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Petr M, Haller BC, Ralph PL, Racimo F. slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. PEER COMMUNITY JOURNAL 2023; 3:e121. [PMID: 38984034 PMCID: PMC11233137 DOI: 10.24072/pcjournal.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.
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Affiliation(s)
- Martin Petr
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
| | - Benjamin C Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
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2
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Seaborn T, Landguth EL, Caudill CC. Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP. Mol Ecol Resour 2023; 23:1458-1472. [PMID: 37081173 PMCID: PMC11081408 DOI: 10.1111/1755-0998.13799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/22/2023]
Abstract
Adaptive capacity can present challenges for modelling as it encompasses multiple ecological and evolutionary processes such as natural selection, genetic drift, gene flow and phenotypic plasticity. Spatially explicit, individual-based models provide an outlet for simulating these complex interacting eco-evolutionary processes. We expanded the existing Cost-Distance Meta-POPulation (CDMetaPOP) framework with inducible plasticity modelled as a habitat selection behaviour, using temperature or habitat quality variables, with a genetically based selection threshold conditioned on past individual experience. To demonstrate expected results in the new module, we simulated hypothetical populations and then evaluated model performance in populations of redband trout (Oncorhynchus mykiss gairdneri) across three watersheds where temperatures induce physiological stress in parts of the stream network. We ran simulations using projected warming stream temperature data under four scenarios for alleles that: (1) confer thermal tolerance, (2) bestow plastic habitat selection, (3) give both thermal tolerance and habitat selection preference and (4) do not provide either thermal tolerance or habitat selection. Inclusion of an adaptive allele decreased declines in population sizes, but this impact was greatly reduced in the relatively cool stream networks. As anticipated with the new module, high-temperature patches remained unoccupied by individuals with the allele operating plastically after exposure to warm temperatures. Using complete habitat avoidance above the stressful temperature threshold, habitat selection reduced the overall population size due to the opportunity cost of avoiding areas with increased, but not guaranteed, mortality. Inclusion of plasticity within CDMetaPOP will provide the potential for genetic or plastic traits and 'rescue' to affect eco-evolutionary dynamics for research questions and conservation applications.
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Affiliation(s)
- Travis Seaborn
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, USA
- School of Natural Resource Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Erin L. Landguth
- Computational Ecology Laboratory & Center for Population Health Research, University of Montana, Missoula, Montana, USA
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3
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Gould MJ, Cain JW, Atwood TC, Harding LE, Johnson HE, Onorato DP, Winslow FS, Roemer GW. Pleistocene-Holocene vicariance, not Anthropocene landscape change, explains the genetic structure of American black bear ( Ursus americanus) populations in the American Southwest and northern Mexico. Ecol Evol 2022; 12:e9406. [PMID: 36248671 PMCID: PMC9551525 DOI: 10.1002/ece3.9406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
The phylogeography of the American black bear (Ursus americanus) is characterized by isolation into glacial refugia, followed by population expansion and genetic admixture. Anthropogenic activities, including overharvest, habitat loss, and transportation infrastructure, have also influenced their landscape genetic structure. We describe the genetic structure of the American black bear in the American Southwest and northern Mexico and investigate how prehistoric and contemporary forces shaped genetic structure and influenced gene flow. Using a suite of microsatellites and a sample of 550 bears, we identified 14 subpopulations organized hierarchically following the distribution of ecoregions and mountain ranges containing black bear habitat. The pattern of subdivision we observed is more likely a product of postglacial habitat fragmentation during the Pleistocene and Holocene, rather than a consequence of contemporary anthropogenic barriers to movement during the Anthropocene. We used linear mixed-effects models to quantify the relationship between landscape resistance and genetic distance among individuals, which indicated that both isolation by resistance and geographic distance govern gene flow. Gene flow was highest among subpopulations occupying large tracts of contiguous habitat, was reduced among subpopulations in the Madrean Sky Island Archipelago, where montane habitat exists within a lowland matrix of arid lands, and was essentially nonexistent between two isolated subpopulations. We found significant asymmetric gene flow supporting the hypothesis that bears expanded northward from a Pleistocene refugium located in the American Southwest and northern Mexico and that major highways were not yet affecting gene flow. The potential vulnerability of the species to climate change, transportation infrastructure, and the US-Mexico border wall highlights conservation challenges and opportunities for binational collaboration.
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Affiliation(s)
- Matthew J. Gould
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA
- Department of BiologyNew Mexico State UniversityLas CrucesNew MexicoUSA
- U.S. Geological Survey, Northern Rocky Mountain Science CenterBozemanMontanaUSA
| | - James W. Cain
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA
- Department of BiologyNew Mexico State UniversityLas CrucesNew MexicoUSA
- U.S. Geological Survey New Mexico Cooperative Fish and Wildlife Research UnitNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Todd C. Atwood
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | | | | | - Dave P. Onorato
- Fish and Wildlife Research InstituteFlorida Fish and Wildlife Conservation CommissionNaplesFloridaUSA
| | | | - Gary W. Roemer
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA
- Department of BiologyNew Mexico State UniversityLas CrucesNew MexicoUSA
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4
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Rezić A, Safner T, Iacolina L, Bužan E, Šprem N. Traces of past reintroduction in genetic diversity: The case of the Balkan chamois (Mammalia, Artiodactyla). Zookeys 2022; 1116:57-70. [PMID: 36760981 PMCID: PMC9848663 DOI: 10.3897/zookeys.1116.84577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022] Open
Abstract
The translocation of wild animal species became a common practice worldwide to re-establish local populations threatened with extinction. Archaeological data confirm that chamois once lived in the Biokovo Mountain but, prior to their reintroduction in the 1960s, there was no written evidence of their recent existence in the area. The population was reintroduced in the period 1964-1969, when 48 individuals of Balkan chamois from the neighbouring mountains in Bosnia and Herzegovina were released. The main objective of this study was to determine the accuracy of the existing historical data on the origin of the Balkan chamois population from the Biokovo Mountain and to assess the genetic diversity and population structure of the source and translocated populations 56 years after reintroduction. Sixteen microsatellite loci were used to analyse the genetic structure of three source chamois populations from Prenj, Čvrsnica and Čabulja Mountains and from Biokovo Mountain. Both STRUCTURE and GENELAND analyses showed a clear separation of the reintroduced population on Biokovo from Prenj's chamois and considerable genetic similarity between the Biokovo population and the Čvrsnica-Čabulja population. This suggests that the current genetic composition of the Biokovo population does not derive exclusively from Prenj, as suggested by the available literature and personal interviews, but also from Čvrsnica and Čabulja. GENELAND analysis recognised the Balkan chamois from Prenj as a separate cluster, distinct from the populations of Čvrsnica and Čabulja. Our results thus highlight the need to implement genetic monitoring of both reintroduced and source populations of endangered Balkan chamois to inform sustainable management and conservation strategies in order to maximise the chances of population persistence.
