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Uttam V, Vohra V, Chhotaray S, Santhosh A, Diwakar V, Patel V, Gahlyan RK. Exome-wide comparative analyses revealed differentiating genomic regions for performance traits in Indian native buffaloes. Anim Biotechnol 2024; 35:2277376. [PMID: 37934017 DOI: 10.1080/10495398.2023.2277376] [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: 11/08/2023]
Abstract
In India, 20 breeds of buffalo have been identified and registered, yet limited studies have been conducted to explore the performance potential of these breeds, especially in the Indian native breeds. This study is a maiden attempt to delineate the important variants and unique genes through exome sequencing for milk yield, milk composition, fertility, and adaptation traits in Indian local breeds of buffalo. In the present study, whole exome sequencing was performed on Chhattisgarhi (n = 3), Chilika (n = 4), Gojri (n = 3), and Murrah (n = 4) buffalo breeds and after stringent quality control, 4333, 6829, 4130, and 4854 InDels were revealed, respectively. Exome-wide FST along 100-kb sliding windows detected 27, 98, 38, and 35 outlier windows in Chhattisgarhi, Chilika, Gojri, and Murrah, respectively. The comparative exome analysis of InDels and subsequent gene ontology revealed unique breed specific genes for milk yield (CAMSAP3), milk composition (CLCN1, NUDT3), fertility (PTGER3) and adaptation (KCNA3, TH) traits. Study provides insight into mechanism of how these breeds have evolved under natural selection, the impact of these events on their respective genomes, and their importance in maintaining purity of these breeds for the traits under study. Additionally, this result will underwrite to the genetic acquaintance of these breeds for breeding application, and in understanding of evolution of these Indian local breeds.
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Affiliation(s)
- Vishakha Uttam
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Vikas Vohra
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Supriya Chhotaray
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Ameya Santhosh
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Vikas Diwakar
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Vaibhav Patel
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Rajesh Kumar Gahlyan
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
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2
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Bernardi G, Azzurro E, Bariche M, Jimenez C, Kalogirou S, Kleitou P. Invasion genomics of lionfish in the Mediterranean Sea. Ecol Evol 2024; 14:e11087. [PMID: 38450316 PMCID: PMC10915480 DOI: 10.1002/ece3.11087] [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: 01/27/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
The rate of biological invasions is steadily increasing, with major ecological and economic impacts accounting for billions of dollars in damage as a result. One spectacular example is the western Atlantic invasion by lionfishes. In the Mediterranean Sea, invasions from the Red Sea via the Suez Canal (termed Lessepsian invasions) comprise more than 100 fish species, including a recent invasion by lionfish. In light of the devastating effects of lionfish in the Caribbean Sea, understanding the dynamics of Mediterranean lionfish invasion is crucial. The Lessepsian lionfish invasion started in 2012, and rapidly spread to the central Mediterranean. Here, we used thousands of RAD seq genomic markers to study the population dynamics of this invasion. While we did not find a reduction in genetic diversity between source (Red Sea) and invasive (Mediterranean) populations (i.e., bottleneck effects), we found evidence of population structure within the invasive range in the Mediterranean Sea. We found that loci that are potentially under selection may play an important role in invasion success (in particular, genes involved in osmoregulation and fin spine sizes). Genomic approaches proved powerful in examining the ecological and evolutionary patterns of successful invaders and may be used as tools to understand and potentially mitigate future invasions.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | - Ernesto Azzurro
- CNR‐IRBIM, National Research CouncilInstitute of Biological Resources and Marine BiotechnologiesAnconaItaly
- Zoological Station A. DohrnNaplesItaly
| | - Michel Bariche
- Department of BiologyAmerican University of BeirutBeirutLebanon
| | - Carlos Jimenez
- Enalia Physis Environmental Research Centre (ENALIA)NicosiaCyprus
- The Cyprus InstituteEnergy Environment and Water Research CenterNicosiaCyprus
| | - Stefanos Kalogirou
- Hellenic Centre for Marine Research, Institute for Marine Biological Resources and Inland WatersHydrobiological Station of RhodesRhodesGreece
