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Tan WJ, Carver S, Martin AM, Fountain-Jones NM, Proft KM, Burridge CP. Sex and landscape influence spatial genetic variation in a large fossorial mammal, the Bare-nosed Wombat ( Vombatus ursinus). J Mammal 2024; 105:481-489. [PMID: 38812925 PMCID: PMC11130529 DOI: 10.1093/jmammal/gyae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/27/2024] [Indexed: 05/31/2024] Open
Abstract
Dispersal is an important process that is widely studied across species, and it can be influenced by intrinsic and extrinsic factors. Intrinsic factors commonly assessed include the sex and age of individuals, while landscape features are frequently-tested extrinsic factors. Here, we investigated the effects of both sex and landscape composition and configuration on genetic distances among bare-nosed wombats (Vombatus ursinus)-one of the largest fossorial mammals in the world and subject to habitat fragmentation, threats from disease, and human persecution including culling as an agricultural pest. We analyzed a data set comprising 74 Tasmanian individuals (30 males and 44 females), genotyped for 9,064 single-nucleotide polymorphisms. We tested for sex-biased dispersal and the influence of landscape features on genetic distances including land use, water, vegetation, elevation, and topographic ruggedness. We detected significant female-biased dispersal, which may be related to females donating burrows to their offspring due to the energetic cost of excavation, given their large body sizes. Land use, waterbodies, and elevation appeared to be significant landscape predictors of genetic distance. Land use potentially reflects land clearing and persecution over the last 200 years. If our findings based on a limited sample size are valid, retention and restoration of nonanthropogenic landscapes in which wombats can move and burrow may be important for gene flow and maintenance of genetic diversity.
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Affiliation(s)
- Woei Jiun Tan
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Scott Carver
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
- Odum School of Ecology, University of Georgia, Athens, GA 30602, United States
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA 30602, United States
| | - Alynn M Martin
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
- Caesar Kleberg Wildlife Research Institute, Texas A&M University–Kingsville, Kingsville, TX 78363, United States
| | - Nicholas M Fountain-Jones
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Kirstin M Proft
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
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Chambers EA, Bishop AP, Wang IJ. Individual-based landscape genomics for conservation: An analysis pipeline. Mol Ecol Resour 2023. [PMID: 37883295 DOI: 10.1111/1755-0998.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/18/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.
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Affiliation(s)
- E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Anusha P Bishop
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
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The European Ground Squirrel’s Genetic Diversity in Its Ancestral Land: Landscape Insights and Conservation Implications. DIVERSITY 2023. [DOI: 10.3390/d15030365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The European ground squirrel is an endangered rodent whose populations are declining throughout its range. Only in Bulgaria, the genetic hotspot of the species, are some abundant populations still present. We employed 12 microsatellite loci in ten Bulgarian populations to look at population structure, gene flow and recent bottlenecks. We found that the populations are in good condition in terms of heterozygosity, where values ranged from 0.55 to 0.78. However, the inbreeding index (FIS) was significant for most populations. A recent bottleneck was detected in only one population. Based on Bayesian clustering methods, the populations in Bulgaria were attributed to two groups, northern and southern, with admixture in the northern one. The AMOVA test between these groups showed no differentiation in genetic diversity. The mean value of FST was 0.184, which shows strong diversification among all populations. Hence, gene flow is probably limited. All these results indicate that Bulgaria is the main area to focus the efforts for conservation of the species by ensuring that the complex and rich genetic structure of Bulgarian populations is preserved.
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Martin SA, Peterman WE, Lipps GJ, Gibbs HL. Inferring population connectivity in eastern massasauga rattlesnakes (Sistrurus catenatus) using landscape genetics. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2793. [PMID: 36482809 DOI: 10.1002/eap.2793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Assessing the environmental factors that influence the ability of a threatened species to move through a landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited, making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the eastern massasauga rattlesnake (Sistrurus catenatus). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity was impacted by both contemporary land-cover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and least-cost paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for S. catenatus movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmented landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.
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Affiliation(s)
- Scott A Martin
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - William E Peterman
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
- School of Environmental and Natural Resources, The Ohio State University, Columbus, Ohio, USA
| | - Gregory J Lipps
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
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Jabin G, Dolker S, Joshi BD, Singh SK, Chandra K, Sharma LK, Thakur M. Lahaul–Zanskar–Sham Valley Corridor in Indian Trans Himalayan Region Facilitates Dispersal and Gene Flow in Himalayan Ibex. BIOLOGY 2023; 12:biology12030382. [PMID: 36979074 PMCID: PMC10045165 DOI: 10.3390/biology12030382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Wildlife corridors that connect mosaic habitats in heterogeneous mountainous landscapes can be of high significance as they facilitate the genetic and demographic stability of free-ranging populations. Peripheral populations of widespread species are usually ignored in conservation planning. However, these populations retain locally common alleles and are genetic reservoir under the changing climatic conditions. Capra sibirica has widespread distribution, and its southern peripheral population is distributed in the Indian trans-Himalayan region (ITR). In the present study, we studied the spatial distribution and genetic make-up of Himalayan ibex from the ITR following the landscape genetics approach. We obtained 16 haplotypes at the mitochondrial d-loop region and found a stable demography in the past with a recent decline. With 10 nuclear microsatellites, we ascertained 111 unique individuals assigned into two clusters following Bayesian and non-Bayesian clustering analysis with several admixed individuals. We also recorded 25 first-generation migrants that reflected relatively high dispersal and gene-flow across the range. We identified a 19,835 sq.km suitable area with 13,311 sq.km in Ladakh and 6524 sq.km in Lahaul-Spiti. We identified a novel movement corridor for Himalayan ibex across the Lahaul–Zanskar–Sham valley (L–Z–SV) that displayed a fairly good conductance with low genetic divergence among the samples collected on the L–Z–SV corridor. We propose declaring a protected area in the Lahaul and Kargil districts to prioritize dedicated conservation efforts for the Himalayan ibex and other sympatric ungulates that impart a major role in the diet of large carnivore and balancing ecosystem services in the trans-Himalayan region.
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Affiliation(s)
- Gul Jabin
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Stanzin Dolker
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Sujeet Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Correspondence:
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Effects of Anthropogenic Habitat Fragmentation on the Genetic Connectivity of the Threatened and Endemic Campylorhynchus yucatanicus (Aves, Trogloditydae) in the Yucatan Peninsula, Mexico. DIVERSITY 2022. [DOI: 10.3390/d14121108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identifying connectivity patterns among remnant bird populations and their relationships with land use practices and adjacent habitat fragments is key to implementing appropriate long-term management strategies for species conservation. The coastal scrub and dune vegetation complex of the northern Yucatan Peninsula is rich in endemisms and has been affected by human development, which threatens the survival of the Yucatan Wren (Campylorhynchus yucatanicus) population, an endemic bird species. To identify possible anthropogenic barriers to the connectivity of C. yucatanicus along 14 localities in the Yucatan (Mexico) coastal north, we explored the relationship between the species population’s genetic variability at each sampled site and landscape structure using regression models, in addition to the relationship between genetic distance and landscape resistance. Seven nuclear microsatellite loci were used as genetic markers. Four genetic populations were highlighted by the clustering method implemented in the Geneland program. Human settlement and availability of adequate habitat were significantly related to genetic distance (Fst), suggesting limited connectivity among sites due to ongoing land use changes. We suggest changing the IUCN threat category of C. yucatanicus to endangered as we found a significant loss of genetic variability in addition to restricted distribution, small population, habitat degradation, and loss of connectivity.
