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Herman RW, Clucas G, Younger J, Bates J, Robinson B, Reddy S, Stepanuk J, O'Brien K, Veeramah K, Lynch HJ. Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird. Mol Ecol 2024; 33:e17282. [PMID: 38299701 DOI: 10.1111/mec.17282] [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: 06/02/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500-800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.
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Affiliation(s)
- Rachael W Herman
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Gemma Clucas
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Jane Younger
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - John Bates
- Negaunee Integrative Research Center, The Field Museum of Natural History, Chicago, Illinois, USA
| | - Bryce Robinson
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Sushma Reddy
- Bell Museum of Natural History and Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Julia Stepanuk
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Katie O'Brien
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Heather J Lynch
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
- Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, New York, USA
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Folkertsma R, Charbonnel N, Henttonen H, Heroldová M, Huitu O, Kotlík P, Manzo E, Paijmans JLA, Plantard O, Sándor AD, Hofreiter M, Eccard JA. Genomic signatures of climate adaptation in bank voles. Ecol Evol 2024; 14:e10886. [PMID: 38455148 PMCID: PMC10918726 DOI: 10.1002/ece3.10886] [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: 05/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.
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Affiliation(s)
- Remco Folkertsma
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Comparative Cognition Unit, Messerli Research InstituteUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | - Marta Heroldová
- Department of Forest Ecology, FFWTMendel University in BrnoBrnoCzech Republic
| | - Otso Huitu
- Natural Resources Institute FinlandHelsinkiFinland
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and GeneticsCzech Academy of SciencesLiběchovCzech Republic
| | - Emiliano Manzo
- Fondazione Ethoikos, Convento dell'OsservanzaRadicondoliItaly
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Present address:
Evolutionary Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Attila D. Sándor
- HUN‐RENClimate Change: New Blood‐Sucking Parasites and Vector‐Borne Pathogens Research GroupBudapestHungary
- Department of Parasitology and ZoologyUniversity of Veterinary MedicineBudapestHungary
- Department of Parasitology and Parasitic DiseasesUniversity of Agricultural Sciences and Veterinary MedicineCluj‐NapocaRomania
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
| | - Jana A. Eccard
- Animal Ecology, Institute for Biochemistry and Biology, Faculty of ScienceBerlin‐Brandenburg Institute for Biodiversity ResearchUniversity of PotsdamPotsdamGermany
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3
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Labutin A, Heckel G. Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus Evol 2024; 10:veae002. [PMID: 38361825 PMCID: PMC10868551 DOI: 10.1093/ve/veae002] [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: 03/14/2023] [Revised: 11/08/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.
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Affiliation(s)
- Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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Campos DP, Granger-Neto HP, Júnior JES, Faux P, Santos FR. Population Genomics of the Critically Endangered Brazilian Merganser. Animals (Basel) 2023; 13:3759. [PMID: 38136797 PMCID: PMC10741106 DOI: 10.3390/ani13243759] [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: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The Brazilian merganser (Mergus octosetaceus) is one of the most endangered bird species in South America and comprises less than 250 mature individuals in wild environments. This is a species extremely sensitive to environmental disturbances and restricted to a few "pristine" freshwater habitats in Brazil, and it has been classified as Critically Endangered on the IUCN Red List since 1994. Thus, biological conservation studies are vital to promote adequate management strategies and to avoid the decline of merganser populations. In this context, to understand the evolutionary dynamics and the current genetic diversity of remaining Brazilian merganser populations, we used the "Genotyping by Sequencing" approach to genotype 923 SNPs in 30 individuals from all known areas of occurrence. These populations revealed a low genetic diversity and high inbreeding levels, likely due to the recent population decline associated with habitat loss. Furthermore, it showed a moderate level of genetic differentiation between all populations located in four separated areas of the highly threatened Cerrado biome. The results indicate that urgent actions for the conservation of the species should be accompanied by careful genetic monitoring to allow appropriate in situ and ex situ management to increase the long-term species' survival in its natural environment.
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Affiliation(s)
- Davidson P. Campos
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (D.P.C.); (H.P.G.-N.); (J.E.S.J.)
| | - Henry Paul Granger-Neto
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (D.P.C.); (H.P.G.-N.); (J.E.S.J.)
| | - José E. Santos Júnior
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (D.P.C.); (H.P.G.-N.); (J.E.S.J.)
| | - Pierre Faux
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet-Tolosan, France;
| | - Fabrício R. Santos
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (D.P.C.); (H.P.G.-N.); (J.E.S.J.)
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Hofmeister NR, Stuart KC, Warren WC, Werner SJ, Bateson M, Ball GF, Buchanan KL, Burt DW, Cardilini APA, Cassey P, De Meyer T, George J, Meddle SL, Rowland HM, Sherman CDH, Sherwin WB, Vanden Berghe W, Rollins LA, Clayton DF. Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions. Mol Ecol 2023. [PMID: 37933429 DOI: 10.1111/mec.17195] [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: 11/04/2022] [Revised: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.
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Affiliation(s)
- Natalie R Hofmeister
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Katarina C Stuart
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Wesley C Warren
- Department of Animal Sciences and Surgery, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
| | - Scott J Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Melissa Bateson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gregory F Ball
- Department of Psychology, University of Maryland, College Park, Maryland, USA
| | | | - David W Burt
- Office of the Deputy Vice-Chancellor (Research and Innovation), The University of Queensland, Brisbane, Queensland, Australia
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Adam P A Cardilini
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia
| | - Phillip Cassey
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, South Australia, Australia
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Julia George
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Simone L Meddle
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Hannah M Rowland
- Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Craig D H Sherman
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - William B Sherwin
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University Antwerp, Antwerp, Belgium
| | - Lee Ann Rollins
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - David F Clayton
- Department of Genetics & Biochemistry, Clemson University, Clemson, South Carolina, USA
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6
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Colunga-Salas P, Marines-Macías T, Hernández-Canchola G, Barbosa S, Ramírez C, Searle JB, León-Paniagua L. Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat. MAMMAL RES 2023. [DOI: 10.1007/s13364-022-00667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Abstract
Genomic tools are now commonly used to assess the genetic diversity and genetic structure of species and populations, and they provide the ability to describe and address the negative effects of population declines and fragmentation. However, such studies are lacking for arboreal mammals despite their contribution to various ecosystem services, especially in uncommon and critically endangered ecosystems such as cloud forests. The aim of this work was to evaluate and compare the genetic diversity and population structure of two endemic arboreal mice from Mexican cloud forests that are associated with areas with different levels of impacts from human activities. We performed genotyping-by-sequencing in 47 Habromys schmidlyi and 17 Reithrodontomys wagneri individuals to evaluate genetic diversity and differentiation. In both species, the genetic diversity was low compared to other cricetid species, and we observed different population structure patterns, potentially linked to the different ecological associations. We detected two genetic groups in H. schmidlyi, that is a territorial species present in areas of low incline, while a single genetic group was found in R. wagneri, which forms family groups in areas with steep slopes. Overall, these results highlight how species’ genetic diversity can be differentially impacted depending on differential ecological associations within the same ecosystem. This information is essential for the development of the adequate conservation and management of these species.
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7
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Pina-Martins F, Caperta AD, Conceição SIR, Nunes VL, Marques I, Paulo OS. A first look at sea-lavenders genomics - can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex? BMC PLANT BIOLOGY 2023; 23:34. [PMID: 36642719 PMCID: PMC9841708 DOI: 10.1186/s12870-022-03974-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Sea-lavenders (Limonium Mill., Plumbaginaceae) are a cosmopolitan group of diploid and polyploid plants often adapted to extreme saline environments, with a mostly Tethyan distribution, occurring in the Mediterranean, Irano-Turanian, Euro-Siberian and in the New World. The halophylic Limonium vulgare polyploid complex in particular, presents a large distribution throughout extreme salt-marsh habitats and shows little morphological but high taximetric variation, frequently blurring species delimitation. In this work we pursue three main goals: assert whether SNP data from polyploid individuals has the resolution to distinguish the seven sampled species, to better understand how genetically structured Limonium vulgare is, and attempt to identify specific molecular mechanisms for the differentiation between L. maritimum and L. vulgare. For this purpose, 95 individuals were genotyped using Genotyping by Sequencing (GBS), which were assembled as two independent datasets using IPYRAD. All analyses performed downstream of assembly were fully automated. Phylogenetic inference, PCA, and admixture plots were used to infer answers to the study's main goals. RESULTS Close to 10,000 SNPs were obtained for each dataset. Phylogenetic analyses reveal that polyploid data can be used to infer species relationships. Population structure analyses suggest a genetically structured L. vulgare. A set of 34 SNPs were found to be fully segregated between L. vulgare and L. maritimum, two of which are potentially linked to proteins that might be involved in the speciation process. CONCLUSION Despite polyploid data analyses shortcomings, GBS generated SNPs have the resolution to discern all seven included species. Limonium vulgare revealed pronounced genetic structure along a geographical north-south cline. L. maritimum always appears as a distinct genetic entity. Segregated SNPs between L. vulgare and L. maritimum indicate salinity response and morphological trait control genes as potentially interesting to follow up for studying these species' divergence process.
