analysis of other aquatic species.
Collapse
Affiliation(s)
- Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
31
|
Bouhali A, Homrani A, Ferrand N, Lopes S, Emam AM. Assessment of genetic diversity among native Algerian rabbit populations using microsatellite markers. Arch Anim Breed 2023; 66:207-215. [PMID: 37560355 PMCID: PMC10407306 DOI: 10.5194/aab-66-207-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
Having higher adaptability against abiotic stress, which is characterized in rural areas in developing countries, local farm animal genetic resources (FAGRs) are increasingly precarious for random and unsystematic crossing with exotic breeds. In this study, 85 microsatellite loci were utilized to assess genetic diversity among native Algerian rabbits (NARs) sampled from an area of 753 km (from north to south) and 919 km (from east to west). Those distances covered 25 significant geographical points in seven rural areas (El Taref, Mostaganem, Sidi Bel Abbès, M'Sila, Dar Chioukh, Faidh El Botma, and Laghouat). A total of 558 alleles were observed in this study. The highest genetic diversity was registered in the southern direction among NAR populations. The mean number of alleles per locus (MNa) and the inbreeding coefficient (F IS ) were highest in Laghouat (4.482 and 0.232), while they were lowest in El Taref (4.000 and 0.149). In the current study, the number of private alleles (Pa) ranged from 9 to 23. In addition, the average of observed heterozygosity (0.427) was lower than the expected value (0.524) due to high levels of inbreeding. The discriminant analysis of principal components (DAPC), the neighbor-joining tree (NJ), and the analysis of STRUCTURE software confirmed the classification of populations according to geographical zones into four main groups (east, west, south, and middle). The results of the current study are useful for breeding improvement and conservation plan research in relation to local animal genetic resources in Algeria.
Collapse
Affiliation(s)
- Abdelbaki Bouhali
- Laboratory of Sciences and Technics for Animal Production (LSTAP),
Department of Agronomic Sciences, Faculty of Nature Sciences and Life,
Abdelhamid Ibn Badis Mostaganem University, Mostaganem, Algeria
- École Normale Supérieur Taleb abderrahmane Laghouat, Laghouat,
4033, Algeria
| | - Abdelkader Homrani
- Laboratory of Sciences and Technics for Animal Production (LSTAP),
Department of Agronomic Sciences, Faculty of Nature Sciences and Life,
Abdelhamid Ibn Badis Mostaganem University, Mostaganem, Algeria
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigacao em Biodiversidade e Recursos
Geneticos, Campus Agrario de Vairao, Universidade do Porto, 4485-661,
Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciencias, Universidade do
Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Susana Lopes
- CIBIO/InBIO, Centro de Investigacao em Biodiversidade e Recursos
Geneticos, Campus Agrario de Vairao, Universidade do Porto, 4485-661,
Vairão, Portugal
| | - Ahmed Mostafa Emam
- Animal Production Research Institute, Agricultural Research Centre,
Ministry of Agriculture, Nadi El Saiid street, 12618, Dokkii, Giza, Egypt
| |
Collapse
|
32
|
Aung KM, Oo WH, Maung TZ, Min MH, Somsri A, Nam J, Kim KW, Nawade B, Lee CY, Chu SH, Park YJ. Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1225445. [PMID: 37560030 PMCID: PMC10407808 DOI: 10.3389/fpls.2023.1225445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.
