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Coexistence of two newt species in a transition zone of range overlap. CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Theory suggests that spatial segregation of similar, co-occurring species may be driven by alternative innate life history and dispersal strategies, and that it operates through catastrophic events. An inventory of the evolutionary closely related small-bodied newts Lissotriton helveticus and L. vulgaris in the northwest of France demonstrated the species’ spatial partitioning, with L. vulgaris dominating in two pond-rich and historically disturbed coastal areas and L. helveticus prevailing inland where ponds are sparser. Population numbers were followed over several decades (1975–2021) in a pond within the narrow (ca. 2000 m wide) species transition zone. Early in the temporal survey (1986) a massive die-off was observed of two-third of the L. helveticus breeding population from a late frost event. Yet, the contribution of L. helveticus to the newt assemblage was more or less stable around 60%, even though the total population size fluctuated by an order of magnitude. Lissotriton vulgaris and a third species, Ichthyosaura alpestris, made up ca. 30% and 10% of the total till 1993, after which date their relative contributions reversed. These data suggest that a state shift may have occurred among the latter two species and that the assumed two-species dynamics of Lissotriton underlying the study has been an oversimplification. The local decline of L. vulgaris is paralleled by the loss of well-vegetated ponds from the wider agricultural terrain that affects this species more than L. helveticus and I. alpestris.
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Albert EM, García-Navas V. Population structure and genetic diversity of the threatened pygmy newt Triturus pygmaeus in a network of natural and artificial ponds. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01437-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractPond physical characteristics (connectivity, hydroperiod) have shown to be highly relevant in explaining species presence, reproductive success, and survival in breeding-pond amphibians. However, few studies have addressed the influence that these factors may have on the genetic variability of pond populations. We examined genetic variation at 11 microsatellite loci in Iberian endemic, the pygmy newt (Triturus pygmaeus), from 58 breeding ponds in the Doñana National Park (Andalusia), including both temporary ponds and artificially deepened ponds that remain wet during the whole year. Temporary ponds are located in the North part of the region where the surrounding habitat-wet meadows-facilitates the connectivity among populations, whereas the deepest ponds (‘zacallones’) are located in the southern edge embedded in a matrix of unsuitable habitat (thickets and dry underbrush). We investigated genetic diversity and structure within and among ponds. Our results show that both regions (Doñana-North and Doñana-South) are well-differentiated and form two main clusters. We found higher genetic diversity within ponds from the North region, which also exhibited a higher degree of genetic admixture in comparison with populations from the southern edge. Although we found an isolation-by-distance pattern within each cluster, it arose due to the effect of a few isolated ponds located on the edge of each zone, suggesting the existence of substantial gene flow between ponds in the core area. According to our findings, landscape’s permeability to movement (pond connectivity) may constitute a more important factor than hydroperiod length in determining the genetic diversity and viability of pygmy newt populations in this area. Although Doñana populations show a good state, more peripheral and isolated populations present a more worrisome condition as a result of fragmentation and thus, require conservation efforts. Our study provides key insights that could help guide management practices of this threatened and poorly-studied salamander.
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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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Connectivity of Alpine newt populations (Ichthyosaura alpestris) exacerbates the risk of Batrachochytrium salamandrivorans outbreaks in European fire salamanders (Salamandra salamandra). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01377-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThe pathogenic chytrid fungus Batrachochytrium salamandrivorans (Bsal) was introduced from Asia to Europe, most likely via the pet trade. It is currently causing a severe local decline in populations of the European fire salamanders (Salamandra salamandra). Laboratory tests confirmed that all infected individuals succumbed to the disease within two weeks. Furthermore, mass mortality events in the wild were observed in Germany, Belgium and the Netherlands. Some newt species, including the Alpine newt (Ichthyosaura alpestris), can also become infected with Bsal. However, they seem to be ‘tolerant’ and can often survive the disease, but maintain an infectious load, which they could spread among connected populations. It is, therefore, hypothesized that this species functions as a vector of the disease and threatens syntopic populations of susceptible species such as the European fire salamander. To assess the risk of Alpine newts as vectors for Bsal, we sampled 233 individuals from 50 sites in 2017 and performed a genetic population connectivity analysis using microsatellites. The results showed that populations of Alpine newts are not spatially structured, suggesting high gene flow across the study area. Tests for Bsal of all Alpine newts and 150 individuals of two other newt species confirmed five infected individuals. Infected newts can thus function as reservoirs and vectors of Bsal and spread it through dispersal. As a result, the risk of European fire salamander declines in this region is further exacerbated by the connectivity of syntopic Alpine newt populations.