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Affiliation(s)
- Andrea Rezić
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Toni Safner
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia,University of Zagreb, Faculty of Agriculture, Department of Plant Breeding, Genetics and Biometrics, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Laura Iacolina
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia,Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000, Zagreb, Croatia,University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Department of Biodiversity, Glagoljaška 8, 6000, Koper, Slovenia
| | - Elena Bužan
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000, Zagreb, Croatia,Aalborg University, Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Nikica Šprem
- University of Zagreb, Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Svetošimunska c. 25, 10000, Zagreb, Croatia
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5
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Landscape Features Fail to Explain Spatial Genetic Structure in White‐Tailed Deer Across Ohio, USA. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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New insights into the past and recent evolutionary history of the Corsican mouflon (Ovis gmelini musimon) to inform its conservation. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01399-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Marcus J, Ha W, Barber RF, Novembre J. Fast and flexible estimation of effective migration surfaces. eLife 2021; 10:61927. [PMID: 34328078 PMCID: PMC8324296 DOI: 10.7554/elife.61927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Spatial population genetic data often exhibits ‘isolation-by-distance,’ where genetic similarity tends to decrease as individuals become more geographically distant. The rate at which genetic similarity decays with distance is often spatially heterogeneous due to variable population processes like genetic drift, gene flow, and natural selection. Petkova et al., 2016 developed a statistical method called Estimating Effective Migration Surfaces (EEMS) for visualizing spatially heterogeneous isolation-by-distance on a geographic map. While EEMS is a powerful tool for depicting spatial population structure, it can suffer from slow runtimes. Here, we develop a related method called Fast Estimation of Effective Migration Surfaces (FEEMS). FEEMS uses a Gaussian Markov Random Field model in a penalized likelihood framework that allows for efficient optimization and output of effective migration surfaces. Further, the efficient optimization facilitates the inference of migration parameters per edge in the graph, rather than per node (as in EEMS). With simulations, we show conditions under which FEEMS can accurately recover effective migration surfaces with complex gene-flow histories, including those with anisotropy. We apply FEEMS to population genetic data from North American gray wolves and show it performs favorably in comparison to EEMS, with solutions obtained orders of magnitude faster. Overall, FEEMS expands the ability of users to quickly visualize and interpret spatial structure in their data.
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Affiliation(s)
- Joseph Marcus
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Wooseok Ha
- Department of Statistics, University of California, Berkeley, Berkeley, United States
| | | | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
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8
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Ariyaraphong N, Laopichienpong N, Singchat W, Panthum T, Farhan Ahmad S, Jattawa D, Duengkae P, Muangmai N, Suwanasopee T, Koonawootrittriron S, Srikulnath K. High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing. Animals (Basel) 2021; 11:ani11061680. [PMID: 34199963 PMCID: PMC8227385 DOI: 10.3390/ani11061680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup "I", were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.
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Affiliation(s)
- Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Danai Jattawa
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok 10900, Thailand
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9
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Danusevičius D, Kembrytė R, Buchovska J, Baliuckas V, Kavaliauskas D. Genetic signature of the natural gene pool of Tilia cordata Mill. in Lithuania: Compound evolutionary and anthropogenic effects. Ecol Evol 2021; 11:6260-6275. [PMID: 34141216 PMCID: PMC8207418 DOI: 10.1002/ece3.7473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/25/2022] Open
Abstract
Tilia cordata Mill. is a valuable tree species enriching the ecological values of the coniferous-dominated boreal forests in Europe. Following the historical decline, spreading of Tilia sp. is challenged by the elevated inbreeding and habitat fragmentation. We studied the geographical distribution of genetic diversity of Tilia cordata populations in Lithuania. We used 14 genomic microsatellite markers to genotype 543 individuals from 23 wild-growing populations. We found that Tilia cordata retained high levels of genetic diversity (population F IS = 0-0.15, H o = 0.53-0.69, H e = 0.56-0.75). AMOVA, Bayesian clustering, and Monmonier's barrier detection indicate weak but significant differentiation among the populations (F ST = 0.037***) into geographically interpretable clusters of (a) western Lithuania with high genetic heterogeneity but low genetic diversity, bottleneck effects, (b) relatively higher genetic diversity of Tilia cordata on rich and most soils of midland lowland, and (c) the most differentiated populations on poor soils of the coolest northeastern highland possessing the highest rare allele frequency but elevated inbreeding and bottleneck effects. Weak genetic differentiation among the Tilia cordata populations in Lithuania implies common ancestry, absence of strong adaptive gradients, and effective genetic exchange possible mediated via the riparian networks. A hypothesis on riparian networks as gene flow mediators in Tilia cordata was raised based on results of this study.
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Affiliation(s)
| | | | - Jurata Buchovska
- Forestry InstituteLithuanian Research Centre for Agriculture and ForestryKaunasLithuania
| | - Virgilijus Baliuckas
- Forestry InstituteLithuanian Research Centre for Agriculture and ForestryKaunasLithuania
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10
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Carress H, Lawson DJ, Elhaik E. Population genetic considerations for using biobanks as international resources in the pandemic era and beyond. BMC Genomics 2021; 22:351. [PMID: 34001009 PMCID: PMC8127217 DOI: 10.1186/s12864-021-07618-x] [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: 10/16/2020] [Accepted: 04/14/2021] [Indexed: 12/11/2022] Open
Abstract
The past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limits the global understanding of disease risk but also inhibits viable research into the genomic differences between carriers and patients. Whilst the community has agreed that more diverse samples are required, it is not enough to blindly increase diversity; the diversity must be quantified, compared and annotated to lead to insight. Genetic annotations from separate biobanks need to be comparable and computable and to operate without access to raw data due to privacy concerns. Comparability is key both for regular research and to allow international comparison in response to pandemics. Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner. The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally), increase the accuracy of association analyses and inform developmental efforts.
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Affiliation(s)
- Hannah Carress
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Daniel John Lawson
- School of Mathematics and Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK. .,Department of Biology, Lund University, Lund, Sweden.