Collapse
Affiliation(s)
- Kyaw Myo Aung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Win Htet Oo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Jungrye Nam
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Kyu-Won Kim
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Bhagwat Nawade
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan, Republic of Korea
| | - Sang-Ho Chu
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| |
Collapse
|
33
|
Kundu S, Kamalakannan M, Kim AR, Hegde VD, Banerjee D, Jung WK, Kim YM, Kim HW. Morphology and Mitochondrial Lineage Investigations Corroborate the Systematic Status and Pliocene Colonization of Suncus niger (Mammalia: Eulipotyphla) in the Western Ghats Biodiversity Hotspot of India. Genes (Basel) 2023; 14:1493. [PMID: 37510398 PMCID: PMC10379166 DOI: 10.3390/genes14071493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
The Indian highland shrew, Suncus niger (Horsfield, 1851), is the least studied soricid species from its original range distribution in Southern India, with several systematics conundrums. Following its discovery in 1851, the species was synonymized with Suncus montanus (Kelaart, 1850) (endemic to Sri Lanka) and subsequently identified as a separate Indian population. However, the systematic status of S. niger from topotype specimens in Southern India has yet to be determined through an integrated approach. Both taxonomy and mitochondrial genetic data (Cytochrome b and 16S ribosomal RNA) were used to re-examine the systematics of S. niger. The mtCytb gene clearly distinguished topotypic S. niger from other Suncus species, with high genetic divergences varying from 8.49% to 26.29%. Further, the Bayesian and maximum likelihood topologies clearly segregated S. niger from other congeners and corroborated the sister relationship with S. stoliczkanus with expected divergence in the late Pliocene (2.62 MYA). The TimeTree analysis also exhibits a strong matrilineal affinity of S. dayi (endemic to India) toward the African species. The current study hypothesizes that the ancestor of the soricids evolved in Africa and that genetic lineages were subsequently shifted by plate tectonic events that subsequently colonized different continents as distinct species during the late Miocene (Tortonian) to the Holocene era. In addition to the new range expansion and elevation records of S. niger in the Central Western Ghats, we propose that additional sampling across its distribution, as well as the use of multiple genetic markers, may be useful in determining the genetic diversity and population structure of this endemic species. The present study also recommends that more molecular data on the Soricomorphs lineages, and estimates of their divergence times, will shed light on the evolution of these small mammals on Earth.
Collapse
Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Manokaran Kamalakannan
- Mammal and Osteology Section, Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
| | - Ah Ran Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Vishwanath D Hegde
- Mammal and Osteology Section, Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
| | - Dhriti Banerjee
- Mammal and Osteology Section, Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
| | - Won-Kyo Jung
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| |
Collapse
|
34
|
Whitney JL, Coleman RR, Deakos MH. Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays. BMC Ecol Evol 2023; 23:31. [PMID: 37422622 PMCID: PMC10329317 DOI: 10.1186/s12862-023-02130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 06/07/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Reef manta rays (Mobula alfredi) are globally distributed in tropical and subtropical seas. Their life history traits (slow growth, late maturity, low reproductive output) make them vulnerable to perturbations and therefore require informed management strategies. Previous studies have reported wide-spread genetic connectivity along continental shelves suggesting high gene flow along continuous habitats spanning hundreds of kilometers. However, in the Hawaiian Islands, tagging and photo-identification evidence suggest island populations are isolated despite proximity, a hypothesis that has not yet been evaluated with genetic data. RESULTS This island-resident hypothesis was tested by analyzing whole mitogenome haplotypes and 2048 nuclear single nucleotide polymorphisms (SNPs) between M. alfredi (n = 38) on Hawai'i Island and Maui Nui (the 4-island complex of Maui, Moloka'i, Lāna'i and Kaho'olawe). Strong divergence in the mitogenome (ΦST = 0.488) relative to nuclear genome-wide SNPs (neutral FST = 0.003; outlier FST = 0.186), and clustering of mitochondrial haplotypes among islands provides robust evidence that female reef manta rays are strongly philopatric and do not migrate between these two island groups. Combined with restricted male-mediated migration, equivalent to a single male moving between islands every 2.2 generations (~ 64 years), we provide evidence these populations are significantly demographically isolated. Estimates of contemporary effective population size (Ne) are 104 (95% CI: 99-110) in Hawai'i Island and 129 (95% CI: 122-136) in Maui Nui. CONCLUSIONS Concordant with evidence from photo identification and tagging studies, these genetic results indicate reef manta rays in Hawai'i have small, genetically-isolated resident island populations. We hypothesize that due to the Island Mass Effect, large islands provide sufficient resources to support resident populations, thereby making crossing deep channels separating island groups unnecessary. Small effective population size, low genetic diversity, and k-selected life history traits make these isolated populations vulnerable to region-specific anthropogenic threats, which include entanglement, boat strikes, and habitat degradation. The long-term persistence of reef manta rays in the Hawaiian Islands will require island-specific management strategies.