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Affiliation(s)
- Francisco Pina-Martins
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Ana D Caperta
- LEAF-Linking Landscape, Environment, Agriculture and Food, Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Sofia I R Conceição
- LEAF-Linking Landscape, Environment, Agriculture and Food, Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
- LASIGE Computer Science and Engineering Research Centre, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Vera L Nunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Isabel Marques
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- Forest Research Centre (CEF) & Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017, Lisbon, Portugal
| | - Octávio S Paulo
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
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Pilowsky JA, Colwell RK, Rahbek C, Fordham DA. Process-explicit models reveal the structure and dynamics of biodiversity patterns. SCIENCE ADVANCES 2022; 8:eabj2271. [PMID: 35930641 PMCID: PMC9355350 DOI: 10.1126/sciadv.abj2271] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
With ever-growing data availability and computational power at our disposal, we now have the capacity to use process-explicit models more widely to reveal the ecological and evolutionary mechanisms responsible for spatiotemporal patterns of biodiversity. Most research questions focused on the distribution of diversity cannot be answered experimentally, because many important environmental drivers and biological constraints operate at large spatiotemporal scales. However, we can encode proposed mechanisms into models, observe the patterns they produce in virtual environments, and validate these patterns against real-world data or theoretical expectations. This approach can advance understanding of generalizable mechanisms responsible for the distributions of organisms, communities, and ecosystems in space and time, advancing basic and applied science. We review recent developments in process-explicit models and how they have improved knowledge of the distribution and dynamics of life on Earth, enabling biodiversity to be better understood and managed through a deeper recognition of the processes that shape genetic, species, and ecosystem diversity.
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Affiliation(s)
- Julia A. Pilowsky
- The Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (J.A.P.); (D.A.F.)
| | - Robert K. Colwell
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University of Colorado Museum of Natural History, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Departmento de Ecología, Universidade Federal de Goiás, Goiás, Brazil
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Ecology, Peking University, Beijing, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Damien A. Fordham
- The Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (J.A.P.); (D.A.F.)
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Kotlík P, Marková S, Horníková M, Escalante MA, Searle JB. The Bank Vole (Clethrionomys glareolus) as a Model System for Adaptive Phylogeography in the European Theater. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The legacy of climatic changes during the Pleistocene glaciations allows inferences to be made about the patterns and processes associated with range expansion/colonization, including evolutionary adaptation. With the increasing availability of population genomic data, we have the opportunity to examine these questions in detail and in a variety of non-traditional model species. As an exemplar, here we review more than two decades of work by our group and others that illustrate the potential of a single “non-model model” mammal species - the bank vole (Clethrionomys glareolus), which is particularly well suited to illustrate the complexities that may be associated with range expansion and the power of genomics (and other datasets) to uncover them. We first summarize early phylogeographic work using mitochondrial DNA and then describe new phylogeographic insights gained from population genomic analysis of genome-wide SNP data to highlight the bank vole as one of the most compelling examples of a forest mammal, that survived in cryptic extra-Mediterranean (“northern”) glacial refugia in Europe, and as one of the species in which substantial replacement and mixing of lineages originating from different refugia occurred during end-glacial colonization. Our studies of bank vole hemoglobin structure and function, as well as our recent ecological niche modeling study examining differences among bank vole lineages, led us to develop the idea of “adaptive phylogeography.” This is what we call the study of the role of adaptive differences among populations in shaping phylogeographic patterns. Adaptive phylogeography provides a link between past population history and adaptation that can ultimately help predict the potential of future species responses to climate change. Because the bank vole is part of a community of organisms whose range has repeatedly contracted and then expanded in the past, what we learn from the bank vole will be useful for our understanding of a broad range of species.
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Genomic Analysis Reveals Subdivision of Black Rats (Rattus rattus) in India, Origin of the Worldwide Species Spread. Genes (Basel) 2022; 13:genes13020267. [PMID: 35205312 PMCID: PMC8871742 DOI: 10.3390/genes13020267] [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: 12/19/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
In contrast to the detailed and globally extensive studies on the spread of the commensal black rat, Rattus rattus, there has been relatively little work on the phylogeography of the species within India, from where this spread originated. Taking a genomic approach, we typed 27 R. rattus samples from Peninsular India using the genotyping-by-sequencing (GBS) method. Filtering and alignment of the FASTQ files yielded 1499 genome-wide SNPs. Phylogenomic tree reconstruction revealed a distinct subdivision in the R. rattus population, manifested as two clusters corresponding to the east and west coasts of India. We also identified signals of admixture between these two subpopulations, separated by an Fst of 0.20. This striking genomic difference between the east and west coast populations mirrors what has previously been described with mitochondrial DNA sequencing. It is notable that the west coast population of R. rattus has been spread globally, reflecting the origins of commensalism of the species in Western India and the subsequent transport by humans worldwide.
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11
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Saxenhofer M, Labutin A, White TA, Heckel G. Host genetic factors associated with the range limit of a European hantavirus. Mol Ecol 2021; 31:252-265. [PMID: 34614264 PMCID: PMC9298007 DOI: 10.1111/mec.16211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 11/30/2022]
Abstract
The natural host ranges of many viruses are restricted to very specific taxa. Little is known about the molecular barriers between species that lead to the establishment of this restriction or generally prevent virus emergence in new hosts. Here, we identify genomic polymorphisms in a natural rodent host associated with a strong genetic barrier to the transmission of European Tula orthohantavirus (TULV). We analysed the very abrupt spatial transition between two major phylogenetic clades in TULV across the comparatively much wider natural hybrid zone between evolutionary lineages of their reservoir host, the common vole (Microtus arvalis). Genomic scans of 79,225 single nucleotide polymorphisms (SNPs) in 323 TULV‐infected host individuals detected 30 SNPs that were consistently associated with the TULV clades CEN.S or EST.S in two replicate sampling transects. Focusing the analysis on 199 voles with evidence of genomic admixture at the individual level (0.1–0.9) supported statistical significance for all 30 loci. Host genomic variation at these SNPs explained up to 37.6% of clade‐specific TULV infections. Genes in the vicinity of associated SNPs include SAHH, ITCH and two members of the Syngr gene family, which are involved in functions related to immune response or membrane transport. This study demonstrates the relevance of natural hybrid zones as systems not only for studying processes of evolutionary divergence and speciation, but also for the detection of evolving genetic barriers for specialized parasites.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
| | - Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Thomas A White
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
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12
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Parasitic nematodes of the genus Syphacia Seurat, 1916 infecting Cricetidae in the British Isles: the enigmatic status of Syphacia nigeriana. Parasitology 2021; 149:76-94. [PMID: 34608855 PMCID: PMC8862137 DOI: 10.1017/s0031182021001578] [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] [Indexed: 11/13/2022]
Abstract
Oxyurid nematodes (Syphacia spp.) from bank (Myodes glareolus) and field/common (Microtus spp.) voles, from disparate geographical sites in the British Isles, were examined morphologically and genetically. The genetic signatures of 118 new isolates are provided, based primarily on the rDNA internal transcribed spacers (ITS1-5.8S-ITS2) region and for representative isolates also on the small subunit 18S rDNA region and cytochrome c oxidase subunit 1 (cox-1) gene locus. Genetic data on worms recovered from Microtus spp. from the European mainland and from other rodent genera from the Palaearctic, North America and West Africa are also included. We test historical hypotheses indicating that S. nigeriana is a generalist species, infecting a range of different rodent genera. Our results establish that S. nigeriana is a parasite of both bank and field voles in the British Isles. An identical genotype was also recorded from Hubert's multimammate mouse (Mastomys huberti) from Senegal, but Mastomys spp. from West Africa were additionally parasitized by a related, although genetically distinct Syphacia species. We found no evidence for S. petrusewiczi in voles from the British Isles but isolates from Russia and North America were genetically distinct and formed their own separate deep branch in maximum likelihood molecular phylogenetic trees.
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13
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McManus A, Holland CV, Henttonen H, Stuart P. The Invasive Bank Vole ( Myodes glareolus): A Model System for Studying Parasites and Ecoimmunology during a Biological Invasion. Animals (Basel) 2021; 11:2529. [PMID: 34573495 PMCID: PMC8464959 DOI: 10.3390/ani11092529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/16/2022] Open
Abstract
The primary driver of the observed increase in emerging infectious diseases (EIDs) has been identified as human interaction with wildlife and this increase has emphasized knowledge gaps in wildlife pathogens dynamics. Wild rodent models have proven excellent for studying changes in parasite communities and have been a particular focus of eco-immunological research. Helminth species have been shown to be one of the factors regulating rodent abundance and indirectly affect disease burden through trade-offs between immune pathways. The Myodes glareolus invasion in Ireland is a unique model system to explore the invasion dynamics of helminth species. Studies of the invasive population of M. glareolus in Ireland have revealed a verifiable introduction point and its steady spread. Helminths studies of this invasion have identified enemy release, spillover, spillback and dilution taking place. Longitudinal studies have the potential to demonstrate the interplay between helminth parasite dynamics and both immune adaptation and coinfecting microparasites as M. glareolus become established across Ireland. Using the M. glareolus invasion as a model system and other similar wildlife systems, we can begin to fill the large gap in our knowledge surrounding the area of wildlife pathogen dynamics.
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Affiliation(s)
- Andrew McManus
- Department of Biological and Pharmaceutical Sciences, Munster Technological University, Clash, V92 CX88 Tralee, Ireland;
| | - Celia V. Holland
- Department of Zoology, Trinity College Dublin, the University of Dublin, College Green, D02 PN40 Dublin, Ireland;
| | - Heikki Henttonen
- Wildlife Ecology, Natural Resources Institute Finland (Luke), FI 00790 Helsinki, Finland;
| | - Peter Stuart
- Department of Biological and Pharmaceutical Sciences, Munster Technological University, Clash, V92 CX88 Tralee, Ireland;
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14
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Tepolt CK, Grosholz ED, de Rivera CE, Ruiz GM. Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity. Mol Ecol 2021; 31:55-69. [PMID: 34431151 DOI: 10.1111/mec.16143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/24/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022]
Abstract
Adaptation across environmental gradients has been demonstrated in numerous systems with extensive dispersal, despite high gene flow and consequently low genetic structure. The speed and mechanisms by which such adaptation occurs remain poorly resolved, but are critical to understanding species spread and persistence in a changing world. Here, we investigate these mechanisms in the European green crab Carcinus maenas, a globally distributed invader. We focus on a northwestern Pacific population that spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1500 km, we examine genetic structure using 9376 single nucleotide polymorphisms (SNPs). We find high connectivity among five locations, with significant structure between these locations and an enclosed lagoon with limited connectivity to the coast. Among the five highly connected locations, the only structure observed was a cline driven by a handful of SNPs strongly associated with latitude and winter temperature. These SNPs are almost exclusively found in a large cluster of genes in strong linkage disequilibrium that was previously identified as a candidate for cold tolerance adaptation in this species. This region may represent a balanced polymorphism that evolved to promote rapid adaptation in variable environments despite high gene flow, and which now contributes to successful invasion and spread in a novel environment. This research suggests an answer to the paradox of genetically depauperate yet successful invaders: populations may be able to adapt via a few variants of large effect despite low overall diversity.