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11
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Reiner G, Rumpel M, Zimmer K, Willems H. Genetic Differentiation of Wild Boar Populations in a Region Endangered by African Swine Fever. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gerald Reiner
- Working Group Wildlife Biology Justus‐Liebig University 35392 Giessen Germany
| | - Martin Rumpel
- Working Group Wildlife Biology Justus‐Liebig University 35392 Giessen Germany
| | - Karl Zimmer
- Institute of Veterinary Diagnostics Landesuntersuchungsamt 56068 Koblenz Germany
| | - Hermann Willems
- Working Group Wildlife Biology Justus‐Liebig University 35392 Giessen Germany
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12
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Yannic G, Helfer V, Sermier R, Schmidt BR, Fumagalli L. Fine scale genetic structure in fire salamanders (Salamandra salamandra) along a rural-to-urban gradient. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01335-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Moir M, Richards LR, Rambau RV, Wannenburgh A, Cherry MI. Fragmentation does not affect gene flow in forest populations of the dusky pipistrelle bat on the eastern seaboard of South Africa. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The Eastern Cape Province harbors almost half of the indigenous forest in South Africa, but these forests are threatened by large-scale agricultural and urban development planned for the coming decade. Additional anthropogenic development is likely to cause further fragmentation and degradation of forests inhabited by the dusky pipistrelle bat (Pipistrellus hesperidus). We used eight microsatellite markers to study the genetic diversity, population structure, and migration, of P. hesperidus (n = 120) across 14 sites in the Eastern Cape and KwaZulu-Natal provinces of South Africa. We examined the effect of contemporary land cover types on genetic differentiation to assess whether current levels of urbanization and agricultural development affect gene flow. High gene flow and low population structure were evident across sampled sites, apart from genetic discontinuities at the northern (Oribi Gorge Nature Reserve) and southern (Alexandria Forest) ends of the seaboard. Genetic discontinuity at Oribi Gorge may relate to anthropogenic modification of two rivers surrounding the forest, while the Alexandria-linked barrier is a climatic break known as the Bedford gap. Migration rates generally were low between sites except for one Scarp forest, Manubi State Forest, from which individuals dispersed to other sites. The Amatole Mistbelt forests supported high genetic diversity, and likely served as a refugium for P. hesperidus during the Last Glacial Maximum. The composition of land cover classes between sites was a poor predictor of genetic differentiation, although it seems likely that P. hesperidus uses riparian habitats and wetlands for dispersal. Lastly, urban and agricultural development did not have a significant effect on genetic differentiation, which may reflect the wide niche breadth and intermediate distribution range of the species. This study provides insights into genetic diversity and gene flow of P. hesperidus across the study region prior to agricultural intensification and large-scale urbanization.
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Affiliation(s)
- Monika Moir
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | | | - Ramugondo V Rambau
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Andrew Wannenburgh
- Natural Resource Management, Department of Environmental Affairs, Cape Town, South Africa
| | - Michael I Cherry
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
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14
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Sartori RQ, Lopes AG, Aires LPN, Bianchi RDC, de Mattos CCB, Morales AC, Castiglioni L. Identifying Priority Giant Anteater ( Myrmecophaga tridactyla) Populations for Conservation in São Paulo State, Brazil. Ecol Evol 2021; 11:700-713. [PMID: 33520159 PMCID: PMC7820152 DOI: 10.1002/ece3.6809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 11/11/2022] Open
Abstract
Habitat loss is the main threat to biodiversity conservation worldwide. Some species may be particularly susceptible to the effects of fragmentation and the isolation of populations. The impacts of human activity on wild animal populations may be understood through relationships between individual genetic data and spatial landscape variables, particularly when considering local population dynamics influenced by fragmented habitats. Thus, the objective of this study was to analyze the population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla) using an individual sampling scheme (ISS) on a regional geographic scale. Data were collected from 41 specimens from twenty different locations in São Paulo State, Brazil, and six polymorphic microsatellite loci were genotyped. Our results indicate that barriers to gene flow exist and have segregated individuals of the farther away areas into two spatially structured clusters. The populations were also found to have high genetic diversity. The experimental sampling approach used herein enabled an analysis of the population dynamics of the giant anteater on a regional scale, as well as the identification of priority populations for genetic resource conservation for this species. The results reflect the need for adequate management plans. The efficacy of the sampling scheme may vary based on the study model used, but we argue that the use of an ISS combined with suitable molecular markers and statistical methods may serve as an important tool for initial analyses of threatened or vulnerable species, particularly in anthropized regions where populations are small or hard to characterize.
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Affiliation(s)
- Ricardo Quiterio Sartori
- School of Biosciences, Humanities, and Exact SciencesGraduate Program in BiosciencesSão Paulo State University (UNESP)São José do Rio PretoSão Paulo StateBrazil
| | - Alessandro Garcia Lopes
- School of Biosciences, Humanities, and Exact SciencesGraduate Program in BiosciencesSão Paulo State University (UNESP)São José do Rio PretoSão Paulo StateBrazil
| | | | - Rita de Cassia Bianchi
- School of Agricultural and Veterinary ScienceSão Paulo State University (UNESP)JaboticabalSão Paulo StateBrazil
| | | | - Adriana Coletto Morales
- School of Agricultural and Veterinary ScienceSão Paulo State University (UNESP)JaboticabalSão Paulo StateBrazil
| | - Lilian Castiglioni
- School of Biosciences, Humanities, and Exact SciencesGraduate Program in BiosciencesSão Paulo State University (UNESP)São José do Rio PretoSão Paulo StateBrazil
- São José do Rio Preto Medical School (FAMERP)São José do Rio PretoSão Paulo StateBrazil
- Rio Preto University Center (UNIRP)São José do Rio PretoSão Paulo StateBrazil
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15
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Miller WL, Miller‐Butterworth CM, Diefenbach DR, Walter WD. Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease. Ecol Evol 2020; 10:3977-3990. [PMID: 32489625 PMCID: PMC7244803 DOI: 10.1002/ece3.6161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/04/2020] [Accepted: 01/24/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding the geographic extent and connectivity of wildlife populations can provide important insights into the management of disease outbreaks but defining patterns of population structure is difficult for widely distributed species. Landscape genetic analyses are powerful methods for identifying cryptic structure and movement patterns that may be associated with spatial epizootic patterns in such cases.We characterized patterns of population substructure and connectivity using microsatellite genotypes from 2,222 white-tailed deer (Odocoileus virginianus) in the Mid-Atlantic region of the United States, a region where chronic wasting disease was first detected in 2009. The goal of this study was to evaluate the juxtaposition between population structure, landscape features that influence gene flow, and current disease management units.Clustering analyses identified four to five subpopulations in this region, the edges of which corresponded to ecophysiographic provinces. Subpopulations were further partitioned into 11 clusters with subtle (F ST ≤ 0.041), but significant genetic differentiation. Genetic differentiation was lower and migration rates were higher among neighboring genetic clusters, indicating an underlying genetic cline. Genetic discontinuities were associated with topographic barriers, however.Resistance surface modeling indicated that gene flow was diffuse in homogenous landscapes, but the direction and extent of gene flow were influenced by forest cover, traffic volume, and elevational relief in subregions heterogeneous for these landscape features. Chronic wasting disease primarily occurred among genetic clusters within a single subpopulation and along corridors of high landscape connectivity.These results may suggest a possible correlation between population substructure, landscape connectivity, and the occurrence of diseases for widespread species. Considering these factors may be useful in delineating effective management units, although only the largest features produced appreciable differences in subpopulation structure. Disease mitigation strategies implemented at the scale of ecophysiographic provinces are likely to be more effective than those implemented at finer scales.