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Burgess SM, Garrick RC. The effect of sampling density and study area size on landscape genetics inferences for the Mississippi slimy salamander ( Plethodon mississippi). Ecol Evol 2021; 11:6289-6304. [PMID: 34141218 PMCID: PMC8207395 DOI: 10.1002/ece3.7481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual's dispersal distance, for low-mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal-limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite-based genetic distances among individuals were divided into three datasets representing sparse sampling across a large study area, dense sampling across a small study area, or sparse sampling across the same small study area. These datasets were a proxy for gene flow (i.e., the response variable) in maximum-likelihood population effects models that assessed the nature and strength of their relationship with each of five land-use classes (i.e., potential predictor variables). Comparisons of outcomes were based on the rank order of effect, sign of effect (i.e., gene flow resistance vs. facilitation), spatial scale of effect, and functional relationship with gene flow. The best-fit model for each dataset had the same sign of effect for hardwood forests, manmade structures, and pine forests, indicating the impacts of these land-use classes on dispersal and gene flow in P. mississippi are robust to sampling scheme. Contrasting sampling densities led to a different inferred functional relationship between agricultural areas and gene flow. Study area size appeared to influence the scale of effect of manmade structures and the sign of effect of pine forests. Our findings provided evidence for an influence of sampling density, study area size, and sampling effort upon inferences. Accordingly, we recommend iterative subsampling of empirical datasets and continued investigation into the sensitivities of landscape genetic analyses using simulations.
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Yannic G, Helfer V, Sermier R, Schmidt BR, Fumagalli L. Fine scale genetic structure in fire salamanders (Salamandra salamandra) along a rural-to-urban gradient. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01335-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Genes in space: what Mojave desert tortoise genetics can tell us about landscape connectivity. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01251-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Joly P. Behavior in a Changing Landscape: Using Movement Ecology to Inform the Conservation of Pond-Breeding Amphibians. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00155] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Cayuela H, Rougemont Q, Prunier JG, Moore JS, Clobert J, Besnard A, Bernatchez L. Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review. Mol Ecol 2018; 27:3976-4010. [DOI: 10.1111/mec.14848] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/17/2018] [Accepted: 08/19/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jérôme G. Prunier
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Aurélien Besnard
- CNRS; PSL Research University; EPHE; UM, SupAgro, IRD; INRA; UMR 5175 CEFE; Montpellier France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
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Costanzi JM, Mège P, Boissinot A, Isselin-Nondedeu F, Guérin S, Lourdais O, Trochet A, Le Petitcorps Q, Legrand A, Varenne F, Grillet P, Morin-Pinaud S, Picard D. Agricultural landscapes and the Loire River influence the genetic structure of the marbled newt in Western France. Sci Rep 2018; 8:14177. [PMID: 30242196 PMCID: PMC6155057 DOI: 10.1038/s41598-018-32514-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 09/10/2018] [Indexed: 11/26/2022] Open
Abstract
Amphibians are particularly sensitive to landscape fragmentation. Potential barriers between breeding sites can negatively influence the dispersal of individuals and increase genetic structure between populations. In this study, we genotyped 10 microsatellites for 334 marbled newts (Triturus marmoratus) at 11 different locations in Western France. Samples were collected in different regions with contrasting agricultural landscapes (low and high proportion of arable land in the north and south, respectively). We found a strong genetic structure between the northern and southern sampling sites. Isolation by distance was recorded after 62 km, but within the northern region, little or no genetic structure was detected over large distances (up to 114 km). Genetic structure at shorter distance (43 km) was found between sites situated in landscapes with larger amounts of arable lands. A significant positive relationship was found between the pairwise genetic distance (Fst) between sites and the amount of arable land together with the distance between sites. Our results suggest that the Loire River might act as a corridor for the marbled newt, while arable land might act as a barrier. Finally, although a large city is located between sampling sites, no effect was detected on population structure.
