101
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High gene flow through pollen partially compensates spatial limited gene flow by seeds for a Neotropical tree in forest conservation and restoration areas. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01344-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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102
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Henderson D, Zhu S(J, Cole CB, Lunter G. Demographic inference from multiple whole genomes using a particle filter for continuous Markov jump processes. PLoS One 2021; 16:e0247647. [PMID: 33651801 PMCID: PMC7924771 DOI: 10.1371/journal.pone.0247647] [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: 05/04/2020] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Demographic events shape a population's genetic diversity, a process described by the coalescent-with-recombination model that relates demography and genetics by an unobserved sequence of genealogies along the genome. As the space of genealogies over genomes is large and complex, inference under this model is challenging. Formulating the coalescent-with-recombination model as a continuous-time and -space Markov jump process, we develop a particle filter for such processes, and use waypoints that under appropriate conditions allow the problem to be reduced to the discrete-time case. To improve inference, we generalise the Auxiliary Particle Filter for discrete-time models, and use Variational Bayes to model the uncertainty in parameter estimates for rare events, avoiding biases seen with Expectation Maximization. Using real and simulated genomes, we show that past population sizes can be accurately inferred over a larger range of epochs than was previously possible, opening the possibility of jointly analyzing multiple genomes under complex demographic models. Code is available at https://github.com/luntergroup/smcsmc.
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Affiliation(s)
| | - Sha (Joe) Zhu
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
- Big Data Institute, Oxford, United Kingdom
| | - Christopher B. Cole
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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103
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Barr K, Beichman AC, Kalhori P, Rajbhandary J, Bay RA, Ruegg K, Smith TB. Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird ( Agelaius tricolor). Evol Appl 2021; 14:674-684. [PMID: 33767743 PMCID: PMC7980274 DOI: 10.1111/eva.13147] [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: 06/18/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD-Seq) from samples collected across the species' range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K = 1), and comparisons of genetic differentiation (average FST = 0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Annabel C. Beichman
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Pooneh Kalhori
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Jasmine Rajbhandary
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCAUSA
| | - Kristen Ruegg
- Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
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104
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Pečnerová P, Garcia-Erill G, Liu X, Nursyifa C, Waples RK, Santander CG, Quinn L, Frandsen P, Meisner J, Stæger FF, Rasmussen MS, Brüniche-Olsen A, Hviid Friis Jørgensen C, da Fonseca RR, Siegismund HR, Albrechtsen A, Heller R, Moltke I, Hanghøj K. High genetic diversity and low differentiation reflect the ecological versatility of the African leopard. Curr Biol 2021; 31:1862-1871.e5. [PMID: 33636121 DOI: 10.1016/j.cub.2021.01.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position at the top of the trophic pyramid is associated with small population sizes. Accordingly, low genetic diversity at the whole-genome level has been reported for all big cat species, including the widely distributed leopard. However, all previous whole-genome analyses of leopards are based on the Far Eastern Amur leopards that live at the extremity of the species' distribution and therefore are not necessarily representative of the whole species. We sequenced 53 whole genomes of African leopards. Strikingly, we found that the genomic diversity in the African leopard is 2- to 5-fold higher than in other big cats, including the Amur leopard, likely because of an exceptionally high effective population size maintained by the African leopard throughout the Pleistocene. Furthermore, we detected ongoing gene flow and very low population differentiation within African leopards compared with those of other big cats. We corroborated this by showing a complete absence of an otherwise ubiquitous equatorial forest barrier to gene flow. This sets the leopard apart from most other widely distributed large African mammals, including lions. These results revise our understanding of trophic sensitivity and highlight the remarkable resilience of the African leopard, likely because of its extraordinary habitat versatility and broad dietary niche.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Ryan K Waples
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Copenhagen Zoo, Research and Conservation, Roskildevej 32, 2000 Frederiksberg, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Frederik Filip Stæger
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe Sebro Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anna Brüniche-Olsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Department of Forestry and Natural Resources, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | | | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
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105
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Zhao P, Liu S, Zhou Y, Lynch T, Lu W, Zhang T, Yang H. Estimating animal population size with very high-resolution satellite imagery. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:316-324. [PMID: 32839996 DOI: 10.1111/cobi.13613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Very high-resolution (VHR) satellite sensors can be used to estimate the size of animal populations, a critical factor in wildlife management, and acquire animal spatial distributions in an economical, easy, and precise way. We developed a method for satellite population size estimation that includes a noninvasive photogrammetry, from which the animal's average orthographic area is calculated, and an imagery interpretation method that estimates population size based on the ratio of an observed animal population area to the average individual area. As a proof of concept, we used this method to estimate the population size of Whooper Swans (Cygnus cygnus) in a national nature reserve in China. To reduce errors, the reserve was subdivided into regions of interest based on locations of Whooper Swan and background brightness. Estimates from the satellite pixels were compared with manual counts made over 2 years, at 3 locations, and in 3 land-cover types. Our results showed 1124 Whooper Swans occupied a national nature reserve on 15 February 2013, and the average percent error was 3.16% (SE = 1.37). These results demonstrate that our method produced robust data for population size estimation that were indistinguishable from manual count data. Our method may be used generally to estimate population sizes of visible and gregarious animals that exhibit high contrast relative to their environments and may inform estimations of populations in complex backgrounds.
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Affiliation(s)
- Peng Zhao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Marine Data & Information Service, Tianjin, 300171, China
| | - Shuming Liu
- National Marine Data & Information Service, Tianjin, 300171, China
| | - Yi Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Tim Lynch
- CSIRO Oceans and Atmosphere Flagship, Hobart, 7001, Australia
| | - Wenhu Lu
- National Marine Data & Information Service, Tianjin, 300171, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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106
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Lang AR, Boveng P, Quakenbush L, Robertson K, Lauf M, Rode KD, Ziel H, Taylor BL. Re-examination of population structure in Arctic ringed seals using DArTseq genotyping. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although Arctic ringed seals Phoca hispida hispida are currently abundant and broadly distributed, their numbers are projected to decline substantially by the year 2100 due to climate warming. While understanding population structure could provide insight into the impact of environmental changes on this subspecies, detecting demographically important levels of exchange can be difficult in taxa with high abundance. We used a next-generation sequencing approach (DArTseq) to genotype ~5700 single nucleotide polymorphisms in 79 seals from 4 Pacific Arctic regions. Comparison of the 2 most geographically separated strata (eastern Bering vs. northeastern Chukchi-Beaufort Seas) revealed a statistically significant level of genetic differentiation (FST = 0.001, p = 0.005) that, while small, was 1 to 2 orders of magnitude greater than expected based on divergence estimated for similarly sized populations connected by low (1% yr-1) dispersal. A relatively high proportion (72 to 88%) of individuals within these strata could be genetically assigned to their stratum of origin. These results indicate that demographically important structure may be present among Arctic ringed seals breeding in different areas, increasing the risk that declines in the number of seals breeding in areas most negatively affected by environmental warming could occur.
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Affiliation(s)
- AR Lang
- Ocean Associates, Inc., Arlington, VA 22207, USA, under contract to the Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - P Boveng
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115, USA
| | - L Quakenbush
- Arctic Marine Mammal Program, Alaska Department of Fish and Game, Fairbanks, AK 99701, USA
| | - K Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - M Lauf
- Ocean Associates, Inc., Arlington, VA 22207, USA, under contract to the Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - KD Rode
- Alaska Science Center, US Geological Survey, Anchorage, AK 99508, USA
| | - H Ziel
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115, USA
| | - BL Taylor
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
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107
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Carlen E, Munshi‐South J. Widespread genetic connectivity of feral pigeons across the Northeastern megacity. Evol Appl 2021; 14:150-162. [PMID: 33519962 PMCID: PMC7819573 DOI: 10.1111/eva.12972] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/31/2022] Open
Abstract
Urbanization may restrict, facilitate, or have no effect on gene flow, depending on the organism and extent of urbanization. In human commensals, with high dispersal ability, urbanization can facilitate gene flow by providing continuous suitable habitat across a wide range. Additionally, suburban or rural areas with lower human population density may act as a barrier to gene flow for these human commensals. Spatial population genetic approaches provide a means to understand genetic connectivity across geographically expansive areas that encompass multiple metropolitan areas. Here, we examined the spatial genetic patterns of feral pigeons (Columba livia) living in cities in the eastern United States. We focused our sampling on the Northeastern megacity, which is a region covering six large cities (Boston, Providence, New York City, Philadelphia, Baltimore, and Washington, DC). We performed ddRAD-Seqon 473 samples, recovered 35,200 SNPs, and then used multiple evolutionary clustering analyses to investigate population structuring. These analyses revealed that pigeons formed two genetic clusters-a northern cluster containing samples from Boston and Providence and a southern cluster containing all other samples. This substructuring is possibly due to reduced urbanization across coastal Connecticut that separates Boston and Providence from New York and mid-Atlantic cities. We found that pairs of pigeons within 25 km are highly related (Mantel r = 0.217, p = .001) and that beyond 50 km, pigeons are no more related than they would be at random. Our analysis detected higher-than-expected gene flow under an isolation by distance model within each city. We conclude that the extreme urbanization characteristic of the Northeastern megacity is likely facilitating gene flow in feral pigeons.
