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Burnett HA, Bieker VC, Le Moullec M, Peeters B, Rosvold J, Pedersen ÅØ, Dalén L, Loe LE, Jensen H, Hansen BB, Martin MD. Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer. Evol Appl 2023; 16:1531-1548. [PMID: 37752961 PMCID: PMC10519417 DOI: 10.1111/eva.13585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.
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Affiliation(s)
- Hamish A. Burnett
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Vanessa C. Bieker
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Jørgen Rosvold
- Department of Terrestrial BiodiversityNorwegian Institute for Nature Research (NINA)TrondheimNorway
| | | | - Love Dalén
- Centre for PalaeogeneticsStockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
- Department of ZoologyStockholm UniversityStockholmSweden
| | - Leif Egil Loe
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesAasNorway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Brage B. Hansen
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Terrestrial EcologyNorwegian Institute for Nature Research (NINA)TrondheimNorway
| | - Michael D. Martin
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
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2
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Gajdárová B, Belotti E, Bufka L, Volfová J, Wölfl S, Mináriková T, Hollerbach L, Duľa M, Kleven O, Kutal M, Nowak C, Ozoliņš J, Tám B, Bryja J, Koubek P, Krojerová-Prokešová J. Long-term genetic monitoring of a reintroduced Eurasian lynx population does not indicate an ongoing loss of genetic diversity. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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3
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Poutanen J, Fuller AK, Pusenius J, Royle JA, Wikström M, Brommer JE. Density-habitat relationships of white-tailed deer ( Odocoileus virginianus) in Finland. Ecol Evol 2023; 13:e9711. [PMID: 36644703 PMCID: PMC9831969 DOI: 10.1002/ece3.9711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
In heterogeneous landscapes, resource selection constitutes a crucial link between landscape and population-level processes such as density. We conducted a non-invasive genetic study of white-tailed deer in southern Finland in 2016 and 2017 using fecal DNA samples to understand factors influencing white-tailed deer density and space use in late summer prior to the hunting season. We estimated deer density as a function of landcover types using a spatial capture-recapture (SCR) model with individual identities established using microsatellite markers. The study revealed second-order habitat selection with highest deer densities in fields and mixed forest, and third-order habitat selection (detection probability) for transitional woodlands (clear-cuts) and closeness to fields. Including landscape heterogeneity improved model fit and increased inferred total density compared with models assuming a homogenous landscape. Our findings underline the importance of including habitat covariates when estimating density and exemplifies that resource selection can be studied using non-invasive methods.
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Affiliation(s)
- Jenni Poutanen
- Department of BiologyUniversity Hill, University of TurkuTurkuFinland,Natural Resources Institute FinlandTurkuFinland
| | - Angela K. Fuller
- Department of Natural Resources and the Environment, U.S. Geological Survey, New York Cooperative Fish and Wildlife Research UnitCornell UniversityIthacaNew YorkUSA
| | | | - J. Andrew Royle
- U.S. Geological SurveyEastern Ecological Science CenterLaurelMarylandUSA
| | | | - Jon E. Brommer
- Department of BiologyUniversity Hill, University of TurkuTurkuFinland,NOVIA University of Applied SciencesEkenäsFinland
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Lim QL, Yong CSY, Ng WL, Ismail A, Rovie-Ryan JJ, Rosli N, Inoue-Murayama M, Annavi G. Population genetic structure of wild Malayan tapirs (Tapirus indicus) in Peninsular Malaysia revealed by nine cross-species microsatellite markers. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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5
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Kelly CL, Schwarzkopf L, Gordon IJ, Hirsch B. Population growth lags in introduced species. Ecol Evol 2021; 11:4577-4587. [PMID: 33976832 PMCID: PMC8093750 DOI: 10.1002/ece3.7352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 11/17/2022] Open
Abstract
When introduced to new ecosystems, species' populations often grow immediately postrelease. Some introduced species, however, maintain a low population size for years or decades before sudden, rapid population growth is observed. Because exponential population growth always starts slowly, it can be difficult to distinguish species experiencing the early phases of slow exponential population growth (inherent lags) from those with actively delayed growth rates (prolonged lags). Introduced ungulates provide an excellent system in which to examine lags, because some introduced ungulate populations have demonstrated rapid population growth immediately postintroduction, while others have not. Using studies from the literature, we investigated which exotic ungulate species and populations (n = 36) showed prolonged population growth lags by comparing the doubling time of real ungulate populations to those predicted from exponential growth models for theoretical populations. Having identified the specific populations that displayed prolonged lags, we examined the impacts of several environmental and biological variables likely to influence the length of lag period. We found that seventeen populations (47%) showed significant prolonged population growth lags. We could not, however, determine the specific factors that contributed to the length of these lag phases, suggesting that these ungulate populations' growth is idiosyncratic and difficult to predict. Introduced species that exhibit delayed growth should be closely monitored by managers, who must be proactive in controlling their growth to minimize the impact such populations may have on their environment.
