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Batalha-Filho H, Barreto SB, Silveira MHB, Miyaki CY, Afonso S, Ferrand N, Carneiro M, Sequeira F. Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil. Heredity (Edinb) 2024; 132:77-88. [PMID: 37985738 PMCID: PMC10844224 DOI: 10.1038/s41437-023-00662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.
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Affiliation(s)
- Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil.
| | - Silvia Britto Barreto
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Mario Henrique Barros Silveira
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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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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Lee SR, Son DC. Genetic diversity pattern reveals the primary determinant of burcucumber ( Sicyos angulatus L.) invasion in Korea. FRONTIERS IN PLANT SCIENCE 2022; 13:997521. [PMID: 36457533 PMCID: PMC9706109 DOI: 10.3389/fpls.2022.997521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, South Korea
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Zhang C, Li J, Yang B, Dai Q. habCluster: identifying the geographical boundary among intraspecific units using community detection algorithms in R. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.908012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conservation management for a species generally rests on intraspecific units, while identification of their geographic boundaries is necessary for the implementation. Intraspecific units can be discriminated using population genetic methods, yet an analytical approach is still lacking for detecting their geographic boundaries. Here, based on landscape connectivity, we present a raster-based geographical boundary delineation method, habCluster, using community detection algorithms. Community detection is a technique in graph theory used to identify clusters of highly connected nodes within a network. We assume that the habitat raster cells with better connections tend to form a continuous habitat patch than the others, thus making the range of an intraspecific unit. The method was tested on the gray wolf (Canis lupus) habitat in Europe and the giant panda (Ailuropoda melanoleuca) habitat in China. The habitat suitability index (HSI) maps for gray wolves and giant pandas were evaluated using species distribution models. Each cell in the HSI raster is treated as a node and directly connected with its eight neighbor cells. The edge weight between nodes is the reciprocal of the relative distance between the centers of the nodes weighted by the average of their HSI values. We implement habCluster using the R programming language with the inline C++ code to speed up the computing. We found that the boundaries of the clusters delineated using habCluster could serve as a good indicator of habitat patches. In the giant panda case, the clusters match generally well with nature reserves. habCluster can provide a spatial analysis basis for conservation management plans such as monitoring, translocation and reintroduction, and population structure research.
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Selection and localised genetic structure in the threatened Manauense Harlequin Frog (Bufonidae: Atelopus manauensis). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01436-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Huang K, Peng L, Wang X, Chen T. Integrating Landscape Connectivity and Natural-Anthropogenic Interaction to Understand Karst Vegetation Restoration: A Case Study of Guizhou Province, China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Because of implementation of ecological projects, the restoration of vegetation not only changes the typological composition and spatial structure of the landscape, but also improves the regional ecosystem function. The present study considered the effects of natural-anthropogenic factors and landscape connectivity on vegetation restoration. It also explored the impact and underlying mechanisms by which structural changes in landscape connectivity affect vegetation coverage in the karst region of Guizhou Province and provided a novel perspective for the maintenance of regional ecological security. We used morphological spatial pattern analysis (MSPA) and integrated valuation of ecosystem services and tradeoffs (InVEST) and circuit theory to identify ecological networks and explore the changes in landscape structure. We performed a Theil-Sen Median trend analysis and a Mann-Kendall (MK) trend test to determine spatiotemporal variations in vegetation coverage. We conducted a coupling analysis to discover correlations between the average cumulative current density (CCD) and the normalized difference vegetation index (NDVI) in various karst landform counties. We also implemented a geographical detector to detect the factors affecting the NDVI trend and disclose interactions among factors. The results showed that (1) Though the total area of forests and core areas was reduced, the ecological networks and landscape connectivity steadily improved. (2) Areas with improved vegetation coverage accounted for 77.77% of the total. By contrast, the degraded areas covered 14.28% while the remaining 7.95% was stable. (3) The relationships between the average CCD and the NDVI were inconsistent among various geomorphological counties. The counties with the highest proportions of karst landforms presented with negative correlations between the average CCD and the NDVI in 2005 and positive correlations between these parameters in 2018. (4) The NDVI trend was influenced by several factors. Of these, anthropogenic activity played a dominant role. Nevertheless, changes in landscape connectivity was also implicated. Attention should be paid to the impact of landscape connectivity on ecological restoration. The foregoing results indicated that the rocky desertification projects effectively improved landscape connectivity and vegetation coverage and provided a reference for developing policies establishing and maintaining ecological security of the karst ecosystem and coordinating sustainable development in this region.