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108
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Luikart G, Antao T, Hand BK, Muhlfeld CC, Boyer MC, Cosart T, Trethewey B, Al-Chockhachy R, Waples RS. Detecting population declines via monitoring the effective number of breeders (N b ). Mol Ecol Resour 2020; 21:379-393. [PMID: 32881365 DOI: 10.1111/1755-0998.13251] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Estimating the effective population size and effective number of breeders per year (Nb ) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one-sample LDNe estimator of Nb in age-structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5%-10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence Nb estimation. Precision was higher for 100 SNPs (H ≈ 0.30) than for 15 microsatellites (H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when Nb was small (Nb < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that Nb = 50 when the true Nb = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject Nb = 500 when the true Nb = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in Nb when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate Nb for age structured populations (https://github.com/popgengui/agestrucnb/), which should help biologists develop sensitive monitoring programmes for early detection of changes in Nb and population declines.
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Affiliation(s)
- Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Tiago Antao
- The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Brian K Hand
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Clint C Muhlfeld
- Northern Rocky Mountain Science Center, U.S. Geological Survey, Glacier National Park, Northern Rocky Mountain Science Center, West Glacier, MT, USA
| | | | - Ted Cosart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Brian Trethewey
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Robert Al-Chockhachy
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT, USA
| | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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109
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Barrow LN, Masiero da Fonseca E, Thompson CEP, Carstens BC. Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data. Mol Ecol Resour 2020; 21:2818-2831. [PMID: 33249725 DOI: 10.1111/1755-0998.13303] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/11/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
The growing availability of genetic data sets, in combination with machine learning frameworks, offers great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we analysed repurposed data using machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this data set, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contained low genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful data sets with greater utility for understanding global biodiversity.
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Affiliation(s)
- Lisa N Barrow
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | - Coleen E P Thompson
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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110
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Genetic diversity and population structure of the endangered plant Salix taishanensis based on CDDP markers. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01242] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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111
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Olah G, Stojanovic D, Webb MH, Waples RS, Heinsohn R. Comparison of three techniques for genetic estimation of effective population size in a critically endangered parrot. Anim Conserv 2020. [DOI: 10.1111/acv.12655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Olah
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
- Wildlife Messengers Richmond VA USA
| | - D. Stojanovic
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
| | - M. H. Webb
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
| | - R. S. Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle WA USA
| | - R. Heinsohn
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
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112
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Genetic Consequences of Multiple Translocations of the Banded Hare-Wallaby in Western Australia. DIVERSITY 2020. [DOI: 10.3390/d12120448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many Australian mammal species now only occur on islands and fenced mainland havens free from invasive predators. The range of one species, the banded hare-wallaby (Lagostrophus fasciatus), had contracted to two offshore islands in Western Australia. To improve survival, four conservation translocations have been attempted with mixed success, and all occurred in the absence of genetic information. Here, we genotyped seven polymorphic microsatellite markers in two source (Bernier Island and Dorre Island), two historic captive, and two translocated L. fasciatus populations to determine the impact of multiple translocations on genetic diversity. Subsequently, we used population viability analysis (PVA) and gene retention modelling to determine scenarios that will maximise demographic resilience and genetic richness of two new populations that are currently being established. One translocated population (Wadderin) has undergone a genetic bottleneck and lost 8.1% of its source population’s allelic diversity, while the other (Faure Island) may be inbred. We show that founder number is a key parameter when establishing new L. fasciatus populations and 100 founders should lead to high survival probabilities. Our modelling predicts that during periodic droughts, the recovery of source populations will be slower post-harvest, while 75% more animals—about 60 individuals—are required to retain adequate allelic diversity in the translocated population. Our approach demonstrates how genetic data coupled with simulations of stochastic environmental events can address central questions in translocation programmes.
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113
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Skorupski J. Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals? Genes (Basel) 2020; 11:E1332. [PMID: 33187363 PMCID: PMC7696698 DOI: 10.3390/genes11111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-914-441-685
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
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114
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Levasseur KE, Stapleton SP, Quattro JM. Precise natal homing and an estimate of age at sexual maturity in hawksbill turtles. Anim Conserv 2020. [DOI: 10.1111/acv.12657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- K. E. Levasseur
- Department of Biological Sciences University of South Carolina Columbia SC USA
- Jumby Bay Hawksbill Project St John’s Antigua and Barbuda
| | - S. P. Stapleton
- Jumby Bay Hawksbill Project St John’s Antigua and Barbuda
- Department of Fisheries, Wildlife and Conservation Biology University of Minnesota St. Paul MN USA
| | - J. M. Quattro
- Department of Biological Sciences University of South Carolina Columbia SC USA
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115
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Klein JD, der Merwe AEBV, Dicken ML, Emami-Khoyi A, Mmonwa KL, Teske PR. A globally threatened shark, Carcharias taurus, shows no population decline in South Africa. Sci Rep 2020; 10:17959. [PMID: 33087802 PMCID: PMC7578018 DOI: 10.1038/s41598-020-75044-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.
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Affiliation(s)
- Juliana D Klein
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Matthew L Dicken
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, 4320, South Africa
- Department of Development Studies, School of Economics, Development and Tourism, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Kolobe L Mmonwa
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, 4320, South Africa
| | - Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa.
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116
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Chung MY, Son S, Herrando-Moraira S, Tang CQ, Maki M, Kim YD, López-Pujol J, Hamrick JL, Chung MG. Incorporating differences between genetic diversity of trees and herbaceous plants in conservation strategies. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1142-1151. [PMID: 31994789 DOI: 10.1111/cobi.13467] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/09/2019] [Accepted: 01/10/2020] [Indexed: 05/22/2023]
Abstract
Reviews that summarize the genetic diversity of plant species in relation to their life history and ecological traits show that forest trees have more genetic diversity at population and species levels than annuals or herbaceous perennials. In addition, among-population genetic differentiation is significantly lower in trees than in most herbaceous perennials and annuals. Possible reasons for these differences between trees and herbaceous perennials and annuals have not been discussed critically. Several traits, such as high rates of outcrossing, long-distance pollen and seed dispersal, large effective population sizes (Ne ), arborescent stature, low population density, longevity, overlapping generations, and occurrence in late successional communities, may make trees less sensitive to genetic bottlenecks and more resistant to habitat fragmentation or climate change. We recommend that guidelines for genetic conservation strategies be designed differently for tree species versus other types of plant species. Because most tree species fit an LH scenario (low [L] genetic differentiation and high [H] genetic diversity), tree seeds could be sourced from a few populations distributed across the species' range. For the in situ conservation of trees, translocation is a viable option to increase Ne . In contrast, rare herbaceous understory species are frequently HL (high differentiation and low diversity) species. Under the HL scenario, seeds should be taken from many populations with high genetic diversity. In situ conservation efforts for herbaceous plants should focus on protecting habitats because the typically small populations of these species are vulnerable to the loss of genetic diversity. The robust allozyme genetic diversity databases could be used to develop conservation strategies for species lacking genetic information. As a case study of reforestation with several tree species in denuded areas on the Korean Peninsula, we recommend the selection of local genotypes as suitable sources to prevent adverse effects and to insure the successful restoration in the long term.