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Affiliation(s)
- Catherine L. Kelly
- Division of Tropical Environments and SocietiesJames Cook UniversityTownsvilleQldAustralia
| | - Lin Schwarzkopf
- Division of Tropical Environments and SocietiesJames Cook UniversityTownsvilleQldAustralia
| | - Iain J. Gordon
- Fenner School of Environment & SocietyAustralian National UniversityCanberraACTAustralia
- James Hutton InstituteAberdeenUK
- Australian Tropical Science and Innovation PrecinctCSIROTownsvilleQldAustralia
- Central Queensland UniversityTownsvilleQldAustralia
| | - Ben Hirsch
- Division of Tropical Environments and SocietiesJames Cook UniversityTownsvilleQldAustralia
- Smithsonian Tropical Research InstitutePanama CityPanama
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6
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Blanco G, Morinha F. Genetic signatures of population bottlenecks, relatedness, and inbreeding highlight recent and novel conservation concerns in the Egyptian vulture. PeerJ 2021; 9:e11139. [PMID: 33828925 PMCID: PMC8005290 DOI: 10.7717/peerj.11139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/01/2021] [Indexed: 11/20/2022] Open
Abstract
The assessment of temporal variation in genetic features can be particularly informative on the factors behind demography and viability of wildlife populations and species. We used molecular methods to evaluate neutral genetic variation, relatedness, bottlenecks, and inbreeding in a declining population of Egyptian vulture (Neophron percnopterus) in central Spain. The results show that the genetic diversity remained relatively stable over a period of twelve years despite the decline in census and effective population sizes in the last decades. A relatively high proportion of nestlings from different and distant territories showed high relatedness in each study year. We also found support for an increasing impact of severe recent (contemporary) rather than distant (historical) past demographic bottlenecks, and the first evidence of inbred mating between full siblings coinciding with lethal malformations in offspring. The inbred nestling with feather malformations was positive to beak and feather disease virus recorded for the first time in this species. These results alert on recent and novel threats potentially affecting health and reducing the adaptive potential of individuals in this threatened species.
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Affiliation(s)
- Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Francisco Morinha
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
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Nelson SL, Taylor SA, Reuter JD. An isolated white-tailed deer ( Odocoileus virginianus) population on St. John, US Virgin Islands shows low inbreeding and comparable heterozygosity to other larger populations. Ecol Evol 2021; 11:2775-2781. [PMID: 33767835 PMCID: PMC7981213 DOI: 10.1002/ece3.7230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
This is the first study to document the genetic diversity of the white-tailed deer population on St. John, US Virgin Islands. The island population was founded by a small number of animals, has very limited hunting or predation, and recently experienced a reduction in size following an extended drought in 2015. DNA samples were collected from hair from 23 anesthetized adult deer (13 males, 10 females) ranging in age from 1 to 8 years (3.36 ± 1.9 years) and also from fecal DNA samples, for a total of 42 individuals analyzed for genetic diversity. The St. John deer data set averaged 4.19 alleles per marker and demonstrates the second lowest number of alleles (A) when compared to other populations of Odocoileus virginianus (4.19). Heterozygosity was similar to the other studies (0.54) with little evidence of inbreeding. To explain the level of heterozygosity and level of inbreeding within the St. John population, three hypotheses are proposed, including the effect of intrinsic biological traits within the population, a recent infusion of highly heterogeneous loci from North American populations, and a consistent level of immigration from a nearby island. Additional work is needed to further understand the genetic history of the St. John and regional deer populations.