| | - Periklis Kleitou
- Marine & Environmental Research (MER) LabLimassolCyprus
- School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
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3
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Wang YL, Li L, Paudel BR, Zhao JL. Genomic Insights into High-Altitude Adaptation: A Comparative Analysis of Roscoea alpina and R. purpurea in the Himalayas. Int J Mol Sci 2024; 25:2265. [PMID: 38396942 PMCID: PMC10889555 DOI: 10.3390/ijms25042265] [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: 12/22/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Environmental stress at high altitudes drives the development of distinct adaptive mechanisms in plants. However, studies exploring the genetic adaptive mechanisms of high-altitude plant species are scarce. In the present study, we explored the high-altitude adaptive mechanisms of plants in the Himalayas through whole-genome resequencing. We studied two widespread members of the Himalayan endemic alpine genus Roscoea (Zingiberaceae): R. alpina (a selfing species) and R. purpurea (an outcrossing species). These species are distributed widely in the Himalayas with distinct non-overlapping altitude distributions; R. alpina is distributed at higher elevations, and R. purpurea occurs at lower elevations. Compared to R. purpurea, R. alpina exhibited higher levels of linkage disequilibrium, Tajima's D, and inbreeding coefficient, as well as lower recombination rates and genetic diversity. Approximately 96.3% of the genes in the reference genome underwent significant genetic divergence (FST ≥ 0.25). We reported 58 completely divergent genes (FST = 1), of which only 17 genes were annotated with specific functions. The functions of these genes were primarily related to adapting to the specific characteristics of high-altitude environments. Our findings provide novel insights into how evolutionary innovations promote the adaptation of mountain alpine species to high altitudes and harsh habitats.
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Affiliation(s)
- Ya-Li Wang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
| | - Li Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
| | - Babu Ram Paudel
- Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur 44613, Nepal
| | - Jian-Li Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
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4
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Scucchia F, Wong K, Zaslansky P, Putnam HM, Goodbody-Gringley G, Mass T. Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda. J Struct Biol 2023; 215:108036. [PMID: 37832837 DOI: 10.1016/j.jsb.2023.108036] [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: 06/21/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
The widespread decline of shallow-water coral reefs has fueled interest in assessing whether mesophotic reefs can act as refugia replenishing deteriorated shallower reefs through larval exchange. Here we explore the morphological and molecular basis facilitating survival of planulae and adults of the coral Porites astreoides (Lamarck, 1816; Hexacorallia: Poritidae) along the vertical depth gradient in Bermuda. We found differences in micro-skeletal features such as bigger calyxes and coarser surface of the skeletal spines in shallow corals. Yet, tomographic reconstructions reveal an analogous mineral distribution between shallow and mesophotic adults, pointing to similar skeleton growth dynamics. Our study reveals patterns of host genetic connectivity and minimal symbiont depth-zonation across a broader depth range than previously known for this species in Bermuda. Transcriptional variations across life stages showed different regulation of metabolism and stress response functions, unraveling molecular responses to environmental conditions at different depths. Overall, these findings increase our understanding of coral acclimatory capability across broad vertical gradients, ultimately allowing better evaluation of the refugia potential of mesophotic reefs.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H. Charney School of Marine Sciences University of Haifa, Israel; The Interuniversity Institute of Marine Sciences, Eilat, Israel.
| | - Kevin Wong
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Paul Zaslansky
- Department for Operative, Preventive and Pediatric Dentistry, Charité-Universitätsmedizin, Berlin, Germany
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Gretchen Goodbody-Gringley
- Central Caribbean Marine Institute, Little Cayman, Cayman Islands; Bermuda Institute of Ocean Sciences, St. George's, Bermuda
| | - Tali Mass
- Department of Marine Biology, Leon H. Charney School of Marine Sciences University of Haifa, Israel.