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Affiliation(s)
- Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Edwin D Grosholz
- Department of Environmental Science and Policy, University of California, Davis, California, USA
| | - Catherine E de Rivera
- Department of Environmental Science and Management, Portland State University, Portland, Oregon, USA
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, Smithsonian Institution, Edgewater, Maryland, USA
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15
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Chen Y, Gao Y, Huang X, Li S, Zhan A. Local environment-driven adaptive evolution in a marine invasive ascidian ( Molgula manhattensis). Ecol Evol 2021; 11:4252-4266. [PMID: 33976808 PMCID: PMC8093682 DOI: 10.1002/ece3.7322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/04/2022] Open
Abstract
Elucidating molecular mechanisms of environment-driven adaptive evolution in marine invaders is crucial for understanding invasion success and further predicting their future invasions. Although increasing evidence suggests that adaptive evolution could contribute to organisms' adaptation to varied environments, there remain knowledge gaps regarding how environments influence genomic variation in invaded habitats and genetic bases underlying local adaptation for most marine invaders. Here, we performed restriction-site-associated DNA sequencing (RADseq) to assess population genetic diversity and further investigate genomic signatures of local adaptation in the marine invasive ascidian, Molgula manhattensis. We revealed that most invasive populations exhibited significant genetic differentiation, low recent gene flow, and no signal of significant population bottleneck. Based on three genome scan approaches, we identified 109 candidate loci potentially under environmental selection. Redundancy analysis and variance partitioning analysis suggest that local environmental factors, particularly the salinity-related variables, represent crucial evolutionary forces in driving adaptive divergence. Using the newly developed transcriptome as a reference, 14 functional genes were finally obtained with potential roles in salinity adaptation, including SLC5A1 and SLC9C1 genes from the solute carrier gene (SLC) superfamily. Our findings confirm that differed local environments could rapidly drive adaptive divergence among invasive populations and leave detectable genomic signatures in marine invaders.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Yangchun Gao
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
- Guangdong Key Laboratory of Animal Conservation and Resource UtilizationInstitute of ZoologyGuangdong Academy of SciencesHaizhu DistrictGuangzhouChina
| | - Xuena Huang
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
| | - Shiguo Li
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Aibin Zhan
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
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16
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Barr K, Beichman AC, Kalhori P, Rajbhandary J, Bay RA, Ruegg K, Smith TB. Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird ( Agelaius tricolor). Evol Appl 2021; 14:674-684. [PMID: 33767743 PMCID: PMC7980274 DOI: 10.1111/eva.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD-Seq) from samples collected across the species' range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K = 1), and comparisons of genetic differentiation (average FST = 0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Annabel C. Beichman
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Pooneh Kalhori
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Jasmine Rajbhandary
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCAUSA
| | - Kristen Ruegg
- Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
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17
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Hill T, Unckless RL. Adaptation, ancestral variation and gene flow in a 'Sky Island' Drosophila species. Mol Ecol 2021; 30:83-99. [PMID: 33089581 PMCID: PMC7945764 DOI: 10.1111/mec.15701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Over time, populations of species can expand, contract, fragment and become isolated, creating subpopulations that must adapt to local conditions. Understanding how species maintain variation after divergence as well as adapt to these changes in the face of gene flow is of great interest, especially as the current climate crisis has caused range shifts and frequent migrations for many species. Here, we characterize how a mycophageous fly species, Drosophila innubila, came to inhabit and adapt to its current range which includes mountain forests in south-western USA separated by large expanses of desert. Using population genomic data from more than 300 wild-caught individuals, we examine four populations to determine their population history in these mountain forests, looking for signatures of local adaptation. In this first extensive study, establishing D. innubila as a key genomic "Sky Island" model, we find D. innubila spread northwards during the previous glaciation period (30-100 KYA) and have recently expanded even further (0.2-2 KYA). D. innubila shows little evidence of population structure, consistent with a recent establishment and genetic variation maintained since before geographic stratification. We also find some signatures of recent selective sweeps in chorion proteins and population differentiation in antifungal immune genes suggesting differences in the environments to which flies are adapting. However, we find little support for long-term recurrent selection in these genes. In contrast, we find evidence of long-term recurrent positive selection in immune pathways such as the Toll signalling system and the Toll-regulated antimicrobial peptides.
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Affiliation(s)
- Tom Hill
- 4055 Haworth Hall, The Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045
| | - Robert L. Unckless
- 4055 Haworth Hall, The Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045
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18
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Charbonnel N, Galan M, Tatard C, Loiseau A, Diagne C, Dalecky A, Parrinello H, Rialle S, Severac D, Brouat C. Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal. Sci Rep 2020; 10:18257. [PMID: 33106535 PMCID: PMC7589499 DOI: 10.1038/s41598-020-75060-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/28/2020] [Indexed: 01/09/2023] Open
Abstract
Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. However, what determines the successful establishment and spread of introduced populations remains unclear. Here, we explore several hypotheses linking invasion success and immune phenotype traits, including those based on the evolution of increased competitive ability concept. We compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal (West Africa). Transcriptome analyses identified differential expression between anciently and recently established populations for 364 mouse genes and 83 rat genes. All immune-related genes displaying differential expression along the mouse invasion route were overexpressed at three of the four recently invaded sites studied. Complement activation pathway genes were overrepresented among these genes. By contrast, no particular immunological process was found to be overrepresented among the differentially expressed genes of black rat. Changes in transcriptome profiles were thus observed along invasion routes, but with different specific patterns between the two invasive species. These changes may be driven by increases in infection risks at sites recently invaded by the house mouse, and by stochastic events associated with colonization history for the black rat. These results constitute a first step toward the identification of immune eco-evolutionary processes potentially involved in the invasion success of these two rodent species.
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Affiliation(s)
- Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | - Maxime Galan
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Caroline Tatard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Christophe Diagne
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.,Départment de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Fann, Dakar, Senegal
| | | | - Hugues Parrinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Stephanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Carine Brouat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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19
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Miller TEX, Angert AL, Brown CD, Lee-Yaw JA, Lewis M, Lutscher F, Marculis NG, Melbourne BA, Shaw AK, Szűcs M, Tabares O, Usui T, Weiss-Lehman C, Williams JL. Eco-evolutionary dynamics of range expansion. Ecology 2020; 101:e03139. [PMID: 32697876 DOI: 10.1002/ecy.3139] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/05/2020] [Accepted: 06/08/2020] [Indexed: 01/31/2023]
Abstract
Understanding the movement of species' ranges is a classic ecological problem that takes on urgency in this era of global change. Historically treated as a purely ecological process, range expansion is now understood to involve eco-evolutionary feedbacks due to spatial genetic structure that emerges as populations spread. We synthesize empirical and theoretical work on the eco-evolutionary dynamics of range expansion, with emphasis on bridging directional, deterministic processes that favor evolved increases in dispersal and demographic traits with stochastic processes that lead to the random fixation of alleles and traits. We develop a framework for understanding the joint influence of these processes in changing the mean and variance of expansion speed and its underlying traits. Our synthesis of recent laboratory experiments supports the consistent role of evolution in accelerating expansion speed on average, and highlights unexpected diversity in how evolution can influence variability in speed: results not well predicted by current theory. We discuss and evaluate support for three classes of modifiers of eco-evolutionary range dynamics (landscape context, trait genetics, and biotic interactions), identify emerging themes, and suggest new directions for future work in a field that stands to increase in relevance as populations move in response to global change.
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Affiliation(s)
- Tom E X Miller
- Program in Ecology and Evolutionary Biology, Department of BioSciences, Rice University, Houston, Texas, 77005, USA
| | - Amy L Angert
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z2, Canada
| | - Carissa D Brown
- Department of Geography, Memorial University, 230 Elizabeth Avenue, St John's, Newfoundland and Labrador, A1B 3X9, Canada
| | - Julie A Lee-Yaw
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z2, Canada.,Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Mark Lewis
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada
| | - Frithjof Lutscher
- Department of Mathematics and Statistics, and Department of Biology, University of Ottawa, Ottawa, Ottawa, K1N 6N5, Canada
| | - Nathan G Marculis
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada.,Department of Environmental Science and Policy, University of California-Davis, Davis, California, 95616, USA
| | - Brett A Melbourne
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Allison K Shaw
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Marianna Szűcs
- Department of Entomology, Michigan State University, 288 Farm Lane, East Lansing, Michigan, 48824, USA
| | - Olivia Tabares
- Department of Geography and Biodiversity Research Centre, University of British Columbia, 1984 West Mall, Vancouver, British Columbia, V6T 1Z2, Canada
| | - Takuji Usui
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z2, Canada
| | - Christopher Weiss-Lehman
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Jennifer L Williams
- Department of Geography and Biodiversity Research Centre, University of British Columbia, 1984 West Mall, Vancouver, British Columbia, V6T 1Z2, Canada
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20
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Philopatry at the frontier: A demographically driven scenario for the evolution of multilevel societies in baboons (Papio). J Hum Evol 2020; 146:102819. [PMID: 32736063 DOI: 10.1016/j.jhevol.2020.102819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 04/25/2020] [Accepted: 04/25/2020] [Indexed: 11/23/2022]
Abstract
The baboons (Papio sp.) exhibit marked interspecies variation in social behavior. The thesis presented here argues, first, that male philopatry is a crucial factor, arguably the crucial factor, underlying the other distinctive features (one-male units, multilevel society) shared by hamadryas and Guinea baboons, but not other species of Papio. The second suggestion is that male philopatry as a population norm was not an adaptation to a particular habitat or set of ecological circumstances but evolved in the common ancestor of hamadryas and Guinea baboons as a response to natural selection in the demographic context peculiar to the frontier of a rapidly expanding population. Other derived features of social structure (male-male tolerance, some facultative female dispersal) subsequently evolved to accommodate male philopatry. The mitochondrial genetic population structure of extant baboons preserves a footprint of the initial expansion of 'modern' Papio. Immediately after the expansion, male-philopatric, multilevel populations with a general physical and behavioral resemblance to Guinea baboons occupied the whole northern hemisphere range of the genus. Behavioral and physical autapomorphies of hamadryas baboons evolved in a subpopulation of this ancestral northern base, in response to a less productive habitat of the Horn of Africa. Subsequently, ancestral olive baboons 'reinvented' male dispersal. They and yellow baboons, another male-dispersing species, then replaced most of the male-philopatric northern populations, by male-driven introgression and nuclear swamping.