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Affiliation(s)
- William L. Miller
- Pennsylvania Cooperative Fish and Wildlife Research UnitDepartment of Ecosystem Science and ManagementIntercollege Graduate Degree Program in EcologyThe Pennsylvania State UniversityUniversity ParkPAUSA
| | | | - Duane R. Diefenbach
- U.S. Geological SurveyPennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - W. David Walter
- U.S. Geological SurveyPennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPAUSA
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16
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Peñaloza‐Ramírez JM, Rodríguez‐Correa H, González‐Rodríguez A, Rocha‐Ramírez V, Oyama K. High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae). Ecol Evol 2020; 10:4204-4219. [PMID: 32489590 PMCID: PMC7246204 DOI: 10.1002/ece3.6189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/19/2022] Open
Abstract
The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans-Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified, and 29 of these haplotypes were restricted to single populations. The within-population genetic diversity was high (mean h S = 0.72), and among-population genetic differentiation showed a strong phylogeographic structure (N ST = 0.630 > G ST = 0.266; p < .001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure, and ecological niche models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.
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Affiliation(s)
- Juan Manuel Peñaloza‐Ramírez
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMéxico
| | - Hernando Rodríguez‐Correa
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMéxico
| | | | | | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMéxico
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17
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Wogan GOU, Voelker G, Oatley G, Bowie RCK. Biome stability predicts population structure of a southern African aridland bird species. Ecol Evol 2020; 10:4066-4081. [PMID: 32489631 PMCID: PMC7244808 DOI: 10.1002/ece3.6175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 11/07/2022] Open
Abstract
Environments are heterogeneous in space and time, and the permeability of landscape and climatic barriers to gene flow may change over time. When barriers are present, they may start populations down the path toward speciation, but if they become permeable before the process of speciation is complete, populations may once more merge. In Southern Africa, aridland biomes play a central role in structuring the organization of biodiversity. These biomes were subject to substantial restructuring during Plio-Pleistocene climatic fluctuations, and the imprint of this changing environment should leave genetic signatures on the species living there. Here, we investigate the role of adjacent aridland biome boundaries in structuring the genetic diversity within a widespread generalist bird, the Cape Robin-chat (Cossypha caffra). We find evidence supporting a central role for aridland biomes in structuring populations across Southern Africa. Our findings support a scenario wherein populations were isolated in different biome refugia, due to separation by the exceptionally arid Nama Karoo biome. This biome barrier may have arisen through a combination of habitat instability and environmental unsuitability, and was highly unstable throughout the Plio-Pleistocene. However, we also recovered a pattern of extensive contemporary gene flow and admixture across the Nama Karoo, potentially driven by the establishment of homesteads over the past 200 years. Thus, the barrier has become permeable, and populations are currently merging. This represents an instance where initial formation of a barrier to gene flow enabled population differentiation, with subsequent gene flow and the merging of populations after the barrier became permeable.
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Affiliation(s)
- Guinevere O. U. Wogan
- Department of Integrative BiologyMuseum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCAUSA
| | - Gary Voelker
- Department of Wildlife and Fisheries SciencesBiodiversity Research and Teaching CollectionsTexas A&M UniversityCollege StationTXUSA
| | - Graeme Oatley
- Department of GeographyCollege of Life and Environmental SciencesUniversity of ExeterExeterUK
- DST/NRF Centre of Excellence at the Percy FitzPatrick InstituteUniversity of Cape TownRondeboschSouth Africa
| | - Rauri C. K. Bowie
- Department of Integrative BiologyMuseum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCAUSA
- DST/NRF Centre of Excellence at the Percy FitzPatrick InstituteUniversity of Cape TownRondeboschSouth Africa
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18
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Naino Jika AK, Le Ru B, Capdevielle-Dulac C, Chardonnet F, Silvain JF, Kaiser L, Dupas S. Population genetics of the Mediterranean corn borer (Sesamia nonagrioides) differs between wild and cultivated plants. PLoS One 2020; 15:e0230434. [PMID: 32191750 PMCID: PMC7081988 DOI: 10.1371/journal.pone.0230434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 03/01/2020] [Indexed: 11/19/2022] Open
Abstract
The population genetic structure of crop pest populations gives information about their spatial ecology, which helps in designing management strategies. In this paper, we investigated the genetic structure of the Mediterranean Corn Borer (MCB), Sesamia nonagrioides Lefèbvre (Lepidoptera: Noctuidae), one of the most important maize pests in the Mediterranean countries, using microsatellite markers for the first time in this species. Insects were collected in twenty-five locations in southwest and southeast France from cultivated and wild host plants (Zea mays, Sorghum halepense and Typha domingensis). Contrary to what has been reported so far in France, we found that MCB populations could be locally abundant on wild poales plants. Analysis was carried out at 11 polymorphic microsatellite markers. Molecular variance was significantly determined by geography, then by host plant, with 17% and 4%, respectively, when considered as a major effect, and with 14% and 1%, respectively, when considered as a marginal effect in permutational analysis. Multidimensional scaling (MDS) and GENELAND Bayesian clustering suggested that populations infecting wild plants (T. domingensis and S. halepense) were more structured locally than those affecting cultivated maize. In S. halepense, significant Isolation By Distance (IBD) indicated that this factor could explain genetic differentiation of the moth populations. In T. domingensis, local population differentiation was strong but did not depend on distance. The implication of this absence of population structure in maize and the heterogeneity of population genetics patterns in wild plants are discussed in the context of the population dynamics hypothesis and population management strategies.