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Affiliation(s)
- Mi Yoon Chung
- Research Institute of Natural Science (RINS), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Sungwon Son
- Division of Plant Resources, Korea National Arboretum, Yangpyeong, 12519, Republic of Korea
| | - Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, 08038, Spain
| | - Cindy Q Tang
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Aoba, Sendai, 980-0862, Japan
| | - Young-Dong Kim
- Department of Life Sciences, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, 08038, Spain
| | - James L Hamrick
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, U.S.A
| | - Myong Gi Chung
- Division of Life Science and the RINS, Gyeongsang National University, Jinju, 52828, Republic of Korea
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117
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Hecht LB, Thompson PC, Rosenthal BM. Assessing the evolutionary persistence of ecological relationships: A review and preview. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 84:104441. [PMID: 32622083 PMCID: PMC7327472 DOI: 10.1016/j.meegid.2020.104441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022]
Abstract
Species interactions, such as pollination, parasitism and predation, form the basis of functioning ecosystems. The origins and resilience of such interactions therefore merit attention. However, fossils only occasionally document ancient interactions, and phylogenetic methods are blind to recent interactions. Is there some other way to track shared species experiences? "Comparative demography" examines when pairs of species jointly thrived or declined. By forging links between ecology, epidemiology, and evolutionary biology, this method sheds light on biological adaptation, species resilience, and ecosystem health. Here, we describe how this method works, discuss examples, and suggest future directions in hopes of inspiring interest, imitators, and critics.
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Affiliation(s)
| | - Peter C. Thompson
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD 20705 USA
| | - Benjamin M. Rosenthal
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD 20705 USA,Corresponding author
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118
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Abstract
AbstractMany species on endangered species lists such as the IUCN Red List (RL) are categorized using demographic factors such as numbers of mature individuals. Genetic factors are not currently used in the RL even though their explicit consideration, including effective population size (Ne) and expected heterozygosity-loss (H-loss), could improve the assessment of extinction risk. Here, we consider the estimation of Ne and H-loss in the context of RL species. First, we investigate the reporting of number of mature individuals for RL Endangered species, which is needed to estimate Ne and H-loss. We found 77% of species assessments studied here did not report methods used to estimate the number of mature adults, and that these assessments rarely report other important determinants of Ne (e.g., sex ratio, variance in family size). We therefore applied common rules of thumb to estimate Ne, and found that Ne was likely < 50 for at least 25% of the 170 RL Endangered species studied here. We also estimated mean expected H-loss for these species over the next 100 years, and found it to be 9–29%. These estimates of high H-loss and low Ne suggest that some species listed as Endangered likely warrant listing as Critically Endangered if genetic considerations were included. We recommend that RL and other assessment frameworks (i) report methods used for estimating the number of mature adults, (ii) include standardized information on species traits that influence Ne to facilitate Ne estimation, and (iii) consider using concepts like Ne and heterozygosity-loss in risk assessments.
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119
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Dellinger JA, Gustafson KD, Gammons DJ, Ernest HB, Torres SG. Minimum habitat thresholds required for conserving mountain lion genetic diversity. Ecol Evol 2020; 10:10687-10696. [PMID: 33072289 PMCID: PMC7548186 DOI: 10.1002/ece3.6723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022] Open
Abstract
Jointly considering the ecology (e.g., habitat use) and genetics (e.g., population genetic structure and diversity) of a species can increase understanding of current conservation status and inform future management practices. Previous analyses indicate that mountain lion (Puma concolor) populations in California are genetically structured and exhibit extreme variation in population genetic diversity. Although human development may have fragmented gene flow, we hypothesized the quantity and quality of remaining habitat available would affect the genetic viability of each population. Our results indicate that area of suitable habitat, determined via a resource selection function derived using 843,500 location fixes from 263 radio‐collared mountain lions, is strongly and positively associated with population genetic diversity and viability metrics, particularly with effective population size. Our results suggested that contiguous habitat of ≥10,000 km2 may be sufficient to alleviate the negative effects of genetic drift and inbreeding, allowing mountain lion populations to maintain suitable effective population sizes. Areas occupied by five of the nine geographic–genetic mountain lion populations in California fell below this habitat threshold, and two (Santa Monica Area and Santa Ana) of those five populations lack connectivity to nearby populations. Enhancing ecological conditions by protection of greater areas of suitable habitat and facilitating positive evolutionary processes by increasing connectivity (e.g., road‐crossing structures) might promote persistence of small or isolated populations. The conservation status of suitable habitat also appeared to influence genetic diversity of populations. Thus, our results demonstrate that both the area and status (i.e., protected or unprotected) of suitable habitat influence the genetic viability of mountain lion populations.
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Affiliation(s)
| | - Kyle D Gustafson
- Department of Biological Sciences Arkansas State University Jonesboro Arkansas USA.,Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Daniel J Gammons
- California Department of Fish and Wildlife Sacramento California USA
| | - Holly B Ernest
- Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Steven G Torres
- California Department of Fish and Wildlife Sacramento California USA
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120
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Population Genetic Assessment of Anadromous and Resident Striped Bass (Morone saxatilis) in the Roanoke River System, Eastern United States. FISHES 2020. [DOI: 10.3390/fishes5030024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Striped bass is the subject of important commercial and sport fisheries in North America. The Roanoke River drainage—especially Smith Mountain Lake, Leesville Lake, and Kerr Reservoir—has popular recreational striped bass fisheries. After construction of five hydroelectric dams, populations became landlocked, declined, and have been supplemented by stocking. A key basis for responsibly augmenting populations is to characterize genetic variation and incorporate the findings into responsible hatchery and stocking practices. Genetic variation at 12 microsatellite DNA loci was evaluated among 837 striped bass representing 16 collections across the native range; populations from rivers in South Carolina, North Carolina, Chesapeake Bay, and Hudson River were screened to provide context for assessing genetic structure within the Roanoke system. Analysis of population genetic differentiation showed landlocked Roanoke River striped bass to be distinctive. Subject to genetic isolation, high M ratios, and relatively low Ne estimates suggest loss of genetic variation, and relatedness analysis showed heightened frequencies of related individuals. These insights into population genetics, demographics, and existing guidelines for broodstock acquisition and mating designs can inform genetically cognizant hatchery management and stocking for striped bass in the Roanoke River drainage. In particular, we recommend the use of larger numbers of breeders and factorial mating designs to increase the genetic diversity of propagated striped bass stocked within the Roanoke River drainage.
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121
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Ausband DE, Waits L. Does harvest affect genetic diversity in grey wolves? Mol Ecol 2020; 29:3187-3195. [PMID: 32657476 DOI: 10.1111/mec.15552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 01/01/2023]
Abstract
Harvest can affect vital rates such as reproduction and survival, but also genetic measures of individual and population health. Grey wolves (Canis lupus) live and breed in groups, and effective population size is a small fraction of total abundance. As a result, genetic diversity of wolves may be particularly sensitive to harvest. We evaluated how harvest affected genetic diversity and relatedness in wolves. We hypothesized that harvest would (a) reduce relatedness of individuals within groups in a subpopulation but increase relatedness of individuals between groups due to increased local immigration, (b) increase individual heterozygosity and average allelic richness across groups in subpopulations and (c) add new alleles to a subpopulation and decrease the number of private alleles in subpopulations due to an increase in breeding opportunities for unrelated individuals. We found harvest had no effect on observed heterozygosity of individuals or allelic richness at loci within subpopulations but was associated with a small, biologically insignificant effect on within-group relatedness values in grey wolves. Harvest was, however, positively associated with increased relatedness of individuals between groups and a net gain (+16) of alleles into groups in subpopulations monitored since harvest began, although the number of private alleles in subpopulations overall declined. Harvest likely created opportunities for wolves to immigrate into nearby groups and breed, thereby making groups in subpopulations more related over time. Harvest appears to affect genetic diversity in wolves at the group and population levels, but its effects are less apparent at the individual level given the population sizes we studied.
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Affiliation(s)
- David E Ausband
- Idaho Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Idaho, Moscow, ID, USA
| | - Lisette Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
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122
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Cooper L, Bunnefeld L, Hearn J, Cook JM, Lohse K, Stone GN. Low-coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp. Mol Ecol 2020; 29:3649-3666. [PMID: 32567765 DOI: 10.1111/mec.15523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Population divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide data sets allows discrimination between alternative scenarios for these processes even in nonmodel taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum [bSFS], the second on the pairwise sequentially Markovian coalescent [PSMC]) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia and are separated into The Northern population is to the north of the Southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of postdivergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196 kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57 kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, nonmodel organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.
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Affiliation(s)
- Lisa Cooper
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Lynsey Bunnefeld
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Jack Hearn
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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123
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Nikolic N, Thompson P, de Bruyn M, Macé M, Chevalet C. Evolutionary history of a Scottish harbour seal population. PeerJ 2020; 8:e9167. [PMID: 32728487 PMCID: PMC7357561 DOI: 10.7717/peerj.9167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/19/2020] [Indexed: 12/02/2022] Open
Abstract
Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area.