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Predicting burrowing owl flight trajectories in urban environments. Urban Ecosyst 2021. [DOI: 10.1007/s11252-021-01170-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Marcus J, Ha W, Barber RF, Novembre J. Fast and flexible estimation of effective migration surfaces. eLife 2021; 10:61927. [PMID: 34328078 PMCID: PMC8324296 DOI: 10.7554/elife.61927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Spatial population genetic data often exhibits ‘isolation-by-distance,’ where genetic similarity tends to decrease as individuals become more geographically distant. The rate at which genetic similarity decays with distance is often spatially heterogeneous due to variable population processes like genetic drift, gene flow, and natural selection. Petkova et al., 2016 developed a statistical method called Estimating Effective Migration Surfaces (EEMS) for visualizing spatially heterogeneous isolation-by-distance on a geographic map. While EEMS is a powerful tool for depicting spatial population structure, it can suffer from slow runtimes. Here, we develop a related method called Fast Estimation of Effective Migration Surfaces (FEEMS). FEEMS uses a Gaussian Markov Random Field model in a penalized likelihood framework that allows for efficient optimization and output of effective migration surfaces. Further, the efficient optimization facilitates the inference of migration parameters per edge in the graph, rather than per node (as in EEMS). With simulations, we show conditions under which FEEMS can accurately recover effective migration surfaces with complex gene-flow histories, including those with anisotropy. We apply FEEMS to population genetic data from North American gray wolves and show it performs favorably in comparison to EEMS, with solutions obtained orders of magnitude faster. Overall, FEEMS expands the ability of users to quickly visualize and interpret spatial structure in their data.
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Affiliation(s)
- Joseph Marcus
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Wooseok Ha
- Department of Statistics, University of California, Berkeley, Berkeley, United States
| | | | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
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Toffoli R, Cucco M. Habitat Suitability, Connection Analysis and Effectiveness of Protected Areas for Conservation of the Barbastelle Bat Barbastella barbastellus in NW Italy. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.2.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Roberto Toffoli
- Associazione Chirosphera, Via Tetti Barbiere 11, 10026 Santena, Italy
| | - Marco Cucco
- Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15100 Alessandria, Italy
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Is There an Equivalence between Measures of Landscape Structural and Functional Connectivity for Plants in Conservation Assessments of the Cerrado? LAND 2020. [DOI: 10.3390/land9110459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Landscape connectivity can be assessed based on the physical connection (structural connectivity) or the maintenance of flow among habitats depending on the species (functional connectivity). The lack of empirical data on the dispersal capacity of species can lead to the use of simple structural measures. Comparisons between these approaches can improve decision-making processes for the conservation or restoration of habitats in fragmented landscapes, such as the Cerrado biome. This study aimed to understand the correspondence between the measures of landscape structural and functional connectivity for Cerrado plants. Three landscapes with cerradão patches in a pasture matrix were selected for the application of these metrics based on the functional connectivity of four profiles of plant dispersal capacity. The results showed divergent interpretations between the measures of landscape structural and functional connectivity, indicating that the assessment of biodiversity conservation and landscape connectivity is dependent on the set of metrics chosen. Structurally, the studied landscapes had the same number of cerradão patches but varied in optimal resource availability, isolation, heterogeneity, and aggregation. Functional connectivity was low for all profiles (based on the integral index of connectivity—IIC) and null for species with a low dispersal capacity (based on the connectance index—CONNECT), indicating that species with a medium- to long-distance dispersal capacity may be less affected by the history of losses and fragmentation of the Cerrado in the pasture matrix. The functional connectivity metrics used allowed a more robust analysis and, apparently, better reflected reality, but the lack of empirical data on dispersal capacity and the difficulty in choosing an indicator organism can limit their use in the management and planning of conservation and restoration areas.