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Affiliation(s)
- Abdel Kader Naino Jika
- Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS, IRD & Université Paris-Sud Orsay, Gif-sur-Yvette cedex, France
- * E-mail:
| | - B. Le Ru
- Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS, IRD & Université Paris-Sud Orsay, Gif-sur-Yvette cedex, France
- ICIPE- African Insect Science for Food and Health, Kasarani, Nairobi, Kenya
| | - C. Capdevielle-Dulac
- Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS, IRD & Université Paris-Sud Orsay, Gif-sur-Yvette cedex, France
| | - F. Chardonnet
- Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS, IRD & Université Paris-Sud Orsay, Gif-sur-Yvette cedex, France
| | - J. F. Silvain
- Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS, IRD & Université Paris-Sud Orsay, Gif-sur-Yvette cedex, France
| | - L. Kaiser
- Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS, IRD & Université Paris-Sud Orsay, Gif-sur-Yvette cedex, France
| | - S. Dupas
- Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS, IRD & Université Paris-Sud Orsay, Gif-sur-Yvette cedex, France
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Donkpegan ASL, Piñeiro R, Heuertz M, Duminil J, Daïnou K, Doucet JL, Hardy OJ. Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis reveals no significant past fragmentation of their distribution ranges. AMERICAN JOURNAL OF BOTANY 2020; 107:498-509. [PMID: 32200549 DOI: 10.1002/ajb2.1449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
PREMISE Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. METHODS We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. RESULTS Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. CONCLUSIONS These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
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Affiliation(s)
- Armel S L Donkpegan
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- Univ. Bordeaux, INRAE, BFP, 71 Avenue Edouard Bourlaux, F-33882, Villenave d'Ornon, France
| | - Rosalía Piñeiro
- University of Exeter, Geography, College of Life and Environmental Sciences, Stocker road, EX44QD, Exeter, UK
- Evolutionary Genomics, Centre for Geogenetics - Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Myriam Heuertz
- Univ. Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, F-33610, Cestas, France
| | - Jérôme Duminil
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- DIADE, IRD, University of Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Bioversity International, Forest Genetic Resources and Restoration Programme, Sub-Regional Office for Central Africa, P.O. Box 2008, Messa, Yaoundé, Cameroon
| | - Kasso Daïnou
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- Université d'Agriculture de Kétou, BP: 43, Kétou, Benin
| | - Jean-Louis Doucet
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
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20
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Landguth EL, Forester BR, Eckert AJ, Shirk AJ, Menon M, Whipple A, Day CC, Cushman SA. Modelling multilocus selection in an individual‐based, spatially‐explicit landscape genetics framework. Mol Ecol Resour 2019; 20:605-615. [DOI: 10.1111/1755-0998.13121] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Erin L. Landguth
- School of Public and Community Health Sciences University of Montana Missoula MT USA
| | | | - Andrew J. Eckert
- Department of Biology Virginia Commonwealth University Richmond VA USA
| | - Andrew J. Shirk
- Climate Impacts Group College of the Environment University of Washington Seattle WA USA
| | - Mitra Menon
- Integrative Life Sciences Virginian Commonwealth University Richmond VA USA
| | - Amy Whipple
- Department of Biological Sciences and Merriam‐Powell Center for Environmental Research Northern Arizona University Flagstaff AZ USA
| | - Casey C. Day
- School of Public and Community Health Sciences University of Montana Missoula MT USA
| | - Samuel A. Cushman
- USDA Forest Service Rocky Mountain Research Station Flagstaff AZ USA
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21
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Chroni A, Stefanović M, Djan M, Vujić A, Šašić Zorić L, Kočiš Tubić N, Petanidou T. Connecting the dots: Bridging genetic and spatial differentiation of the genus
Eumerus
(Diptera: Syrphidae) in the Mediterranean Basin and Balkans. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Antonia Chroni
- Department of Biology, Institute for Genomics and Evolutionary Medicine Temple University Philadelphia Pennsylvania
- Department of Geography University of the Aegean Mytilene Greece
| | - Milomir Stefanović
- Faculty of Sciences, Department of Biology and Ecology University of Novi Sad Novi Sad Serbia
| | - Mihajla Djan
- Faculty of Sciences, Department of Biology and Ecology University of Novi Sad Novi Sad Serbia
| | - Ante Vujić
- Faculty of Sciences, Department of Biology and Ecology University of Novi Sad Novi Sad Serbia
| | - Ljiljana Šašić Zorić
- Laboratory for Biosystems Research, BioSense Institute – Research Institute for Information Technologies in Biosystems University of Novi Sad Novi Sad Serbia
| | - Nataša Kočiš Tubić
- Faculty of Sciences, Department of Biology and Ecology University of Novi Sad Novi Sad Serbia
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22
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Pan T, Zhou K, Zhang S, Shu Y, Zhang J, Li E, Wang M, Yan P, Wu H. Effects of dispersal barriers and geographic distance on the genetic structure of a narrowly distributed frog in a spatially structured landscape. J Zool (1987) 2019. [DOI: 10.1111/jzo.12730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Pan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - K. Zhou
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - S.‐L. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - Y.‐L. Shu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - J.‐H. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - E. Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - M.‐S. Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - P. Yan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - H.‐L. Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
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23
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Tolley KA, Hopkins KP, da Silva JM. Genetic structure associated with habitat diversification supports the independent evolution of ecomorphs inBradypodion pumilum. AFR J HERPETOL 2019. [DOI: 10.1080/21564574.2019.1646324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Krystal A Tolley
- South African National Biodiversity Institute, Cape Town, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - Kevin P Hopkins
- South African National Biodiversity Institute, Cape Town, South Africa
| | - Jessica M da Silva
- South African National Biodiversity Institute, Cape Town, South Africa
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
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24
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Carroll RP, Litvaitis MK, Clements SJ, Stevens CL, Litvaitis JA. History matters: contemporary versus historic population structure of bobcats in the New England region, USA. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01170-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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The sarolga: conservation implications of genetic and visual evidence for hybridization between the brolga Antigone rubicunda and the Australian sarus crane Antigone antigone gillae. ORYX 2019. [DOI: 10.1017/s003060531800073x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractTo investigate the extent of suspected hybridization between the brolga Antigone rubicunda and the Australian sarus crane Antigone antigone gillae, first noted in the 1970s, we analysed the genetic diversity of 389 feathers collected from breeding and flocking areas in north Queensland, Australia. We compared these with 15 samples from birds of known identity, or that were phenotypically typical. Bayesian clustering based on 10 microsatellite loci identified nine admixed birds, confirming that Australian cranes hybridize in the wild. Four of these were backcrosses, also confirming that wild Australian crane hybrids are fertile. Genetic analyses identified 10 times more hybrids than our accompanying visual field observations. Our analyses also provide the first definitive evidence that both brolgas and sarus cranes migrate between the Gulf Plains, the principal breeding area for sarus cranes, and major non-breeding locations on the Atherton Tablelands. We suggest that genetic analysis of shed feathers could potentially offer a cost-effective means to provide ongoing monitoring of this migration. The first observations of hybrids coincided with significantly increased opportunities for interaction between the two species when foraging on agricultural crops, which have developed significantly in the Atherton Tablelands flocking area since the 1960s. As the sarus crane is declining in much of its Asian range, challenges to the genetic integrity of the Australian sarus crane populations have international conservation significance.