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21
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Garcia-Elfring A, Barrett RDH, Millien V. Genomic Signatures of Selection along a Climatic Gradient in the Northern Range Margin of the White-Footed Mouse (Peromyscus leucopus). J Hered 2020; 110:684-695. [PMID: 31300816 DOI: 10.1093/jhered/esz045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Identifying genetic variation involved in thermal adaptation is likely to yield insights into how species adapt to different climates. Physiological and behavioral responses associated with overwintering (e.g., torpor) are thought to serve important functions in climate adaptation. In this study, we use 2 isolated Peromyscus leucopus lineages on the northern margin of the species range to identify single nucleotide polymorphisms (SNPs) showing a strong environmental association and test for evidence of parallel evolution. We found signatures of clinal selection in each lineage, but evidence of parallelism was limited, with only 2 SNPs showing parallel allele frequencies across transects. These parallel SNPs map to a gene involved in protection against iron-dependent oxidative stress (Fxn) and to a gene with unknown function but containing a forkhead-associated domain (Fhad1). Furthermore, within transects, we find significant clinal patterns in genes enriched for functions associated with glycogen homeostasis, synaptic function, intracellular Ca2+ balance, H3 histone modification, as well as the G2/M transition of cell division. Our results are consistent with recent literature on the cellular and molecular basis of climate adaptation in small mammals and provide candidate genomic regions for further study.
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Affiliation(s)
- Alan Garcia-Elfring
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Virginie Millien
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
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22
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Lado P, Smith ML, Carstens BC, Klompen H. Population genetic structure and demographic history of the lone star tick, Amblyomma americanum (Ixodida: Ixodidae): New evidence supporting old records. Mol Ecol 2020; 29:2810-2823. [PMID: 32574413 DOI: 10.1111/mec.15524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 01/25/2023]
Abstract
Range expansions are a potential outcome of changes in habitat suitability, which commonly result as a consequence of climate change. Hypotheses on such changes in the geographic distribution of a certain species can be evaluated using population genetic structure and demography. In this study we explore the population genetic structure, genetic variability, demographic history of, and habitat suitability for Amblyomma americanum, a North American tick species that is a known vector of several pathogenic microorganisms. We used a double digestion restriction site-associated DNA sequencing technique (dd-RAD seq) and discovered 8,181 independent single nucleotide polymorphisms (SNPs) in 189 ticks from across the geographic range of the species. Genetic diversity was low, particularly when considering the broad geographic range of this species. The edge populations were less diverse than populations belonging to the historic range, possibly indicative of a range expansion, but this hypothesis was not statistically supported by a test based on genetic data. Nonetheless, moderate levels of population structure and substructure were detected between geographic regions. For New England, demographic and species distribution models support a scenario where A. americanum was present in more northern locations in the past, underwent a bottleneck, and subsequently recovered. These results are consistent with a hypothesis that this species is re-establishing in this area, rather than one focused on range expansion from the south. This hypothesis is consistent with old records describing the presence of A. americanum in the northeastern US in the early colonial period.
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Affiliation(s)
- Paula Lado
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Hans Klompen
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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23
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Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics 2020; 35:4480-4483. [PMID: 31077292 PMCID: PMC6821363 DOI: 10.1093/bioinformatics/btz311] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
SUMMARY SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework. The new capabilities include long-distance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a large variety of DNA mutation models. These implementations have been applied independently to various studies, but grouped together in the current version. AVAILABILITY AND IMPLEMENTATION SPLATCHE3 is written in C++ and is freely available for non-commercial use from the website http://www.splatche.com/splatche3. It includes console versions for Linux, MacOs and Windows and a user-friendly GUI for Windows, as well as detailed documentation and ready-to-use examples.
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Affiliation(s)
- Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva 1211, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, Vigo 36310, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo 36310, Spain
| | - Claudio S Quilodràn
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Nicolas Ray
- Institute of Global Health, GeoHealth Group, University of Geneva, Geneva 1205, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva 1205, Switzerland
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24
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Marková S, Horníková M, Lanier HC, Henttonen H, Searle JB, Weider LJ, Kotlík P. High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonizations and end-glacial refugia. Mol Ecol 2020; 29:1730-1744. [PMID: 32248595 DOI: 10.1111/mec.15427] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/10/2020] [Accepted: 03/25/2020] [Indexed: 01/08/2023]
Abstract
The history of repeated northern glacial cycling and southern climatic stability has long dominated explanations for how genetic diversity is distributed within temperate species in Eurasia and North America. However, growing evidence indicates the importance of cryptic refugia for northern colonization dynamics. An important geographic region to assess this is Fennoscandia, where recolonization at the end of the last glaciation was restricted to specific routes and temporal windows. We used genomic data to analyse genetic diversity and colonization history of the bank vole (Myodes glareolus) throughout Europe (>800 samples) with Fennoscandia as the northern apex. We inferred that bank voles colonized Fennoscandia multiple times by two different routes; with three separate colonizations via a southern land-bridge route deriving from a "Carpathian" glacial refugium and one via a north-eastern route from an "Eastern" glacial refugium near the Ural Mountains. Clustering of genome-wide SNPs revealed high diversity in Fennoscandia, with eight genomic clusters: three of Carpathian origin and five Eastern. Time estimates revealed that the first of the Carpathian colonizations occurred before the Younger Dryas (YD), meaning that the first colonists survived the YD in Fennoscandia. Results also indicated that introgression between bank and northern red-backed voles (Myodes rutilus) took place in Fennoscandia just after end-glacial colonization. Therefore, multiple colonizations from the same and different cryptic refugia, temporal and spatial separations and interspecific introgression have shaped bank vole genetic variability in Fennoscandia. Together, these processes drive high genetic diversity at the apex of the northern expansion in this emerging model species.
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Affiliation(s)
- Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA.,Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | | | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Lawrence J Weider
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
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25
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Faux P, Oliveira JC, Campos DP, Dantas GP, Maia TA, Dergan CG, Cassemiro PM, Hajdu GL, Santos-Júnior JE, Santos FR. Fast genomic analysis of aquatic bird populations from short single-end reads considering sex-related pitfalls. ECOL INFORM 2020. [DOI: 10.1016/j.ecoinf.2020.101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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The hidden faces of a biological invasion: parasite dynamics of invaders and natives. Int J Parasitol 2020; 50:111-123. [PMID: 31981672 DOI: 10.1016/j.ijpara.2019.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/02/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023]
Abstract
One of the primary drivers of emerging infectious diseases (EIDs) is human intervention via host or parasite translocations. A unique opportunity to study host and parasite dispersal during a bio-invasion currently exists in Ireland due to the introduction of the bank vole (Myodes glareolus) in the 1920s. The continuing range expansion of M. glareolus within Ireland presents a natural large-scale perturbation experiment. This study used the Irish M. glareolus model to conduct a spatiotemporal study analysing the parasite dynamics of native and invasive species throughout their range. Myodes glareolus and native Apodemus sylvaticus were trapped in woodlands across Ireland and surveyed for their helminth parasites. Myodes glareolus in Ireland were found to have lower parasite diversity in comparison to records of M. glareolus from across Europe and A. sylvaticus in Ireland. Increased density of M. glareolus resulted in a dilution effect, with significantly lower levels of parasitism overall in native hosts, where M. glareolus has been established longest. However, three helminth parasite species of A. sylvaticus increased in abundance in the presence of M. glareolus. Furthermore, M. glareolus at the expansion front were less parasitised (lower abundance and prevalence of certain parasites and lower parasite diversity) than M. glareolus from the core population. This "enemy release" is believed to be mediating the continued successful spread of the invader across Ireland. Our results identify two important variables, seasonality and the stage of the invasion, which should not be overlooked when investigating or managing the changing distribution of hosts and their parasites. Studies of bio-invasions and parasite transmission have primarily focused on the invasive host species or the native host species in cases where virulent pathogen spillover is observed. Our results demonstrate how the concurrent study of invasive and native hosts, and the careful identification of their parasite communities, allows the dynamic processes influencing the parasite component and intracommunity to be identified.