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Campos FS, Lourenço-de-Moraes R, Ruas DS, Mira-Mendes CV, Franch M, Llorente GA, Solé M, Cabral P. Searching for Networks: Ecological Connectivity for Amphibians Under Climate Change. ENVIRONMENTAL MANAGEMENT 2020; 65:46-61. [PMID: 31832730 DOI: 10.1007/s00267-019-01240-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Ecological connectivity depends on key elements within the landscape, which can support ecological fluxes, species richness and long-term viability of a biological community. Landscape planning requires clear aims and quantitative approaches to identify which key elements can reinforce the spatial coherence of protected areas design. We aim to explore the probability of the ecological connectivity of forest remnants and amphibian species distributions for current and future climate scenarios across the Central Corridor of the Brazilian Atlantic Forest. Integrating amphibian conservation, climate change and ecological corridors, we design a landscape ranking based on graph and circuit theories. To identify the sensitivity of connected areas to climate-dependent changes, we use the Model for Interdisciplinary Research on Climate by means of simulations for 2080-2100, representing a moderated emission scenario within an optimistic context. Our findings indicate that more than 70% of forest connectivity loss by climate change may drastically reduce amphibian dispersal in this region. We show that high amphibian turnover rates tend to be greater in the north-eastern edges of the corridor across ensembles of forecasts. Our spatial analysis reveals a general pattern of low-conductance areas in landscape surface, yet with some well-connected patches suggesting potential ecological corridors. Atlantic Forest reserves are expected to be less effective in a near future. For improved conservation outcomes, we recommend some landscape paths with low resistance values across space and time. We highlight the importance of maintaining forest remnants in the southern Bahia region by drafting a blueprint for functional biodiversity corridors.
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Affiliation(s)
- Felipe S Campos
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain.
- NOVA Information Management School (NOVA IMS), Universidade Nova de Lisboa, Campus de Campolide, 1070-312, Lisboa, Portugal.
| | - Ricardo Lourenço-de-Moraes
- Programa de Pós-graduação em Ecologia e Monitoramento Ambiental (PPGEMA), Universidade Federal da Paraíba, Campus IV-Litoral Norte, Rio Tinto, PB, 58297-000, Brazil
| | - Danilo S Ruas
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, BA, 45662-000, Brazil
| | - Caio V Mira-Mendes
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, BA, 45662-000, Brazil
| | - Marc Franch
- CICGE - Centro de Investigação em Ciências Geo-Espaciais, Observatório Astronómico Prof. Manuel de Barros, Universidade do Porto, 4430-146, Vila Nova de Gaia, Portugal
| | - Gustavo A Llorente
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Mirco Solé
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, 45662-000, Brazil
| | - Pedro Cabral
- NOVA Information Management School (NOVA IMS), Universidade Nova de Lisboa, Campus de Campolide, 1070-312, Lisboa, Portugal
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Carvalho CS, Lanes ÉCM, Silva AR, Caldeira CF, Carvalho-Filho N, Gastauer M, Imperatriz-Fonseca VL, Nascimento Júnior W, Oliveira G, Siqueira JO, Viana PL, Jaffé R. Habitat Loss Does Not Always Entail Negative Genetic Consequences. Front Genet 2019; 10:1011. [PMID: 31798621 PMCID: PMC6863885 DOI: 10.3389/fgene.2019.01101] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022] Open
Abstract
Although habitat loss has large, consistently negative effects on biodiversity, its genetic consequences are not yet fully understood. This is because measuring the genetic consequences of habitat loss requires accounting for major methodological limitations like the confounding effect of habitat fragmentation, historical processes underpinning genetic differentiation, time-lags between the onset of disturbances and genetic outcomes, and the need for large numbers of samples, genetic markers, and replicated landscapes to ensure sufficient statistical power. In this paper we overcame all these challenges to assess the genetic consequences of extreme habitat loss driven by mining in two herbs endemic to Amazonian savannas. Relying on genotyping-by-sequencing of hundreds of individuals collected across two mining landscapes, we identified thousands of neutral and independent single-nucleotide polymorphisms (SNPs) in each species and used these to evaluate population structure, genetic diversity, and gene flow. Since open-pit mining in our study region rarely involves habitat fragmentation, we were able to assess the independent effect of habitat loss. We also accounted for the underlying population structure when assessing landscape effects on genetic diversity and gene flow, examined the sensitivity of our analyses to the resolution of spatial data, and used annual species and cross-year analyses to minimize and quantify possible time-lag effects. We found that both species are remarkably resilient, as genetic diversity and gene flow patterns were unaffected by habitat loss. Whereas historical habitat amount was found to influence inbreeding; heterozygosity and inbreeding were not affected by habitat loss in either species, and gene flow was mainly influenced by geographic distance, pre-mining land cover, and local climate. Our study demonstrates that it is not possible to generalize about the genetic consequences of habitat loss, and implies that future conservation efforts need to consider species-specific genetic information.