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Affiliation(s)
- Jean-Marc Costanzi
- Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway, Gullbringvegen 36, Bø i Telemark, 3800, Norway.
| | - Pascal Mège
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
| | - Alexandre Boissinot
- Centre d'Études Biologiques de Chizé, CNRS et Université de la Rochelle - UMR 7372, F-79360, Villiers en Bois, France
| | - Francis Isselin-Nondedeu
- Ecole Polytechnique de l'Université François Rabelais, Département d'Aménagement et d'Environnement, UMR 7324 - CNRS CITERES 33-35 allée Ferdinand de Lesseps, 37200, Tours, France
- IMBE, UMR Université Aix-Marseille Avignon, 7223-CNRS, 237-IRD IRPNC (Ingénierie de la Restauration des Patrimoines Naturels et Culturels), Avignon, France
| | - Sandra Guérin
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
- EPHE, PSL Research University, CNRS, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, F-34293, Montpellier, France
| | - Olivier Lourdais
- Centre d'Études Biologiques de Chizé, CNRS et Université de la Rochelle - UMR 7372, F-79360, Villiers en Bois, France
| | - Audrey Trochet
- CNRS, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Université Paul Sabatier, 118 route de Narbonne, Toulouse, F-31062, France
- Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, F-09200, France
| | - Quentin Le Petitcorps
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
| | - Agathe Legrand
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
| | | | | | - Sophie Morin-Pinaud
- Office National de la Chasse et de la Faune Sauvage - Unité Avifaune migratrice, Direction de la Recherche et de l'Expertise, F-79360, Villiers en Bois, France
| | - Damien Picard
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
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Clevenot L, Carré C, Pech P. A Review of the Factors That Determine Whether Stormwater Ponds Are Ecological Traps And/or High-Quality Breeding Sites for Amphibians. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Balbi M, Ernoult A, Poli P, Madec L, Guiller A, Martin MC, Nabucet J, Beaujouan V, Petit EJ. Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum). Mol Ecol 2018; 27:1357-1370. [PMID: 29412498 DOI: 10.1111/mec.14521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/11/2022]
Abstract
Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multiscale analysis to determine how landscape composition, configuration and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side by side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analysed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavourable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results and shows how multiscale analyses provide insight into scale-dependent processes.
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Affiliation(s)
- Manon Balbi
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Aude Ernoult
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Pedro Poli
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Luc Madec
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Annie Guiller
- Edysan FRE 3498, CNRS, Université de Picardie Jules Vernes, Amiens, France
| | - Marie-Claire Martin
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Jean Nabucet
- UMR LETG, CNRS, Université de Rennes 2, Rennes Cedex, France
| | | | - Eric J Petit
- ESE, Ecology and Ecosystem Health, INRA, Rennes, France
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No distinct barrier effects of highways and a wide river on the genetic structure of the Alpine newt (Ichthyosaura alpestris) in densely settled landscapes. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1046-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Soanes K, Taylor AC, Sunnucks P, Vesk PA, Cesarini S, Ree R. Evaluating the success of wildlife crossing structures using genetic approaches and an experimental design: Lessons from a gliding mammal. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12966] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kylie Soanes
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Vic. Australia
| | - Andrea C. Taylor
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Peter A. Vesk
- School of BioSciences The University of Melbourne Parkville Vic. Australia
| | - Silvana Cesarini
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Rodney Ree
- School of BioSciences The University of Melbourne Parkville Vic. Australia
- Ecology and Infrastructure International Wantirna Vic. Australia
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Quaternary history, population genetic structure and diversity of the cold-adapted Alpine newt Ichthyosaura alpestris in peninsular Italy. Sci Rep 2017; 7:2955. [PMID: 28592856 PMCID: PMC5462806 DOI: 10.1038/s41598-017-03116-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022] Open
Abstract
Mediterranean peninsulas are major biodiversity hotspots, and cold-adapted species are an important component of this biodiversity. However, cold-adapted species contributed surprisingly little to our knowledge of the intimate links between Quaternary environmental changes, species' responses to these changes, and current patterns of intraspecific biodiversity. Here, we investigated the genetic structure and evolutionary history of a cold-adapted amphibian, the Alpine newt Ichthyosaura alpestris, within the Italian peninsula. Nuclear and mitochondrial markers consistently identified three distinct genetic lineages, whose divergence dates to the Early Pleistocene (1.9 and 0.8 million years ago). Our results show that the Italian peninsula provided multiple Pleistocene refugia to this cold-adapted species, and suggest that allopatric fragmentation followed by secondary admixture have been key events in the formation of its current pattern of genetic diversity. Indeed, estimates of population genetic diversity clearly identified contact populations as those achieving the highest levels of diversity. Such concordance among cold-adapted and temperate species in terms of processes triggering the formation of regional patterns of genetic diversity provides strong support for the hypothesis that gene exchange between divergent lineages, rather than long-term stability of refugial populations, has been the main step toward the formation of hotspots of intraspecific biodiversity.