Collapse
Affiliation(s)
- Jonathan L Whitney
- National Oceanic and Atmospheric Administration, Pacific Islands Fisheries Science Center, Honolulu, Hawai'i, USA.
| | - Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - Mark H Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, Maui, Hawai'i, USA
| |
Collapse
|
35
|
Johnson JA, Athrey G, Anderson CM, Bell DA, Dixon A, Kumazawa Y, Maechtle T, Meeks GW, Mindell D, Nakajima K, Novak B, Talbot S, White C, Zhan X. Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies. Ecol Evol 2023; 13:e10347. [PMID: 37484928 PMCID: PMC10361364 DOI: 10.1002/ece3.10347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
In efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The assumption that all small populations require measures to increase their genetic diversity may be unwarranted, and limited resources for conservation may be better utilized elsewhere. We test this assumption in a case study focused on the peregrine falcon (Falco peregrinus), a cosmopolitan circumpolar species with 19 named subspecies. We used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies. Our analyses revealed extensive variation among subspecies, with many island-restricted and nonmigratory populations possessing lower overall genomic diversity, elevated inbreeding coefficients (F ROH)-among the highest reported, and extensive runs of homozygosity (ROH) compared to mainland and migratory populations. Similarly, the majority of subspecies that are either nonmigratory or restricted to islands show a much longer history of low effective population size (N e). While mutational load analyses indicated an increased proportion of homozygous-derived deleterious variants (i.e., drift load) among nonmigrant and island populations compared to those that are migrant or reside on the mainland, no significant differences in the proportion of heterozygous deleterious variants (i.e., inbreeding load) was observed. Our results provide evidence that high levels of inbreeding may not be an existential threat for some populations or taxa. Additional factors such as the timing and severity of population declines are important to consider in management decisions about extinction potential.
Collapse
Affiliation(s)
- Jeff A. Johnson
- Department of Biological SciencesUniversity of North TexasDentonTexasUSA
- Wolf Creek Operating FoundationWolfWyomingUSA
| | - Giridhar Athrey
- Department of Poultry Science & Faculty of Ecology and Evolutionary BiologyTexas A&M UniversityCollege StationTexasUSA
| | | | - Douglas A. Bell
- East Bay Regional Park DistrictOaklandCaliforniaUSA
- California Academy of SciencesSan FranciscoCaliforniaUSA
| | - Andrew Dixon
- The Mohamed Bin Zayed Raptor Conservation FundAbu DhabiUnited Arab Emirates
- International Wildlife ConsultantsCarmarthenUK
| | - Yoshinori Kumazawa
- Research Center for Biological DiversityNagoya City UniversityNagoyaJapan
| | | | - Garrett W. Meeks
- Department of Biological SciencesUniversity of North TexasDentonTexasUSA
| | - David Mindell
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Keiya Nakajima
- Research Center for Biological DiversityNagoya City UniversityNagoyaJapan
- The Japan Falconiformes CenterOwariasahiJapan
| | - Ben Novak
- Revive & RestoreSausalitoCaliforniaUSA
| | - Sandra Talbot
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
| | | | | |
Collapse
|
36
|
Santos AS, Cazetta E, Faria D, Lima TM, Lopes MTG, Carvalho CDS, Alves‐Pereira A, Morante‐Filho JC, Gaiotto FA. Tropical forest loss and geographic location drive the functional genomic diversity of an endangered palm tree. Evol Appl 2023; 16:1257-1273. [PMID: 37492151 PMCID: PMC10363835 DOI: 10.1111/eva.13525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 07/27/2023] Open
Abstract
Human activity has diminished forests in different terrestrial ecosystems. This is well illustrated in the Brazilian Atlantic Forest, which still hosts high levels of species richness and endemism, even with only 28% of its original extent remaining. The consequences of such forest loss in remaining populations can be investigated with several approaches, including the genomic perspective, which allows a broader understanding of how human disturbance influences the genetic variability in natural populations. In this context, our study investigated the genomic responses of Euterpe edulis Martius, an endangered palm tree, in forest remnants located in landscapes presenting different forest cover amount and composed by distinct bird assemblage that disperse its seeds. We sampled 22 areas of the Brazilian Atlantic Forest in four regions using SNP markers inserted into transcribed regions of the genome of E. edulis, distinguishing neutral loci from those putatively under natural selection (outlier). We demonstrate that populations show patterns of structure and genetic variability that differ between regions, as a possible reflection of deforestation and biogeographic histories. Deforested landscapes still maintain high neutral genetic diversity due to gene flow over short distances. Overall, we not only support previous evidence with microsatellite markers, but also show that deforestation can influence the genetic variability outlier, in the scenario of selective pressures imposed by these stressful environments. Based on our findings, we suggest that, to protect genetic diversity in the long term, it is necessary to reforest and enrich deforested areas, using seeds from populations in the same management target region.