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Affiliation(s)
| | | | - Amanda R. Silva
- Instituto Tecnológico Vale, Belém, Brazil
- Departamento de Botânica, Museu Paraense Emílio Goeldi, Belém, Brazil
| | | | | | | | | | | | | | | | - Pedro L. Viana
- Departamento de Botânica, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Belém, Brazil
- Departamento de Ecologia, Universidade de São Paulo, São Paulo, Brazil
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Duchatel F, Bronsvoort BMDC, Lycett S. Phylogeographic Analysis and Identification of Factors Impacting the Diffusion of Foot-and-Mouth Disease Virus in Africa. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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14
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Torres-Morales L, Guillén A, Ruiz-Sanchez E. Distinct Patterns of Genetic Connectivity Found for Two Frugivorous Bat Species in Mesoamerica. ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2019.21.1.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Laura Torres-Morales
- División de Posgrado, Instituto de Ecología, A.C., Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91070, Mexico
| | - Antonio Guillén
- Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91070, Mexico
| | - Eduardo Ruiz-Sanchez
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Nextipac, Zapopán, Jalisco 45200, Mexico
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15
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Berkman LK, Nielsen CK, Roy CL, Heist EJ. A landscape genetic analysis of swamp rabbits (Sylvilagus aquaticus) suggests forest canopy cover enhances gene flow in an agricultural matrix. CAN J ZOOL 2018. [DOI: 10.1139/cjz-2017-0116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Habitat loss and fragmentation pose a continued and immediate threat to wildlife and create a persistent need for ecological information at the landscape scale to guide conservation efforts. Landscape features influence population connectivity for many species and genetic analyses can be employed to determine which of these features are most important. Because population connectivity through dispersal is important to the persistence of swamp rabbits (Sylvilagus aquaticus (Bachman, 1837)) at the northern edge of their range, we used a landscape genetic approach to relate gene flow to landscape features that may impact dispersal success. We tested resistance values for attributes of land cover, watercourse corridors, canopy cover, and roads and used causal modeling and redundancy analysis to relate these representations of landscapes to genetic distance for swamp rabbits in southern Illinois, USA. Models that included canopy cover had the strongest correlations with genetic distance and were supported by our methods whereas other models were not. We concluded that high tree canopy cover enhances gene flow and landscape connectivity for swamp rabbits in southern Illinois. Our study provides important empirical evidence that landscape variables may impact the habitat connectivity of swamp rabbits. Preserving dispersal routes for swamp rabbits should focus on improving canopy cover, in both bottomland and upland, to connect suitable habitat.