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Brasil SNR, Kelemen EP, Rehan SM. Historic DNA uncovers genetic effects of climate change and landscape alteration in two wild bee species. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01488-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Cordonnier M, Felten D, Trindl A, Heinze J, Bernadou A. Absence of genetic isolation across highly fragmented landscape in the ant Temnothorax nigriceps. BMC Ecol Evol 2022; 22:91. [PMID: 35840881 PMCID: PMC9284864 DOI: 10.1186/s12862-022-02044-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Human activities, including changes in agricultural landscapes, often impact biodiversity through habitat fragmentation. This potentially reduces genetic exchange between previously connected populations. Using a combination of nuclear and mitochondrial markers, we investigated (i) genetic diversity and population structure at multiple spatial scales and (ii) colony genetic structure and queen mating frequency in the ant species Temnothorax nigriceps in a highly anthropized environment.
Results
Although the results highlighted genetic structure on a European spatial scale, they did not reveal an impact of fragmentation on a regional scale, and we did not observe any genetic population structure on a regional scale. Across all populations, regardless of their geographical location, colony structure suggested monogyny (a single queen per colony) and monandry (single mating). However, nestmates were more related than expected, indicating that large-scale dispersal does not fully prevent genetic isolation.
Conclusions
Despite living in fragmented patches of habitat, populations of Temnothorax nigriceps are apparently genetically not isolated at a regional scale. However, large-scale dispersal alone does not prevent genetic isolation. The ecological requirements of T. nigriceps may explain their resilience to habitat fragmentation by allowing them to survive in very small patches of suitable habitat. The deeper investigation of the diversity of functional habitats for this species should allow to appreciate better the mechanisms permitting this species to overcome the negative impacts of fragmentation.
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The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
AbstractThe negative impact of habitat fragmentation due to human activities may be different in different species that co-exist in the same area, with consequences on the development of environmental protection plans. Here we aim at understanding the effects produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations, one generalist and one specialist, sampled in the same locations. We collected and genotyped 194 wood mice (generalist species) and 199 bank voles (specialist species) from 15 woodlands in a fragmented landscape characterized by different potential barriers to dispersal. Genetic variation and structure were analyzed in the two species, respectively. Effective migration surfaces, isolation-by-resistance (IBR) analysis, and regression with randomization were used to investigate isolation-by-distance (IBD) and the relative importance of land cover elements on gene flow. We observed similar patterns of heterozygosity and IBD for both species, but the bank vole showed higher genetic differences among geographic areas. The IBR analysis suggests that (i) connectivity is reduced in both species by urban areas but more strongly in the specialist bank vole; (ii) cultivated areas act as dispersal corridors in both species; (iii) woodlands appear to be an important factor in increasing connectivity in the bank vole, and less so in the wood mouse. The difference in dispersal abilities between a generalist and specialist species was reflected in the difference in genetic structure, despite extensive habitat changes due to human activities. The negative effects of fragmentation due to the process of urbanization were, at least partially, mitigated by another human product, i.e., cultivated terrains subdivided by hedgerows, and this was true for both species.
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Hernández-Leal MS, Suárez-Atilano M, Nicasio-Arzeta S, Piñero D, González-Rodríguez A. Landscape genetics of the tropical willow Salix humboldtiana: influence of climate, salinity, and orography in an altitudinal gradient. AMERICAN JOURNAL OF BOTANY 2022; 109:456-469. [PMID: 35191023 DOI: 10.1002/ajb2.1824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
PREMISE Gene flow in riparian ecosystems is influenced by landscape features such as orography, climate, and salinity. The downstream increase in genetic diversity (DIGD) hypothesis states that the unidirectionality of the watercourse causes an accumulation of genetic diversity toward downstream populations, while upstream populations are more structured and less diverse, especially in water-dispersed organisms. METHODS We used chloroplast and nuclear microsatellites to characterize genetic diversity, structure, and gene flow patterns among populations of Salix humboldtiana across an elevation and salinity gradient on three rivers (Actopan, Antigua, and Blanco) in Mexico. We used optimization of resistance surface methods to determine whether genetic distances between populations are correlated with landscape features. RESULTS Positive FIS values evidenced biparental inbreeding in some populations, particularly at higher elevations where lower niche availability constrains colonization and persistence. Four genetic groups were distinguished, corresponding to populations on the Actopan and Antigua rivers and upstream and downstream on the Blanco, but with high admixture between populations on the Actopan and Antigua rivers. Higher gene flow rates were found among proximate populations on the same river than among different rivers. Genetic diversity increased toward the river mouths, in support of the DIGD hypothesis, probably due to greater niche availability and larger population size. Differences among rivers in precipitation patterns and salinity, as well as geographic distance, were significant predictors of gene flow. CONCLUSIONS Our results depict that the DIGD and gene flow patterns in S. humboldtiana result from the complex interaction among physiography, climate, river salinity, and life-history traits of the species.
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Affiliation(s)
- Mariana S Hernández-Leal
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190 Michoacán, México
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Marco Suárez-Atilano
- Department of Integrative Biology, University of California, 3101A Valley life Sciences Building, Berkeley, CA 94720-3160, USA
| | - Sergio Nicasio-Arzeta
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190 Michoacán, México
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190 Michoacán, México
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Miao J, Farhat P, Wang W, Ruhsam M, Milne R, Yang H, Tso S, Li J, Xu J, Opgenoorth L, Miehe G, Mao K. Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau. ANNALS OF BOTANY 2021; 128:903-918. [PMID: 34472580 PMCID: PMC8577208 DOI: 10.1093/aob/mcab114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP). METHODS The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species. KEY RESULTS Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter. CONCLUSIONS This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.
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Affiliation(s)
- Jibin Miao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Perla Farhat
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Wentao Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Richard Milne
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Sonam Tso
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jingjing Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lars Opgenoorth
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Georg Miehe
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
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Veliz D, Rojas-Hernández N, Fibla P, Dewitte B, Cornejo-Guzmán S, Parada C. High levels of connectivity over large distances in the diadematid sea urchin Centrostephanus sylviae. PLoS One 2021; 16:e0259595. [PMID: 34735545 PMCID: PMC8568165 DOI: 10.1371/journal.pone.0259595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Most benthic marine invertebrates with sedentary benthic adult phases have planktonic larvae that permit connectivity between geographically isolated populations. Planktonic larval duration and oceanographic processes are vital to connecting populations of species inhabiting remote and distant islands. In the present study, we analyzed the population genetic structure of the sea urchin Centrostephanus sylviae, which inhabits only the Juan Fernández Archipelago and the Desventuradas islands, separated by more than 800 km. For 92 individuals collected from Robinson Crusoe and Selkirk Islands (Juan Fernández Archipelago) and San Ambrosio Island (Desventuradas Islands), 7,067 single nucleotide polymorphisms (SNPs) were obtained. The results did not show a spatial genetic structure for C. sylviae; relative high migration rates were revealed between the islands. An analysis of the water circulation pattern in the area described a predominant northward water flow with periods of inverted flow, suggesting that larvae could move in both directions. Overall, this evidence suggests that C. sylviae comprises a single large population composed of individuals separated by more than 800 km.
