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Prakas P, Butkauskas D, Balčiauskienė L, Balčiauskas L. Low Genetic Variability of the Tundra Vole in Lithuania. Animals (Basel) 2024; 14:270. [PMID: 38254439 PMCID: PMC10812506 DOI: 10.3390/ani14020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
The distribution and spread of the tundra vole (Alexandromys oeconomus) in Lithuania have been documented over the last 70 years, but the genetic diversity of the species has not been studied. In this study, we examined A. oeconomus trapped in three sites in northern and western Lithuania using mtDNA sequence analysis of the cytb and control region. The western and northern sites are separated by anthropogenic landscape barriers. The western site is subject to regular spring flooding. Phylogenetic analyses of the studied individuals placed them in the Central European phylogroup, suggesting that Lithuanian A. oeconomus originated from northeastern Poland. In Lithuania, the genetic diversity of A. oeconomus at both mtDNA loci was relatively low (Hd < 0.6, π < 0.002) compared to that found in other European samples (Hd = 0.833-0.958; π = 0.00402-0.01552). Individuals analyzed in Lithuania were genetically different from samples collected in Poland and Northern Europe (ΦST > 0.15, p < 0.05). The genetic divergence between the western and northern samples of A. oeconomus in Lithuania, together with the low genetic variability among the voles studied, provides new insights into the phylogeography of the species and the influence of barriers on the colonization of the country.
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Affiliation(s)
- Petras Prakas
- Nature Research Centre, Akademijos Str. 2, LT-08412 Vilnius, Lithuania; (D.B.); (L.B.); (L.B.)
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Rose JP, Kim R, Schoenig EJ, Lien PC, Halstead BJ. Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models. PLoS One 2023; 18:e0292379. [PMID: 37796777 PMCID: PMC10553336 DOI: 10.1371/journal.pone.0292379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023] Open
Abstract
For endangered species persisting in a few populations, reintroductions to unoccupied habitat are a popular conservation action to increase viability in the long term. Identifying the reintroduction strategy that is most likely to result in viable founder and donor populations is essential to optimally use resources available for conservation. The San Francisco gartersnake (Thamnophis sirtalis tetrataenia) is an endangered sub-species that persists in a small number of populations in a highly urbanized region of California. Most of the extant populations of San Francisco gartersnakes have low adult abundance and effective population size, heightening the need for establishment of more populations for insurance against the risk of extinction. We used simulations from demographic models to project the probability of quasi-extinction for reintroduced populations of San Francisco gartersnakes based on the release of neonate, juvenile, adult, or mixed-age propagules. Our simulation results indicated that the release of head-started juveniles resulted in the greatest viability of reintroduced populations, and that releases would need to continue for at least 15 years to ensure a low probability of quasi-extinction. Releasing captive-bred juvenile snakes would also have less effect on the viability of the donor population, compared to strategies that require more adult snakes to be removed from the donor population for translocation. Our models focus on snake demography, but the genetic makeup of donor, captive, and reintroduced populations will also be a major concern for any proposed reintroduction plan. This study demonstrates how modeling can be used to inform reintroduction strategies for highly imperiled species.
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Affiliation(s)
- Jonathan P. Rose
- U.S. Geological Survey, Western Ecological Research Center, Santa Cruz, California, United States of America
| | - Richard Kim
- U.S. Geological Survey, Western Ecological Research Center, Dixon, California, United States of America
| | - Elliot J. Schoenig
- U.S. Geological Survey, Western Ecological Research Center, Dixon, California, United States of America
| | - Patrick C. Lien
- U.S. Geological Survey, Western Ecological Research Center, Dixon, California, United States of America
| | - Brian J. Halstead
- U.S. Geological Survey, Western Ecological Research Center, Dixon, California, United States of America
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Rose JP, Kim R, Schoenig EJ, Lien PC, Halstead BJ. Integrating growth and survival models for flexible estimation of size‐dependent survival in a cryptic, endangered snake. Ecol Evol 2022; 12:e8799. [PMID: 35414900 PMCID: PMC8987119 DOI: 10.1002/ece3.8799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/31/2022] [Accepted: 03/10/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jonathan P. Rose
- U.S. Geological Survey Western Ecological Research Center Santa Cruz Field Station Santa Cruz California USA
| | - Richard Kim
- U.S. Geological Survey Western Ecological Research Center Dixon California USA
| | - Elliot J. Schoenig
- U.S. Geological Survey Western Ecological Research Center Dixon California USA
| | - Patrick C. Lien
- U.S. Geological Survey Western Ecological Research Center Dixon California USA
| | - Brian J. Halstead
- U.S. Geological Survey Western Ecological Research Center Dixon California USA
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Dyson CJ, Piscano OL, Durham RM, Thompson VJ, Johnson CH, Goodisman MAD. Temporal Analysis of Effective Population Size and Mating System in a Social Wasp. J Hered 2021; 112:626-634. [PMID: 34558622 DOI: 10.1093/jhered/esab057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/20/2021] [Indexed: 02/07/2023] Open
Abstract
Highly social species are successful because they cooperate in obligately integrated societies. We examined temporal genetic variation in the eusocial wasp Vespula maculifrons to gain a greater understanding of evolution in highly social taxa. First, we wished to test if effective population sizes of eusocial species were relatively low due to the reproductive division of labor that characterizes eusocial taxa. We thus estimated the effective population size of V. maculifrons by examining temporal changes in population allele frequencies. We sampled the genetic composition of a V. maculifrons population at 3 separate timepoints spanning a 13-year period. We found that effective population size ranged in the hundreds of individuals, which is similar to estimates in other, non-eusocial taxa. Second, we estimated levels of polyandry in V. maculifrons in different years to determine if queen mating system varied over time. We found no significant change in the number or skew of males mated to queens. In addition, mating skew was not significant within V. maculifrons colonies. Therefore, our data suggest that queen mate number may be subject to stabilizing selection in this taxon. Overall, our study provides novel insight into the selective processes operating in eusocial species by analyzing temporal genetic changes within populations.
