1
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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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2
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Ding K, Xu Q, Zhao L, Li Y, Li Z, Shi W, Zeng Q, Wang X, Zhang X. Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis). BMC Genomics 2024; 25:373. [PMID: 38627659 PMCID: PMC11022445 DOI: 10.1186/s12864-024-10268-4] [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: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.
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Affiliation(s)
- Kui Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Liyuan Zhao
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Zhong Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Wenge Shi
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Qianhui Zeng
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xianyan Wang
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China.
- National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, Xi'an, China.
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Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024; 15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [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] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.
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Affiliation(s)
- Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Rui Resende Pinto
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jonas Meisner
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Research Centre for Mental Health, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Rute R da Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Springer AL, Gompert Z. Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii. Mol Ecol 2024; 33:e17310. [PMID: 38441401 DOI: 10.1111/mec.17310] [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: 10/03/2023] [Revised: 11/26/2023] [Accepted: 02/15/2024] [Indexed: 03/26/2024]
Abstract
Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure, in turn, can reveal signatures of isolation by distance (IBD), barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by IBD, isolation by resistance (IBR) (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping-by-sequencing (GBS) approach coupled with host preference assays, Bayesian modelling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of IBR and simple IBD, was the major driver of contemporary patterns of differentiation in this narrow endemic species.
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Affiliation(s)
- Amy L Springer
- Department of Biology, Utah State University, Logan, Utah, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA
- Ecology Center, Utah State University, Logan, Utah, USA
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Ghouri S, Reich MS, Lopez-Mañas R, Talavera G, Bowen GJ, Vila R, Talla VNK, Collins SC, Martins DJ, Bataille CP. A hydrogen isoscape for tracing the migration of herbivorous lepidopterans across the Afro-Palearctic range. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9675. [PMID: 38211347 DOI: 10.1002/rcm.9675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/06/2023] [Accepted: 11/03/2023] [Indexed: 01/13/2024]
Abstract
RATIONALE Many insect species undertake multigenerational migrations in the Afro-tropical and Palearctic ranges, and understanding their migratory connectivity remains challenging due to their small size, short life span and large population sizes. Hydrogen isotopes (δ2 H) can be used to reconstruct the movement of dispersing or migrating insects, but applying δ2 H for provenance requires a robust isotope baseline map (i.e. isoscape) for the Afro-Palearctic. METHODS We analyzed the δ2 H in the wings (δ2 Hwing ) of 142 resident butterflies from 56 sites across the Afro-Palearctic. The δ2 Hwing values were compared to the predicted local growing-season precipitation δ2 H values (δ2 HGSP ) using a linear regression model to develop an insect wing δ2 H isoscape. We used multivariate linear mixed models and high-resolution and time-specific remote sensing climate and environmental data to explore the controls of the residual δ2 Hwing variability. RESULTS A strong linear relationship was found between δ2 Hwing and δ2 HGSP values (r2 = 0.53). The resulting isoscape showed strong patterns across the Palearctic but limited variation and high uncertainty for the Afro-tropics. Positive residuals of this relationship were correlated with dry conditions for the month preceding sampling whereas negative residuals were correlated with more wet days for the month preceding sampling. High intra-site δ2 Hwing variance was associated with lower relative humidity for the month preceding sampling and higher elevation. CONCLUSION The δ2 Hwing isoscape is applicable for tracing herbivorous lepidopteran insects that migrate across the Afro-Palearctic range but has limited geolocation potential in the Afro-tropics. The spatial analysis of uncertainty using high-resolution climatic data demonstrated that many African regions with highly variable evaporation rates and relative humidity have δ2 Hwing values that are less related to δ2 HGSP values. Increasing geolocation precision will require new modeling approaches using more time-specific environmental data and/or independent geolocation tools.