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Affiliation(s)
- Natacha Nikolic
- ARBRE (Reunion Island Biodiversity Research Agency), Saint-Leu, La Réunion
- Génétique Physiologie et Systèmes d’Elevage - UMR1388, INRAE, Castanet Tolosan, France
| | - Paul Thompson
- Lighthouse Field Station, Sciences School of Biological Sciences, University of Aberdeen, Cromarty, United Kingdom
| | - Mark de Bruyn
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Matthias Macé
- Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse - UMR 5288, CNRS, Toulouse, France
| | - Claude Chevalet
- Génétique Physiologie et Systèmes d’Elevage - UMR1388, INRAE, Castanet Tolosan, France
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124
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Olarte Ó, SÁnchez-Montes G, MartÍnez-Solano Í. Integrative demographic study of the Iberian painted frog (Discoglossus galganoi): inter-annual variation in the effective to census population size ratio, with insights on mating system and breeding success. Integr Zool 2020; 15:498-510. [PMID: 32333629 DOI: 10.1111/1749-4877.12452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the face of worldwide amphibian declines, integrative studies combining individual-based information and genetic data represent a powerful approach to produce robust, reliable, and comparable assessments of demographic dynamics. The Iberian painted frog (Discoglossus galganoi) is endemic to Spain and Portugal and shows decreasing population trends across its range, but few studies have attempted to estimate census sizes or assess genetic diversity in wild populations, and little is known about their reproductive biology. We applied an integrative approach based on the combination of capture-mark-recapture data and multilocus genotypes to monitor a breeding population of D. galganoi in central Spain during two consecutive breeding seasons, focusing on the estimation of demographic parameters and their temporal variation. Specifically, we estimated the number of adults (Na ), the effective population size (Ne ), and the effective number of breeders (Nb ), as well as survival and migration rates. We documented a >50% decrease in the estimated number of adults of both sexes between the breeding seasons of 2018 and 2019, probably associated with reduced rainfall in the latter. Estimates of Nb and the Nb /Na ratio were low in both seasons, with a 20-30% decrease in Nb and a 47% increase in the Nb /Na ratio in 2019. Based on the reconstruction of pedigrees from larval and adult genotypes, we provide the first genetic evidence of polygamy in males and females of D. galganoi and the first estimates of breeding success in the species.
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Affiliation(s)
- Óscar Olarte
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Íñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
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125
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Abstract
Megafishes are important to people and ecosystems worldwide. These fishes attain a maximum body weight of ≥30 kg. Global population declines highlight the need for more information about megafishes’ conservation status to inform management and conservation. The northern Cambodian Mekong River and its major tributaries are considered one of the last refugia for Mekong megafishes. We collected data on population abundance and body size trends for eight megafishes in this region to better understand their conservation statuses. Data were collected in June 2018 using a local ecological knowledge survey of 96 fishers in 12 villages. Fishers reported that, over 20 years, most megafishes changed from common to uncommon, rare, or locally extirpated. The most common and rarest species had mean last capture dates of 4.5 and 95 months before the survey, respectively. All species had declined greatly in body size. Maximum body weights reported by fishers ranged from 11–88% of their recorded maxima. Fishers identified 10 threats to megafishes, seven of which were types of illegal fishing. Electrofishing was the most prevalent. Results confirm that Mekong megafishes are severely endangered. Species Conservation Strategies should be developed and must address pervasive illegal fishing activities, alongside habitat degradation and blocked migrations, to recover declining populations.
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126
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Determinants of genetic variation across eco-evolutionary scales in pinnipeds. Nat Ecol Evol 2020; 4:1095-1104. [PMID: 32514167 DOI: 10.1038/s41559-020-1215-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/28/2020] [Indexed: 11/09/2022]
Abstract
The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent Ne for 17 pinniped species represented by 36 population samples (total n = 458 individuals). Ne estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with NC ([Formula: see text] = 0.59; P = 0.0002). Ne/NC ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species' ecological and life-history variables such as breeding habitat. Residual variation in Ne/NC, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary NC than would be expected from their long-term Ne. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention.
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127
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Wood DA, Rose JP, Halstead BJ, Stoelting RE, Swaim KE, Vandergast AG. Combining genetic and demographic monitoring better informs conservation of an endangered urban snake. PLoS One 2020; 15:e0231744. [PMID: 32369486 PMCID: PMC7200000 DOI: 10.1371/journal.pone.0231744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/05/2020] [Indexed: 11/24/2022] Open
Abstract
Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T. s. tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T. s. tetrataenia populations could promote persistence of this endangered snake.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Jonathan P. Rose
- U.S. Geological Survey, Western Ecological Research Center, Santa Cruz Field Station, Santa Cruz, California, United States of America
| | - Brian J. Halstead
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, United States of America
| | - Ricka E. Stoelting
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Karen E. Swaim
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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128
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CapellÀ-Marzo B, SÁnchez-Montes G, MartÍnez-Solano I. Contrasting demographic trends and asymmetric migration rates in a spatially structured amphibian population. Integr Zool 2020; 15:482-497. [PMID: 32329558 DOI: 10.1111/1749-4877.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural populations often persist at the landscape scale as metapopulations, with breeding units (subpopulations) experiencing temporal extinction and recolonization events. Important parameters to forecast population viability in these systems include the ratio of the effective number of breeders (Nb ) to the total number of adults (Na ) and migration rates among subpopulations. Here, we present the results of a 10-year integrative monitoring program of a metapopulation of the Iberian green frog (Pelophylax perezi) in central Spain. We characterized population dynamics at two main breeding ponds (Gravera and Laguna) using capture-mark-recapture data to estimate Na in each breeding season, and multilocus genotypes to estimate the effective population size (Ne ), Nb , individual breeding success, and migration rates. Both ponds experienced population decline after a dry season, with Gravera subsequently recovering and Laguna suffering a bottleneck associated with genetic impoverishment. In this subpopulation, average allelic richness and private alleles decreased from 2010 (10.87 and 1.67, respectively) to 2018 (8.0 and 0.20). The Nb /Na ratio in Laguna in 2018 was twice as high (0.95) than in Gravera (0.41) or in pre-bottleneck Laguna (0.50), suggesting plasticity or genetic compensation through increased individual breeding success. Migration rates were asymmetric between ponds, with a stronger contribution from Gravera to Laguna (29.9% vs. 16.2% in the opposite direction) that may result in a rescue effect. This study emphasizes the importance of integrative demographic approaches for the monitoring of natural populations based on a better understanding of their spatio-temporal dynamics, which provides valuable information for conservation actions.
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Affiliation(s)
- Berta CapellÀ-Marzo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Iñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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129
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Duncan SI, Robertson EP, Fletcher RJ, Austin JD. Urbanization and Population Genetic Structure of the Panama City crayfish (Procambarus econfinae). J Hered 2020; 111:204-215. [PMID: 31746328 DOI: 10.1093/jhered/esz072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
For species with geographically restricted distributions, the impacts of habitat loss and fragmentation on long-term persistence may be particularly pronounced. We examined the genetic structure of Panama City crayfish (PCC), Procambarus econfinae, whose historical distribution is limited to an area approximately 145 km2, largely within the limits of Panama City and eastern Bay County, FL. Currently, PCC occupy approximately 28% of its historical range, with suitable habitat composed of fragmented patches in the highly urbanized western portion of the range and managed plantations in the more contiguous eastern portion of the range. We used 1640 anonymous single-nucleotide polymorphisms to evaluate the effects of anthropogenic habitat modification on the genetic diversity and population structure of 161 PCC sampled from across its known distribution. First, we examined urban habitat patches in the west compared with less-developed habitat patches in the east. Second, we used approximate Bayesian computation to model inferences on the demographic history of eastern and western populations. We found anthropogenic habitat modifications explain the genetic structure of PCC range-wide. Clustering analyses revealed significant genetic structure between and within eastern and western regions. Estimates of divergence between east and west were consistent with urban growth in the mid-20th century. PCC have low genetic diversity and high levels of inbreeding and relatedness, indicating populations are small and isolated. Our results suggest that PCC have been strongly affected by habitat loss and fragmentation and management strategies, including legal protection, translocations, or reintroductions, may be necessary to ensure long-term persistence.