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Herrmann HW, Pozarowski KM, Ochoa A, Schuett GW. An interstate highway affects gene flow in a top reptilian predator (Crotalus atrox) of the Sonoran Desert. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0936-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Isselin-Nondedeu F, Trochet A, Joubin T, Picard D, Etienne R, Chevalier HL, Legrand D, Ribéron A. Spatial genetic structure of Lissotriton helveticus L. following the restoration of a forest ponds network. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0932-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Grilo C, Del Cerro I, Centeno-Cuadros A, Ramiro V, Román J, Molina-Vacas G, Fernández-Aguilar X, Rodríguez J, Porto-Peter F, Fonseca C, Revilla E, Godoy JA. Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 565:706-713. [PMID: 27219505 DOI: 10.1016/j.scitotenv.2016.05.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites.
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Affiliation(s)
- Clara Grilo
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain; Centro Brasileiro de Estudos em Ecologia de Estradas/Setor Ecologia, Departamento de Biologia, Universidade Federal de Lavras, Campus Universitário, 37200-000 Lavras, Minas Gerais, Brazil.
| | - Irene Del Cerro
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Alejandro Centeno-Cuadros
- Department of Molecular Biology and Biochemical Engineering, University Pablo de Olavide, Sevilla, Spain.
| | - Victor Ramiro
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | - Jacinto Román
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain.
| | - Guillem Molina-Vacas
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | | | - Juan Rodríguez
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | - Flávia Porto-Peter
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | - Carlos Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Eloy Revilla
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain.
| | - José A Godoy
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain.
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Richardson JL, Brady SP, Wang IJ, Spear SF. Navigating the pitfalls and promise of landscape genetics. Mol Ecol 2016; 25:849-63. [PMID: 26756865 DOI: 10.1111/mec.13527] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/12/2015] [Accepted: 01/07/2016] [Indexed: 12/17/2022]
Abstract
The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms of techniques appear like clockwork with each new journal issue. The developments are an encouraging, and at times bewildering, sign of progress in an exciting new field of study. However, we suggest that the rapid expansion of landscape genetics has belied important flaws in the development of the field, and we add an air of caution to this breakneck pace of expansion. Specifically, landscape genetic studies often lose sight of the fundamental principles and complex consequences of gene flow, instead favouring simplistic interpretations and broad inferences not necessarily warranted by the data. Here, we describe common pitfalls that characterize such studies, and provide practical guidance to improve landscape genetic investigation, with careful consideration of inferential limits, scale, replication, and the ecological and evolutionary context of spatial genetic patterns. Ultimately, the utility of landscape genetics will depend on translating the relationship between gene flow and landscape features into an understanding of long-term population outcomes. We hope the perspective presented here will steer landscape genetics down a more scientifically sound and productive path, garnering a field that is as informative in the future as it is popular now.
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Affiliation(s)
- Jonathan L Richardson
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI, 02918, USA
| | - Steven P Brady
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA
| | - Stephen F Spear
- The Orianne Society, 100 Phoenix Rd., Athens, GA, 30605, USA
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Epps CW, Keyghobadi N. Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change. Mol Ecol 2015; 24:6021-40. [DOI: 10.1111/mec.13454] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Clinton W. Epps
- Oregon State University; Nash Hall Room 104 Corvallis OR 97331 USA
| | - Nusha Keyghobadi
- Department of Biology; Western University; London ON N6A 5B7 Canada
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Prunier JG, Colyn M, Legendre X, Nimon KF, Flamand MC. Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses. Mol Ecol 2015; 24:263-83. [PMID: 25495950 DOI: 10.1111/mec.13029] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 02/02/2023]
Abstract
Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses.
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Affiliation(s)
- J G Prunier
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
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