Collapse
Affiliation(s)
- Alesandro Souza Santos
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Eliana Cazetta
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Deborah Faria
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Thâmara Moura Lima
- Instituto Federal de Educação, Ciência e Tecnologia da Bahia – Campus SeabraSeabraBrazil
| | | | | | | | - José Carlos Morante‐Filho
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Fernanda Amato Gaiotto
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
| |
Collapse
|
37
|
Lauterbur ME, Cavassim MIA, Gladstein AL, Gower G, Pope NS, Tsambos G, Adrion J, Belsare S, Biddanda A, Caudill V, Cury J, Echevarria I, Haller BC, Hasan AR, Huang X, Iasi LNM, Noskova E, Obsteter J, Pavinato VAC, Pearson A, Peede D, Perez MF, Rodrigues MF, Smith CCR, Spence JP, Teterina A, Tittes S, Unneberg P, Vazquez JM, Waples RK, Wohns AW, Wong Y, Baumdicker F, Cartwright RA, Gorjanc G, Gutenkunst RN, Kelleher J, Kern AD, Ragsdale AP, Ralph PL, Schrider DR, Gronau I. Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations. eLife 2023; 12:RP84874. [PMID: 37342968 DOI: 10.7554/elife.84874] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.
Collapse
Affiliation(s)
- M Elise Lauterbur
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
| | - Maria Izabel A Cavassim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States
| | | | - Graham Gower
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathaniel S Pope
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Georgia Tsambos
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Jeffrey Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
- Ancestry DNA, San Francisco, United States
| | - Saurabh Belsare
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | | | - Victoria Caudill
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Jean Cury
- Universite Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numerique, Orsay, France
| | | | - Benjamin C Haller
- Department of Computational Biology, Cornell University, Ithaca, United States
| | - Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
| | - Xin Huang
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | | | - Ekaterina Noskova
- Computer Technologies Laboratory, ITMO University, St Petersburg, Russian Federation
| | - Jana Obsteter
- Agricultural Institute of Slovenia, Department of Animal Science, Ljubljana, Slovenia
| | | | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - David Peede
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, United States
- Center for Computational Molecular Biology, Brown University, Providence, United States
| | - Manolo F Perez
- Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos, Brazil
| | - Murillo F Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Chris C R Smith
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Jeffrey P Spence
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Anastasia Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
| | - Ryan K Waples
- Department of Biostatistics, University of Washington, Seattle, United States
| | | | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Franz Baumdicker
- Cluster of Excellence - Controlling Microbes to Fight Infections, Eberhard Karls Universit¨at Tubingen, Tubingen, Germany
| | - Reed A Cartwright
- School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, United States
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Andrew D Kern
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
| | - Aaron P Ragsdale
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, United States
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, United States
- Department of Mathematics, University of Oregon, Eugene, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel
| |
Collapse
|
38
|
Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
Collapse
Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
39
|
Bercovitch FB. Conservation and evolution: Inbreeding, small populations, and sex differences in life history. Primates 2023; 64:277-283. [PMID: 37145305 DOI: 10.1007/s10329-023-01069-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Affiliation(s)
- Fred B Bercovitch
- Wildlife Research Center, Kyoto, Japan.