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Affiliation(s)
| | - Ellen P Robertson
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - Robert J Fletcher
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
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130
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Laikre L, Hoban S, Bruford MW, Segelbacher G, Allendorf FW, Gajardo G, Rodríguez AG, Hedrick PW, Heuertz M, Hohenlohe PA, Jaffé R, Johannesson K, Liggins L, MacDonald AJ, OrozcoterWengel P, Reusch TBH, Rodríguez-Correa H, Russo IRM, Ryman N, Vernesi C. Post-2020 goals overlook genetic diversity. Science 2020; 367:1083-1085. [PMID: 32139534 DOI: 10.1126/science.abb2748] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Linda Laikre
- Department of Zoology, Stockholm University, SE 10691 Stockholm. .,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cardiff, UK.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Gernot Segelbacher
- Wildlife Ecology and Management, University Freiburg, Freiburg, Germany.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Gonzalo Gajardo
- Universidad de Los Lagos, Lab Genetics, Aquaculture & Biodiversity, Osorno, Chile
| | - Antonio González Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Myriam Heuertz
- Biodiversity, Genes, & Communities (BIOGECO), Joint Research Unit (UMR) of French National Institute for Agriculture, Food, and Environment (INRAE) and University of Bordeaux, FR-33610 Cestas, France.,Faculté des Sciences, Évolution Biologique et Écologie, Université Libre de Bruxelles, BE-1050 Brussels, Belgium
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051, USA
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale, 66055-090 Belém PA, Brazil.,Department of Ecology, University of São Paulo, 05508-090 São Paulo SP, Brazil.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | | | - Libby Liggins
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Anna J MacDonald
- The John Curtin School of Medical Research/Research School of Biology, The Australian National University, Acton, ACT 2601, Australia.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Pablo OrozcoterWengel
- School of Biosciences, Cardiff University, Cardiff, UK.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | | | - Hernando Rodríguez-Correa
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, México
| | - Isa-Rita M Russo
- School of Biosciences, Cardiff University, Cardiff, UK.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland
| | - Nils Ryman
- Department of Zoology, Stockholm University, SE 10691 Stockholm
| | - Cristiano Vernesi
- Department of Sustainable Agroecosystems and Bioresources, Research and Innovation Centre-Fondazione Edmund Mach, San Michele All'Adige, TN, Italy.,Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), 1196 Gland, Switzerland.,Genomic Biodiversity Knowledge for Resilient Ecosystems (G-BiKE) Action network of the European Cooperation in Science & Technology (COST CA18134) c/o Department of Sustainable Agroecosystems and Bioresources, Research and Innovation Centre-Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
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131
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Paijmans AJ, Stoffel MA, Bester MN, Cleary AC, De Bruyn PJN, Forcada J, Goebel ME, Goldsworthy SD, Guinet C, Lydersen C, Kovacs KM, Lowther A, Hoffman JI. The genetic legacy of extreme exploitation in a polar vertebrate. Sci Rep 2020; 10:5089. [PMID: 32198403 PMCID: PMC7083876 DOI: 10.1038/s41598-020-61560-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arctocephalus gazella), a species that was hunted to the brink of extinction by 18th and 19th century sealers. Molecular genetic data from over 2,000 individuals sampled from all eight major breeding locations across the species' circumpolar geographic distribution, show that at least four relict populations around Antarctica survived commercial hunting. Coalescent simulations suggest that all of these populations experienced severe bottlenecks down to effective population sizes of around 150-200. Nevertheless, comparably high levels of neutral genetic variability were retained as these declines are unlikely to have been strong enough to deplete allelic richness by more than around 15%. These findings suggest that even dramatic short-term declines need not necessarily result in major losses of diversity, and explain the apparent contradiction between the high genetic diversity of this species and its extreme exploitation history.
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Affiliation(s)
- Anneke J Paijmans
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
| | - Martin A Stoffel
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Marthán N Bester
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Alison C Cleary
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
- Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - P J Nico De Bruyn
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Michael E Goebel
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, National Marine Fisheries, National Oceanographic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
- Institute of Marine Science, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Simon D Goldsworthy
- South Australian Research and Development Institute, 2 Hamra Avenue, West Beach, South Australia, 5024, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS and Université de La Rochelle - UMR 7372, 79360, Villiers en Bois, France
| | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | - Andrew Lowther
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
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132
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Population Size and Dynamics of the Lima Leaf-Toed Gecko, Phyllodactylus sentosus, in One of Its Last Refuges. J HERPETOL 2020. [DOI: 10.1670/17-079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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133
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Paudel S, Koprowski JL. Factors affecting the persistence of endangered Ganges River dolphins ( Platanista gangetica gangetica). Ecol Evol 2020; 10:3138-3148. [PMID: 32211183 PMCID: PMC7083702 DOI: 10.1002/ece3.6102] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 11/08/2022] Open
Abstract
The Ganges-Brahmaputra-Meghna and Karnaphuli (GBMK) River Basin in Nepal, India, and Bangladesh is among the world's most biodiverse river basins. However, human-induced habitat modification processes threaten the ecological structure of this river basin. Among the GBMK's diverse flora and fauna of this freshwater ecosystem, the endemic Ganges River dolphin (Platanista gangetica gangetica; GRD) is one of the most charismatic species in this freshwater ecosystem. Though a >50% population size reduction has occurred since 1957, researchers and decision-makers often overlook the persistence (or evolutionary potential) of this species in the highly fragmented GBMK. We define the evolutionary potential as the ability of species/populations to adapt in a changing environment by maintaining their genetic diversity. Here, we review how evolutionary trap mechanisms affect the dynamics and viability of the GRD (hereafter Ganges dolphin) populations after rapid declines in their population size and distribution. We detected six potential trap mechanisms that might affect the Ganges dolphin populations discretely or in combination: (a) habitat modification; (b) occurrence of finite and geographically restricted local populations; (c) ratio of effective to estimate population size; (d) increasing risk of inbreeding depression in genetically isolated groups; (e) at-risk behavioral attributes; and (f) direct fisheries-dolphin interactions. Because evolutionary traps appear most significant during low water season, they adversely affect demographic parameters, which reduce evolutionary potential. These traps have already caused local extirpation events; therefore, we recommend translocation among populations, including restoring and preserving essential habitats as immediate conservation strategies. Integrative evolutionary potential information based on demographic, genetic, and environmental data is still lacking. Thus, we identify gaps in the knowledge and suggest integrative approaches to understand the future of Ganges dolphins in South Asian waterways.
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Affiliation(s)
- Shambhu Paudel
- School of Natural Resources and the Environment University of Arizona Tucson AZ USA
- Institute of Forestry Tribhuvan University Pokhara Nepal
| | - John L Koprowski
- School of Natural Resources and the Environment University of Arizona Tucson AZ USA
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134
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Genetic structure and diversity of Australian freshwater crocodiles (Crocodylus johnstoni) from the Kimberley, Western Australia. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01259-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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135
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Chen W, Li C, Chen F, Li Y, Yang J, Li J, Li X. Phylogeographic analyses of a migratory freshwater fish (Megalobrama terminalis) reveal a shallow genetic structure and pronounced effects of sea-level changes. Gene 2020; 737:144478. [PMID: 32061762 DOI: 10.1016/j.gene.2020.144478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 10/25/2022]
Abstract
Different types of fish taxa generally seem to present diverse phylogeographic structures and show different responses to environmental changes. In southern China, however, a large number of phylogeographic studies have been employed for small and/or benthic fish species, while phylogeographic patterns of larger and migratory species are not well understood. In this study, we chose Megalobrama terminalis, an endemic cyprinid from Southern China with a median size and relatively high migratory potential as a candidate to explore the phylogeographic structure and to seek the relevant driving forces using a multilocus approach (two mitochondrial markers and three nuclear markers). Our results show that M. terminalis exhibits three mtDNA genetic groups, each presenting genetic structure to the local geography, but the differentiation level was much weaker than that of small and/or benthic fish species reported in earlier studies. Nuclear loci did not observe pronounced genetic group subdivision, but did examine noteworthy genetic differentiation between the Hainan Island population and the mainland populations. Divergence time estimation and demographic analyses suggest that sea-level changes associated with the Late Pleistocene glacial cycles have exerted pronounced effects on the divergence of the three groups and the expansion of M. terminalis populations. Above all, our study provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this endemic organism.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Ce Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Fangcan Chen
- Guangzhou Qianjiang Water Ecological Technology Co. LTD, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Jiping Yang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China.