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5
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Scucchia F, Zaslansky P, Boote C, Doheny A, Mass T, Camp EF. The role and risks of selective adaptation in extreme coral habitats. Nat Commun 2023; 14:4475. [PMID: 37507378 PMCID: PMC10382478 DOI: 10.1038/s41467-023-39651-7] [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: 01/25/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The alarming rate of climate change demands new management strategies to protect coral reefs. Environments such as mangrove lagoons, characterized by extreme variations in multiple abiotic factors, are viewed as potential sources of stress-tolerant corals for strategies such as assisted evolution and coral propagation. However, biological trade-offs for adaptation to such extremes are poorly known. Here, we investigate the reef-building coral Porites lutea thriving in both mangrove and reef sites and show that stress-tolerance comes with compromises in genetic and energetic mechanisms and skeletal characteristics. We observe reduced genetic diversity and gene expression variability in mangrove corals, a disadvantage under future harsher selective pressure. We find reduced density, thickness and higher porosity in coral skeletons from mangroves, symptoms of metabolic energy redirection to stress response functions. These findings demonstrate the need for caution when utilizing stress-tolerant corals in human interventions, as current survival in extremes may compromise future competitive fitness.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H, Charney school of Marine Sciences, University of Haifa, Haifa, Israel.
| | - Paul Zaslansky
- Department for Operative, Preventive and Pediatric Dentistry, Charité-Universitätsmedizin, Berlin, Germany
| | - Chloë Boote
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Annabelle Doheny
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Tali Mass
- Department of Marine Biology, Leon H, Charney school of Marine Sciences, University of Haifa, Haifa, Israel
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia.
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6
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Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023; 14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.
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Affiliation(s)
- Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Courage Adobor
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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7
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Byrne D, Scheben A, Scott JK, Webber BL, Batchelor KL, Severn-Ellis AA, Gooden B, Bell KL. Genomics reveals the history of a complex plant invasion and improves the management of a biological invasion from the South African-Australian biotic exchange. Ecol Evol 2022; 12:e9179. [PMID: 36016815 PMCID: PMC9396708 DOI: 10.1002/ece3.9179] [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: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Many plants exchanged in the global redistribution of species in the last 200 years, particularly between South Africa and Australia, have become threatening invasive species in their introduced range. Refining our understanding of the genetic diversity and population structure of native and alien populations, introduction pathways, propagule pressure, naturalization, and initial spread, can transform the effectiveness of management and prevention of further introductions. We used 20,221 single nucleotide polymorphisms to reconstruct the invasion of a coastal shrub, Chrysanthemoides monilifera ssp. rotundata (bitou bush) from South Africa, into eastern Australia (EAU), and Western Australia (WAU). We determined genetic diversity and population structure across the native and introduced ranges and compared hypothesized invasion scenarios using Bayesian modeling. We detected considerable genetic structure in the native range, as well as differentiation between populations in the native and introduced range. Phylogenetic analysis showed the introduced samples to be most closely related to the southern‐most native populations, although Bayesian analysis inferred introduction from a ghost population. We detected strong genetic bottlenecks during the founding of both the EAU and WAU populations. It is likely that the WAU population was introduced from EAU, possibly involving an unsampled ghost population. The number of private alleles and polymorphic SNPs successively decreased from South Africa to EAU to WAU, although heterozygosity remained high. That bitou bush remains an invasion threat in EAU, despite reduced genetic diversity, provides a cautionary biosecurity message regarding the risk of introduction of potentially invasive species via shipping routes.
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Affiliation(s)
- Dennis Byrne
- CSIRO Health & Biosecurity Floreat Western Australia Australia.,School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Armin Scheben
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory Cold Spring, Harbor New York USA
| | - John K Scott
- CSIRO Health & Biosecurity Floreat Western Australia Australia.,School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity Floreat Western Australia Australia.,School of Biological Sciences University of Western Australia Crawley Western Australia Australia.,Western Australian Biodiversity Science Institute Perth Western Australia Australia
| | | | - Anita A Severn-Ellis
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Ben Gooden
- CSIRO Health and Biosecurity Canberra Australian Capital Territory Australia.,Centre for Sustainable Ecosystem Solutions School of Earth, Atmospheric and Life Sciences, University of Wollongong Wollongong New South Wales Australia
| | - Karen L Bell
- CSIRO Health & Biosecurity Floreat Western Australia Australia.,School of Biological Sciences University of Western Australia Crawley Western Australia Australia
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8
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Molecular Evidence Reveals the Sympatric Distribution of Cervus nippon yakushimae and Cervus nippon taiouanus on Jeju Island, South Korea. Animals (Basel) 2022; 12:ani12080998. [PMID: 35454244 PMCID: PMC9029077 DOI: 10.3390/ani12080998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/17/2022] Open
Abstract
Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.