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Affiliation(s)
- Suzanne L. Nelson
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
| | - Scott A. Taylor
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderCOUSA
| | - Jon D. Reuter
- Office of Animal ResourcesDepartment of Psychology and NeuroscienceUniversity of Colorado BoulderBoulderCOUSA
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Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers. Sci Rep 2021; 11:556. [PMID: 33436676 PMCID: PMC7804180 DOI: 10.1038/s41598-020-79575-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/07/2020] [Indexed: 02/01/2023] Open
Abstract
Behavioural and socio-cultural traits are recognized in the restriction of gene flow in species with high cognitive capacity and complex societies. This isolation by social barriers has been generally overlooked in threatened species by assuming disrupted gene flow due to population fragmentation and decline. We examine the genetic structure and ecology of the global population of the Critically Endangered red-fronted macaw (Ara rubrogenys), an endemic species to the inter-Andean valleys of Bolivia. We found a fine-scale genetic structuring in four genetic clusters. Genetic diversity was higher in wild compared to captive-bred macaws, but similar to that of captive wild-caught macaws. We found no clear evidence of severe genetic erosion in the population in recent decades, but it was patent in historic times, overlapping with drastic human habitat transformation and macaw persecution over millennia. We found no evidence of geographical and ecological barriers, owing to the high dispersal ability, nesting and foraging habits between genetic clusters. The lack of genetic intermixing despite long-distance foraging and seasonal movements suggests recruitment in natal colonies and other social factors reinforcing philopatry-related genetic structure. Conservation efforts should be specifically focussed on major threats in each genetic cluster as independent conservation units, and also considered in ex-situ management.
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Yang H, You CJ, Tsui CKM, Tembrock LR, Wu ZQ, Yang DP. Phylogeny and biogeography of the Japanese rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae) based on SNP markers. Ecol Evol 2021; 11:153-173. [PMID: 33437420 PMCID: PMC7790660 DOI: 10.1002/ece3.6982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/23/2020] [Accepted: 10/16/2020] [Indexed: 12/05/2022] Open
Abstract
The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific-locus amplified fragment sequencing (SLAF-seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., T. d. septentrionalis) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise F ST values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF-seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species' range.
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Affiliation(s)
- Huan Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Chong Juan You
- Beijing Key Laboratory for Forest Pest ControlBeijing Forestry UniversityBeijingChina
| | - Clement K. M. Tsui
- Department of PathologySidra MedicineDohaQatar
- Department of Pathology and Laboratory MedicineWeill Cornell Medicine‐QatarAr‐RayyanQatar
- Division of Infectious DiseasesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Luke R. Tembrock
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Zhi Qiang Wu
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - De Po Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
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10
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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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Kalb DM, Delaney DA, DeYoung RW, Bowman JL. Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula. Ecol Evol 2019; 9:11504-11517. [PMID: 31641489 PMCID: PMC6802040 DOI: 10.1002/ece3.5655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/01/2019] [Accepted: 08/26/2019] [Indexed: 01/13/2023] Open
Abstract
The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA, is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on the data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from approximate Bayesian computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately five effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. five individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.
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Affiliation(s)
- David M. Kalb
- Virginia Department of Game and Inland FisheriesMarionVAUSA
| | - Deborah A. Delaney
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research InstituteTexas A&M University‐KingsvilleKingsvilleTXUSA
| | - Jacob L. Bowman
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
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Gajaweera C, Kang JM, Lee DH, Lee SH, Kim YK, Wijayananda HI, Kim JJ, Ha JH, Choi BH, Lee SH. Genetic diversity and population structure of the Sapsaree, a native Korean dog breed. BMC Genet 2019; 20:66. [PMID: 31382890 PMCID: PMC6683530 DOI: 10.1186/s12863-019-0757-5] [Citation(s) in RCA: 5] [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: 08/17/2018] [Accepted: 06/20/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Sapsaree is a breed of dog (Canis familiaris) native to Korea, which became perilously close to extinction in the mid-1980s. However, with systematic genetic conservation and restoration efforts, this breed was rescued from extinction and population sizes have been gradually increasing over the past few decades. The aim of this study was to ascertain novel information about the genetic diversity, population structure, and demographic history of the Sapsaree breed using genome-wide single nucleotide polymorphism data. We characterized the genetic profile of the Sapsaree breed by comparison with seven foreign dog breeds with similar morphologies to estimate genetic differentiation within and among these breeds. RESULTS The results suggest that Sapsarees have higher genetic variance compared with the other breeds analyzed. The majority of the Sapsarees in this study share a discrete genetic pattern, although some individuals were slightly different, possibly as a consequence of the recent restoration process. Concordant results from analyses of linkage disequilibrium, effective population size, genetic diversity, and population structural analyses illustrate a relationship among the Sapsaree and the Tibetan breeds Tibetan terrier and Lhasa Apso, and a small genetic introgression from European breeds. The effective population size of the Sapsaree has contracted dramatically over the past generations, and is currently insufficient to maintain long-term viability of the breed's genetic diversity. CONCLUSIONS This study provides novel insights regarding the genetic diversity and population structure of the native Korean dog breed Sapsaree. Our results suggest the importance of a strategic and systematic approach to ensure the genetic diversity and the authenticity of the Sapsaree breed.