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27
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Prunier J, Lemaçon A, Bastien A, Jafarikia M, Porth I, Robert C, Droit A. LD-annot: A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes. Front Genet 2019; 10:1192. [PMID: 31850063 PMCID: PMC6889475 DOI: 10.3389/fgene.2019.01192] [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: 07/02/2019] [Accepted: 10/28/2019] [Indexed: 11/24/2022] Open
Abstract
A multitude of model and non-model species studies have now taken full advantage of powerful high-throughput genotyping advances such as SNP arrays and genotyping-by-sequencing (GBS) technology to investigate the genetic basis of trait variation. However, due to incomplete genome coverage by these technologies, the identified SNPs are likely in linkage disequilibrium (LD) with the causal polymorphisms, rather than be causal themselves. In addition, researchers could benefit from annotations for the identified candidate SNPs and, simultaneously, for all neighboring genes in genetic linkage. In such case, LD extent estimation surrounding the candidate SNPs is required to determine the regions encompassing genes of interest. We describe here an automated pipeline, “LD-annot,” designed to delineate specific regions of interest for a given experiment and candidate polymorphisms on the basis of LD extent, and furthermore, provide annotations for all genes within such regions. LD-annot uses standard file formats, bioinformatics tools, and languages to provide identifiers, coordinates, and annotations for genes in genetic linkage with each candidate polymorphism. Although the focus lies upon SNP arrays and GBS data as they are being routinely deployed, this pipeline can be applied to a variety of datasets as long as genotypic data are available for a high number of polymorphisms and formatted into a vcf file. A checkpoint procedure in the pipeline allows to test several threshold values for linkage without having to rerun the entire pipeline, thus saving the user computational time and resources. We applied this new pipeline to four different sample sets: two breeding populations GBS datasets, one within-pedigree SNP set coming from whole genome sequencing (WGS), and a very large multi-varieties SNP dataset obtained from WGS, representing variable sample sizes, and numbers of polymorphisms. LD-annot performed within minutes, even when very high numbers of polymorphisms are investigated and thus will efficiently assist research efforts aimed at identifying biologically meaningful genetic polymorphisms underlying phenotypic variation. LD-annot tool is available under a GPL license from https://github.com/ArnaudDroitLab/LD-annot.
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Affiliation(s)
- Julien Prunier
- Genomics Center, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Quebec, QC, Canada.,Forestry Research Centre, Forestry Department, Université Laval, Quebec, QC, Canada
| | - Audrey Lemaçon
- Genomics Center, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Quebec, QC, Canada
| | - Alexandre Bastien
- Faculty of Agricultural and Food Science, Université Laval, Quebec, QC, Canada
| | - Mohsen Jafarikia
- Canadian Centre for Swine Improvement, Ottawa, ON, Canada.,Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Ilga Porth
- Forestry Research Centre, Forestry Department, Université Laval, Quebec, QC, Canada
| | - Claude Robert
- Forestry Research Centre, Forestry Department, Université Laval, Quebec, QC, Canada
| | - Arnaud Droit
- Genomics Center, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Quebec, QC, Canada
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28
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Szewczyk M, Nowak S, Niedźwiecka N, Hulva P, Špinkytė-Bačkaitienė R, Demjanovičová K, Bolfíková BČ, Antal V, Fenchuk V, Figura M, Tomczak P, Stachyra P, Stępniak KM, Zwijacz-Kozica T, Mysłajek RW. Dynamic range expansion leads to establishment of a new, genetically distinct wolf population in Central Europe. Sci Rep 2019; 9:19003. [PMID: 31831858 PMCID: PMC6908625 DOI: 10.1038/s41598-019-55273-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/06/2019] [Indexed: 11/12/2022] Open
Abstract
Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (Canis lupus) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset (881 identified individuals) of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies. In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf genetic structure in Central Europe.
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Affiliation(s)
- Maciej Szewczyk
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.,Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland.,Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Sabina Nowak
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Natalia Niedźwiecka
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Pavel Hulva
- Faculty of Science, Charles University in Prague, Viničná 7, 128 43, Prague, Czech Republic.,Faculty of Science, University of Ostrava, Chittussiho 10, 170 00, Ostrava, Czech Republic
| | | | - Klára Demjanovičová
- Faculty of Science, University of Ostrava, Chittussiho 10, 170 00, Ostrava, Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00, Czech Republic
| | - Vladimír Antal
- State Nature Conservancy of Slovak Republic, Tajovského 28B, 974 01, Banská Bystrica, Slovakia
| | - Viktar Fenchuk
- APB-BirdLife Belarus, Engelsa 34A - 1, 220030, Minsk, Belarus
| | - Michał Figura
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Patrycja Tomczak
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland.,Institute of Romance Studies, Faculty of Modern Languages and Literature, Adam Mickiewicz University in Poznań, Al. Niepodległości 4, 61-874, Poznań, Poland
| | | | - Kinga M Stępniak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.,Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | | | - Robert W Mysłajek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.
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29
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Selechnik D, Richardson MF, Shine R, DeVore JL, Ducatez S, Rollins LA. Increased Adaptive Variation Despite Reduced Overall Genetic Diversity in a Rapidly Adapting Invader. Front Genet 2019; 10:1221. [PMID: 31850072 PMCID: PMC6901984 DOI: 10.3389/fgene.2019.01221] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 11/05/2019] [Indexed: 01/26/2023] Open
Abstract
Invasive species often evolve rapidly following introduction despite genetic bottlenecks that may result from small numbers of founders; however, some invasions may not fit this “genetic paradox”. The invasive cane toad (Rhinella marina) displays high phenotypic variation across its introduced Australian range. Here, we used three genome-wide datasets to characterize their population structure and genetic diversity. We found that toads form three genetic clusters: 1) native range toads, 2) toads from the source population in Hawaii and long-established areas near introduction sites in Australia, and 3) toads from more recently established northern Australian sites. Although we find an overall reduction in genetic diversity following introduction, we do not see this reduction in loci putatively under selection, suggesting that genetic diversity may have been maintained at ecologically relevant traits, or that mutation rates were high enough to maintain adaptive potential. Nonetheless, toads encounter novel environmental challenges in Australia, and the transition between genetic clusters occurs at a point along the invasion transect where temperature rises and rainfall decreases. We identify environmentally associated loci known to be involved in resistance to heat and dehydration. This study highlights that natural selection occurs rapidly and plays a vital role in shaping the structure of invasive populations.
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Affiliation(s)
- Daniel Selechnik
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia.,Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mark F Richardson
- Deakin Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Richard Shine
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Jayna L DeVore
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Simon Ducatez
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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30
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Campbell P, Arévalo L, Martin H, Chen C, Sun S, Rowe AH, Webster MS, Searle JB, Pasch B. Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice ( Onychomys). Ecol Evol 2019; 9:12886-12896. [PMID: 31788222 PMCID: PMC6875671 DOI: 10.1002/ece3.5770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long-distance acoustic signals to attract and localize mates; Onychomys arenicola and Onychomys torridus are acoustically similar and morphologically cryptic whereas Onychomys leucogaster is larger and acoustically distinct. We used genotyping-by-sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, laboratory crosses between O. torridus and O. arenicola produced litters whereas O. leucogaster and O. arenicola crosses did not. Call fundamental frequency in O. torridus and O. arenicola was indistinguishable in allopatry but significantly differentiated in sympatry, a pattern consistent with reproductive character displacement. These results suggest that assortative mating based on a long-distance signal is an important isolating mechanism between O. torridus and O. arenicola and highlight the importance of behavioral barriers in determining the permeability of species boundaries.
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Affiliation(s)
- Polly Campbell
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California, RiversideRiversideCAUSA
| | - Lena Arévalo
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Developmental PathologyUniversity of BonnBonnGermany
| | - Heather Martin
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
| | - Charles Chen
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
| | - Shuzhen Sun
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Forest and Conservation SciencesForest Science CentreThe University of British ColumbiaVancouverBCCanada
| | - Ashlee H. Rowe
- Department of BiologyThe University of OklahomaNormanOKUSA
| | - Michael S. Webster
- Macaulay LibraryCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Department of Neurobiology and BehaviorCornell UniversityIthacaNYUSA
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Bret Pasch
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
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31
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Kalb DM, Delaney DA, DeYoung RW, Bowman JL. Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula. Ecol Evol 2019; 9:11504-11517. [PMID: 31641489 PMCID: PMC6802040 DOI: 10.1002/ece3.5655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/01/2019] [Accepted: 08/26/2019] [Indexed: 01/13/2023] Open
Abstract
The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA, is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on the data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from approximate Bayesian computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately five effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. five individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.
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Affiliation(s)
- David M. Kalb
- Virginia Department of Game and Inland FisheriesMarionVAUSA
| | - Deborah A. Delaney
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research InstituteTexas A&M University‐KingsvilleKingsvilleTXUSA
| | - Jacob L. Bowman
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
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32
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Fuller N, Ford AT, Lerebours A, Gudkov DI, Nagorskaya LL, Smith JT. Chronic radiation exposure at Chernobyl shows no effect on genetic diversity in the freshwater crustacean, Asellus aquaticus thirty years on. Ecol Evol 2019; 9:10135-10144. [PMID: 31624541 PMCID: PMC6787803 DOI: 10.1002/ece3.5478] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022] Open
Abstract
Analysis of genetic diversity represents a fundamental component of ecological risk assessments in contaminated environments. Many studies have assessed the genetic implications of chronic radiation exposure at Chernobyl, generally recording an elevated genetic diversity and mutation rate in rodents, plants, and birds inhabiting contaminated areas. Only limited studies have considered genetic diversity in aquatic biota at Chernobyl, despite the large number of freshwater systems where elevated dose rates will persist for many years. Consequently, the present study aimed to assess the effects of chronic radiation exposure on genetic diversity in the freshwater crustacean, Asellus aquaticus, using a genome-wide SNP approach (Genotyping-by-sequencing). It was hypothesized that genetic diversity in A. aquaticus would be positively correlated with dose rate. A. aquaticus was collected from six lakes in Belarus and the Ukraine ranging in dose rate from 0.064 to 27.1 µGy/hr. Genotyping-by-sequencing analysis was performed on 74 individuals. A significant relationship between geographical distance and genetic differentiation confirmed the Isolation-by-Distance model. Conversely, no significant relationship between dose rate and genetic differentiation suggested no effect of the contamination gradient on genetic differentiation between populations. No significant relationship between five measures of genetic diversity and dose rate was recorded, suggesting that radiation exposure has not significantly influenced genetic diversity in A. aquaticus at Chernobyl. This is the first study to adopt a genome-wide SNP approach to assess the impacts of environmental radiation exposure on biota. These findings are fundamental to understanding the long-term success of aquatic populations in contaminated environments at Chernobyl and Fukushima.