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Affiliation(s)
- David Veliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable (ESMOI), Coquimbo, Chile
- Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile
- * E-mail:
| | - Noemi Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Fibla
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Boris Dewitte
- Núcleo Milenio de Ecología y Manejo Sustentable (ESMOI), Coquimbo, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
- Université de Toulouse, CERFACS/CNRS, Toulouse, France
| | - Sebastián Cornejo-Guzmán
- Núcleo Milenio de Ecología y Manejo Sustentable (ESMOI), Coquimbo, Chile
- Departamento de Geofísica, Universidad de Concepción, Concepción, Chile
| | - Carolina Parada
- Núcleo Milenio de Ecología y Manejo Sustentable (ESMOI), Coquimbo, Chile
- Departamento de Geofísica, Universidad de Concepción, Concepción, Chile
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Gauffre B, Boissinot A, Quiquempois V, Leblois R, Grillet P, Morin S, Picard D, Ribout C, Lourdais O. Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction. Mol Ecol 2021; 31:119-133. [PMID: 34674328 DOI: 10.1111/mec.16236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farmland, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation-by-distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess differences in effective population density and dispersal between the contrasted landscapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.
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Affiliation(s)
- Bertrand Gauffre
- INRAE, UR 1115 PSH, Plantes et Systèmes de culture Horticoles, Avignon, France.,School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Alexandre Boissinot
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,Réserve Naturelle Régionale du Bocage des Antonins - Deux-Sèvres Nature Environnement, Niort, France
| | | | - Raphael Leblois
- CBGP UMR 1062, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France.,Institut de Biologie Computationnelle, Univ. Montpellier, Montpelier, France
| | - Pierre Grillet
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Sophie Morin
- Office Français de la Biodiversité, Villiers-en-Bois, France
| | - Damien Picard
- Département de Biologie, UFR Sciences, Angers, France
| | - Cécile Ribout
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Olivier Lourdais
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
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14
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Guerrini M, Panayides P, Niktoreh Mofrad N, Kassinis N, Ioannou I, Forcina G, Hadjigerou P, Barbanera F. Spatial genetic structure and Ovis haplogroup as a tool for an adaptive conservation management of the endangered Cyprus mouflon. ZOOLOGY 2021; 148:125959. [PMID: 34474331 DOI: 10.1016/j.zool.2021.125959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022]
Abstract
The mouflon (Ovis gmelini ophion) is the largest wild terrestrial mammal of Cyprus. Regarded as the local flagship species, its population range is limited to the mountainous Paphos Forest and adjacent areas including part of Troodos National Forest Park (> 700 Km2). This species, protected by both national and international legislation, is classified as Endangered by the IUCN, with livestock intrusion, poaching and habitat loss as the main threatening factors. We determined the spatial genetic structure by investigating sexes separately and shed further light on the Cyprus mouflon placement among Ovis haplogroups (HGs) to enforce its protection within an adaptive conservation framework. We genotyped 108 samples collected across the entire species' range at both14 loci of the microsatellite DNA and the mitochondrial DNA Control Region (CR). Microsatellite genotyping indicated that the wild population retained low genetic variability, which, however, was not associated with a level of inbreeding raising particular concern (FIS = 0.12). An overall weak spatial genetic structure was disclosed, consistently with the limited extension of the mouflon range, the lack of significant physical barriers to dispersal and the intense gene flow mostly occurring along a northeast-southwest axis across the forest. Nevertheless, evidences of structure were found for females in compliance with their philopatric behaviour. The disclosure of unique features compared to Mediterranean and Near East conspecifics, such as the occurrence of a six-fold 76 bp-long repeated motif in the Cyprus mouflon CR, along with the outcome of a phylogenetic reconstruction (based on a far higher number of Ovis GenBank records and Cyprus haplotypes than in previous studies) inspired the proposal of a new haplogroup (HGC2) which included the Anatolian mouflon (O. g. anatolica, former HGX) as sister taxon. While both high habitat heterogeneity and low human disturbance were the main drivers in determining the overall spatial structure, future conservation efforts to preserve this valuable genetic resource should focus on avoiding possible introgressive hybridisation with co-grazing livestock to the edge of its range.
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Affiliation(s)
- Monica Guerrini
- Department of Biology, Via A. Volta 4, University of Pisa, 56126, Pisa, Italy
| | | | | | | | | | - Giovanni Forcina
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | | | - Filippo Barbanera
- Department of Biology, Via A. Volta 4, University of Pisa, 56126, Pisa, Italy.
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15
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Hellwig T, Abbo S, Sherman A, Ophir R. Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110957. [PMID: 34315583 DOI: 10.1016/j.plantsci.2021.110957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/12/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Plant breeders and conservationist depend on knowledge about the genetic variation of their species of interest. Pisum fulvum, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of P. fulvum from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of P. fulvum is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 %-18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1,354 markers were significantly correlated with environmental factors, 1,233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of P. fulvum. Climate changeis likely to cause further erosion of genetic diversity in P. fulvum. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.
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Affiliation(s)
- Timo Hellwig
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel; Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Shahal Abbo
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Ron Ophir
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel.
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16
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Major EI, Höhn M, Avanzi C, Fady B, Heer K, Opgenoorth L, Piotti A, Popescu F, Postolache D, Vendramin GG, Csilléry K. Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.). Mol Ecol 2021; 30:5247-5265. [PMID: 34365696 PMCID: PMC9291806 DOI: 10.1111/mec.16107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 12/03/2022]
Abstract
Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.
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Affiliation(s)
- Enikő I Major
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Mária Höhn
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Camilla Avanzi
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Bruno Fady
- Ecology of Mediterranean Forests (URFM), INRAE, UR629, Avignon, France
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Marburg, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Marburg, Germany.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Flaviu Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Dragos Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Katalin Csilléry
- Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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17
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Dong Z, Li C, Zhang Q, Li L, Lu Z, Ouyang F, Song Y, Yu Y, Men X. Landscape genetic analyses reveal host association of mitochondrial haplotypes in the Asian corn borer, Ostrinia furnacalis. INSECT SCIENCE 2021; 28:1169-1178. [PMID: 32383529 DOI: 10.1111/1744-7917.12798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/26/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Crop expansion often leads to high pest pressure. These pests may have fitness trade-offs related to host use, and some host-associated genotypes may benefit and increase in frequency. However, evidence concerning the effect of host availability on spatial distribution and frequency of mitochondrial haplotypes is scarce. We studied genetic variation of the Asian corn borer, Ostrinia furnacalis (Guenée), across a large area during 2 years (2016 and 2017). Mitochondrial sequence data were obtained from 530 individuals collected from 79 locations in Shandong Province, China. In total, 155 haplotypes were found based on the combined cytochrome oxidase subunit 1 (COI) and COII genes. Three haplotypes (H2, H12, and H23) were dominant, whereas most of the other haplotypes occurred in low frequency. A haplotype network showed that the 155 haplotypes can be grouped into three clusters. Haplotype clusters seemed to be randomly distributed. The frequency of H12 (in Cluster 1) was positively correlated with maize crop proportion, but negatively correlated with other crops (primarily vegetables, oilseed crops, and cotton) at all spatial scales (1-, 3-, and 5-km radius). Cluster 2 had haplotype H23, and this cluster was negatively correlated with semi-natural habitats. Cluster 3 had no dominant haplotype and was not affected by landscape factors. We conclude that H12 may be a maize-associated haplotype. Further study is needed to verify the possibility that the carriers of this haplotype may possess some fitness trade-offs. Our study highlights the importance of host availability in O. furnacalis haplotype distribution and frequency.