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Affiliation(s)
- Chandima Gajaweera
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
- Department of Animal Science, Faculty of Agriculture, University of Ruhuna, Matara, Sri Lanka
| | - Ji Min Kang
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Doo Ho Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Soo Hyun Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Yeong Kuk Kim
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hasini I. Wijayananda
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749 Republic of Korea
| | - Ji Hong Ha
- School of Life Science, Kyungpook National University, Daegu, 41940 Republic of Korea
| | - Bong Hwan Choi
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Seung Hwan Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
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Conservation genetic analysis of a Central-European range-margin population of the yellow-bellied toad (Bombina v. variegata). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01156-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Poutanen J, Pusenius J, Wikström M, Brommer JE. Estimating Population Density of the White-Tailed Deer in Finland using Non-Invasive Genetic Sampling and Spatial Capture–Recapture. ANN ZOOL FENN 2019. [DOI: 10.5735/086.056.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jenni Poutanen
- Department of Biology, University Hill, FI-20014 University of Turku, Finland
| | - Jyrki Pusenius
- Natural Resources Institute Finland, Yliopistokatu 6, FI-80100 Joensuu, Finland
| | - Mikael Wikström
- Finnish Wildlife Agency, Sompiontie 1, FI-00730 Helsinki, Finland
| | - Jon E. Brommer
- Department of Biology, University Hill, FI-20014 University of Turku, Finland
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Baker SJ, Anthonysamy WJB, Davis MA, Dreslik MJ, Douglas MR, Douglas ME, Phillips CA. Temporal Patterns of Genetic Diversity in an Imperiled Population of the Eastern Massasauga Rattlesnake (Sistrurus catenatus). COPEIA 2018. [DOI: 10.1643/cg-17-682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Successful worldwide invasion of the veined rapa whelk, Rapana venosa, despite a dramatic genetic bottleneck. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1774-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Crowdsourcing-based nationwide tick collection reveals the distribution of Ixodes ricinus and I. persulcatus and associated pathogens in Finland. Emerg Microbes Infect 2017; 6:e31. [PMID: 28487561 PMCID: PMC5584484 DOI: 10.1038/emi.2017.17] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/27/2017] [Accepted: 02/06/2017] [Indexed: 11/08/2022]
Abstract
A national crowdsourcing-based tick collection campaign was organized in 2015 with the objective of producing novel data on tick distribution and tick-borne pathogens in Finland. Nearly 20 000 Ixodes ticks were collected. The collected material revealed the nationwide distribution of I. persulcatus for the first time and a shift northwards in the distribution of I. ricinus in Finland. A subset of 2038 tick samples containing both species was screened for Borrelia burgdorferi sensu lato (the prevalence was 14.2% for I. ricinus and 19.8% for I. persulcatus), B. miyamotoi (0.2% and 0.4%, respectively) and tick-borne encephalitis virus (TBEV; 0.2% and 3.0%, respectively). We also report new risk areas for TBEV in Finland and, for the first time, the presence of B. miyamotoi in ticks from mainland Finland. Most importantly, our study demonstrates the overwhelming power of citizen science in accomplishing a collection effort that would have been impossible with the scientific community alone.