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Affiliation(s)
- Leah K. Berkman
- Cooperative Wildlife Research Laboratory, Department of Zoology, Southern Illinois University, Carbondale, IL 62901-6504, USA
| | - Clayton K. Nielsen
- Cooperative Wildlife Research Laboratory, Department of Forestry, Southern Illinois University, Carbondale, IL 62901-6504, USA
| | - Charlotte L. Roy
- Forest Wildlife Populations and Research Group, Minnesota Department of Natural Resources, Grand Rapids, MN 55744, USA
| | - Edward J. Heist
- Department of Zoology, Southern Illinois University, Carbondale, IL 62901-6501, USA
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Environmental factors affecting population level genetic divergence of the striped field mouse (Apodemus agrarius) in South Korea. Ecol Res 2018. [DOI: 10.1007/s11284-018-1613-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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17
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Morente-López J, García C, Lara-Romero C, García-Fernández A, Draper D, Iriondo JM. Geography and Environment Shape Landscape Genetics of Mediterranean Alpine Species Silene ciliata Poiret. (Caryophyllaceae). FRONTIERS IN PLANT SCIENCE 2018; 9:1698. [PMID: 30538712 PMCID: PMC6277476 DOI: 10.3389/fpls.2018.01698] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/31/2018] [Indexed: 05/22/2023]
Abstract
The study of the drivers that shape spatial genetic structure across heterogeneous landscapes is one of the main approaches used to understand population dynamics and responses in changing environments. While the Isolation-by-Distance model (IBD) assumes that genetic differentiation increases among populations with geographical distance, the Isolation-by-Resistance model (IBR) also considers geographical barriers and other landscape features that impede gene flow. On the other hand, the Isolation-by-Environment model (IBE) explains genetic differentiation through environmental differences between populations. Although spatial genetic studies have increased significantly in recent years, plants from alpine ecosystems are highly underrepresented, even though they are great suitable systems to disentangle the role of the different factors that structure genetic variation across environmental gradients. Here, we studied the spatial genetic structure of the Mediterranean alpine specialist Silene ciliata across its southernmost distribution limit. We sampled three populations across an altitudinal gradient from 1850 to 2400 m, and we replicated this sample over three mountain ranges aligned across an E-W axis in the central part of the Iberian Peninsula. We genotyped 20 individuals per population based on eight microsatellite markers and used different landscape genetic tools to infer the role of topographic and environmental factors in shaping observed patterns along the altitudinal gradient. We found a significant genetic structure among the studied Silene ciliata populations which was related to the orography and E-W configuration of the mountain ranges. IBD pattern arose as the main factor shaping population genetic differentiation. Geographical barriers between mountain ranges also affected the spatial genetic structure (IBR pattern). Although environmental variables had a significant effect on population genetic diversity parameters, no IBE pattern was found on genetic structure. Our study reveals that IBD was the driver that best explained the genetic structure, whereas environmental factors also played a role in determining genetic diversity values of this dominant plant of Mediterranean alpine environments.
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Affiliation(s)
- Javier Morente-López
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
- *Correspondence: Javier Morente-López, José María Iriondo,
| | - Cristina García
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Plant Biology Group, CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Universidade do Porto, Porto, Portugal
| | - Carlos Lara-Romero
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
- Global Change Research Group, Mediterranean Institute for Advanced Studies (IMEDEA), Consejo Superior de Investigaciones Científicas (CSIC), Esporles, Spain
| | - Alfredo García-Fernández
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
| | - David Draper
- Natural History and Systematics Research Group, cE3c, Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisbon, Portugal
- UBC Botanical Garden and Centre for Plant Research, Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - José María Iriondo
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
- *Correspondence: Javier Morente-López, José María Iriondo,
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18
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Shirk AJ, Cushman SA. Spatially-explicit estimation of Wright's neighborhood size in continuous populations. Front Ecol Evol 2014. [DOI: 10.3389/fevo.2014.00062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Simulating Pattern-Process Relationships to Validate Landscape Genetic Models. INTERNATIONAL JOURNAL OF ECOLOGY 2012. [DOI: 10.1155/2012/539109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Landscapes may resist gene flow and thereby give rise to a pattern of genetic isolation within a population. The mechanism by which a landscape resists gene flow can be inferred by evaluating the relationship between landscape models and an observed pattern of genetic isolation. This approach risks false inferences because researchers can never feasibly test all plausible alternative hypotheses. In this paper, rather than infer the process of gene flow from an observed genetic pattern, we simulate gene flow and determine if the simulated genetic pattern is related to the observed empirical genetic pattern. This is a form of inverse modeling and can be used to independently validate a landscape genetic model. In this study, we used this approach to validate a model of landscape resistance based on elevation, landcover, and roads that was previously related to genetic isolation among mountain goats (Oreamnos americanus) inhabiting the Cascade Range, Washington (USA). The strong relationship between the empirical and simulated patterns of genetic isolation we observed provides independent validation of the resistance model and demonstrates the utility of this approach in supporting landscape genetic inferences.
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