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Affiliation(s)
- Zhaoke Dong
- Institute of Plant Protection, Shandong Academy of Agricultural Science, Jinan, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chao Li
- Institute of Plant Protection, Shandong Academy of Agricultural Science, Jinan, China
| | - Qingqing Zhang
- Institute of Plant Protection, Shandong Academy of Agricultural Science, Jinan, China
| | - Lili Li
- Institute of Plant Protection, Shandong Academy of Agricultural Science, Jinan, China
| | - Zengbin Lu
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, China
| | - Fang Ouyang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yingying Song
- Institute of Plant Protection, Shandong Academy of Agricultural Science, Jinan, China
| | - Yi Yu
- Institute of Plant Protection, Shandong Academy of Agricultural Science, Jinan, China
| | - Xingyuan Men
- Institute of Plant Protection, Shandong Academy of Agricultural Science, Jinan, China
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18
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Byer NW, Holding ML, Crowell MM, Pierson TW, Dilts TE, Larrucea ES, Shoemaker KT, Matocq MD. Adaptive divergence despite low effective population size in a peripherally isolated population of the pygmy rabbit, Brachylagus idahoensis. Mol Ecol 2021; 30:4173-4188. [PMID: 34166550 DOI: 10.1111/mec.16040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022]
Abstract
Local adaptation can occur when spatially separated populations are subjected to contrasting environmental conditions. Historically, understanding the genetic basis of adaptation has been difficult, but increased availability of genome-wide markers facilitates studies of local adaptation in non-model organisms of conservation concern. The pygmy rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on sagebrush for forage and cover. This reliance has led to widespread population declines following reductions in the distribution of sagebrush, leading to geographic separation between populations. In this study, we used >20,000 single nucleotide polymorphisms, genotype-environment association methods, and demographic modeling to examine neutral genetic variation and local adaptation in the pygmy rabbit in Nevada and California. We identified 308 loci as outliers, many of which had functional annotations related to metabolism of plant secondary compounds. Likewise, patterns of spatial variation in outlier loci were correlated with landscape and climatic variables including proximity to streams, sagebrush cover, and precipitation. We found that populations in the Mono Basin of California probably diverged from other Great Basin populations during late Pleistocene climate oscillations, and that this region is adaptively differentiated from other regions in the southern Great Basin despite limited gene flow and low effective population size. Our results demonstrate that peripherally isolated populations can maintain adaptive divergence.
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Affiliation(s)
- Nathan W Byer
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Matthew L Holding
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Miranda M Crowell
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, Georgia, USA
| | - Thomas E Dilts
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | | | - Kevin T Shoemaker
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
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19
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Rönkä N, Pakanen VM, Pauliny A, Thomson RL, Nuotio K, Pehlak H, Thorup O, Lehikoinen P, Rönkä A, Blomqvist D, Koivula K, Kvist L. Genetic differentiation in an endangered and strongly philopatric, migrant shorebird. BMC Ecol Evol 2021; 21:125. [PMID: 34147062 PMCID: PMC8214799 DOI: 10.1186/s12862-021-01855-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background Populations living in fragmented habitats may suffer from loss of genetic variation and reduced between-patch dispersal, which are processes that can result in genetic differentiation. This occurs frequently in species with reduced mobility, whereas genetic differentiation is less common among mobile species such as migratory birds. The high dispersal capacity in the latter species usually allows for gene flow even in fragmented landscapes. However, strongly philopatric behaviour can reinforce relative isolation and the degree of genetic differentiation. The Southern Dunlin (Calidris alpina schinzii) is a philopatric, long-distance migratory shorebird and shows reduced dispersal between isolated breeding patches. The endangered population of the Southern Dunlin breeding at the Baltic Sea has suffered from habitat deterioration and fragmentation of coastal meadows. We sampled DNA across the entire population and used 12 polymorphic microsatellite loci to examine whether the environmental changes have resulted in genetic structuring and loss of variation. Results We found a pattern of isolation-by-distance across the whole Baltic population and genetic differentiation between local populations, even within the southern Baltic. Observed heterozygosity was lower than expected throughout the range and internal relatedness values were positive indicating inbreeding. Conclusions Our results provide long-term, empirical evidence for the theoretically expected links between habitat fragmentation, population subdivision, and gene flow. They also demonstrate a rare case of genetic differentiation between populations of a long-distance migratory species. The Baltic Southern Dunlin differs from many related shorebird species that show near panmixia, reflecting its philopatric life history and the reduced connectivity of its breeding patches. The results have important implications as they suggest that reduced connectivity of breeding habitats can threaten even long-distance migrants if they show strong philopatry during breeding. The Baltic Southern Dunlin warrants urgent conservation efforts that increase functional connectivity and gene flow between breeding areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01855-0.
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Affiliation(s)
- Nelli Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Veli-Matti Pakanen
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland.,Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Angela Pauliny
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Robert L Thomson
- Section of Ecology, Department of Biology, University of Turku, 20014, Turku, Finland.,Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kimmo Nuotio
- Environmental Agency, Valtakatu 11, 28100, Pori, Finland
| | - Hannes Pehlak
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia.,OÜ Xenus, Koguva, 94724, Muhu Island, Saare, Estonia
| | - Ole Thorup
- , V. Vedsted Byvej 32, Vester Vedsted, 6760, Ribe, Denmark
| | - Petteri Lehikoinen
- The Helsinki Lab of Ornithology, Finnish Museum of Natural History, University of Helsinki, 00014, Helsinki, Finland
| | - Antti Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Donald Blomqvist
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden.
| | - Kari Koivula
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
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20
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Snow Leopard (Panthera uncia) Genetics: The Knowledge Gaps, Needs, and Implications for Conservation. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00236-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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21
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Westphal D, Mancini AN, Baden AL. Primate landscape genetics: A review and practical guide. Evol Anthropol 2021; 30:171-184. [PMID: 33720482 DOI: 10.1002/evan.21891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/12/2020] [Accepted: 02/17/2021] [Indexed: 11/06/2022]
Abstract
Landscape genetics is an emerging field that integrates population genetics, landscape ecology, and spatial statistics to investigate how geographical and environmental features and evolutionary processes such as gene flow, genetic drift, and selection structure genetic variation at both the population and individual levels, with implications for ecology, evolution, and conservation biology. Despite being particularly well suited for primatologists, this method is currently underutilized. Here, we synthesize the current state of research on landscape genetics in primates. We begin by outlining how landscape genetics has been used to disentangle the drivers of diversity, followed by a review of how landscape genetic methods have been applied to primates. This is followed by a section highlighting special considerations when applying the methods to primates, and a practical guide to facilitate further landscape genetics studies using both existing and de novo datasets. We conclude by exploring future avenues of inquiry that could be facilitated by recent developments as well as underdeveloped applications of landscape genetics to primates.
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Affiliation(s)
- Darice Westphal
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Andrea L Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA.,Department of Anthropology, Hunter College, New York, New York, USA
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22
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Garrison NL, Johnson PD, Whelan NV. Conservation genomics reveals low genetic diversity and multiple parentage in the threatened freshwater mussel, Margaritifera hembeli. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01329-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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23
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Martín-Rodríguez I, Escudero A, García-Fernández A. Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist. PeerJ 2021; 9:e10533. [PMID: 33505788 PMCID: PMC7789860 DOI: 10.7717/peerj.10533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/19/2020] [Indexed: 11/20/2022] Open
Abstract
Background Gypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the species Lepidium subulatum, a dominant Iberian shrubby gypsophyte. Methods We tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier. Results Results showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, like FST and FIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants. Discussion Natural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions.