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Affiliation(s)
- Neil Fuller
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Alex T. Ford
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Adélaïde Lerebours
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Dmitri I. Gudkov
- Department of Freshwater RadioecologyInstitute of HydrobiologyKievUkraine
| | - Liubov L. Nagorskaya
- Applied Science Center for Bioresources of the National Academy of Sciences of BelarusMinskBelarus
| | - Jim T. Smith
- School of Earth & Environmental SciencesUniversity of PortsmouthPortsmouthUK
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33
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Pujol‐Buxó E, Garcia‐Cisneros A, Miaud C, Llorente GA. Genetic relationships and diversity patterns within the invasive range of the Mediterranean Painted Frog. J Zool (1987) 2019. [DOI: 10.1111/jzo.12703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Pujol‐Buxó
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona Barcelona Spain
- IrBio, Institut de Recerca de la Biodiversitat University of Barcelona Barcelona Spain
| | - A. Garcia‐Cisneros
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona Barcelona Spain
- Center for Advanced Studies of Blanes (CEAB‐CSIC) Blanes Spain
| | - C. Miaud
- EPHE, UMR 5175 CEFE, CNRS, UM, Univ. P. Valéry, SupAgro, IRD, INRA, Biogéographie et Écologie des Vertébrés PSL Research University Montpellier France
| | - G. A. Llorente
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona Barcelona Spain
- IrBio, Institut de Recerca de la Biodiversitat University of Barcelona Barcelona Spain
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34
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Li H, Heckel G, Huang Y, Fan W, Ślipiński A, Pang H. Genomic changes in the biological control agent Cryptolaemus montrouzieri associated with introduction. Evol Appl 2019; 12:989-1000. [PMID: 31080510 PMCID: PMC6503826 DOI: 10.1111/eva.12774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 11/20/2018] [Accepted: 01/13/2019] [Indexed: 01/01/2023] Open
Abstract
Biological control is the main purpose of intentionally introducing non-native invertebrate species. The evolutionary changes that occur in the populations of the introduced biological control agents may determine the agent's efficiency and the environmental safety. Here, to explore the pattern and extent of potential genomic changes in the worldwide introduced predatory ladybird beetle Cryptolaemus montrouzieri, we used a reduced-representation sequencing method to analyze the genome-wide differentiation of the samples from two native and five introduced locations. Our analyses based on a total of 53,032 single nucleotide polymorphism loci showed that beetles from the introduced locations in Asia and Europe exhibited significant reductions in genetic diversity and high differentiation compared with the samples from the native Australian range. Each introduced population belonged to a unique genetic cluster, while the beetles from two native locations were much more similar. These genomic patterns were also detected when the dataset was pruned for genomic outlier loci (52,318 SNPs remaining), suggesting that random genetic drift was the main force shaping the genetic diversity and population structure of this biological control agent. Our results provide a genome-wide characterization of polymorphisms in a biological control agent and reveal genomic differences that were influenced by the introduction history. These differences might complicate assessments of the efficiency of biological control and the invasion potential of this species but also indicate the feasibility of selective breeding.
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Affiliation(s)
- Hao‐Sen Li
- State Key Laboratory of Biocontrol, Ecology and Evolution, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Gerald Heckel
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Yu‐Hao Huang
- State Key Laboratory of Biocontrol, Ecology and Evolution, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Wei‐Jian Fan
- College of Life SciencesTianjin Normal UniversityTianjinChina
| | - Adam Ślipiński
- State Key Laboratory of Biocontrol, Ecology and Evolution, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Australian National Insect Collection, National Research CollectionsCSIROCanberraAustralian Capital TerritoryAustralia
| | - Hong Pang
- State Key Laboratory of Biocontrol, Ecology and Evolution, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
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35
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Riddle BR, Jezkova T. How is phylogeography shaping our understanding of the geography of diversity, diversification, and range dynamics in mammals? J Mammal 2019. [DOI: 10.1093/jmammal/gyz027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Brett R Riddle
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Tereza Jezkova
- Department of Biology, Miami University of Ohio, Oxford, OH, USA
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36
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Braasch J, Barker BS, Dlugosch KM. Expansion history and environmental suitability shape effective population size in a plant invasion. Mol Ecol 2019; 28:2546-2558. [PMID: 30993767 DOI: 10.1111/mec.15104] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/19/2022]
Abstract
The margins of an expanding range are predicted to be challenging environments for adaptation. Marginal populations should often experience low effective population sizes (Ne ) where genetic drift is high due to demographic expansion and/or census population size is low due to unfavourable environmental conditions. Nevertheless, invasive species demonstrate increasing evidence of rapid evolution and potential adaptation to novel environments encountered during colonization, calling into question whether significant reductions in Ne are realized during range expansions in nature. Here we report one of the first empirical tests of the joint effects of expansion dynamics and environment on effective population size variation during invasive range expansion. We estimate contemporary values of Ne using rates of linkage disequilibrium among genome-wide markers within introduced populations of the highly invasive plant Centaurea solstitialis (yellow starthistle) in North America (California, USA), and within native Eurasian populations. As predicted, we find that Ne within the invaded range is positively correlated with both expansion history (time since founding) and habitat quality (abiotic climate). History and climate had independent additive effects with similar effect sizes, indicating an important role for both factors in this invasion. These results support theoretical expectations for the population genetics of range expansion, though whether these processes can ultimately arrest the spread of an invasive species remains an unanswered question.
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Affiliation(s)
- Joseph Braasch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Brittany S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona.,Integrated Plant Protection Center and Department of Horticulture, Oregon State University, Corvallis, Oregon
| | - Katrina M Dlugosch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
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37
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Billerman SM, Cicero C, Bowie RCK, Carling MD. Phenotypic and genetic introgression across a moving woodpecker hybrid zone. Mol Ecol 2019; 28:1692-1708. [DOI: 10.1111/mec.15043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/22/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Shawn M. Billerman
- Department of Zoology and Physiology University of Wyoming Laramie Wyoming
- Program in Ecology University of Wyoming Laramie Wyoming
| | - Carla Cicero
- Museum of Vertebrate Zoology University of California Berkeley California
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology University of California Berkeley California
- Department of Integrative Biology University of California Berkeley California
| | - Matthew D. Carling
- Department of Zoology and Physiology University of Wyoming Laramie Wyoming
- Program in Ecology University of Wyoming Laramie Wyoming
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38
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Gralka M, Hallatschek O. Environmental heterogeneity can tip the population genetics of range expansions. eLife 2019; 8:e44359. [PMID: 30977724 PMCID: PMC6513619 DOI: 10.7554/elife.44359] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/11/2019] [Indexed: 12/12/2022] Open
Abstract
The population genetics of most range expansions is thought to be shaped by the competition between Darwinian selection and random genetic drift at the range margins. Here, we show that the evolutionary dynamics during range expansions is highly sensitive to additional fluctuations induced by environmental heterogeneities. Tracking mutant clones with a tunable fitness effect in bacterial colonies grown on randomly patterned surfaces we found that environmental heterogeneity can dramatically reduce the efficacy of selection. Time-lapse microscopy and computer simulations suggest that this effect arises generically from a local 'pinning' of the expansion front, whereby stretches of the front are slowed down on a length scale that depends on the structure of the environmental heterogeneity. This pinning focuses the range expansion into a small number of 'lucky' individuals with access to expansion paths, altering the neutral evolutionary dynamics and increasing the importance of chance relative to selection.
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Affiliation(s)
- Matti Gralka
- Department of PhysicsUniversity of California, BerkeleyBerkeleyUnited States
| | - Oskar Hallatschek
- Department of PhysicsUniversity of California, BerkeleyBerkeleyUnited States
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyUnited States
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39
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Stepien CA, Snyder MR, Elz AE. Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection. PLoS One 2019; 14:e0203012. [PMID: 30917127 PMCID: PMC6436794 DOI: 10.1371/journal.pone.0203012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/05/2019] [Indexed: 11/19/2022] Open
Abstract
In the 1970s, the introduced silver carp Hypophthalmichthys molitrix (which is indigenous to eastern Asia) escaped from southern U.S. aquaculture to spread throughout the Mississippi River basin, and since has steadily moved northward. This large, prolific filter-feeder reduces food availability for other fishes. It now has reached the threshold of the Laurentian Great Lakes, where it likely will significantly impact food chains and fisheries. Our study evaluates population genetic variability and differentiation of the silver carp using 10 nuclear DNA microsatellite loci, and sequences of two mitochondrial genes-cytochrome b and cytochrome c oxidase subunit 1, along with the nuclear ribosomal protein S7 gene intron 1. We analyze population samples from: two primary Great Lakes' invasion fronts (at the Illinois River outside of Chicago, IL in Lake Michigan and in the Wabash River, which leads into the Maumee River and western Lake Erie), the original establishment "core" in the Lower Mississippi River, and expansion areas in the Upper Mississippi and Missouri rivers. We analyze and compare our results with bighead and other invasive carps, and cyprinid relatives. Results reveal that the silver carp invasion possesses moderate levels of genetic diversity, with more mtDNA haplotypes and unique microsatellite alleles in the "core" Lower Mississippi River population, which also diverges the most. The two invasion fronts also significantly genetically differ. About 3% of individuals (including all populations except the Illinois River) contain a unique and very divergent mtDNA haplotype, which likely stems from historic introgression in Asia with female largescale silver carp H. harmandi. The nuclear microsatellites and S7 sequences of the introgressed individuals do not differ from silver carp and are very distant from bighead carp. These sequence variation data are employed to design and evaluate a targeted high-throughput metabarcoding sequence assay that identifies and distinguishes among species of invasive carps (i.e., silver, bighead, grass, black, and common carps, along with goldfish), as well as native cyprinids, using cytochrome b. Our assay further differentiates among selected silver carp haplotypes (including between H. molitrix and H. harmandi), for use in population genetics and future analyses of spread pathways. We test and evaluate this assay on environmental (e)DNA water samples from 48 bait shops in the Great Lakes' region (along the Lake Erie, Lake St. Clair, and Wabash River watersheds), using positive and negative controls and custom bioinformatic processing. Test results discern silver carp eDNA in four of the shops-three in Lake Erie and one in the Wabash River watershed-and bighead carp from one of the same Lake Erie venues, suggesting that retailers (who often source from established southerly populations) comprise another introduction vector. Our overall findings thus provide key population genetic and phylogenetic data for understanding and tracing introductions, vectors, and spread pathways for silver carp, their variants, and their relatives.