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Affiliation(s)
- Sana Ghouri
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Megan S Reich
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Roger Lopez-Mañas
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona, Catalonia, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona, Catalonia, Spain
| | - Gabriel J Bowen
- Geology and Geophysics, University of Utah, Salt Lake City, Utah, USA
| | - Roger Vila
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Catalonia, Spain
| | - Valery N K Talla
- Laboratory of Applied Biology and Ecology, Faculty of Science, University of Dschang, Dschang, West Region, Cameroon
| | | | - Dino J Martins
- Mpala Research Centre, Nanyuki, Kenya
- Turkana Basin Institute, Stony Brook University NY, Stony Brook, New York, USA
| | - Clement P Bataille
- Department of Earth and Environmental Sciences, University of Ottawa, Ottawa, Ontario, Canada
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James DG. Monarch Butterflies in Western North America: A Holistic Review of Population Trends, Ecology, Stressors, Resilience and Adaptation. INSECTS 2024; 15:40. [PMID: 38249046 PMCID: PMC10817040 DOI: 10.3390/insects15010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024]
Abstract
Monarch butterfly populations in western North America suffered a substantial decline, from millions of butterflies overwintering in California in the 1980s to less than 400,000 at the beginning of the 21st century. The introduction of neonicotinoid insecticides in the mid-1990s and their subsequent widespread use appears to be the most likely major factor behind this sudden decline. Habitat loss and unfavorable climates (high temperatures, aridity, and winter storms) have also played important and ongoing roles. These factors kept overwintering populations stable but below 300,000 during 2001-2017. Late winter storm mortality and consequent poor spring reproduction drove winter populations to less than 30,000 butterflies during 2018-2019. Record high temperatures in California during the fall of 2020 appeared to prematurely terminate monarch migration, resulting in the lowest overwintering population (1899) ever recorded. Many migrants formed winter-breeding populations in urban areas. Normal seasonal temperatures in the autumns of 2021 and 2022 enabled overwintering populations to return to around the 300,000 level, characteristic of the previous two decades. Natural enemies (predators, parasitoids, parasites, and pathogens) may be important regional or local drivers at times but they are a consistent and fundamental part of monarch ecology. Human interference (capture, rearing) likely has the least impact on monarch populations. The rearing of monarch caterpillars, particularly by children, is an important human link to nature that has positive ramifications for insect conservation beyond monarch butterflies and should be encouraged.
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Affiliation(s)
- David G James
- Department of Entomology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA 99350, USA
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Marino A, Reboud EL, Chevalier E, Tilak MK, Contreras-Garduño J, Nabholz B, Condamine FL. Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies. G3 (BETHESDA, MD.) 2023; 13:jkad239. [PMID: 37847748 PMCID: PMC10700114 DOI: 10.1093/g3journal/jkad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
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Affiliation(s)
- Alba Marino
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Eliette L Reboud
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Emmanuelle Chevalier
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Jorge Contreras-Garduño
- Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
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Bergman J, Pedersen RØ, Lundgren EJ, Lemoine RT, Monsarrat S, Pearce EA, Schierup MH, Svenning JC. Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change. Nat Commun 2023; 14:7679. [PMID: 37996436 PMCID: PMC10667484 DOI: 10.1038/s41467-023-43426-5] [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: 03/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32-76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92-95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.
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Affiliation(s)
- Juraj Bergman
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Rasmus Ø Pedersen
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Erick J Lundgren
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Rhys T Lemoine
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Sophie Monsarrat
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Rewilding Europe, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Elena A Pearce
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
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Zheng L, Wang H, Lin J, Zhou Y, Xiao J, Li K. Population genomics provides insights into the genetic diversity and adaptation of the Pieris rapae in China. PLoS One 2023; 18:e0294521. [PMID: 37972203 PMCID: PMC10653512 DOI: 10.1371/journal.pone.0294521] [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: 03/14/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
The cabbage white butterfly (Pieris rapae), a major agricultural pest, has become one of the most abundant and destructive butterflies in the world. It is widely distributed in a large variety of climates and terrains of China due to its strong adaptability. To gain insight into the population genetic characteristics of P. rapae in China, we resequenced the genome of 51 individuals from 19 areas throughout China. Using population genomics approaches, a dense variant map of P. rapae was observed, indicating a high level of polymorphism that could result in adaptation to a changing environment. The feature of the genetic structure suggested considerable genetic admixture in different geographical groups. Additionally, our analyses suggest that physical barriers may have played a more important role than geographic distance in driving genetic differentiation. Population history showed the effective population size of P. rapae was greatly affected by global temperature changes, with mild periods (i.e., temperatures warmer than those during glaciation but not excessively hot) leading to an increase in population size. Furthermore, by comparing populations from south and north China, we have identified selected genes related to sensing temperature, growth, neuromodulation and immune response, which may reveal the genetic basis of adaptation to different environments. Our study is the first to illustrate the genetic signatures of P. rapae in China at the population genomic level, providing fundamental knowledge of the genetic diversity and adaptation of P. rapae.