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26
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Jensen AM, O'Neil NP, Iwaniuk AN, Burg TM. Landscape effects on the contemporary genetic structure of Ruffed Grouse ( Bonasa umbellus) populations. Ecol Evol 2019; 9:5572-5592. [PMID: 31160983 PMCID: PMC6540679 DOI: 10.1002/ece3.5112] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/28/2019] [Accepted: 02/08/2019] [Indexed: 01/01/2023] Open
Abstract
The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.
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Affiliation(s)
- Ashley M. Jensen
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Nicholas P. O'Neil
- Canadian Centre for Behavioural NeuroscienceUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Andrew N. Iwaniuk
- Canadian Centre for Behavioural NeuroscienceUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
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Gelmi-Candusso TA, Hämäläinen AM. Seeds and the City: The Interdependence of Zoochory and Ecosystem Dynamics in Urban Environments. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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28
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Berkman LK, Frair JL, Marquardt PE, Donner DM, Kilgo JC, Whipps CM. Spatial genetic analysis of coyotes in New York State. WILDLIFE SOC B 2019. [DOI: 10.1002/wsb.960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leah K. Berkman
- The State University of New York College of Environmental Science and Forestry1 Forestry DriveSyracuseNY13210USA
| | - Jacqueline L. Frair
- The State University of New York College of Environmental Science and Forestry1 Forestry DriveSyracuseNY13210USA
| | - Paula E. Marquardt
- U.S. Department of Agriculture Forest ServiceNorthern Research Station5985 Highway KRhinelanderWI54501USA
| | - Deahn M. Donner
- U.S. Department of Agriculture Forest ServiceNorthern Research Station5985 Highway KRhinelanderWI54501USA
| | - John C. Kilgo
- U.S. Department of Agriculture Forest ServiceSouthern Research StationP.O. Box 700New EllentonSC29809USA
| | - Christopher M. Whipps
- The State University of New York College of Environmental Science and Forestry1 Forestry DriveSyracuseNY13210USA
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Demastes JW, Hafner DJ, Hafner MS, Light JE, Spradling TA. Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei. Mol Ecol 2019; 28:703-720. [PMID: 30589151 DOI: 10.1111/mec.14997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023]
Abstract
Understanding the genetic consequences of changes in species distributions has wide-ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25-year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935 G. aurei lice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post-bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225-generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid-based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow.
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Affiliation(s)
- James W Demastes
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa
| | - David J Hafner
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| | - Mark S Hafner
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas
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Small-scale spatial genetic structure of Alpine chamois (Rupicapra rupicapra) in Northern Dinarides. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1259-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Shallow Genetic Structure among the European Populations of the Six-Toothed Bark Beetle Ips sexdentatus (Coleoptera, Curculionidae, Scolytinae). FORESTS 2019. [DOI: 10.3390/f10020136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The six-toothed bark beetle, Ips sexdentatus, is one of the most abundant scolytid species of the central and southern European countries. It mostly feeds on Pinus sp., whereas during population outbreaks it can also attack Picea sp. In spite of its broad distribution, its phylogeography has never been studied before. To do that, we employed an mtDNA marker on 489 individuals that covered most of its native range in Europe. Geographic distribution of the 86 haplotypes showed that at least three glacial refugia have played a significant role in shaping the currently observed pattern of genetic divergence in Europe, without excluding the contribution of minor refugial areas that acted in a similar manner. The revealed shallow structure can be considered an artifact of factors that reduced intraspecific diversity, at the same time favoring gene flow. As such, biological traits of the species itself (flying ability and host preference) and even human-mediated transport of wood seem to be the most prevailing and probable reasons that gave rise to the observed pattern.
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Wu WD, Liu WH, Sun M, Zhou JQ, Liu W, Zhang CL, Zhang XQ, Peng Y, Huang LK, Ma X. Genetic diversity and structure of Elymus tangutorum accessions from western China as unraveled by AFLP markers. Hereditas 2019; 156:8. [PMID: 30733654 PMCID: PMC6352457 DOI: 10.1186/s41065-019-0082-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/17/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Understanding genetic diversity of wild plant germplasm and the relationships between ecogeographic and genetic characteristics may provide insights for better utilizing and conserving genetic resources. Elymus tangutorum (Nevski) Hand.-Mazz, a cool-season hexaploid perennial, is an important pasture bunchgrass species used for forages and grassland restoration in Qinghai-Tibet Plateau and northwest China. In this study, 27 E. tangutorum accessions from diverse origins of western China were evaluated using AFLP markers in an effort to delve into the genetic relationships among them. The effects of eco-environmental factors and geographical isolation on the genetic diversity and population structure were also elucidated. RESULTS On account of 554 polymorphic fragments amplified with 14 primer combinations, the mean values of some marker parameters including polymorphic information content, resolving power and marker index were 0.2504, 14.10 and 23.07, respectively, validating the high efficiency and reliability of the markers selected. Genetic dissimilarity index values among accessions ranged from 0.1024 to 0.7137 with a mean of 0.2773. STRUCTURE, UPGMA clustering and PCoA analyses showed that all accessions could be divided into the three main clusters; however, this results do not exactly coincide with geographic groups. We found medium differentiation (F ST = 0.162) between Qinghai-Tibet Plateau (QTP) and Xinjiang (XJC), and high differentiation (F ST = 0.188) among three Bayesian subgroups. A significant correlation (r = 0.312) between genetic and geographical distance was observed by Mantel test in the species level, while the weak correlation was detected between genetic and environmental distance for all accessions and most of geographical groups. In addition, a significant ecological influence of average annual precipitation on genetic distance was revealed in XJC group and the Bayesian subgroup A. CONCLUSION This study indicates that AFLP technique are a useful tool to measure genetic diversity in E. tangutorum, showing that geographical and environmental factors (especially precipitation) together, play a crucial role in genetic differentiation patterns. These findings underline the importance of local adaptation in shaping patterns of genetic variability and population structure in E. tangutorum germplasm collected in Western China.