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Affiliation(s)
- Carol A. Stepien
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Matthew R. Snyder
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Anna E. Elz
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
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40
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Bors EK, Herrera S, Morris JA, Shank TM. Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure. Ecol Evol 2019; 9:3306-3320. [PMID: 30962894 PMCID: PMC6434604 DOI: 10.1002/ece3.4952] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 01/10/2023] Open
Abstract
Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo-Pacific lionfish, Pterois volitans, into waters off the US East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 single nucleotide polymorphism loci sequenced by restriction enzyme-associated DNA sequencing for nine P. volitans sampling areas in the invaded range, including Florida and other sites throughout the Caribbean, as well as mitochondrial control region D-loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from initial reports of between-basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant in sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an F ST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.
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Affiliation(s)
- Eleanor K. Bors
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
- Marine Mammal Institute, Department of Fisheries and WildlifeOregon State UniversityNewportOregon
| | - Santiago Herrera
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvania
| | - James A. Morris
- National Oceanic and Atmospheric Administration, National Ocean ServiceNational Centers for Coastal Ocean ScienceBeaufortNorth Carolina
| | - Timothy M. Shank
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
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41
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Heppenheimer E, Brzeski KE, Hinton JW, Patterson BR, Rutledge LY, DeCandia AL, Wheeldon T, Fain SR, Hohenlohe PA, Kays R, White BN, Chamberlain MJ, vonHoldt BM. High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote ( Canis latrans) populations. Ecol Evol 2018; 8:12641-12655. [PMID: 30619570 PMCID: PMC6309008 DOI: 10.1002/ece3.4688] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 12/29/2022] Open
Abstract
Range expansion is a widespread biological process, with well-described theoretical expectations associated with the colonization of novel ranges. However, comparatively few empirical studies address the genomic outcomes accompanying the genome-wide consequences associated with the range expansion process, particularly in recent or ongoing expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction-associated DNA sequencing (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well-publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts.
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Affiliation(s)
| | - Kristin E. Brzeski
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMichigan
| | - Joseph W. Hinton
- Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgia
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources and ForestryPeterboroughOntarioCanada
- Trent UniversityPeterboroughOntario
| | - Linda Y. Rutledge
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- Trent UniversityPeterboroughOntario
| | | | - Tyler Wheeldon
- Ontario Ministry of Natural Resources and ForestryPeterboroughOntarioCanada
- Trent UniversityPeterboroughOntario
| | | | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
| | - Roland Kays
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth Carolina
- North Carolina Museum of Natural SciencesRaleighNorth Carolina
| | | | | | - Bridgett M. vonHoldt
- Department of Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
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42
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Walker TWN, Weckwerth W, Bragazza L, Fragner L, Forde BG, Ostle NJ, Signarbieux C, Sun X, Ward SE, Bardgett RD. Plastic and genetic responses of a common sedge to warming have contrasting effects on carbon cycle processes. Ecol Lett 2018; 22:159-169. [PMID: 30556313 PMCID: PMC6334510 DOI: 10.1111/ele.13178] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 02/02/2023]
Abstract
Climate warming affects plant physiology through genetic adaptation and phenotypic plasticity, but little is known about how these mechanisms influence ecosystem processes. We used three elevation gradients and a reciprocal transplant experiment to show that temperature causes genetic change in the sedge Eriophorum vaginatum. We demonstrate that plants originating from warmer climate produce fewer secondary compounds, grow faster and accelerate carbon dioxide (CO2) release to the atmosphere. However, warmer climate also caused plasticity in E. vaginatum, inhibiting nitrogen metabolism, photosynthesis and growth and slowing CO2 release into the atmosphere. Genetic differentiation and plasticity in E. vaginatum thus had opposing effects on CO2 fluxes, suggesting that warming over many generations may buffer, or reverse, the short‐term influence of this species over carbon cycle processes. Our findings demonstrate the capacity for plant evolution to impact ecosystem processes, and reveal a further mechanism through which plants will shape ecosystem responses to climate change.
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Affiliation(s)
- Tom W N Walker
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Centre for Ecology and Hydrology, Lancaster, LA1 4AP, UK.,Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Wolfram Weckwerth
- Department of Ecogenomics & Systems Biology, University of Vienna, 1090, Vienna, Austria.,Vienna Metabolomics Centre (VIME), University of Vienna, 1090, Vienna, Austria
| | - Luca Bragazza
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 1015, Lausanne, Switzerland.,Ecological Systems Laboratory (ECOS), École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Department of Life Science and Biotechnologies, University of Ferrara, 44100, Ferrara, Italy
| | - Lena Fragner
- Department of Ecogenomics & Systems Biology, University of Vienna, 1090, Vienna, Austria.,Vienna Metabolomics Centre (VIME), University of Vienna, 1090, Vienna, Austria
| | - Brian G Forde
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Nicholas J Ostle
- Centre for Ecology and Hydrology, Lancaster, LA1 4AP, UK.,Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Constant Signarbieux
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 1015, Lausanne, Switzerland.,Ecological Systems Laboratory (ECOS), École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Xiaoliang Sun
- Department of Ecogenomics & Systems Biology, University of Vienna, 1090, Vienna, Austria.,Vienna Metabolomics Centre (VIME), University of Vienna, 1090, Vienna, Austria
| | - Susan E Ward
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Richard D Bardgett
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
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43
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Rohfritsch A, Galan M, Gautier M, Gharbi K, Olsson G, Gschloessl B, Zeimes C, VanWambeke S, Vitalis R, Charbonnel N. Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden. Ecol Evol 2018; 8:11273-11292. [PMID: 30519443 PMCID: PMC6262921 DOI: 10.1002/ece3.4603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Natural reservoirs of zoonotic pathogens generally seem to be capable of tolerating infections. Tolerance and its underlying mechanisms remain difficult to assess using experiments or wildlife surveys. High-throughput sequencing technologies give the opportunity to investigate the genetic bases of tolerance, and the variability of its mechanisms in natural populations. In particular, population genomics may provide preliminary insights into the genes shaping tolerance and potentially influencing epidemiological dynamics. Here, we addressed these questions in the bank vole Myodes glareolus, the specific asymptomatic reservoir host of Puumala hantavirus (PUUV), which causes nephropathia epidemica (NE) in humans. Despite the continuous spatial distribution of M. glareolus in Sweden, NE is endemic to the northern part of the country. Northern bank vole populations in Sweden might exhibit tolerance strategies as a result of coadaptation with PUUV. This may favor the circulation and maintenance of PUUV and lead to high spatial risk of NE in northern Sweden. We performed a genome-scan study to detect signatures of selection potentially correlated with spatial variations in tolerance to PUUV. We analyzed six bank vole populations from Sweden, sampled from northern NE-endemic to southern NE-free areas. We combined candidate gene analyses (Tlr4, Tlr7, and Mx2 genes) and high-throughput sequencing of restriction site-associated DNA (RAD) markers. Outlier loci showed high levels of genetic differentiation and significant associations with environmental data including variations in the regional number of NE human cases. Among the 108 outliers that matched to mouse protein-coding genes, 14 corresponded to immune-related genes. The main biological pathways found to be significantly enriched corresponded to immune processes and responses to hantavirus, including the regulation of cytokine productions, TLR cascades, and IL-7, VEGF, and JAK-STAT signaling. In the future, genome-scan replicates and functional experimentations should enable to assess the role of these biological pathways in M. glareolus tolerance to PUUV.
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Affiliation(s)
- Audrey Rohfritsch
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Karim Gharbi
- Norwich Research ParkEarlham InstituteNorwich, NorfolkUK
| | - Gert Olsson
- Department of Wildlife, Fish, and Environmental StudiesSLUUmeåSweden
| | - Bernhard Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Caroline Zeimes
- Georges Lemaître Centre for Earth and Climate Research, Earth and Life InstituteUniversité Catholique de Louvain (UCL)Louvain‐la‐NeuveBelgium
| | - Sophie VanWambeke
- Georges Lemaître Centre for Earth and Climate Research, Earth and Life InstituteUniversité Catholique de Louvain (UCL)Louvain‐la‐NeuveBelgium
| | - Renaud Vitalis
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Nathalie Charbonnel
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
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44
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Barbosa S, Mestre F, White TA, Paupério J, Alves PC, Searle JB. Integrative approaches to guide conservation decisions: Using genomics to define conservation units and functional corridors. Mol Ecol 2018; 27:3452-3465. [PMID: 30030869 DOI: 10.1111/mec.14806] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/01/2018] [Accepted: 07/05/2018] [Indexed: 01/13/2023]
Abstract
Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long-term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation by distance and phylogeographic history. We evaluate our approach on a Near Threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: We defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision-making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia and that the pre-Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential and that this framework needs a strong evolutionary basis.
