51
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Range-wide genetic differentiation of Eugenia dysenterica (Myrtaceae) populations in Brazilian Cerrado. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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52
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Wang IJ, Bradburd GS. Isolation by environment. Mol Ecol 2014; 23:5649-62. [DOI: 10.1111/mec.12938] [Citation(s) in RCA: 505] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/07/2014] [Accepted: 09/21/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Ian J. Wang
- Department of Environmental Science, Policy, and Management; University of California; 130 Mulford Hall #3114 Berkeley CA 94705 USA
| | - Gideon S. Bradburd
- Center for Population Biology; Department of Evolution and Ecology; University of California; 2320 Storer Hall 1 Shields Ave Davis CA 95616 USA
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53
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Dell'Acqua M, Zuccolo A, Tuna M, Gianfranceschi L, Pè ME. Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach. BMC Genomics 2014; 15:801. [PMID: 25236859 PMCID: PMC4177692 DOI: 10.1186/1471-2164-15-801] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/04/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environment depends on how well they adapt to local pedoclimatic conditions. Genomic tools can be used to identify adaptive traits at a DNA level and to further our understanding of evolutionary processes. Here we report the use of genotyping-by-sequencing on local groups of the sequenced monocot model species Brachypodium distachyon. Exploiting population genetics, landscape genomics and genome wide association studies, we evaluate B. distachyon role as a natural probe for identifying genomic loci involved in environmental adaptation. RESULTS Brachypodium distachyon individuals were sampled in nine locations with different ecologies and characterized with 16,697 SNPs. Variations in sequencing depth showed consistent patterns at 8,072 genomic bins, which were significantly enriched in transposable elements. We investigated the structuration and diversity of this collection, and exploited climatic data to identify loci with adaptive significance through i) two different approaches for genome wide association analyses considering climatic variation, ii) an outlier loci approach, and iii) a canonical correlation analysis on differentially sequenced bins. A linkage disequilibrium-corrected Bonferroni method was applied to filter associations. The two association methods jointly identified a set of 15 genes significantly related to environmental adaptation. The outlier loci approach revealed that 5.7% of the loci analysed were under selection. The canonical correlation analysis showed that the distribution of some differentially sequenced regions was associated to environmental variation. CONCLUSIONS We show that the multi-faceted approach used here targeted different components of B. distachyon adaptive variation, and may lead to the discovery of genes related to environmental adaptation in natural populations. Its application to a model species with a fully sequenced genome is a modular strategy that enables the stratification of biological material and thus improves our knowledge of the functional loci determining adaptation in near-crop species. When coupled with population genetics and measures of genomic structuration, methods coming from genome wide association studies may lead to the exploitation of model species as natural probes to identify loci related to environmental adaptation.
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Affiliation(s)
| | | | | | | | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
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54
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Rhodes MK, Fant JB, Skogen KA. Local topography shapes fine-scale spatial genetic structure in the Arkansas Valley evening primrose, Oenothera harringtonii (Onagraceae). J Hered 2014; 105:806-15. [PMID: 25189774 DOI: 10.1093/jhered/esu051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Identifying factors that shape the spatial distribution of genetic variation is crucial to understanding many population- and landscape-level processes. In this study, we explore fine-scale spatial genetic structure in Oenothera harringtonii (Onagraceae), an insect-pollinated, gravity-dispersed herb endemic to the grasslands of south-central and southeastern Colorado, USA. We genotyped 315 individuals with 11 microsatellite markers and utilized a combination of spatial autocorrelation analyses and landscape genetic models to relate life history traits and landscape features to dispersal processes. Spatial genetic structure was consistent with theoretical expectations of isolation by distance, but this pattern was weak (Sp = 0.00374). Anisotropic analyses indicated that spatial genetic structure was markedly directional, in this case consistent with increased dispersal along prominent slopes. Landscape genetic models subsequently confirmed that spatial genetic variation was significantly influenced by local topographic heterogeneity, specifically that geographic distance, elevation and aspect were important predictors of spatial genetic structure. Among these variables, geographic distance was ~68% more important than elevation in describing spatial genetic variation, and elevation was ~42% more important than aspect after removing the effect of geographic distance. From these results, we infer a mechanism of hydrochorous seed dispersal along major drainages aided by seasonal monsoon rains. Our findings suggest that landscape features may shape microevolutionary processes at much finer spatial scales than typically considered, and stress the importance of considering how particular dispersal vectors are influenced by their environmental context.