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Affiliation(s)
- Wen-Dan Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Wen-Hui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, 81108 China
| | - Ming Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Ji-Qiong Zhou
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Wei Liu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Cheng-Lin Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xing-Quan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Lin-Kai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
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Seckfort D, Montgomery Pettitt B. Price of disorder in the lac repressor hinge helix. Biopolymers 2019; 110:e23239. [PMID: 30485404 PMCID: PMC6335174 DOI: 10.1002/bip.23239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.
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Affiliation(s)
- Danielle Seckfort
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas
| | - B Montgomery Pettitt
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
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Genetic source–sink dynamics among naturally structured and anthropogenically fragmented puma populations. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1125-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bertl J, Ringbauer H, Blum MG. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ 2018; 6:e5325. [PMID: 30294507 PMCID: PMC6171497 DOI: 10.7717/peerj.5325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 07/01/2018] [Indexed: 11/20/2022] Open
Abstract
Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.
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Affiliation(s)
- Johanna Bertl
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Michael G.B. Blum
- Laboratoire TIMC-IMAG, UMR 5525, Université Grenoble Alpes, CNRS, Grenoble, France
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Cayuela H, Rougemont Q, Prunier JG, Moore JS, Clobert J, Besnard A, Bernatchez L. Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review. Mol Ecol 2018; 27:3976-4010. [DOI: 10.1111/mec.14848] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/17/2018] [Accepted: 08/19/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jérôme G. Prunier
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Aurélien Besnard
- CNRS; PSL Research University; EPHE; UM, SupAgro, IRD; INRA; UMR 5175 CEFE; Montpellier France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
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Thapa K, Manandhar S, Bista M, Shakya J, Sah G, Dhakal M, Sharma N, Llewellyn B, Wultsch C, Waits LP, Kelly MJ, Hero JM, Hughes J, Karmacharya D. Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape. PLoS One 2018; 13:e0193495. [PMID: 29561865 PMCID: PMC5862458 DOI: 10.1371/journal.pone.0193495] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/12/2018] [Indexed: 11/18/2022] Open
Abstract
With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal’s first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (He = 0.61, AR = 3.51) and genetic differentiation (FST = 0.14) across the landscape. We detected 3–7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.
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Affiliation(s)
- Kanchan Thapa
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | | | - Manisha Bista
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Jivan Shakya
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Govind Sah
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Maheshwar Dhakal
- Department of National Parks and Wildlife Conservation, Kathmandu, Nepal
| | - Netra Sharma
- Environment Team, U.S. Agency for International Development, Kathmandu, Nepal
| | - Bronwyn Llewellyn
- Environment Team, U.S. Agency for International Development, Kathmandu, Nepal
| | - Claudia Wultsch
- American Natural History Museum, New York City, New York, United States of America
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Jean-Marc Hero
- School of Environment, Griffith University, Nathan, Queensland, Australia
| | - Jane Hughes
- School of Environment, Griffith University, Nathan, Queensland, Australia
| | - Dibesh Karmacharya
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
- School of Environment, Griffith University, Nathan, Queensland, Australia
- * E-mail:
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38
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Recolonizing lost habitat—how European beavers (Castor fiber) return to south-western Germany. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0360-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ringbauer H, Kolesnikov A, Field DL, Barton NH. Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns. Genetics 2018; 208:1231-1245. [PMID: 29311149 PMCID: PMC5844333 DOI: 10.1534/genetics.117.300638] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/23/2017] [Indexed: 11/18/2022] Open
Abstract
In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well-separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that uses this signal to detect and estimate the strength of a linear barrier to gene flow in two dimensions. We use a diffusion approximation to model the effects of a barrier on the geographic spread of ancestry backward in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographic covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to an Antirrhinum majus (snapdragon) flower-color hybrid zone, where we do not detect any signal of a strong genome-wide barrier to gene flow.
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Affiliation(s)
- Harald Ringbauer
- Institute of Science and Technology Austria, Klosterneuburg A-3400, Austria
| | | | - David L Field
- Department of Botany and Biodiversity Research, University of Vienna, A-1030, Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria, Klosterneuburg A-3400, Austria
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No distinct barrier effects of highways and a wide river on the genetic structure of the Alpine newt (Ichthyosaura alpestris) in densely settled landscapes. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1046-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Bao W, Wuyun T, Li T, Liu H, Jiang Z, Zhu X, Du H, Bai YE. Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies. PLoS One 2017; 12:e0188685. [PMID: 29186199 PMCID: PMC5706700 DOI: 10.1371/journal.pone.0188685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 11/11/2017] [Indexed: 02/01/2023] Open
Abstract
Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%-36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.
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Affiliation(s)
- Wenquan Bao
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Tana Wuyun
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
- * E-mail:
| | - Tiezhu Li
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Huimin Liu
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Zhongmao Jiang
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Xuchun Zhu
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Hongyan Du
- Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, People’s Republic of China
| | - Yu-e Bai
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
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Ruppert JLW, James PMA, Taylor EB, Rudolfsen T, Veillard M, Davis CS, Watkinson D, Poesch MS. Riverscape genetic structure of a threatened and dispersal limited freshwater species, the Rocky Mountain Sculpin (Cottus sp.). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0938-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Samarasin P, Shuter BJ, Wright SI, Rodd FH. The problem of estimating recent genetic connectivity in a changing world. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2017; 31:126-135. [PMID: 27235331 DOI: 10.1111/cobi.12765] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 03/16/2016] [Accepted: 05/22/2016] [Indexed: 05/27/2023]
Abstract
Accurate understanding of population connectivity is important to conservation because dispersal can play an important role in population dynamics, microevolution, and assessments of extirpation risk and population rescue. Genetic methods are increasingly used to infer population connectivity because advances in technology have made them more advantageous (e.g., cost effective) relative to ecological methods. Given the reductions in wildlife population connectivity since the Industrial Revolution and more recent drastic reductions from habitat loss, it is important to know the accuracy of and biases in genetic connectivity estimators when connectivity has declined recently. Using simulated data, we investigated the accuracy and bias of 2 common estimators of migration (movement of individuals among populations) rate. We focused on the timing of the connectivity change and the magnitude of that change on the estimates of migration by using a coalescent-based method (Migrate-n) and a disequilibrium-based method (BayesAss). Contrary to expectations, when historically high connectivity had declined recently: (i) both methods over-estimated recent migration rates; (ii) the coalescent-based method (Migrate-n) provided better estimates of recent migration rate than the disequilibrium-based method (BayesAss); (iii) the coalescent-based method did not accurately reflect long-term genetic connectivity. Overall, our results highlight the problems with comparing coalescent and disequilibrium estimates to make inferences about the effects of recent landscape change on genetic connectivity among populations. We found that contrasting these 2 estimates to make inferences about genetic-connectivity changes over time could lead to inaccurate conclusions.