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Affiliation(s)
- Irene Martín-Rodríguez
- Área de Biodiversidad y Conservación. Departamento de Biología y Geología, Física y Química Orgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación. Departamento de Biología y Geología, Física y Química Orgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Alfredo García-Fernández
- Área de Biodiversidad y Conservación. Departamento de Biología y Geología, Física y Química Orgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
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24
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Draheim HM, Moore JA, Winterstein SR, Scribner KT. Spatial genetic structure and landscape connectivity in black bears: Investigating the significance of using different land cover datasets and classifications in landscape genetics analyses. Ecol Evol 2021; 11:978-989. [PMID: 33520180 PMCID: PMC7820153 DOI: 10.1002/ece3.7111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 11/13/2022] Open
Abstract
Landscape genetic analyses allow detection of fine-scale spatial genetic structure (SGS) and quantification of effects of landscape features on gene flow and connectivity. Typically, analyses require generation of resistance surfaces. These surfaces characteristically take the form of a grid with cells that are coded to represent the degree to which landscape or environmental features promote or inhibit animal movement. How accurately resistance surfaces predict association between the landscape and movement is determined in large part by (a) the landscape features used, (b) the resistance values assigned to features, and (c) how accurately resistance surfaces represent landscape permeability. Our objective was to evaluate the performance of resistance surfaces generated using two publicly available land cover datasets that varied in how accurately they represent the actual landscape. We genotyped 365 individuals from a large black bear population (Ursus americanus) in the Northern Lower Peninsula (NLP) of Michigan, USA at 12 microsatellite loci, and evaluated the relationship between gene flow and landscape features using two different land cover datasets. We investigated the relative importance of land cover classification and accuracy on landscape resistance model performance. We detected local spatial genetic structure in Michigan's NLP black bears and found roads and land cover were significantly correlated with genetic distance. We observed similarities in model performance when different land cover datasets were used despite 21% dissimilarity in classification between the two land cover datasets. However, we did find the performance of land cover models to predict genetic distance was dependent on the way the land cover was defined. Models in which land cover was finely defined (i.e., eight land cover classes) outperformed models where land cover was defined more coarsely (i.e., habitat/non-habitat or forest/non-forest). Our results show that landscape genetic researchers should carefully consider how land cover classification changes inference in landscape genetic studies.
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Affiliation(s)
- Hope M. Draheim
- Department of ZoologyMichigan State UniversityEast LansingMichiganUSA
| | | | - Scott R. Winterstein
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | - Kim T. Scribner
- Department of ZoologyMichigan State UniversityEast LansingMichiganUSA
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
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25
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Ranger survey reveals conservation issues across Protected and outside Protected Areas in southern India. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Visser J, Robinson T, Jansen van Vuuren B. Spatial genetic structure in the rock hyrax (Procavia capensis) across the Namaqualand and western Fynbos areas of South Africa — a mitochondrial and microsatellite perspective. CAN J ZOOL 2020. [DOI: 10.1139/cjz-2019-0154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interplay between biotic and abiotic environments is increasingly recognized as a major determinant of spatial genetic patterns. Among spatial genetic studies, saxicolous or rock-dwelling species remain underrepresented in spite of their strict dependence on landscape structure. Here we investigated patterns and processes operating at different spatial (fine and regional scales) and time scales (using mitochondrial and microsatellite markers) in the rock hyrax (Procavia capensis (Pallas, 1766)). Our focus was on the western seaboard of South Africa and included two recognized biodiversity hotspots (Cape Floristic Region and Succulent Karoo). At fine spatial scale, significant genetic structure was present between four rocky outcrops in an isolated population, likely driven by the social system of this species. At a broader spatial scale, ecological dependence on rocky habitat and population-level processes, in conjunction with landscape structure, appeared to be the main drivers of genetic diversity and structure. Large areas devoid of suitable rocky habitat (e.g., the Knersvlakte, Sandveld, and Cape Flats, South Africa) represent barriers to gene flow in the species, although genetic clusters closely follow climatic, geological, and phytogeographic regions, possibly indicating ecological specialization or adaptation as contributing factors enforcing isolation. Taken together, our study highlights the need to consider both intrinsic and extrinsic factors when investigating spatial genetic structures within species.
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Affiliation(s)
- J.H. Visser
- Department of Botany and Zoology, University of Stellenbosch, Private Bag XI, Matieland 7602, South Africa
| | - T.J. Robinson
- Department of Botany and Zoology, University of Stellenbosch, Private Bag XI, Matieland 7602, South Africa
| | - B. Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, P.O. Box 524, Auckland Park 2000, South Africa
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Sherpa S, Renaud J, Guéguen M, Besnard G, Mouyon L, Rey D, Després L. Landscape does matter: Disentangling founder effects from natural and human-aided post-introduction dispersal during an ongoing biological invasion. J Anim Ecol 2020; 89:2027-2042. [PMID: 32597498 DOI: 10.1111/1365-2656.13284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/19/2020] [Indexed: 11/28/2022]
Abstract
Environmental features impacting the spread of invasive species after introduction can be assessed using population genetic structure as a quantitative estimation of effective dispersal at the landscape scale. However, in the case of an ongoing biological invasion, deciphering whether genetic structure represents landscape connectivity or founder effects is particularly challenging. We examined the modes of dispersal (natural and human-aided) and the factors (landscape or founders history) shaping genetic structure in range edge invasive populations of the Asian tiger mosquito, Aedes albopictus, in the region of Grenoble (Southeast France). Based on detailed occupancy-detection data and environmental variables (climatic, topographic and land-cover), we modelled A. albopictus potential suitable area and its expansion history since first introduction. The relative role of dispersal modes was estimated using biological dispersal capabilities and landscape genetics approaches using genome-wide SNP dataset. We demonstrate that both natural and human-aided dispersal have promoted the expansion of populations. Populations in diffuse urban areas, representing highly suitable habitat for A. albopictus, tend to disperse less, while roads facilitate long-distance dispersal. Yet, demographic bottlenecks during introduction played a major role in shaping the genetic variability of these range edge populations. The present study is one of the few investigating the role of founder effects and ongoing expansion processes in shaping spatial patterns of genetic variation in an invasive species at the landscape scale. The combination of several dispersal modes and large proportions of continuous suitable habitats for A. albopictus promoted range filling of almost its entire potential distribution in the region of Grenoble only few years after introduction.