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Affiliation(s)
- Soraia Barbosa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Frederico Mestre
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade de Évora/InBIO Laboratório Associado, Évora, Portugal
| | - Thomas A White
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Joana Paupério
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal
| | - Paulo C Alves
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Jeremy B Searle
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
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45
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Matsukawa M, Tasaki M, Doi K, Ito K, Kawakita K, Tanaka T. Regional population differences of the brown planthopper (Nilaparvata lugens Stål) in Cambodia using genotyping-by-sequencing. BULLETIN OF ENTOMOLOGICAL RESEARCH 2018; 108:471-478. [PMID: 29061206 DOI: 10.1017/s0007485317000992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The brown planthopper Nilaparvata lugens Stål (BPH) can be found year-round in tropical region and causes severe damage to rice. Although there has been documented BPH damage to rice crops in the past decade in Cambodia, the extent of this epidemic is poorly understood. Here, we examined the time variation of BPH population in the abundance of morphotypes in 13 main rice-producing provinces (86 sites) by aspirator method and in the Takeo Province (five sites) by yellow sticky trap method. At least three generations were observed during the 3-month collection period in the rainy growing season. Regarding the occurrence of BPH morphotypes, in July the macropterous adults were restricted to south Cambodia and in August all morphotypes, adults (macropterous and brachypterous) and nymphs, appeared in all sampling sites. To explain the difference of regional distribution, the genetic differentiation was analyzed in south and northwest Cambodia (three sites) by using single nucleotide polymorphisms (SNP) analysis via genotyping-by-sequencing (GBS) using next-generation sequencing. The 2455 SNPs obtained by GBS clarified the three sub-populations and they corresponded to the expected dissemination patterns. These results provide a clue to understand the differentiation and epidemic of BPH in Cambodia.
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Affiliation(s)
- M Matsukawa
- Graduate School of Bioagricultural Sciences,Nagoya University,Chikusa,Nagoya,Aichi 464-8601,Japan
| | - Mikako Tasaki
- International Cooperation Center for Agricultural Education,Nagoya University,Chikusa,Nagoya,Aichi 464-8601,Japan
| | - Kazuyuki Doi
- Graduate School of Bioagricultural Sciences,Nagoya University,Chikusa,Nagoya,Aichi 464-8601,Japan
| | - Kasumi Ito
- International Cooperation Center for Agricultural Education,Nagoya University,Chikusa,Nagoya,Aichi 464-8601,Japan
| | - Kazuhito Kawakita
- Graduate School of Bioagricultural Sciences,Nagoya University,Chikusa,Nagoya,Aichi 464-8601,Japan
| | - Toshiharu Tanaka
- International Cooperation Center for Agricultural Education,Nagoya University,Chikusa,Nagoya,Aichi 464-8601,Japan
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Ruiz Daniels R, Taylor RS, Serra-Varela MJ, Vendramin GG, González-Martínez SC, Grivet D. Inferring selection in instances of long-range colonization: The Aleppo pine (Pinus halepensis) in the Mediterranean Basin. Mol Ecol 2018; 27:3331-3345. [PMID: 29972881 DOI: 10.1111/mec.14786] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 05/31/2018] [Accepted: 06/14/2018] [Indexed: 01/03/2023]
Abstract
Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase in genetic drift at the edges of range expansions ("allele surfing") can be a confounding factor. To address this potential issue, we first assess the long-range colonization history of the Aleppo pine across the Mediterranean Basin, using molecular markers. We then look for single nucleotide polymorphisms (SNPs) involved in local adaptation using: (a) environmental correlation methods (bayenv2), focusing on bioclimatic variables important for the species' adaptation (i.e., temperature, precipitation and water availability); and (b) FST -related methods (pcadapt). To assess the rate of false positives caused by the allele surfing effect, these results are compared with results from simulated SNP data that mimics the species' past range expansions and the effect of genetic drift, but with no selection. We find that the Aleppo pine shows a previously unsuspected complex genetic structure across its range, as well as evidence of selection acting on SNPs involved with the response to bioclimatic variables such as drought. This study uses an original approach to disentangle the confounding effects of drift and selection in range margin populations. It also contributes to the increased evidence that plant populations are able to adapt to new environments despite the expected accumulation of deleterious mutations that takes place during long-range colonizations.
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Affiliation(s)
- Rose Ruiz Daniels
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
| | | | - María Jesús Serra-Varela
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Department of Plant Production and Forest Resources, University of Valladolid, Palencia, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, FI, Italy
| | - Santiago C González-Martínez
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
- BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
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47
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Gomez‐Uchida D, Cañas‐Rojas D, Riva‐Rossi CM, Ciancio JE, Pascual MA, Ernst B, Aedo E, Musleh SS, Valenzuela‐Aguayo F, Quinn TP, Seeb JE, Seeb LW. Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon ( Oncorhynchus tshawytscha). Ecol Evol 2018; 8:6192-6209. [PMID: 29988411 PMCID: PMC6024130 DOI: 10.1002/ece3.4036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/31/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022] Open
Abstract
Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (Nb) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high-diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low-diversity natural populations were likely subsequently founded from a reduced number of individuals.
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Affiliation(s)
- Daniel Gomez‐Uchida
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Núcleo Milenio INVASALConcepciónChile
| | - Diego Cañas‐Rojas
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Núcleo Milenio INVASALConcepciónChile
| | - Carla M. Riva‐Rossi
- Instituto de Diversidad y Evolución AustralIDEAUS‐CONICETCentro Nacional PatagónicoPuerto MadrynArgentina
| | - Javier E. Ciancio
- Centro para el estudio de Sistemas MarinosCESIMAR‐CONICETCentro Nacional PatagónicoPuerto MadrynArgentina
| | - Miguel A. Pascual
- Instituto Patagónico para el estudio de Ecosistemas ContinentalesIPEEC‐CONICETCentro Nacional PatagónicoPuerto MadrynArgentina
| | - Billy Ernst
- Núcleo Milenio INVASALConcepciónChile
- Department of OceanographyUniversidad de ConcepciónConcepciónChile
- Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
| | - Eduardo Aedo
- Centro TrapanandaUniversidad Austral de ChileCoyhaiqueChile
| | - Selim S. Musleh
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Núcleo Milenio INVASALConcepciónChile
| | - Francisca Valenzuela‐Aguayo
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Present address:
Department of Aquatic SystemsFaculty of Environmental Sciences and EULA‐CentreUniversidad de ConcepciónConcepciónChile
| | - Thomas P. Quinn
- Núcleo Milenio INVASALConcepciónChile
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - James E. Seeb
- Núcleo Milenio INVASALConcepciónChile
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Lisa W. Seeb
- Núcleo Milenio INVASALConcepciónChile
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
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48
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Bourne SD, Hudson J, Holman LE, Rius M. Marine Invasion Genomics: Revealing Ecological and Evolutionary Consequences of Biological Invasions. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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49
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Leydet KP, Grupstra CGB, Coma R, Ribes M, Hellberg ME. Host-targeted RAD-Seq reveals genetic changes in the coralOculina patagonicaassociated with range expansion along the Spanish Mediterranean coast. Mol Ecol 2018; 27:2529-2543. [DOI: 10.1111/mec.14702] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Karine Posbic Leydet
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
| | - Carsten G. B. Grupstra
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam The Netherlands
- Institut de Ciències del mar; Barcelona Spain
| | - Rafel Coma
- Centre d'Estudis Avançats de Blanes; Blanes Girona Spain
| | - Marta Ribes
- Institut de Ciències del mar; Barcelona Spain
| | - Michael E. Hellberg
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
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50
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The Microtus voles: Resolving the phylogeny of one of the most speciose mammalian genera using genomics. Mol Phylogenet Evol 2018; 125:85-92. [PMID: 29574272 DOI: 10.1016/j.ympev.2018.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/03/2018] [Accepted: 03/14/2018] [Indexed: 11/24/2022]
Abstract
Sequential rapid radiations pose some of the greatest difficulties in phylogenetics, especially when analysing only a small number of genetic markers. Given that most of the speciation events occur in quick succession at various points in time, this creates particular challenges in determining phylogenetic relationships, i.e. branching order and divergence times. With the development of high throughput sequencing, thousands of markers can now readily be used to tackle these issues. Microtus is a speciose genus currently composed of 65 species that evolved over the last 2 million years. Although it is a well-studied group, there is still phylogenetic uncertainty at various divergence levels. Building upon previous studies that generally used small numbers of mitochondrial and/or nuclear loci, in this genomic-scale study we used both mitochondrial and nuclear data to study the rapid radiation within Microtus, using partial mitogenomes and genotyping-by-sequencing (GBS) on seven species representing five Microtus subgenera and the main biogeographic ranges where this group occurs. Both types of genome (mitochondrial and nuclear) generated similar tree topologies, with a basal split of the Nearctic (M. ochrogaster) and Holarctic (M. oeconomus) species, and then a subdivision of the five Palearctic species into two subgroups. These data support the occurrence of two European radiations, one North American radiation, and a later expansion of M. oeconomus from Asia to both Europe and North America. We further resolved the positioning of M. cabrerae as sister group of M. agrestis and refute the claim that M. cabrerae should be elevated to its own genus (Iberomys). Finally, the data support ongoing speciation events, especially within M. agrestis, with high levels of genetic divergence between the three Evolutionarily Significant Units (ESUs) previously identified. Similar high levels of divergence were also found among ESUs within M. oeconomus and M. arvalis.
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