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Affiliation(s)
- Carl J Dyson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Olivia L Piscano
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rebecca M Durham
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Veronica J Thompson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Catherine H Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Lettoof DC, Thomson VA, Cornelis J, Bateman PW, Aubret F, Gagnon MM, von Takach B. Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow. PLoS One 2021; 16:e0259124. [PMID: 34714831 PMCID: PMC8555784 DOI: 10.1371/journal.pone.0259124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.
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Affiliation(s)
- Damian C. Lettoof
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jari Cornelis
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Philip W. Bateman
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fabien Aubret
- Station d’Ecologie Théorique et Expérimentale, CNRS, Moulis, France
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Marthe M. Gagnon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Brenton von Takach
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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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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Correction: Combining genetic and demographic monitoring better informs conservation of an endangered urban snake. PLoS One 2021; 16:e0257374. [PMID: 34499684 PMCID: PMC8428562 DOI: 10.1371/journal.pone.0257374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Delgado-Acevedo J, Zamorano A, DeYoung RW, Campbell TA. Genetic Population Structure of Wild Pigs in Southern Texas. Animals (Basel) 2021; 11:ani11010168. [PMID: 33445721 PMCID: PMC7828165 DOI: 10.3390/ani11010168] [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: 11/20/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Wild pigs are the most abundant wild exotic ungulate in the United States. In Texas, particularly, they are abundant and represent a threat to ecosystems, agriculture and humans. Our objective was to apply a landscape-scale analysis of population genetic structure of wild pigs to aid in their management in southern Texas. We used microsatellites to assist large-scale applied management. We found that some populations were isolated from one another. However, many individuals and local populations were admixed, which indicates that multiple introductions and artificial movement of individuals has occurred. Wild pig management efficiency and effectiveness may be able to improve if illegal translocations stop (e.g., enforcing laws) and if management cooperatives are created to manage spatially extensive areas of southern Texas. Abstract Wild pigs (Sus scrofa) alter ecosystems, affect the economy, and carry diseases that can be transmitted to livestock, humans, and wildlife. Understanding wild pig movements and population structure data, including natural population boundaries and dispersal, may potentially increase the efficiency and effectiveness of management actions. We trapped, conducted aerial shootings, and hunted wild pigs from 2005 to 2009 in southern Texas. We used microsatellites to assist large-scale applied management. We quantify broad-scale population structure among 24 sites across southern Texas by computing an overall FST value, and a Bayesian clustering algorithm both with and without considering the spatial location of samples. At a broad geographic scale, pig populations displayed a moderate degree of genetic structure (FST = 0.11). The best partition for number of populations, based on 2nd order rate of change of the likelihood distribution, was K = 10 genetic clusters. The spatially explicit Bayesian clustering algorithm produced similar results, with minor differences in designation of admixed sites. We found evidence of past (and possibly ongoing) translocations; many populations were admixed. Our original goal was to identify landscape features, such as barriers or dispersal corridors, that could be used to aid management. Unfortunately, the extensive admixture among clusters made this impossible. This research shows that large-scale management of wild pigs may be necessary to achieve control and ameliorate damages. Reduction or cessation of translocations is necessary to prevent human-mediated dispersion of wild pigs.
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Affiliation(s)
- Johanna Delgado-Acevedo
- Texas A&M University-Commerce, STC 262, Commerce, TX 75429, USA
- Correspondence: ; Tel.: +1-903-468-3333
| | - Angeline Zamorano
- Caesar Kleberg Wildlife Research Institute, Texas A&M University-Kingsville, Kingsville, TX 78363, USA; (A.Z.); (R.W.D.)
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research Institute, Texas A&M University-Kingsville, Kingsville, TX 78363, USA; (A.Z.); (R.W.D.)
| | - Tyler A. Campbell
- East Foundation, 200 Concord Plaza Dr., Suite 410, San Antonio, TX 78216, USA;
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