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Affiliation(s)
- Stéphanie Sherpa
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
| | - Julien Renaud
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
| | - Maya Guéguen
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
| | - Gilles Besnard
- Entente Interdépartementale Rhône Alpes pour la Démoustication (EID), Chindrieux, France
| | - Loic Mouyon
- Entente Interdépartementale Rhône Alpes pour la Démoustication (EID), Chindrieux, France
| | - Delphine Rey
- Entente Interdépartementale Rhône Alpes pour la Démoustication (EID), Chindrieux, France
| | - Laurence Després
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
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Winiarski KJ, Peterman WE, McGarigal K. Evaluation of the R package ‘
resistancega
’: A promising approach towards the accurate optimization of landscape resistance surfaces. Mol Ecol Resour 2020; 20:1583-1596. [DOI: 10.1111/1755-0998.13217] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 06/01/2020] [Accepted: 06/15/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Kristopher Jonathan Winiarski
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
- Northeast Climate Adaptation Science Center University of Massachusetts Amherst MA USA
| | - William E. Peterman
- School of Environment and Natural Resources Ohio State University Columbus OH USA
| | - Kevin McGarigal
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
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Klass K, Van Belle S, Estrada A. Demographic population structure of black howler monkeys in fragmented and continuous forest in Chiapas, Mexico: Implications for conservation. Am J Primatol 2020; 82:e23163. [PMID: 32602598 DOI: 10.1002/ajp.23163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 01/16/2023]
Abstract
For wild primates, demography studies are increasingly recognized as necessary for assessing the viability of vulnerable populations experiencing rapid environmental change. In particular, anthropogenic changes such as habitat loss and fragmentation can cause ecological and behavioral changes in small, isolated populations, which may, over time, alter population density and demographic structure (age/sex classes and group composition) in fragment populations relative to continuous forest populations. We compared our study population of Endangered black howler monkeys (Alouatta pigra) in 34 forest fragments around Palenque National Park (PNP), Mexico (62 groups, 407 individuals), to the adjacent population in PNP, protected primary forest (21 groups, 134 individuals), and to previous research on black howlers in fragments in our study area (18 groups, 115 individuals). We used χ2 and Mann-Whitney U tests to address the questions: (a) what is the current black howler demographic population structure in unprotected forest fragments around PNP? (b) How does it compare to PNP's stable, continuous population? (c) How has it changed over time? Compared to the PNP population, the fragment populations showed higher density, a significantly lower proportion of multimale groups, and significantly fewer adult males per group. The population's age/sex structure in the fragmented landscape has been stable over the last 17 years, but differed in a higher proportion of multifemale groups, higher density, and higher patch occupancy in the present. In the context of conservation, some of our results may be positive as they indicate possible population growth over time. However, long-term scarcity of adult males in fragments and associated effects on population demographic structure might be cause for concern, in that it may affect gene flow and genetic diversity. The scarcity of adult males might stem from males experiencing increased mortality while dispersing in the fragmented landscape, whereas females might be becoming more philopatric in fragments.
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Affiliation(s)
- Keren Klass
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Sarie Van Belle
- Department of Anthropology, University of Texas at Austin, Austin, Texas
| | - Alejandro Estrada
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Thatte P, Chandramouli A, Tyagi A, Patel K, Baro P, Chhattani H, Ramakrishnan U. Human footprint differentially impacts genetic connectivity of four wide‐ranging mammals in a fragmented landscape. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.13022] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Prachi Thatte
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Anuradha Chandramouli
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Abhinav Tyagi
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Kaushal Patel
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Phulmani Baro
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Himanshu Chhattani
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Uma Ramakrishnan
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
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García-Zubia LC, Hernández-Velasco J, Hernández-Díaz JC, Simental-Rodríguez SL, López-Sánchez CA, Quiñones-Pérez CZ, Carrillo-Parra A, Wehenkel C. Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico. PeerJ 2019; 7:e8002. [PMID: 31844562 PMCID: PMC6910111 DOI: 10.7717/peerj.8002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/07/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Spatial genetic structure (SGS) analysis is a powerful approach to quantifying gene flow between trees, thus clarifying the functional connectivity of trees at population and landscape scales. The findings of SGS analysis may be useful for conservation and management of natural populations and plantations. Pinus cembroides is a widely distributed tree species, covering an area of about 2.5 million hectares in Mexico. The aim of this study was to examine five natural seed stands of P. cembroides in the Sierra Madre Occidental to determine the SGS at population (within the seed stand) and landscape (among seed stands) levels in order to establish guidelines for the conservation and management of the species. We hypothesized that P. cembroides, in which the seeds are dispersed by birds and mammals, creates weaker SGS than species with wind-dispersed seeds. METHODS DNA fingerprinting was performed using the amplified fragment length polymorphism (AFLP) technique. In order to estimate the SGS at population and landscape levels, we measured the geographical (spatial) distance as the Euclidean distance. We also estimated the genetic distances between individuals using the pairwise kinship coefficient. RESULTS The results showed non-significant autocorrelation in four out of five seed stands studied (i.e., a mainly random distribution in the space of the genetic variants of P. cembroides at population level). DISCUSSION SGS was detected at the landscape scale, supporting the theory of isolation by distance as a consequence of restricted pollen and seed dispersal. However, the SGS may also have been generated by our sampling strategy. We recommended establishing a close network of seed stands of P. cembroides to prevent greater loss of local genetic variants and alteration of SGS. We recommend seed stands of P. cembroides of a minimum width of 225 m.
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Affiliation(s)
- Luis C. García-Zubia
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | - Javier Hernández-Velasco
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | - José C. Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | | | - Carlos A. López-Sánchez
- Department of Biology of Organisms and Systems, Mieres Polytechnic School, University of Oviedo, Campus Universitario de Mieres, C/Gonzalo Gutiérrez Quirós S/N, Mieres, Spain
| | | | - Artemio Carrillo-Parra
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
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32
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Le Chevalier H, Marí‐Mena N, Carro B, Prunier JG, Bossu C, Darnet E, Souchet J, Guillaume O, Calvez O, Bertrand R, Barthe L, Pottier G, Martínez‐Sylvestre A, Verdaguer‐Foz I, Mossoll‐Torres M, Trochet A, Aubret F. Isolation and characterization of fourteen polymorphic microsatellite markers in the viperine snake Natrix maura. Ecol Evol 2019; 9:11227-11231. [PMID: 31641467 PMCID: PMC6802021 DOI: 10.1002/ece3.5623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 11/07/2022] Open
Abstract
Nineteen polymorphic microsatellite loci were identified and developed for Natrix maura. Polymorphism was assessed for 120 individuals sampled across four sampling sites from the French Pyrenees Mountains. The number of alleles per locus ranged from 3 to 15, and expected heterozygosity per locus ranged from 0.227 to 0.863. We tested for deviation from Hardy-Weinberg equilibrium and linkage disequilibrium and assessed the presence of null alleles for all loci, resulting in a selection of 14 high-quality polymorphic markers. These markers will be extremely useful in identifying fine-scale genetic structures and providing insight into conservation management plans of this species.