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Affiliation(s)
- Matthew K Rhodes
- From the Division of Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA (Rhodes, Fant, and Skogen); and the Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, O.T. Hogan Hall, Room 2-144, Evanston, IL 60208, USA (Rhodes).
| | - Jeremie B Fant
- From the Division of Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA (Rhodes, Fant, and Skogen); and the Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, O.T. Hogan Hall, Room 2-144, Evanston, IL 60208, USA (Rhodes)
| | - Krissa A Skogen
- From the Division of Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA (Rhodes, Fant, and Skogen); and the Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, O.T. Hogan Hall, Room 2-144, Evanston, IL 60208, USA (Rhodes)
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55
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Diniz-Filho JAF, Soares TN, Telles MPDC. Pattern-oriented modelling of population genetic structure. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12373] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Thannya Nascimento Soares
- Departamento de Genética; Instituto de Ciências Biológicas; Universidade Federal de Goiás; CP 131 Campus II 74001-970 Goiânia GO Brazil
| | - Mariana Pires De Campos Telles
- Departamento de Genética; Instituto de Ciências Biológicas; Universidade Federal de Goiás; CP 131 Campus II 74001-970 Goiânia GO Brazil
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56
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Galpern P, Peres-Neto PR, Polfus J, Manseau M. MEMGENE: Spatial pattern detection in genetic distance data. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12240] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paul Galpern
- Faculty of Environmental Design; University of Calgary; 2500 University Drive NW Calgary AB T2N 1N4 Canada
- Natural Resources Institute; University of Manitoba; 70 Dysart Road Winnipeg MB R3T 2N2 Canada
| | - Pedro R. Peres-Neto
- Canada Research Chair in Spatial Modelling and Biodiversity; Département des sciences biologiques; Université du Québec à Montréal; Montréal QC H3C 3P8 Canada
| | - Jean Polfus
- Natural Resources Institute; University of Manitoba; 70 Dysart Road Winnipeg MB R3T 2N2 Canada
| | - Micheline Manseau
- Natural Resources Institute; University of Manitoba; 70 Dysart Road Winnipeg MB R3T 2N2 Canada
- Parks Canada; 145 McDermot Avenue Winnipeg MB R3B 0R9 Canada
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57
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Marrotte RR, Gonzalez A, Millien V. Landscape resistance and habitat combine to provide an optimal model of genetic structure and connectivity at the range margin of a small mammal. Mol Ecol 2014; 23:3983-98. [DOI: 10.1111/mec.12847] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 05/22/2014] [Accepted: 05/30/2014] [Indexed: 02/05/2023]
Affiliation(s)
- R. R. Marrotte
- Redpath Museum; McGill University; 859 Sherbrooke Street W. Montréal Québec Canada H3A 0C4
- Department of Biology; McGill University; 1205 Ave Docteur Penfield Montréal Québec Canada H3A 1B1
| | - A. Gonzalez
- Department of Biology; McGill University; 1205 Ave Docteur Penfield Montréal Québec Canada H3A 1B1
| | - V. Millien
- Redpath Museum; McGill University; 859 Sherbrooke Street W. Montréal Québec Canada H3A 0C4
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58
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Rioux Paquette S, Talbot B, Garant D, Mainguy J, Pelletier F. Modelling the dispersal of the two main hosts of the raccoon rabies variant in heterogeneous environments with landscape genetics. Evol Appl 2014; 7:734-49. [PMID: 25469156 PMCID: PMC4227855 DOI: 10.1111/eva.12161] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 03/22/2014] [Indexed: 12/25/2022] Open
Abstract
Predicting the geographic spread of wildlife epidemics requires knowledge about the movement patterns of disease hosts or vectors. The field of landscape genetics provides valuable approaches to study dispersal indirectly, which in turn may be used to understand patterns of disease spread. Here, we applied landscape genetic analyses and spatially explicit models to identify the potential path of raccoon rabies spread in a mesocarnivore community. We used relatedness estimates derived from microsatellite genotypes of raccoons and striped skunks to investigate their dispersal patterns in a heterogeneous landscape composed predominantly of agricultural, forested and residential areas. Samples were collected in an area covering 22 000 km2 in southern Québec, where the raccoon rabies variant (RRV) was first detected in 2006. Multiple regressions on distance matrices revealed that genetic distance among male raccoons was strictly a function of geographic distance, while dispersal in female raccoons was significantly reduced by the presence of agricultural fields. In skunks, our results suggested that dispersal is increased in edge habitats between fields and forest fragments in both males and females. Resistance modelling allowed us to identify likely dispersal corridors used by these two rabies hosts, which may prove especially helpful for surveillance and control (e.g. oral vaccination) activities.