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Affiliation(s)
- Linlin Zheng
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Huan Wang
- Department of Plant Science and Technology, Shanghai Vocational College of Agriculture and Forestry, Shanghai, China
| | - Junjie Lin
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Yuxun Zhou
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Junhua Xiao
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Kai Li
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
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10
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Steele C, Ragonese IG, Majewska AA. Extent and impacts of winter breeding in the North American monarch butterfly. CURRENT OPINION IN INSECT SCIENCE 2023; 59:101077. [PMID: 37336490 DOI: 10.1016/j.cois.2023.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
Since the 1960s, scientists have observed the North American monarch butterfly (Danaus plexippus) continuing reproductive activities past the fall migration and into the winter months when the climate is mild. Recent work suggests that small populations of winter breeding monarchs are present in western and southeastern USA, as well as northwestern Mexico, with new winter breeding populations forming in areas where non-native milkweeds are planted. The year-round presence of milkweed plants and temperatures suitable for immature monarch development are vital factors allowing for winter breeding. Non-native milkweeds, in conjunction with novel barriers to migration, are likely contributing to the rise in winter breeding behavior. Warmer climates are already impacting milkweed phenology and range, possibly favoring winter breeding behavior. Similar pressures but different implications are expected for eastern and western winter breeding monarchs given the differences in the migration ecology, milkweed species, and climate changes in the two regions.
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Affiliation(s)
- Christen Steele
- Department of Ecology and Evolutionary Biology, Tulane University, 1430 Annunciation St, New Orleans, LA 70130, USA
| | - Isabella G Ragonese
- Odum School of Ecology, University of Georgia, 140 E Green Street, Athens, GA 30602, USA
| | - Ania A Majewska
- Department of Physiology and Pharmacology College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA 30602, USA.
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11
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Boman J, Zhu Y, Höök L, Vila R, Talavera G, Backström N. Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui). Mol Ecol 2023. [PMID: 37088782 DOI: 10.1111/mec.16957] [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: 01/24/2023] [Revised: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
Seasonal environmental fluctuations provide formidable challenges for living organisms, especially small ectotherms such as butterflies. A common strategy to cope with harsh environments is to enter diapause, but some species avoid unsuitable conditions by migrating. Despite a growing understanding of migration in the life cycles of some butterfly species, it remains unknown how individuals register and store environmental cues to determine whether and where to migrate. Here, we explored how competition and host plant availability during larval development affect patterns of DNA methylation in the migratory painted lady (Vanessa cardui) butterfly. We identify a set of potentially functional methylome shifts associated with differences in the environment, indicating that DNA methylation is involved in the response to different conditions during larval development. By analysing the transcriptome for the same samples used for methylation profiling, we also uncovered a non-monotonic relationship between gene body methylation and gene expression. Our results provide a starting point for understanding the interplay between DNA methylation and gene expression in butterflies in general and how differences in environmental conditions during development can trigger unique epigenetic marks that might be important for behavioural decisions in the adult stage.
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Affiliation(s)
- Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Yishu Zhu
- Animal Ecology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
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12
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Talavera G, García-Berro A, Talla VNK, Ng’iru I, Bahleman F, Kébé K, Nzala KM, Plasencia D, Marafi MAJ, Kassie A, Goudégnon EOA, Kiki M, Benyamini D, Reich MS, López-Mañas R, Benetello F, Collins SC, Bataille CP, Pierce NE, Martins DJ, Suchan T, Menchetti M, Vila R. The Afrotropical breeding grounds of the Palearctic-African migratory painted lady butterflies ( Vanessa cardui). Proc Natl Acad Sci U S A 2023; 120:e2218280120. [PMID: 37036992 PMCID: PMC10120051 DOI: 10.1073/pnas.2218280120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/25/2023] [Indexed: 04/12/2023] Open
Abstract
Migratory insects are key players in ecosystem functioning and services, but their spatiotemporal distributions are typically poorly known. Ecological niche modeling (ENM) may be used to predict species seasonal distributions, but the resulting hypotheses should eventually be validated by field data. The painted lady butterfly (Vanessa cardui) performs multigenerational migrations between Europe and Africa and has become a model species for insect movement ecology. While the annual migration cycle of this species is well understood for Europe and northernmost Africa, it is still unknown where most individuals spend the winter. Through ENM, we previously predicted suitable breeding grounds in the subhumid regions near the tropics between November and February. In this work, we assess the suitability of these predictions through i) extensive field surveys and ii) two-year monitoring in six countries: a large-scale monitoring scheme to study butterfly migration in Africa. We document new breeding locations, year-round phenological information, and hostplant use. Field observations were nearly always predicted with high probability by the previous ENM, and monitoring demonstrated the influence of the precipitation seasonality regime on migratory phenology. Using the updated dataset, we built a refined ENM for the Palearctic-African range of V. cardui. We confirm the relevance of the Afrotropical region and document the missing natural history pieces of the longest migratory cycle described in butterflies.