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Affiliation(s)
- Pasan Samarasin
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Brian J Shuter
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - F Helen Rodd
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
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Cousseau L, Husemann M, Foppen R, Vangestel C, Lens L. A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows. Heredity (Edinb) 2016; 117:259-67. [PMID: 27273323 PMCID: PMC5026754 DOI: 10.1038/hdy.2016.38] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 11/08/2022] Open
Abstract
Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns.
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Affiliation(s)
- L Cousseau
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - M Husemann
- General Zoology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - R Foppen
- Sovon, Dutch Centre for Field Ornithology, Nijmegen, The Netherlands
- Radboud University, Institute for Water and Wetland Research, Department of Animal Ecology and Ecophysiology, Nijmegen, The Netherlands
| | - C Vangestel
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Taxonomy and Phylogeny Unit, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - L Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
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45
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Integration of genetic and demographic data to assess population risk in a continuously distributed species. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0885-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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46
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Cao LJ, Wei SJ, Hoffmann AA, Wen JB, Chen M. Rapid genetic structuring of populations of the invasive fall webworm in relation to spatial expansion and control campaigns. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12486] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Li-Jun Cao
- Beijing Key Laboratory for Forest Pest Control; College of Forestry; Beijing Forestry University; Beijing 100083 China
- Institute of Plant and Environmental Protection; Beijing Academy of Agriculture and Forestry Sciences; Beijing 100097 China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection; Beijing Academy of Agriculture and Forestry Sciences; Beijing 100097 China
| | - Ary Anthony Hoffmann
- School of BioSciences; Bio21 Institute; The University of Melbourne; Melbourne Vic 3010 Australia
| | - Jun-Bao Wen
- Beijing Key Laboratory for Forest Pest Control; College of Forestry; Beijing Forestry University; Beijing 100083 China
| | - Min Chen
- Beijing Key Laboratory for Forest Pest Control; College of Forestry; Beijing Forestry University; Beijing 100083 China
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47
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Kierepka EM, Anderson SJ, Swihart RK, Rhodes OE. Evaluating the influence of life-history characteristics on genetic structure: a comparison of small mammals inhabiting complex agricultural landscapes. Ecol Evol 2016; 6:6376-96. [PMID: 27648250 PMCID: PMC5016657 DOI: 10.1002/ece3.2269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 05/15/2016] [Accepted: 05/31/2016] [Indexed: 01/16/2023] Open
Abstract
Conversion of formerly continuous native habitats into highly fragmented landscapes can lead to numerous negative demographic and genetic impacts on native taxa that ultimately reduce population viability. In response to concerns over biodiversity loss, numerous investigators have proposed that traits such as body size and ecological specialization influence the sensitivity of species to habitat fragmentation. In this study, we examined how differences in body size and ecological specialization of two rodents (eastern chipmunk; Tamias striatus and white‐footed mouse; Peromyscus leucopus) impact their genetic connectivity within the highly fragmented landscape of the Upper Wabash River Basin (UWB), Indiana, and evaluated whether landscape configuration and complexity influenced patterns of genetic structure similarly between these two species. The more specialized chipmunk exhibited dramatically more genetic structure across the UWB than white‐footed mice, with genetic differentiation being correlated with geographic distance, configuration of intervening habitats, and complexity of forested habitats within sampling sites. In contrast, the generalist white‐footed mouse resembled a panmictic population across the UWB, and no landscape factors were found to influence gene flow. Despite the extensive previous work in abundance and occupancy within the UWB, no landscape factor that influenced occupancy or abundance was correlated with genetic differentiation in either species. The difference in predictors of occupancy, abundance, and gene flow suggests that species‐specific responses to fragmentation are scale dependent.
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Affiliation(s)
- Elizabeth M Kierepka
- Savannah River Ecology Laboratory University of Georgia PO Drawer E Aiken South Carolina 29802
| | - Sara J Anderson
- Biosciences Department Minnesota State University Moorhead 1104 7th Ave Moorhead Minnesota 56563
| | - Robert K Swihart
- Department of Forestry and Natural Resources Purdue University 715 W. State Street West Lafayette Indiana 47907
| | - Olin E Rhodes
- Savannah River Ecology Laboratory University of Georgia PO Drawer E Aiken South Carolina 29802
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48
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Landguth EL, Bearlin A, Day CC, Dunham J. CDM
eta
POP
: an individual‐based, eco‐evolutionary model for spatially explicit simulation of landscape demogenetics. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12608] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Erin L. Landguth
- Division of Biological Sciences University of Montana 32 Campus Drive Missoula MT 59846 USA
| | - Andrew Bearlin
- Environmental Affairs Division Seattle City Light 700 5th Avenue Seattle WA 98124 USA
| | - Casey C. Day
- Department of Forestry and Natural Resources Purdue University 195 Marsteller Street West Lafayette IN 47909 USA
| | - Jason Dunham
- Forest and Rangeland Ecosystem Science Center U.S. Geological Survey 3200 SW Jefferson Way Corvallis OR 97330 USA
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49
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Bryson RW, Savary WE, Zellmer AJ, Bury RB, McCormack JE. Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province. Mol Ecol 2016; 25:3731-51. [DOI: 10.1111/mec.13707] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/03/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Robert W. Bryson
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Box 351800 Seattle WA 98195-1800 USA
| | - Warren E. Savary
- Department of Entomology; California Academy of Sciences; 55 Music Concourse Drive, Golden Gate Park San Francisco CA 94118 USA
| | - Amanda J. Zellmer
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
| | | | - John E. McCormack
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
- Moore Laboratory of Zoology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
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50
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Affiliation(s)
- Nikica Šprem
- Faculty of Agriculture; Department of Fisheries, Beekeeping, Game Management and Special Zoology; University of Zagreb; Svetošimunska cesta 25 Zagreb 10000 Croatia
| | - Elena Buzan
- Science and Research Centre; Institute for Biodiversity Studies; University of Primorska; Garibaldijeva 1 Koper 6000 Slovenia
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