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9
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Guragain P, Båtnes AS, Zobolas J, Olsen Y, Bones AM, Winge P. IIb-RAD-sequencing coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice ( Lepeophtheirus salmonis). Ecol Evol 2022; 12:e8809. [PMID: 35414904 PMCID: PMC8986551 DOI: 10.1002/ece3.8809] [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: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 11/29/2022] Open
Abstract
The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19,428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish the differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection was also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.
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Affiliation(s)
- Prashanna Guragain
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Anna Solvang Båtnes
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - John Zobolas
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Yngvar Olsen
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Atle M. Bones
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Per Winge
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
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10
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Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01428-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Poveda-Martínez D, Varone L, Fuentes Corona M, Hight S, Logarzo G, Hasson E. Spatial and host related genomic variation in partially sympatric cactophagous moth species. Mol Ecol 2021; 31:356-371. [PMID: 34662480 DOI: 10.1111/mec.16232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/17/2023]
Abstract
Surveys of patterns of genetic variation in natural sympatric and allopatric populations of recently diverged species are necessary to understand the processes driving intra- and interspecific diversification. The South American moths Cactoblastis cactorum, Cactoblastis doddi and Cactoblastis bucyrus are specialized in the use of cacti as host plants. These species have partially different geographic ranges and differ in patterns of host plant use. However, there are areas that overlap, particularly, in northwestern Argentina, where they are sympatric. Using a combination of genome-wide SNPs and mitochondrial data we assessed intra and interspecific genetic variation and investigated the relative roles of geography and host plants on genetic divergence. We also searched for genetic footprints of hybridization between species. We identified three well delimited species and detected signs of hybridization in the area of sympatry. Our results supported a hypothetical scenario of allopatric speciation in the generalist C. cactorum and genetic interchange during secondary geographic contact with the pair of specialists C. bucyrus and C. doddi that probably speciated sympatrically. In both cases, adaptation to new host plants probably played an important role in speciation. The results also suggested the interplay of geography and host plant use as drivers of divergence and limiting gene flow at intra and interspecific levels.
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Affiliation(s)
- Daniel Poveda-Martínez
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina.,Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Grupo de investigación en Evolución, Ecología y Conservación (EECO), Universidad del Quindío, Armenia, Colombia.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura Varone
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Malena Fuentes Corona
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Stephen Hight
- Insect Behavior and Biocontrol Research Unit (IBBRU), USDA-ARS, Tallahassee, Florida, USA
| | - Guillermo Logarzo
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
| | - Esteban Hasson
- Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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12
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Allen KE, Greenbaum E, Hime PM, Tapondjou N. WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes. Ecol Evol 2021; 11:6133-6152. [PMID: 34141208 PMCID: PMC8207163 DOI: 10.1002/ece3.7429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.
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Affiliation(s)
- Kaitlin E. Allen
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Eli Greenbaum
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTXUSA
| | - Paul M. Hime
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Walter P. Tapondjou N.
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Viktoria V. Sterkhova
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Chifundera Kusamba
- Laboratoire d’Hérpétologie, Département de BiologieCentre de Recherche en Sciences NaturellesLwiroDemocratic Republic of Congo
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Johannes Penner
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Chair of Wildlife Ecology and ManagementUniversity of FreiburgFreiburgGermany
| | - A. Townsend Peterson
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
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Avila-Cervantes J, Arias C, Venegas-Anaya M, Vargas M, Larsson HCE, McMillan WO. Effect of the Central American Isthmus on gene flow and divergence of the American crocodile (Crocodylus acutus). Evolution 2021; 75:245-259. [PMID: 33314048 DOI: 10.1111/evo.14139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 01/22/2023]
Abstract
The final formation of the Central American Isthmus (CAI) about 3.5 million years ago altered global ocean circulation, connected North and South America terrestrial biotas, and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile (Crocodylus acutus) to study the genomic variation of C. acutus on both sides of the CAI, infer its demographic history, and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: (1) Caribbean and the Panama Canal, (2) Pacific coast, and (3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20,000 years ago, which is younger than the formation of the CAI, coinciding with the Last Glacial Maximum. We hypothesize the glacial/interglacial cycles facilitated gene flow between the Caribbean and Pacific crocodile populations after the formation of the CAI, masking any genomic divergence the CAI may have caused. There is no evidence of gene flow associated with the opening of the Panama Canal.