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Krojerová-Prokešová J, Barančeková M, Kawata Y, Oshida T, Igota H, Koubek P. Genetic differentiation between introduced Central European sika and source populations in Japan: effects of isolation and demographic events. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1424-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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McDougall CA, Welsh AB, Gosselin T, Anderson WG, Nelson PA. Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens. PLoS One 2017; 12:e0174269. [PMID: 28329005 PMCID: PMC5362236 DOI: 10.1371/journal.pone.0174269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/06/2017] [Indexed: 12/02/2022] Open
Abstract
Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525–750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013–0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways.
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Affiliation(s)
- Craig A. McDougall
- North/South Consultants Inc., Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
- * E-mail:
| | - Amy B. Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, United States of America
| | | | - W. Gary Anderson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
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Jenkins W, Lipka A, Fogleman A, Delfino K, Malhi R, Hendricks B. Variance in disease risk: rural populations and genetic diversity. Genome 2016; 59:519-25. [DOI: 10.1139/gen-2016-0077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Over 19% of the US population resides in rural areas, where studies of disease risk and disease outcomes are difficult to assess due to smaller populations and lower incidence. While some studies suggest rural disparities for different chronic diseases, the data are inconsistent across geography and definitions of rurality. We reviewed the literature to examine if local variations in population genomic diversity may plausibly explain inconsistencies in estimating disease risk. Many rural communities were founded over 150 years ago by small groups of ethnically and ancestrally similar families. These have since endured relative geographical isolation, similar to groups in other industrialized nations, perhaps resulting in founder effects impacting local disease susceptibility. Studies in Europe and Asia have found that observably different phenotypes may appear in isolated communities within 100 years, and that genomic variation can significantly vary over small geographical scales. Epidemiological studies utilizing common “rural” definitions may miss significant disease differences due to assumptions of risk homogeneity and misinterpretation of administrative definitions of rurality. Local genomic heterogeneity should be an important aspect of chronic disease epidemiology in rural areas, and it is important to consider for designing studies and interpreting results, enabling a better understanding of the heritable components of complex diseases.
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Affiliation(s)
- W.D. Jenkins
- Population Health Science Program, Southern Illinois University School of Medicine, 801 N. Rutledge St., Springfield, IL 62794-9664, USA
| | - A.E. Lipka
- Department of Crop Sciences, University of Illinois, W-201B Turner Hall, 1102 S Goodwin Ave., Urbana IL 61801, USA
| | - A.J. Fogleman
- Center for Clinical Research, Southern Illinois University School of Medicine, 801 N. Rutledge St., Springfield, IL 62794-9664, USA
| | - K.R. Delfino
- Center for Clinical Research, Southern Illinois University School of Medicine, 801 N. Rutledge St., Springfield, IL 62794-9664, USA
| | - R.S. Malhi
- Depts. of Anthropology & Animal Biology, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, 209F Davenport Hall, 607 Matthews Ave., Urbana, IL 61801, USA
| | - B. Hendricks
- Department of History, Southern Illinois University, 1000 Faner Drive, Rm 3374, Carbondale, IL 62901, USA