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136
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Davis AJ, Keiter DA, Kierepka EM, Slootmaker C, Piaggio AJ, Beasley JC, Pepin KM. A comparison of cost and quality of three methods for estimating density for wild pig (Sus scrofa). Sci Rep 2020; 10:2047. [PMID: 32029837 PMCID: PMC7004977 DOI: 10.1038/s41598-020-58937-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/13/2020] [Indexed: 12/02/2022] Open
Abstract
A critical element in effective wildlife management is monitoring the status of wildlife populations; however, resources to monitor wildlife populations are typically limited. We compared cost effectiveness of three common population estimation methods (i.e. non-invasive DNA sampling, camera sampling, and sampling from trapping) by applying them to wild pigs (Sus scrofa) across three habitats in South Carolina, U.S.A where they are invasive. We used mark-recapture analyses for fecal DNA sampling data, spatially-explicit capture-recapture analyses for camera sampling data, and a removal analysis for removal sampling from trap data. Density estimates were similar across methods. Camera sampling was the least expensive, but had large variances. Fecal DNA sampling was the most expensive, although this technique generally performed well. We examined how reductions in effort by method related to increases in relative bias or imprecision. For removal sampling, the largest cost savings while maintaining unbiased density estimates was from reducing the number of traps. For fecal DNA sampling, a reduction in effort only minimally reduced costs due to the need for increased lab replicates while maintaining high quality estimates. For camera sampling, effort could only be marginally reduced before inducing bias. We provide a decision tree for researchers to help make monitoring decisions.
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Affiliation(s)
- Amy J Davis
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA.
| | - David A Keiter
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
- University of Nebraska, School of Natural Resources, Hardin Hall, 3310 Holdrege St., Lincoln, NE, 68583-0961, USA
| | - Elizabeth M Kierepka
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
- Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Chris Slootmaker
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
- Mountain Data Group, 115 N. College Ave. Suite 220, Fort Collins, CO, 80524, USA
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
| | - James C Beasley
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
| | - Kim M Pepin
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
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137
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Whiting JR, Fraser BA. Contingent Convergence: The Ability To Detect Convergent Genomic Evolution Is Dependent on Population Size and Migration. G3 (BETHESDA, MD.) 2020; 10:677-693. [PMID: 31871215 PMCID: PMC7003088 DOI: 10.1534/g3.119.400970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/19/2019] [Indexed: 12/02/2022]
Abstract
Outlier scans, in which the genome is scanned for signatures of selection, have become a prominent tool in studies of local adaptation, and more recently studies of genetic convergence in natural populations. However, such methods have the potential to be confounded by features of demographic history, such as population size and migration, which are considerably varied across natural populations. In this study, we use forward-simulations to investigate and illustrate how several measures of genetic differentiation commonly used in outlier scans (FST, DXY and Δπ) are influenced by demographic variation across multiple sampling generations. In a factorial design with 16 treatments, we manipulate the presence/absence of founding bottlenecks (N of founding individuals), prolonged bottlenecks (proportional size of diverging population) and migration rate between two populations with ancestral and diverged phenotypic optima. Our results illustrate known constraints of individual measures associated with reduced population size and a lack of migration; but notably we demonstrate how relationships between measures are similarly dependent on these features of demography. We find that false-positive signals of convergent evolution (the same simulated outliers detected in independent treatments) are attainable as a product of similar population size and migration treatments (particularly for DXY), and that outliers across different measures (for e.g., FST and DXY) can occur with little influence of selection. Taken together, we show how underappreciated, yet quantifiable measures of demographic history can influence commonly employed methods for detecting selection.
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Affiliation(s)
- James R Whiting
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD
| | - Bonnie A Fraser
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD
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138
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Antaky CC, Conklin EE, Toonen RJ, Knapp IS, Price MR. Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago. PeerJ 2020; 8:e8463. [PMID: 32071808 PMCID: PMC7007978 DOI: 10.7717/peerj.8463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/26/2019] [Indexed: 11/20/2022] Open
Abstract
Seabirds in the order of Procellariiformes have one of the highest proportions of threatened species of any avian order. Species undergoing recovery may be predicted to have a genetic signature of a bottleneck, low genetic diversity, or higher rates of inbreeding. The Hawaiian Band-rumped Storm Petrel ('Akē'akē; Hydrobates castro), a long-lived philopatric seabird, suffered massive population declines resulting in its listing under the Endangered Species Act in 2016 as federally Endangered. We used high-throughput sequencing to assess patterns of genetic diversity and potential for inbreeding in remaining populations in the Hawaiian Islands. We compared a total of 24 individuals, including both historical and modern samples, collected from breeding colonies or downed individuals found on the islands of Kaua'i, O'ahu, Maui, and the Big Island of Hawai'i. Genetic analyses revealed little differentiation between breeding colonies on Kaua'i and the Big Island colonies. Although small sample sizes limit inferences regarding other island colonies, downed individuals from O'ahu and Maui did not assign to known breeding colonies, suggesting the existence of an additional distinct breeding population. The maintenance of genetic diversity in future generations is an important consideration for conservation management. This study provides a baseline of population structure for the remaining nesting colonies that could inform potential translocations of the Endangered H. castro.
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Affiliation(s)
- Carmen C. Antaky
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
| | - Emily E. Conklin
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Ingrid S.S. Knapp
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Melissa R. Price
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
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139
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Lieber L, Hall G, Hall J, Berrow S, Johnston E, Gubili C, Sarginson J, Francis M, Duffy C, Wintner SP, Doherty PD, Godley BJ, Hawkes LA, Witt MJ, Henderson SM, de Sabata E, Shivji MS, Dawson DA, Sims DW, Jones CS, Noble LR. Spatio-temporal genetic tagging of a cosmopolitan planktivorous shark provides insight to gene flow, temporal variation and site-specific re-encounters. Sci Rep 2020; 10:1661. [PMID: 32015388 PMCID: PMC6997447 DOI: 10.1038/s41598-020-58086-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 12/29/2019] [Indexed: 12/30/2022] Open
Abstract
Migratory movements in response to seasonal resources often influence population structure and dynamics. Yet in mobile marine predators, population genetic consequences of such repetitious behaviour remain inaccessible without comprehensive sampling strategies. Temporal genetic sampling of seasonally recurring aggregations of planktivorous basking sharks, Cetorhinus maximus, in the Northeast Atlantic (NEA) affords an opportunity to resolve individual re-encounters at key sites with population connectivity and patterns of relatedness. Genetic tagging (19 microsatellites) revealed 18% of re-sampled individuals in the NEA demonstrated inter/multi-annual site-specific re-encounters. High genetic connectivity and migration between aggregation sites indicate the Irish Sea as an important movement corridor, with a contemporary effective population estimate (Ne) of 382 (CI = 241-830). We contrast the prevailing view of high gene flow across oceanic regions with evidence of population structure within the NEA, with early-season sharks off southwest Ireland possibly representing genetically distinct migrants. Finally, we found basking sharks surfacing together in the NEA are on average more related than expected by chance, suggesting a genetic consequence of, or a potential mechanism maintaining, site-specific re-encounters. Long-term temporal genetic monitoring is paramount in determining future viability of cosmopolitan marine species, identifying genetic units for conservation management, and for understanding aggregation structure and dynamics.
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Affiliation(s)
- Lilian Lieber
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
- School of Chemistry and Chemical Engineering, Queen´s University Belfast, Marine Laboratory, Portaferry, BT22 1PF, Northern Ireland, UK
| | - Graham Hall
- Manx Basking Shark Watch and Manx Wildlife Trust, Peel, Isle of Man, IM9 5PJ, UK
| | - Jackie Hall
- Manx Basking Shark Watch and Manx Wildlife Trust, Peel, Isle of Man, IM9 5PJ, UK
| | - Simon Berrow
- Irish Basking Shark Study Group, Merchants Quay, Kilrush, County Clare, UK
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
| | - Emmett Johnston
- Irish Basking Shark Study Group, Merchants Quay, Kilrush, County Clare, UK
- School of Biological Sciences, Queen´s University Belfast, Belfast, Northern Ireland, UK
| | - Chrysoula Gubili
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
- Hellenic Agricultural Organisation, Fisheries Research Institute, Nea Peramos, Kavala, Macedonia, 64007, Greece
| | - Jane Sarginson
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
- Faculty of Science and Engineering, John Dalton Building, Manchester Metropolitan University, Chester Street, Manchester, M1 5GD, UK
| | - Malcolm Francis
- National Institute of Water and Atmospheric Research, Private Bag 14901, Kilbirnie, Wellington, 6241, New Zealand
| | - Clinton Duffy
- Department of Conservation, Private Bag 68908, Wellesley Street, Auckland, 1141, New Zealand
| | - Sabine P Wintner
- KwaZulu-Natal Sharks Board, Private Bag 2, Umhlanga Rocks, 4320, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Philip D Doherty
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Brendan J Godley
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Lucy A Hawkes
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Matthew J Witt
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Suzanne M Henderson
- Scottish Natural Heritage Great Glen House, Inverness, IV3 8NW, Scotland, UK
| | | | - Mahmood S Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, South Yorkshire, UK
| | - David W Sims
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Waterfront Campus, Southampton, SO14 3ZH, UK
| | - Catherine S Jones
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
| | - Leslie R Noble
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK.