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Affiliation(s)
- Hugo Le Chevalier
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Neus Marí‐Mena
- Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE)Universidade da CoruñaA CoruñaSpain
- All Genetics & Biology SLA CoruñaSpain
| | | | - Jérôme G. Prunier
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Coralie Bossu
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Elodie Darnet
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Jérémie Souchet
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Olivier Guillaume
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Olivier Calvez
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Romain Bertrand
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Laurent Barthe
- Association Nature en Occitanie (NEO)Maison de l'Environnement de Midi‐PyrénéesToulouseFrance
| | - Gilles Pottier
- Association Nature en Occitanie (NEO)Maison de l'Environnement de Midi‐PyrénéesToulouseFrance
| | | | - Isabel Verdaguer‐Foz
- Catalonia Reptile and Amphibian Rescue Center (CRARC)C/Santa Claras/n MasquefaSpain
| | | | - Audrey Trochet
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
| | - Fabien Aubret
- Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321Centre National de la Recherche Scientifique (CNRS)MoulisFrance
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Rutten A, Cox K, Scheppers T, Broecke BV, Leirs H, Casaer J. Analysing the recolonisation of a highly fragmented landscape by wild boar using a landscape genetic approach. WILDLIFE BIOLOGY 2019. [DOI: 10.2981/wlb.00542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | - Karen Cox
- K. Cox, Res. Inst. for Nature and Forest (INBO), Geraardsbergen, Belgium
| | | | - Bram Vanden Broecke
- B. Vanden Broecke and H. Leirs, Dept of Biology, Univ. of Antwerp, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Herwig Leirs
- B. Vanden Broecke and H. Leirs, Dept of Biology, Univ. of Antwerp, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Jim Casaer
- J. Casaer, Res. Inst. for Nature and Forest (INBO), Brussels, Belgium
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Grummer JA, Beheregaray LB, Bernatchez L, Hand BK, Luikart G, Narum SR, Taylor EB. Aquatic Landscape Genomics and Environmental Effects on Genetic Variation. Trends Ecol Evol 2019; 34:641-654. [DOI: 10.1016/j.tree.2019.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 01/17/2023]
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Ashrafzadeh MR, Naghipour AA, Haidarian M, Kusza S, Pilliod DS. Effects of climate change on habitat and connectivity for populations of a vulnerable, endemic salamander in Iran. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00637] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Diversity, genetic structure, and population genomics of the tropical tree Centrolobium tomentosum in remnant and restored Atlantic forests. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01195-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Okamiya H, Kusano T. Effects of landscape features on gene flow among urban frog populations. Ecol Res 2019. [DOI: 10.1111/1440-1703.12011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hisanori Okamiya
- Department of Biological Sciences, Graduate School of Sciences Tokyo Metropolitan University Hachioji‐shi Tokyo Japan
| | - Tamotsu Kusano
- Department of Biological Sciences, Graduate School of Sciences Tokyo Metropolitan University Hachioji‐shi Tokyo Japan
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Toczydlowski RH, Waller DM. Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (
Impatiens capensis
Meerb.) reflect fragmentation of floodplain forests. Mol Ecol 2019; 28:2459-2475. [DOI: 10.1111/mec.15072] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 01/05/2023]
Affiliation(s)
| | - Donald M. Waller
- Department of Botany University of Wisconsin‐Madison Madison Wisconsin
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Tarroso P, Carvalho SB, Velo‐Antón G. Phylin 2.0: Extending the phylogeographical interpolation method to include uncertainty and user‐defined distance metrics. Mol Ecol Resour 2019; 19:1081-1094. [DOI: 10.1111/1755-0998.13010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 02/18/2019] [Accepted: 03/01/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Pedro Tarroso
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Sílvia B. Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Guillermo Velo‐Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
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Seaborn T, Hauser SS, Konrade L, Waits LP, Goldberg CS. Landscape genetic inferences vary with sampling scenario for a pond-breeding amphibian. Ecol Evol 2019; 9:5063-5078. [PMID: 31110662 PMCID: PMC6509389 DOI: 10.1002/ece3.5023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 11/25/2022] Open
Abstract
A critical decision in landscape genetic studies is whether to use individuals or populations as the sampling unit. This decision affects the time and cost of sampling and may affect ecological inference. We analyzed 334 Columbia spotted frogs at 8 microsatellite loci across 40 sites in northern Idaho to determine how inferences from landscape genetic analyses would vary with sampling design. At all sites, we compared a proportion available sampling scheme (PASS), in which all samples were used, to resampled datasets of 2-11 individuals. Additionally, we compared a population sampling scheme (PSS) to an individual sampling scheme (ISS) at 18 sites with sufficient sample size. We applied an information theoretic approach with both restricted maximum likelihood and maximum likelihood estimation to evaluate competing landscape resistance hypotheses. We found that PSS supported low-density forest when restricted maximum likelihood was used, but a combination model of most variables when maximum likelihood was used. We also saw variations when AIC was used compared to BIC. ISS supported this model as well as additional models when testing hypotheses of land cover types that create the greatest resistance to gene flow for Columbia spotted frogs. Increased sampling density and study extent, seen by comparing PSS to PASS, showed a change in model support. As number of individuals increased, model support converged at 7-9 individuals for ISS to PSS. ISS may be useful to increase study extent and sampling density, but may lack power to provide strong support for the correct model with microsatellite datasets. Our results highlight the importance of additional research on sampling design effects on landscape genetics inference.
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Affiliation(s)
- Travis Seaborn
- School of Biological SciencesWashington State UniversityPullmanWashington
| | | | - Lauren Konrade
- Department of Biological SciencesWichita State UniversityWichitaKansas
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdaho
| | - Caren S. Goldberg
- School of the EnvironmentWashington State UniversityPullmanWashington
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Emel SL, Olson DH, Knowles LL, Storfer A. Comparative landscape genetics of two endemic torrent salamander species, Rhyacotriton kezeri and R. variegatus: implications for forest management and species conservation. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01172-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Bouchard C, Tessier N, Lapointe FJ. Watersheds influence the wood turtle’s (Glyptemys insculpta) genetic structure. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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43
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O'Connell KA, Mulder KP, Maldonado J, Currie KL, Ferraro DM. Sampling related individuals within ponds biases estimates of population structure in a pond-breeding amphibian. Ecol Evol 2019; 9:3620-3636. [PMID: 30962914 PMCID: PMC6434569 DOI: 10.1002/ece3.4994] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
Effective conservation and management of pond-breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding-site connectivity. Population-level studies of pond-breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within-pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome-wide SNPs generated using a double-digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within-pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.
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Affiliation(s)
- Kyle A. O'Connell
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Global Genome InitiativeNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Department of BiologyThe University of Texas at ArlingtonArlingtonTexas
| | - Kevin P. Mulder
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO)PortoPortugal
| | - Jose Maldonado
- Department of BiologyThe University of Texas at ArlingtonArlingtonTexas
| | | | - Dennis M. Ferraro
- School of Natural ResourcesUniversity of Nebraska LincolnLincolnNebraska
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44
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Al-Asadi H, Petkova D, Stephens M, Novembre J. Estimating recent migration and population-size surfaces. PLoS Genet 2019; 15:e1007908. [PMID: 30640906 PMCID: PMC6347299 DOI: 10.1371/journal.pgen.1007908] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/25/2019] [Accepted: 12/19/2018] [Indexed: 12/21/2022] Open
Abstract
In many species a fundamental feature of genetic diversity is that genetic similarity decays with geographic distance; however, this relationship is often complex, and may vary across space and time. Methods to uncover and visualize such relationships have widespread use for analyses in molecular ecology, conservation genetics, evolutionary genetics, and human genetics. While several frameworks exist, a promising approach is to infer maps of how migration rates vary across geographic space. Such maps could, in principle, be estimated across time to reveal the full complexity of population histories. Here, we take a step in this direction: we present a method to infer maps of population sizes and migration rates associated with different time periods from a matrix of genetic similarity between every pair of individuals. Specifically, genetic similarity is measured by counting the number of long segments of haplotype sharing (also known as identity-by-descent tracts). By varying the length of these segments we obtain parameter estimates associated with different time periods. Using simulations, we show that the method can reveal time-varying migration rates and population sizes, including changes that are not detectable when using a similar method that ignores haplotypic structure. We apply the method to a dataset of contemporary European individuals (POPRES), and provide an integrated analysis of recent population structure and growth over the last ∼3,000 years in Europe. We introduce a novel statistical method to infer migration rates and population sizes across space in recent time periods. Our approach builds upon the previously developed EEMS method, which infers effective migration rates under a dense lattice. Similarly, we infer demographic parameters under a lattice and use a (Voronoi) prior to regularize parameters of the model. However, our method differs from EEMS in a few key respects. First, we use the coalescent model parameterized by migration rates and population sizes while EEMS uses a resistance model. As another key difference, our method uses haplotype data while EEMS uses the average genetic distance. A consequence of using haplotype data is that our method can separately estimate migration rates and population sizes, which in essence is done by using a recombination rate map to calibrate the decay of haplotypes over time. An additional useful feature of haplotype data is that, by varying the lengths analyzed, we can infer demography associated with different recent time periods. We call our method MAPS for estimating Migration And Population-size Surfaces. To illustrate MAPS on real data, we analyze a genome-wide SNP dataset on 2224 individuals of European ancestry.