- Anne Innis Dagg Foundation, Toronto, Canada.
| |
Collapse
|
40
|
Wilder AP, Supple MA, Subramanian A, Mudide A, Swofford R, Serres-Armero A, Steiner C, Koepfli KP, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK, Ryder OA, Shapiro B, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. The contribution of historical processes to contemporary extinction risk in placental mammals. Science 2023; 380:eabn5856. [PMID: 37104572 PMCID: PMC10184782 DOI: 10.1126/science.abn5856] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.
Collapse
Affiliation(s)
- Aryn P Wilder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | | | | | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Aitor Serres-Armero
- Institute of Evolutionary Biology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Cynthia Steiner
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 30008, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
| | | | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 32, Sweden
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
- Catalan Institution of Research and Advanced Studies, Barcelona 08010, Spain
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Violeta Munoz Fuentes
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kathleen Foley
- College of Law, University of Iowa, Iowa City, IA 52242, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Department of Evolution, Behavior and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92039, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Kundu S, De Alwis PS, Binarao JD, Lee SR, Kim AR, Gietbong FZ, Yi M, Kim HW. Mitochondrial DNA Corroborates the Genetic Variability of Clarias Catfishes (Siluriformes, Clariidae) from Cameroon. Life (Basel) 2023; 13:life13051068. [PMID: 37240713 DOI: 10.3390/life13051068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/07/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries.
Collapse
Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Piyumi S De Alwis
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Jerome D Binarao
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo-Rin Lee
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Myunggi Yi
- Department of Biomedical Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| |
Collapse
|
42
|
Wolf M, Zapf K, Gupta DK, Hiller M, Árnason Ú, Janke A. The genome of the pygmy right whale illuminates the evolution of rorquals. BMC Biol 2023; 21:79. [PMID: 37041515 PMCID: PMC10091562 DOI: 10.1186/s12915-023-01579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales. RESULTS Here, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance. CONCLUSIONS Our results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.
Collapse
Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Konstantin Zapf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Deepak Kumar Gupta
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
| | - Michael Hiller
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-Von-Laue-Str. 9, Frankfurt Am Main, Germany
| | - Úlfur Árnason
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Neurosurgery, Skane University Hospital in Lund, Lund, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
| |
Collapse
|
43
|
Zheng S, Zhang T, Tu K, Li L, Liu Z, Wu B, Zhou L, Sun X. Population Genetics of Manila Clam ( Ruditapes philippinarum) in China Inferred from Microsatellite Markers. BIOLOGY 2023; 12:biology12040557. [PMID: 37106757 PMCID: PMC10135866 DOI: 10.3390/biology12040557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (Ne). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (Ho) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (He) was calculated to be varying from 0.587 to 0.700. Fst values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all Fst values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.