- Faculty of Biosciences and Aquaculture, Nord University, Postboks 1490, 8049, Bodø, Norway.
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140
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Gil-Sánchez JM, Barea-Azcón JM, Jaramillo J, Herrera-Sánchez FJ, Jiménez J, Virgós E. Fragmentation and low density as major conservation challenges for the southernmost populations of the European wildcat. PLoS One 2020; 15:e0227708. [PMID: 31990935 PMCID: PMC6986748 DOI: 10.1371/journal.pone.0227708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/26/2019] [Indexed: 11/18/2022] Open
Abstract
Knowledge of population dynamics of threatened species in the wild is key to effective conservation actions. However, at present, there are many examples of endangered animals for which their current situation is unknown, and not just in remote areas and less developed countries. We have explored this topic by studying the paradigmatic case of the European wildcat (Felis silvestris silvestris), an endangered small carnivore whose status has been subjectively established on the basis of non-systematic approaches and opportunistic records. Little is known about its demographic situation, prompting the need for information to improve conservation measures. However, the secretive behaviour of felines along with its low density in natural conditions have prevented the gathering of sufficient data. We developed a field sampling strategy for one of the largest populations (Andalusia, South Spain, 87,268 km2), based on a logistically viable systematic non-intrusive survey by camera-trapping. This study offers the first large-scale estimation for any European wildcat population, based on analytical approaches applied on Species Distribution Models. A hierarchical approach based on a Maxent model for distribution estimation was used, along with Generalised Linear Models for density estimation from explicit spatial capture-recapture data. Our results show that the distribution range is smaller and more highly fragmented than previously assumed. The overall estimated density was very low (0.069 ±0.0019 wildcats/km2) and the protected areas network seems to be insufficient to cover a significant part of the population or a viable nucleus in demographic terms. Indeed, the most important areas remain unprotected. Our main recommendations are to improve the protected area network and/or vigilance programs in hunting estates, in addition to studying and improving connectivity between the main population patches.
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Affiliation(s)
| | - Jose Miguel Barea-Azcón
- Agencia de Medio Ambiente y Agua (Consejería de Agricultura, Ganadería, Pesca y Desarrollo Sostenible, Junta de Andalucía), Gerencia de Granada, Edificio Zeus III, Granada, Spain
| | - Javier Jaramillo
- Agencia de Medio Ambiente y Agua (Consejería de Agricultura, Ganadería, Pesca y Desarrollo Sostenible, Junta de Andalucía), Gerencia de Granada, Edificio Zeus III, Granada, Spain
| | | | - José Jiménez
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Emilio Virgós
- Department of Biology, Geology, Physics and Inorganic Chemistry, ESCET, Universidad Rey Juan Carlos, C/Tulipán, Móstoles, Madrid, Spain
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141
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The breeding structure for the small ruminant resources in India. Trop Anim Health Prod 2020; 52:1717-1724. [PMID: 31898023 DOI: 10.1007/s11250-019-02188-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 12/22/2019] [Indexed: 10/25/2022]
Abstract
Intense selection for a few desired traits has resulted in reduction of the effective population size (Ne) in most of the plant and livestock populations across the world. The objective of the research was to assess the impact of Ne on the genetic architecture of the population in a simulated data with variable Ne for general population under selection. Along with this, the estimate of Ne and its ratio to adult breeding population (NB) in the census data of small ruminants of India were also investigated. Results indicated that the average inbreeding ([Formula: see text]) decreases with increase in Ne; similarly, increase in [Formula: see text] per generation was highest in population with lowest Ne. Correlation of estimated breeding value (EBV) with true breeding value (TBV) was not much affected with effective population size. An effective number of chromosome segments (Me) in the populations under selection were significantly affected by magnitude of Ne, with linear positive relation between Ne and Me. Results on livestock census data revealed that all the sheep and goat breeds have sufficiently large Ne based on derived and actual census data. The median for ratio of effective population size to adult census size in sheep breeds was 0.120 and for goat breeds was 0.131. Karnah and Poonchi sheep shares the status of endangered breeds due to a smaller number of breeding female population and hence need attention for conservation. The Ne was large in sheep and goat due to less selection pressure as a result of low coverage of breed improvement programs, availability of large number of breeding males, and absence of artificial insemination (AI) in the field flocks. The estimates of Ne and its ratio to the adult census size (NB) excluded several factors such as fluctuating population size and overlapping generations. Study revealed introspection from most of the industrial breeding programs on the issue of Ne for populations under selection. Similarly, in small ruminants, large Ne indicates huge genetic diversity and scope of improvement in the productivity in near future.
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142
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Fuller J, Ferchaud A, Laporte M, Le Luyer J, Davis TB, Côté SD, Bernatchez L. Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (
Odocoileus virginianus
). Mol Ecol 2019; 29:86-104. [DOI: 10.1111/mec.15317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jérémie Fuller
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Jérémy Le Luyer
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | | | - Steeve D. Côté
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
| | - Louis Bernatchez
- Département de Biologie Université Laval Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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143
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Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, Sigfússon AÞ, Jósefsson VA, Frederiksen M, Linnebjerg JF, Samaniego Castruita JA, Niemann J, Sinding MHS, Sandoval-Velasco M, Soares AER, Lacy R, Barilaro C, Best J, Brandis D, Cavallo C, Elorza M, Garrett KL, Groot M, Johansson F, Lifjeld JT, Nilson G, Serjeanston D, Sweet P, Fuller E, Hufthammer AK, Meldgaard M, Fjeldså J, Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife 2019; 8:e47509. [PMID: 31767056 PMCID: PMC6879203 DOI: 10.7554/elife.47509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
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Affiliation(s)
- Jessica E Thomas
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
| | - James Haile
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael D Martin
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Simon YW Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyAustralia
| | | | | | | | | | | | - Jonas Niemann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel-Holger S Sinding
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
| | | | - André ER Soares
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Robert Lacy
- Department of Conservation ScienceChicago Zoological SocietyBrookfieldUnited States
| | | | - Juila Best
- Department of Archaeology, Anthropology and Forensic Science, Faculty of Science and TechnologyBournemouth UniversityPooleUnited Kingdom
- School of History, Archaeology and ReligionCardiff UniversityCardiffUnited Kingdom
| | | | - Chiara Cavallo
- Amsterdam Centre for Ancient Studies and ArchaeologyUniversity of AmsterdamAmsterdamNetherlands
| | - Mikelo Elorza
- Arqueología PrehistóricaSociedad de Ciencias AranzadiSan SebastiánSpain
| | - Kimball L Garrett
- Natural History Museum of Los Angeles CountyLos AngelesUnited States
| | - Maaike Groot
- Institut für Prähistorische ArchäologieFreie Universität BerlinBerlinGermany
| | | | | | - Göran Nilson
- Gothenburg Museum of Natural HistoryGothenburgSweden
| | - Dale Serjeanston
- Humanities ArchaeologyUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Paul Sweet
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkUnited States
| | | | | | | | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural SciencesUniversity of PotsdamPotsdamGermany
| | - John R Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUnited Kingdom
| | - M Thomas P Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
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144
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Lee AM, Myhre AM, Markussen SS, Engen S, Solberg EJ, Haanes H, Røed K, Herfindal I, Heim M, Saether BE. Decomposing demographic contributions to the effective population size with moose as a case study. Mol Ecol 2019; 29:56-70. [PMID: 31732991 DOI: 10.1111/mec.15309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 11/30/2022]
Abstract
Levels of random genetic drift are influenced by demographic factors, such as mating system, sex ratio and age structure. The effective population size (Ne ) is a useful measure for quantifying genetic drift. Evaluating relative contributions of different demographic factors to Ne is therefore important to identify what makes a population vulnerable to loss of genetic variation. Until recently, models for estimating Ne have required many simplifying assumptions, making them unsuitable for this task. Here, using data from a small, harvested moose population, we demonstrate the use of a stochastic demographic framework allowing for fluctuations in both population size and age distribution to estimate and decompose the total demographic variance and hence the ratio of effective to total population size (Ne /N) into components originating from sex, age, survival and reproduction. We not only show which components contribute most to Ne /N currently, but also which components have the greatest potential for changing Ne /N. In this relatively long-lived polygynous system we show that Ne /N is most sensitive to the demographic variance of older males, and that both reproductive autocorrelations (i.e., a tendency for the same individuals to be successful several years in a row) and covariance between survival and reproduction contribute to decreasing Ne /N (increasing genetic drift). These conditions are common in nature and can be caused by common hunting strategies. Thus, the framework presented here has great potential to increase our understanding of the demographic processes that contribute to genetic drift and viability of populations, and to inform management decisions.