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Affiliation(s)
- Gerard Talavera
- Institut Botànic de Barcelona, Consejo Superior de Investigaciones Científicas and Ajuntament de Barcelona, Barcelona, Catalonia08038, Spain
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Aurora García-Berro
- Institut Botànic de Barcelona, Consejo Superior de Investigaciones Científicas and Ajuntament de Barcelona, Barcelona, Catalonia08038, Spain
| | - Valery N. K. Talla
- Laboratory of Applied Biology and Ecology, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Ivy Ng’iru
- Mpala Research Centre, Nanyuki555-10400, Kenya
| | | | - Khadim Kébé
- Department of Chemical Engineering and Applied Biology, Polytechnic Higher School of Dakar, BP 5085Dakar, Senegal
| | | | - Dulce Plasencia
- Asociación Española para la Protección de las Mariposas y su Medio - Zerynthia, Sección Tenerife, E-26004Logroño, Spain
| | - Mohammad A. J. Marafi
- Department of Restoration of Terrestrial and Marine Ecosystems, Public Authority of Agriculture Affairs and Fish Resources, 13075Kuwait City, Kuwait
| | - Abeje Kassie
- Ethiopian Biodiversity Institute, 30726Addis Ababa, Ethiopia
| | - Eude O. A. Goudégnon
- Laboratoire d'Écologie Appliquée, Université d'Abomey-Calavi, BP 526Cotonou, Benin
| | - Martial Kiki
- Laboratoire d'Écologie Appliquée, Université d'Abomey-Calavi, BP 526Cotonou, Benin
| | - Dubi Benyamini
- The Israeli Lepidopterist Society, Beit Arye7194700, Israel
| | - Megan S. Reich
- Department of Biology, University of Ottawa, ONK1N 6N5Ottawa, Canada
| | - Roger López-Mañas
- Institut Botànic de Barcelona, Consejo Superior de Investigaciones Científicas and Ajuntament de Barcelona, Barcelona, Catalonia08038, Spain
| | - Fulvia Benetello
- Dipartimento di Biologia, Università degli Studi di Firenze, 50019Sesto Fiorentino, Italy
| | | | - Clément P. Bataille
- Department of Earth and Environmental Sciences, University of Ottawa, ONK1N 6N5Ottawa, Canada
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Dino J. Martins
- Institut Botànic de Barcelona, Consejo Superior de Investigaciones Científicas and Ajuntament de Barcelona, Barcelona, Catalonia08038, Spain
- Mpala Research Centre, Nanyuki555-10400, Kenya
- Turkana Basin Institute, Stony Brook University, NY11794
| | - Tomasz Suchan
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków31-512, Poland
| | - Mattia Menchetti
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas and Universitat Pompeu Fabra), Barcelona, Catalonia08003, Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas and Universitat Pompeu Fabra), Barcelona, Catalonia08003, Spain
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13
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Bruschini C, Edwards ED, Talavera G, Vaurasi VD, Latu GF, Dapporto L. A complete
COI
library of Samoan butterflies reveals layers of endemic diversity on oceanic islands. ZOOL SCR 2023. [DOI: 10.1111/zsc.12588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- Claudia Bruschini
- ZEN Lab, Dipartimento di Biologia Università degli Studi di Firenze Sesto Fiorentino Italia
| | - Eric D. Edwards
- Department of Conservation Conservation House Wellington New Zealand
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB) CSIC‐Ajuntament de Barcelona Barcelona Spain
| | - Varea D. Vaurasi
- Faculty of Science, National University of Samoa To'omatagi Samoa
| | | | - Leonardo Dapporto
- ZEN Lab, Dipartimento di Biologia Università degli Studi di Firenze Sesto Fiorentino Italia
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