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Guevara EK, Palo JU, Guillén S, Sajantila A. MtDNA and Y-chromosomal diversity in the Chachapoya, a population from the northeast Peruvian Andes-Amazon divide. Am J Hum Biol 2016; 28:857-867. [PMID: 27265853 DOI: 10.1002/ajhb.22878] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVES The ancient Chachapoya were an aggregate of several ethnic groups that shared a common language, religion, and material culture. They inhabited a territory at the juncture of the Andes and the Amazon basin. Their position between those ecozones most likely influenced their genetic composition. We attempted to better understand their population history by assessing the contemporary genetic diversity in the Chachapoya and three of their immediate neighbors (Huancas, Jivaro, and Cajamarca). We inferred signatures of demographic history and genetic affinities, and contrasted the findings with data from other populations on local and continental scales. METHODS We studied mitochondrial DNA (mtDNA; hypervariable segment [HVSI and HVSII]) and Y chromosome (23 short tandem repeats (STRs)) marker data in 382 modern individuals. We used Sanger sequencing for mtDNA and a commercially available kit for Y-chromosomal STR typing. RESULTS The Chachapoya had affinities with various populations of Andean and Amazonian origin. When examining the Native American component, the Chachapoya displayed high levels of genetic diversity. Together with other parameters, for example, large Tajima's D and Fu's Fs, the data indicated no drastic reduction of the population size in the past. CONCLUSION The high level of diversity in the Chachapoya, the lack of evidence of drift in the past, and genetic affinities with a broad range of populations in the Americas reflects an intricate population history in the region. The new genetic data from the Chachapoya indeed seems to point to a genetic complexity that is not yet resolved but beginning to be elucidated. Am. J. Hum. Biol. 28:857-867, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Evelyn K Guevara
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
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Kekkonen J, Wikström M, Ala-Ajos I, Lappalainen V, Brommer JE. Growth and Age Structure in an Introduced and Hunted Cervid Population: White-Tailed Deer in Finland. ANN ZOOL FENN 2016. [DOI: 10.5735/086.053.0206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Tonteri E, Jokelainen P, Matala J, Pusenius J, Vapalahti O. Serological evidence of tick-borne encephalitis virus infection in moose and deer in Finland: sentinels for virus circulation. Parasit Vectors 2016; 9:54. [PMID: 26825371 PMCID: PMC4733276 DOI: 10.1186/s13071-016-1335-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/21/2016] [Indexed: 12/30/2022] Open
Abstract
Background The incidence of tick-borne encephalitis (TBE) in humans has increased in Finland, and the disease has emerged in new foci. These foci have been investigated to determine the circulating virus subtype, the tick host species and the ecological parameters, but countrywide epidemiological information on the distribution of TBEV has been limited. Methods In this study, we screened sera from hunter-harvested wild cervids for the presence of antibodies against tick-borne encephalitis virus (TBEV) with a hemagglutination inhibition test. The positive results were confirmed by a neutralisation assay. Results Nine (0.74 %) of 1213 moose, one (0.74 %) of 135 white-tailed deer, and none of the 17 roe deer were found seropositive for TBEV. A close geographical congruence between seropositive cervids and recently reported human TBE cases was observed: nine of the ten seropositive animals were from known endemic areas. Conclusions Our results confirm the local circulation of TBEV in several known endemic areas. One seropositive moose had been shot in an area where human TBE cases have not been reported, suggesting a possible new focus. Moose appear to be a useful sentinel animal for the presence of TBEV in the taiga region.
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Affiliation(s)
- Elina Tonteri
- Department of Virology, University of Helsinki, Faculty of Medicine, Helsinki, Finland.
| | - Pikka Jokelainen
- Department of Veterinary Biosciences, University of Helsinki, Faculty of Veterinary Medicine, Helsinki, Finland. .,Department of Food Hygiene and Environmental Health, University of Helsinki, Faculty of Veterinary Medicine, Helsinki, Finland. .,Department of Basic Veterinary Sciences and Population Medicine, Estonian University of Life Sciences, Tartu, Estonia.
| | - Juho Matala
- Natural Resources Institute Finland (Luke), Management and Production of Renewable Resources, Joensuu, Finland.
| | - Jyrki Pusenius
- Natural Resources Institute Finland (Luke), Management and Production of Renewable Resources, Joensuu, Finland.
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, Faculty of Medicine, Helsinki, Finland. .,Department of Veterinary Biosciences, University of Helsinki, Faculty of Veterinary Medicine, Helsinki, Finland. .,Department of Virology and Immunology, Hospital district of Helsinki and Uusimaa (HUSLAB), Helsinki, Finland.