Collapse
Affiliation(s)
- Sichen Zheng
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Tianshi Zhang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian 351100, China
| | - Li Li
- National Oceanographic Center, Marine Science Research Institute of Shandong Province, Qingdao 266104, China
| | - Zhihong Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Biao Wu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Liqing Zhou
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiujun Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
44
|
Garcia-Dorado A, Hedrick P. Some hope and many concerns on the future of the vaquita. Heredity (Edinb) 2023; 130:179-182. [PMID: 36333594 PMCID: PMC10076255 DOI: 10.1038/s41437-022-00573-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Aurora Garcia-Dorado
- Departamento de Genetica, Fisiologia y Microbiologia, Facultad de Biologia, Universidad Complutense, 28040, Madrid, Spain.
| | - Philip Hedrick
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| |
Collapse
|
45
|
Ferreira MS, Thurman TJ, Jones MR, Farelo L, Kumar AV, Mortimer SME, Demboski JR, Mills LS, Alves PC, Melo-Ferreira J, Good JM. The evolution of white-tailed jackrabbit camouflage in response to past and future seasonal climates. Science 2023; 379:1238-1242. [PMID: 36952420 DOI: 10.1126/science.ade3984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The genetic basis of adaptive traits has rarely been used to predict future vulnerability of populations to climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits (Lepus townsendii) tracks snow cover and is primarily determined by genetic variation at endothelin receptor type B (EDNRB), corin serine peptidase (CORIN), and agouti signaling protein (ASIP). Winter color variation was associated with deeply divergent alleles at these genes, reflecting selection on both ancestral and introgressed variation. Forecasted reductions in snow cover are likely to induce widespread camouflage mismatch. However, simulated populations with variation for darker winter pelage are predicted to adapt rapidly, providing a trait-based genetic framework to facilitate evolutionary rescue. These discoveries demonstrate how the genetic basis of climate change adaptation can inform conservation.
Collapse
Affiliation(s)
- Mafalda S Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Timothy J Thurman
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Alexander V Kumar
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
- US Fish and Wildlife Service, Fort Collins, CO, USA
| | | | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA
| | - L Scott Mills
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
- Office of Research and Creative Scholarship, University of Montana, Missoula, MT, USA
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| |
Collapse
|
46
|
Kardos M, Zhang Y, Parsons KM, A Y, Kang H, Xu X, Liu X, Matkin CO, Zhang P, Ward EJ, Hanson MB, Emmons C, Ford MJ, Fan G, Li S. Inbreeding depression explains killer whale population dynamics. Nat Ecol Evol 2023; 7:675-686. [PMID: 36941343 DOI: 10.1038/s41559-023-01995-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 01/26/2023] [Indexed: 03/23/2023]
Abstract
Understanding the factors that cause endangered populations to either grow or decline is crucial for preserving biodiversity. Conservation efforts often address extrinsic threats, such as environmental degradation and overexploitation, that can limit the recovery of endangered populations. Genetic factors such as inbreeding depression can also affect population dynamics but these effects are rarely measured in the wild and thus often neglected in conservation efforts. Here we show that inbreeding depression strongly influences the population dynamics of an endangered killer whale population, despite genomic signatures of purging of deleterious alleles via natural selection. We find that the 'Southern Residents', which are currently endangered despite nearly 50 years of conservation efforts, exhibit strong inbreeding depression for survival. Our population models suggest that this inbreeding depression limits population growth and predict further decline if the population remains genetically isolated and typical environmental conditions continue. The Southern Residents also had more inferred homozygous deleterious alleles than three other, growing, populations, further suggesting that inbreeding depression affects population fitness. These results demonstrate that inbreeding depression can substantially limit the recovery of endangered populations. Conservation actions focused only on extrinsic threats may therefore fail to account for key intrinsic genetic factors that also limit population growth.
Collapse
Affiliation(s)
- Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA.
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- BGI-Shenzhen, Shenzhen, China
| | - Kim M Parsons
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Yunga A
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
| | | | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Eric J Ward
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Candice Emmons
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Michael J Ford
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA.
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
- BGI-Shenzhen, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| |
Collapse
|
47
|
Fluctuating selection and the determinants of genetic variation. Trends Genet 2023; 39:491-504. [PMID: 36890036 DOI: 10.1016/j.tig.2023.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023]
Abstract
Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.