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Affiliation(s)
- Aline Magdalena Lee
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ane Marlene Myhre
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stine Svalheim Markussen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Steinar Engen
- Centre for Biodiversity Dynamics, Department of Mathematical Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Hallvard Haanes
- Norwegian Radiation and Nuclear Safety Authority (DSA), Oslo, Norway
| | - Knut Røed
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Ivar Herfindal
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Morten Heim
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Bernt-Erik Saether
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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145
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Perkins LB, Ahlering M, Larson DL. Looking to the future: key points for sustainable management of northern Great Plains grasslands. Restor Ecol 2019. [DOI: 10.1111/rec.13050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lora B. Perkins
- Department of Natural Resource ManagementNative Plant Initiative, South Dakota State University Brookings SD 57007 U.S.A
| | | | - Diane L. Larson
- U.S. Geological SurveyNorthern Prairie Wildlife Research Center St. Paul MN 55108 U.S.A
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146
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Tournayre O, Pons J, Leuchtmann M, Leblois R, Piry S, Filippi‐Codaccioni O, Loiseau A, Duhayer J, Garin I, Mathews F, Puechmaille S, Charbonnel N, Pontier D. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range. Ecol Evol 2019; 9:12272-12290. [PMID: 31832159 PMCID: PMC6854333 DOI: 10.1002/ece3.5714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/06/2022] Open
Abstract
The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals, and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure, and the demographic history of R. ferrumequinum colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque Country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in the near future.
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Affiliation(s)
- Orianne Tournayre
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Jean‐Baptiste Pons
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
| | | | - Raphael Leblois
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Sylvain Piry
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | | | - Anne Loiseau
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Jeanne Duhayer
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
| | - Inazio Garin
- Department of Zoology and Animal Cell BiologyUniversity of the Basque CountryLeioaThe Basque Country
| | - Fiona Mathews
- College of Life SciencesUniversity of SussexFalmerUK
| | - Sébastien Puechmaille
- ISEMUniv MontpellierCNRSEPHEIRDMontpellierFrance
- Groupe Chiroptères de Midi‐Pyrénées (CREN‐GCMP)ToulouseFrance
| | - Nathalie Charbonnel
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Dominique Pontier
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université Lyon 1Université de LyonVilleurbanneFrance
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147
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Billerman SM, Jesmer BR, Watts AG, Schlichting PE, Fortin MJ, Funk WC, Hapeman P, Muths E, Murphy MA. Testing theoretical metapopulation conditions with genotypic data from Boreal Chorus Frogs (Pseudacris maculata). CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The metapopulation concept has far-reaching implications in ecology and conservation biology. Hanski’s criteria operationally define metapopulations, yet testing them is hindered by logistical and financial constraints inherent to the collection of long-term demographic data. Hence, ecologists and conservationists often assume metapopulation existence for dispersal-limited species that occupy patchy habitats. To advance understanding of metapopulation theory and improve conservation of metapopulations, we used population and landscape genetic tools to develop a methodological framework for evaluating Hanski’s criteria. We used genotypic data (11 microsatellite loci) from a purported metapopulation of Boreal Chorus Frogs (Pseudacris maculata (Agassiz, 1850)) in Colorado, U.S.A., to test Hanski’s four criteria. We found support for each criterion: (1) significant genetic differentiation between wetlands, suggesting distinct breeding populations; (2) wetlands had small effective population sizes and recent bottlenecks, suggesting populations do not experience long-term persistence; (3) population graphs provided evidence of gene flow between patches, indicating potential for recolonization; and (4) multiscale bottleneck analyses suggest asynchrony, indicating that simultaneous extinction of all populations was unlikely. Our methodological framework provides a logistically and financially feasible alternative to long-term demographic data for identifying amphibian metapopulations.
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Affiliation(s)
- Shawn M. Billerman
- Program in Ecology, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, U.S.A
- University of Wyoming, Laramie, WY 82071, U.S.A
| | - Brett R. Jesmer
- Program in Ecology, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, U.S.A
- University of Wyoming, Laramie, WY 82071, U.S.A
| | - Alexander G. Watts
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada
| | - Peter E. Schlichting
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79409, U.S.A
- Arizona State University – Polytechnic Campus, Mesa, AZ 85212, U.S.A
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Paul Hapeman
- Department of Biology, Central Connecticut State University, New Britain, CT 06053, U.S.A
| | - Erin Muths
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO 80526, U.S.A
| | - Melanie A. Murphy
- University of Wyoming, Laramie, WY 82071, U.S.A
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, WY 82071, U.S.A
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148
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Chan R, Dunlop J, Spencer PBS. Highly promiscuous paternity in mainland and island populations of the endangered Northern Quoll. J Zool (1987) 2019. [DOI: 10.1111/jzo.12745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Chan
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
| | - J. Dunlop
- Department of Biodiversity, Conservation and Attractions Kensington WA Australia
| | - P. B. S. Spencer
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
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149
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Waples RS, Scribner KT, Moore JA, Draheim HM, Etter D, Boersen M. Accounting for Age Structure and Spatial Structure in Eco-Evolutionary Analyses of a Large, Mobile Vertebrate. J Hered 2019; 109:709-723. [PMID: 29668993 DOI: 10.1093/jhered/esy018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/11/2018] [Indexed: 11/13/2022] Open
Abstract
The idealized concept of a population is integral to ecology, evolutionary biology, and natural resource management. To make analyses tractable, most models adopt simplifying assumptions, which almost inevitably are violated by real species in nature. Here, we focus on both demographic and genetic estimates of effective population size per generation (Ne), the effective number of breeders per year (Nb), and Wright's neighborhood size (NS) for black bears (Ursus americanus) that are continuously distributed in the northern lower peninsula of Michigan, United States. We illustrate practical application of recently developed methods to account for violations of 2 common, simplifying assumptions about populations: 1) reproduction occurs in discrete generations and 2) mating occurs randomly among all individuals. We use a 9-year harvest dataset of >3300 individuals, together with genetic determination of 221 parent-offspring pairs, to estimate male and female vital rates, including age-specific survival, age-specific fecundity, and age-specific variance in fecundity (for which empirical data are rare). We find strong evidence for overdispersed variance in reproductive success of same-age individuals in both sexes, and we show that constraints on litter size have a strong influence on results. We also estimate that another life-history trait that is often ignored (skip breeding by females) has a relatively modest influence, reducing Nb by 9% and increasing Ne by 3%. We conclude that isolation by distance depresses genetic estimates of Nb, which implicitly assume a randomly mating population. Estimated demographic NS (100, based on parent-offspring dispersal) was similar to genetic NS (85, based on regression of genetic distance and geographic distance), indicating that the >36000 km2 study area includes about 4-5 black-bear neighborhoods. Results from this expansive data set provide important insight into effects of violating assumptions when estimating evolutionary parameters for long-lived, free-ranging species. In conjunction with recently developed analytical methodology, the ready availability of nonlethal DNA sampling methods and the ability to rapidly and cheaply survey many thousands of molecular markers should facilitate eco-evolutionary studies like this for many more species in nature.
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Affiliation(s)
- Robin S Waples
- National Marine Fisheries Service, Northwest Fisheries Science Center, Montlake Blvd. East, Seattle, WA
| | - Kim T Scribner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI.,Department of Integrative Biology, Michigan State University, East Lansing, MI
| | - Jennifer A Moore
- Department of Biology, Grand Valley State University, Allendale, MI
| | - Hope M Draheim
- Department of Integrative Biology, Michigan State University, East Lansing, MI
| | - Dwayne Etter
- Michigan Department of Natural Resources, Lansing, MI
| | - Mark Boersen
- Michigan Department of Natural Resources, Lansing, MI
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150
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Hunter EA, Gibbs JP, Cayot LJ, Tapia W, Quinzin MC, Miller JM, Caccone A, Shoemaker KT. Seeking compromise across competing goals in conservation translocations: The case of the ‘extinct’ Floreana Island Galapagos giant tortoise. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
| | - James P. Gibbs
- Department of Environmental and Forest Biology State University of New York College of Environmental Science and Forestry Syracuse NY USA
| | | | | | - Maud C. Quinzin
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Joshua M. Miller
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Kevin T. Shoemaker
- Department of Natural Resources and Environmental Science University of Nevada Reno NV USA
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