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Niemi M, Matala J, Melin M, Eronen V, Järvenpää H. Traffic mortality of four ungulate species in southern Finland. NATURE CONSERVATION 2015. [DOI: 10.3897/natureconservation.11.4416] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Murphy SM, Cox JJ, Clark JD, Augustine BC, Hast JT, Gibbs D, Strunk M, Dobey S. Rapid growth and genetic diversity retention in an isolated reintroduced black bear population in the central appalachians. J Wildl Manage 2015. [DOI: 10.1002/jwmg.886] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sean M. Murphy
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building, Lexington KY 40546 USA
| | - John J. Cox
- Department of Forestry; University of Kentucky; 102 Thomas Poe Cooper Building, Lexington KY 40546 USA
| | - Joseph D. Clark
- United States Geological Survey; Southern Appalachian Research Branch; University of Tennessee; 274 Ellington Plant Sciences Building, Knoxville TN 37996 USA
| | - Ben C. Augustine
- Department of Fish and Wildlife Conservation; Virginia Polytechnic Institute and State University; 318 Cheatham Hall, Blacksburg VA 24061 USA
| | - John T. Hast
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building, Lexington KY 40546 USA
| | - Dan Gibbs
- Tennessee Wildlife Resources Agency; 3030 Wildlife Way, Morristown TN 37814 USA
| | - Michael Strunk
- Kentucky Department of Fish & Wildlife Resources; 11990 N Highway 27, Parkers Lake KY 42634 USA
| | - Steven Dobey
- Kentucky Department of Fish & Wildlife Resources; #1 Sportsman's Lane, Frankfort KY 40601 USA
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Brommer JE, Kekkonen J, Wikström M. Using heterozygosity-fitness correlations to study inbreeding depression in an isolated population of white-tailed deer founded by few individuals. Ecol Evol 2014; 5:357-67. [PMID: 25691963 PMCID: PMC4314268 DOI: 10.1002/ece3.1362] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/11/2014] [Accepted: 11/17/2014] [Indexed: 12/21/2022] Open
Abstract
A heterozygosity–fitness correlations (HFCs) may reflect inbreeding depression, but the extent to which they do so is debated. HFCs are particularly likely to occur after demographic disturbances such as population bottleneck or admixture. We here study HFC in an introduced and isolated ungulate population of white-tailed deer Odocoileus virginianus in Finland founded in 1934 by four individuals. A total of 422 ≥ 1-year-old white-tailed deer were collected in the 2012 hunting season in southern Finland and genotyped for 14 microsatellite loci. We find significant identity disequilibrium as estimated by g2. Heterozygosity was positively associated with size- and age-corrected body mass, but not with jaw size or (in males) antler score. Because of the relatively high identity disequilibrium, heterozygosity of the marker panel explained 51% of variation in inbreeding. Inbreeding explained approximately 4% of the variation in body mass and is thus a minor, although significant source of variation in body mass in this population. The study of HFC is attractive for game- and conservation-oriented wildlife management because it presents an affordable and readily used approach for genetic monitoring that allowing identification of fitness costs associated with genetic substructuring in what may seem like a homogeneous population.
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Affiliation(s)
- Jon E Brommer
- Department of Biology, University Hill 20014 University of Turku, Turku, Finland ; ARONIA Research and Development Institute at NOVIA University of Applied Sciences and Åbo Akademi University Raseborgsvägen 9, 10600, Ekenäs, Finland
| | - Jaana Kekkonen
- Department of Biosciences, University of Helsinki PO Box 65(Viikinkaari 1), 00014, Helsinki, Finland
| | - Mikael Wikström
- Finnish Wildlife Agency Fantsintie 13-14, 00890, Helsinki, Finland
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Nyman T, Valtonen M, Aspi J, Ruokonen M, Kunnasranta M, Palo JU. Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies. Ecol Evol 2014; 4:3420-34. [PMID: 25535558 PMCID: PMC4228616 DOI: 10.1002/ece3.1193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea 'mainland' and two the 'aquatic islands' composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea.
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Affiliation(s)
- Tommi Nyman
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
- Institute for Systematic Botany, University of Zurich, Zollikerstrasse 107Zurich, CH-8008, Switzerland
| | - Mia Valtonen
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jouni Aspi
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Minna Ruokonen
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Mervi Kunnasranta
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jukka U Palo
- Laboratory of Forensic Biology, Hjelt Institute, University of HelsinkiPO Box 40, Helsinki, FI-00014, Finland
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Valtonen M, Palo JU, Aspi J, Ruokonen M, Kunnasranta M, Nyman T. Causes and consequences of fine-scale population structure in a critically endangered freshwater seal. BMC Ecol 2014; 14:22. [PMID: 25005257 PMCID: PMC4106222 DOI: 10.1186/1472-6785-14-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/03/2014] [Indexed: 11/10/2022] Open
Abstract
Background Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland. Results Microsatellite diversity within the subspecies (HE = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST = 0.107) than in maternally inherited mtDNA (FST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females. Conclusions Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.
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Affiliation(s)
- Mia Valtonen
- Department of Biology, University of Eastern Finland, Joensuu, Finland.
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