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Affiliation(s)
| | - Benoit Talbot
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada ; Canada Research Chair in Evolutionary Demography and Conservation, Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Dany Garant
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Julien Mainguy
- Direction générale de l'expertise sur la faune et ses habitats, Direction de la biodiversité et des maladies de la faune, Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs Québec, QC, Canada
| | - Fanie Pelletier
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada ; Canada Research Chair in Evolutionary Demography and Conservation, Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
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59
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Pflüger FJ, Balkenhol N. A plea for simultaneously considering matrix quality and local environmental conditions when analysing landscape impacts on effective dispersal. Mol Ecol 2014; 23:2146-56. [DOI: 10.1111/mec.12712] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 02/23/2014] [Accepted: 03/02/2014] [Indexed: 01/14/2023]
Affiliation(s)
- Femke J. Pflüger
- Department of Wildlife Sciences; University of Goettingen; Buesgenweg 3 Goettingen 37077 Germany
| | - Niko Balkenhol
- Department of Wildlife Sciences; University of Goettingen; Buesgenweg 3 Goettingen 37077 Germany
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60
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Scriber JM. Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes. INSECTS 2013; 5:1-61. [PMID: 26462579 PMCID: PMC4592632 DOI: 10.3390/insects5010001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 01/11/2023]
Abstract
Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.
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Affiliation(s)
- Jon Mark Scriber
- Department of Entomology, Michigan State University, East Lansing, Michigan, MI 48824, USA.
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
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61
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Diniz-Filho JAF, Soares TN, Lima JS, Dobrovolski R, Landeiro VL, de Campos Telles MP, Rangel TF, Bini LM. Mantel test in population genetics. Genet Mol Biol 2013; 36:475-85. [PMID: 24385847 PMCID: PMC3873175 DOI: 10.1590/s1415-47572013000400002] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/10/2013] [Indexed: 01/27/2023] Open
Abstract
The comparison of genetic divergence or genetic distances, estimated by pairwise FST and related statistics, with geographical distances by Mantel test is one of the most popular approaches to evaluate spatial processes driving population structure. There have been, however, recent criticisms and discussions on the statistical performance of the Mantel test. Simultaneously, alternative frameworks for data analyses are being proposed. Here, we review the Mantel test and its variations, including Mantel correlograms and partial correlations and regressions. For illustrative purposes, we studied spatial genetic divergence among 25 populations of Dipteryx alata ("Baru"), a tree species endemic to the Cerrado, the Brazilian savannas, based on 8 microsatellite loci. We also applied alternative methods to analyze spatial patterns in this dataset, especially a multivariate generalization of Spatial Eigenfunction Analysis based on redundancy analysis. The different approaches resulted in similar estimates of the magnitude of spatial structure in the genetic data. Furthermore, the results were expected based on previous knowledge of the ecological and evolutionary processes underlying genetic variation in this species. Our review shows that a careful application and interpretation of Mantel tests, especially Mantel correlograms, can overcome some potential statistical problems and provide a simple and useful tool for multivariate analysis of spatial patterns of genetic divergence.
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Affiliation(s)
| | - Thannya N. Soares
- Departamento de Biologia Geral, Universidade Federal de Goiás, Goiânia, GO,
Brazil
| | - Jacqueline S. Lima
- Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de Goiás, Goiânia, GO,
Brazil
| | - Ricardo Dobrovolski
- Departamento de Zoologia, Universidade Federal da Bahia, Salvador, BA,
Brazil
| | - Victor Lemes Landeiro
- Departamento de Botânica e Ecologia, Universidade Federal de Mato Grosso, Cuiabá, MT,
Brazil
| | | | - Thiago F. Rangel
- Departamento de Ecologia, Universidade Federal de Goiás, Goiânia, GO,
Brazil
| | - Luis Mauricio Bini
- Departamento de Ecologia, Universidade Federal de Goiás, Goiânia, GO,
Brazil
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62
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Alvarado-Serrano DF, Knowles LL. Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol Ecol Resour 2013; 14:233-48. [DOI: 10.1111/1755-0998.12184] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Diego F. Alvarado-Serrano
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
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63
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A new eigenfunction spatial analysis describing population genetic structure. Genetica 2013; 141:479-89. [DOI: 10.1007/s10709-013-9747-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 10/18/2013] [Indexed: 10/26/2022]
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