Collapse
|
48
|
Rahimi M, Ranjbaran E. Investigating the geographical, phenotypic and genetic diversity of Sickleweed populations by bioclimatic parameters, morphological traits and SCoT molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:421-433. [PMID: 37033768 PMCID: PMC10073401 DOI: 10.1007/s12298-023-01296-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/20/2023] [Accepted: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Sickleweed (Falcaria vulgaris) is important due to its nutritional value and medicinal effects on the human body. The 15 different Sickleweed populations were collected based on an unbalanced nest design with 10 replications and nine morphological traits were measured on them. The diversity was investigated with 15 primers of SCoT marker. The genetic diversity was investigated by ANOVA, cluster analysis and Bayesian statistical model based on morphological traits, bioclimatic and SCoT. Grouping the study areas based on bioclimatic parameters by UPGMA method showed that these areas were divided into two groups and were similar in terms of climatic similarities and bioclimatic information. The results of analysis of variance showed that there was a significant difference between populations at the level of one percent for the studied traits. The cluster analysis based traits by the UPGMA method divided these populations into two groups. The phenotypic diversity of these populations was largely consistent with the geographical diversity. The primers used for SCoT marker produced 137 polymorphic bands on the populations, The UPGMA cluster analysis with molecular data placed the studied populations into three groups and four subgroups. Grouping based on the Bayesian method placed the populations into nine groups, although the populations were not differentiated and were a mixture of all nine groups. High genetic diversity for the studied Sickleweed populations have showed valuable insights into the evolution of this plant and provides basic data for designing appropriate management practices for breeding Sickleweed populations.
Collapse
Affiliation(s)
- Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Elaheh Ranjbaran
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| |
Collapse
|
49
|
Chung MY, Merilä J, Kim Y, Mao K, López‐Pujol J, Chung MG. A review on
Q
ST
–
F
ST
comparisons of seed plants: Insights for conservation. Ecol Evol 2023; 13:e9926. [PMID: 37006890 PMCID: PMC10049885 DOI: 10.1002/ece3.9926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Increased access to genome-wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants, regarding both within-population and among-population components. We then introduce the estimates of among-population genetic differentiation in quantitative traits (Q ST) and neutral markers (F ST) to plant biology and summarize conservation applications derived from Q ST-F ST comparisons, particularly on how to capture most AGV and NGV on both in-situ and ex-situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials (n = 18) to capture 99% of NGV and AGV, respectively, whereas four populations would be needed in case of herbaceous perennials (n = 14). On average, Q ST is about 3.6, 1.5, and 1.1 times greater than F ST in woody plants, annuals, and herbaceous perennials, respectively. Hence, conservation and management policies or suggestions based solely on inference on F ST could be misleading, particularly in woody species. To maximize the preservation of the maximum levels of both AGV and NGV, we suggest using maximum Q ST rather than average Q ST. We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, particularly woody species.
Collapse
Affiliation(s)
- Mi Yoon Chung
- Department of Biological SciencesChungnam National UniversityDaejeon34134South Korea
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFI‐00014Finland
- Area of Ecology & BiodiversitySchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Yuseob Kim
- Division of EcoScienceEwha Womans UniversitySeoul03760South Korea
- Department of Life ScienceEwha Womans UniversitySeoul03760South Korea
| | - Kangshan Mao
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of Education, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu610065China
| | - Jordi López‐Pujol
- Botanic Institute of Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelona08038CataloniaSpain
- Universidad Espíritu Santo (UEES)Samborondón091650Ecuador
| | - Myong Gi Chung
- Division of Life Science and RINSGyeongsang National UniversityJinju52828South Korea
| |
Collapse
|
50
|
Hogg CJ, Silver L, McLennan EA, Belov K. Koala Genome Survey: An Open Data Resource to Improve Conservation Planning. Genes (Basel) 2023; 14:genes14030546. [PMID: 36980819 PMCID: PMC10048327 DOI: 10.3390/genes14030546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.
Collapse
|