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Affiliation(s)
- Jose Avila-Cervantes
- McGill University, Redpath Museum 859 Sherbrooke Street West, Montreal, Quebec, H3A 0C4, Canada
| | - Carlos Arias
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Miryam Venegas-Anaya
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Marta Vargas
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Hans C E Larsson
- McGill University, Redpath Museum 859 Sherbrooke Street West, Montreal, Quebec, H3A 0C4, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
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14
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Crossley MS, Snyder WE. What Is the Spatial Extent of a Bemisia tabaci Population? INSECTS 2020; 11:E813. [PMID: 33218155 PMCID: PMC7698913 DOI: 10.3390/insects11110813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
Effective pest management depends on basic knowledge about insect dispersal patterns and gene flow in agroecosystems. The globally invasive sweet potato whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is considered a weak flier whose life history nonetheless predisposes it to frequent dispersal, but the scale over which populations exchange migrants, and should therefore be managed, is uncertain. In this review, we synthesize the emergent literature on B. tabaci population genetics to address the question: What spatial scales define B. tabaci populations? We find that within-species genetic differentiation among sites is often low, and evidence of population structuring by host plant or geography is rare. Heterozygote deficits prevail among populations, indicating that migrants from divergent populations are frequently sampled together. Overall, these results suggest that there is high ongoing gene flow over large spatial extents. However, genetic homogeneity typical of recently invading populations could obscure power to detect real isolation among populations. Genome-wide data collected systematically across space and time could distinguish signatures of invasion history from those of ongoing gene flow. Characterizing the spatial extent of B. tabaci populations could reveal whether insecticide rotations can be tailored to specific commodities or if coordination across linked commodities and regions is justified.
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15
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Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp ( Penaeus monodon) in the Indo-Pacific Region. BIOLOGY 2020; 9:biology9090277. [PMID: 32906759 PMCID: PMC7564732 DOI: 10.3390/biology9090277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise FST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.
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Li H, Qu W, Obrycki JJ, Meng L, Zhou X, Chu D, Li B. Optimizing Sample Size for Population Genomic Study in a Global Invasive Lady Beetle, Harmonia Axyridis. INSECTS 2020; 11:E290. [PMID: 32397374 PMCID: PMC7291016 DOI: 10.3390/insects11050290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/30/2022]
Abstract
Finding optimal sample sizes is critical for the accurate estimation of genetic diversity of large invasive populations. Based on previous studies, we hypothesized that a minimal sample size of 3-8 individuals is sufficient to dissect the population architecture of the harlequin lady beetle, Harmonia axyridis, a biological control agent and an invasive alien species. Here, equipped with a type IIB endonuclease restriction site-associated (2b-RAD) DNA sequencing approach, we identified 13,766 and 13,929 single nucleotide polymorphisms (SNPs), respectively, among native and invasive H. axyridis populations. With this information we simulated populations using a randomly selected 3000 SNPs and a subset of individuals. From this simulation we finally determined that six individuals is the minimum sample size required for the accurate estimation of intra- and inter-population genetic diversity within and across H. axyridis populations. Our findings provide an empirical advantage for population genomic studies of H. axyridis in particular and suggest useful tactics for similar studies on multicellular organisms in general.
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Affiliation(s)
- Hongran Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (L.M.)
| | - Wanmei Qu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (W.Q.); (D.C.)
| | - John J. Obrycki
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA; (J.J.O.); (X.Z.)
| | - Ling Meng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (L.M.)
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA; (J.J.O.); (X.Z.)
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (W.Q.); (D.C.)
| | - Baoping Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (L.M.)
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