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Affiliation(s)
- Hussein Al-Asadi
- Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America.,Department of Statistics, University of Chicago, Illinois, United States of America
| | - Desislava Petkova
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matthew Stephens
- Department of Statistics, University of Chicago, Illinois, United States of America.,Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - John Novembre
- Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America.,Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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45
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Maes J, Van Oosten AR, Van Houtte N, Matthysen E. Genetic structure of natterjack toad (Epidalea calamita) populations in Flanders, Belgium, and its implications for conservation. AMPHIBIA-REPTILIA 2019. [DOI: 10.1163/15685381-17000181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Unique evolutionary potential could be lost when a population goes extinct or when individuals are translocated to other existing populations. Therefore, in order to identify priorities and to predict the efficiency and consequences of conservation actions, information is needed on the genetic structure of natural populations. In the urbanized and diverse landscapes of Flanders, Belgium, natterjack toad (Epidalea calamita) populations have been declining over the last decades. Therefore, this species is subjected to a wide range of different types of conservation measures (e.g. habitat management, corridor development, translocations). However, more information is needed on its genetic population structure. In this study, we sampled egg clutches from six populations and studied their genetic structure with six microsatellite markers. In total, 184 samples from 99 different egg strings were genotyped. Observed heterozygosity was generally high, even for the small and isolated populations (overall mean HO = 0.43). The weak clustering by the Bayesian analyses (STRUCTURE, Adegenet and BAPS) does not allow us to make strong conclusions on the population structure. However, the significant ΦST values between the populations underline the importance of genetic information when conservation priorities are discussed. Unique evolutionary potential could be lost when one or more natterjack toad populations would go extinct, and translocation of individuals to other existing populations should be considered with caution.
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Affiliation(s)
- Joke Maes
- 1Evolutionary Ecology Group, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Arend Raoul Van Oosten
- 1Evolutionary Ecology Group, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
- 2Department of Animal Ecology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Natalie Van Houtte
- 1Evolutionary Ecology Group, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Erik Matthysen
- 1Evolutionary Ecology Group, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
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46
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Hauser SS, Walker L, Leberg PL. Asymmetrical gene flow of the recently delisted passerine black-capped vireo ( Vireo atricapilla) indicates source-sink dynamics in central Texas. Ecol Evol 2019; 9:463-470. [PMID: 30680128 PMCID: PMC6342116 DOI: 10.1002/ece3.4764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/06/2022] Open
Abstract
Habitat fragmentation can produce metapopulations or source-sink systems in which dispersal in crucial for population maintenance. Our objective was to investigate connectivity among black-capped vireo (Vireo atricapilla) populations in tandem with a demographic study (Biological Conservation, 2016, 203, 108-118) to elucidate if central Texas populations act as a source-sink system. We genotyped 343 individuals at 12 microsatellite loci to elucidate the movement ecology of the black-capped vireo in central Texas surrounding Fort Hood; the largest and most stable breeding population of black-capped vireos inhabit Fort Hood. To gain insight into gene flow among populations, we analyzed genetic differentiation, migration rates, number of migrants, and parentage. We found statistically significant, but low levels of genetic differentiation among several populations, suggesting some limited restriction to gene flow. Across approaches to estimate migration, we found consistent evidence for asymmetrical movement from Fort Hood to the other central Texas sites consistent with source-sink dynamics. Our results are complementary to black-capped vireo demographic studies done in tandem showing that portions of Fort Hood are acting as a source population to smaller central Texas populations.
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Affiliation(s)
- Samantha S. Hauser
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisiana
- Present address:
Department of Biological SciencesUniversity of Wisconsin – MilwaukeeMilwaukeeWisconsin
| | - Lauren Walker
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
- Present address:
National Park ServiceYellowstone National ParkMammothWyoming
| | - Paul L. Leberg
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisiana
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47
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Soularue JP, Thöni A, Arnoux L, Le Corre V, Kremer A. Metapop: An individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes. Mol Ecol Resour 2018; 19:296-305. [PMID: 30362291 DOI: 10.1111/1755-0998.12958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 11/27/2022]
Abstract
Metapop is a stochastic individual-based simulation program. It uses quantitative genetics theory to produce an explicit description of the typical life cycle of monoecious and hermaphroditic plant species. Genome structure, the relationship between genotype and phenotype, and the effects of landscape heterogeneity on each individual can be finely parameterized by the user. Unlike most existing simulation packages, Metapop can simulate phenotypic plasticity, which may have a genetic component, and assortative mating, two important features of tree species. Each simulation is parameterized through text files, and raw data are generated recurrently, describing the allelic state of each quantitative trait locus involved in phenotypic variability. The data can be generated in Genepop or Fstat format, and may thus be analysed with other existing packages. Metapop also automatically computes a range of populations statistics, enabling the user to monitor evolutionary dynamics directly, from gene to metapopulation level.
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Affiliation(s)
| | - Armel Thöni
- BIOGECO, INRA, Univ. Bordeaux, Cestas, France
| | - Léo Arnoux
- BIOGECO, INRA, Univ. Bordeaux, Cestas, France
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48
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Kozakiewicz CP, Burridge CP, Funk WC, VandeWoude S, Craft ME, Crooks KR, Ernest HB, Fountain‐Jones NM, Carver S. Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evol Appl 2018; 11:1763-1778. [PMID: 30459828 PMCID: PMC6231466 DOI: 10.1111/eva.12678] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/24/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free-living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host-vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross-disciplinary advances.
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Affiliation(s)
| | | | - W. Chris Funk
- Department of BiologyGraduate Degree Program in EcologyColorado State UniversityFort CollinsColorado
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColorado
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt. PaulMinnesota
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology LaboratoryDepartment of Veterinary SciencesUniversity of WyomingLaramieWyoming
| | | | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
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49
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Langin KM, Aldridge CL, Fike JA, Cornman RS, Martin K, Wann GT, Seglund AE, Schroeder MA, Braun CE, Benson DP, Fedy BC, Young JR, Wilson S, Wolfe DH, Oyler-McCance SJ. Characterizing range-wide divergence in an alpine-endemic bird: a comparison of genetic and genomic approaches. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1115-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Sylvester EVA, Beiko RG, Bentzen P, Paterson I, Horne JB, Watson B, Lehnert S, Duffy S, Clément M, Robertson MJ, Bradbury IR. Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America. Mol Ecol 2018; 27:4026-4040. [PMID: 30152128 DOI: 10.1111/mec.14849] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 12/18/2022]
Abstract
Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine-learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n = 17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate-associated, fine-scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.
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Affiliation(s)
- Emma V A Sylvester
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Ian Paterson
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - John B Horne
- University of Southern Mississippi Gulf Coast Research Laboratory, Ocean Springs, MS, Canada
| | - Beth Watson
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Sarah Lehnert
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Steven Duffy
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, NL, Canada.,Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Martha J Robertson
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada
| | - Ian R Bradbury
- Science Branch, Department of Fisheries and Oceans Canada, St. John's, NL, Canada.,Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada.,Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, Canada
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