Evolutionary history of a Scottish harbour seal population

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.

• Publication year

  2020

• Venue

  PeerJ

• Publication date

  2020-07-10

• Fields of study

  Biology, Medicine, Environmental Science, History

• Identifiers
  DOI 10.7717/peerj.9167PMID 32728487PMCID 7357561
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The status of harbour seals ( Phoca vitulina ) in the UK

  2019influential reference
• The diet of harbour and grey seals around Britain: Examining the role of prey as a potential cause of harbour seal declines

  2019cited by this paper
• Top‐down pressure on a coastal ecosystem by harbor seals

  2019cited by this paper
• Age–length relationships in UK harbour seals during a period of population decline

  2019cited by this paper
• Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

  2018cited by this paper
• Large‐scale genetic panmixia in the blue shark (Prionace glauca): A single worldwide population, or a genetic lag‐time effect of the “grey zone” of differentiation?

  2018cited by this paper
• Harbour seal (Phoca vitulina) abundance within the Firth of Tay and Eden Estuary, Scotland: recent trends and extrapolation to extinction

  2017cited by this paper
• Genetic population structure of harbour seals in the United Kingdom and neighbouring waters

  2017influential reference
• The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem

  2016cited by this paper
• Clumpak: a program for identifying clustering modes and packaging population structure inferences across K

  2015cited by this paper
• Mark‐recapture modeling accounting for state uncertainty provides concurrent estimates of survival and fecundity in a protected harbor seal population

  2014cited by this paper
• VarEff. Variation of Effective size. Software VAREFF (package R in file.zip) and the documentation

  2014cited by this paper
• Detecting past changes of effective population size

  2014influential reference
• Integrating Paleobiology, Archeology, and History to Inform Biological Conservation

  2013cited by this paper
• State-space modelling reveals proximate causes of harbour seal population declines

  2013cited by this paper
• Inferring recent historic abundance from current genetic diversity

  2013influential reference
• Sample Planning Optimization Tool for conservation and population Genetics (SPOTG): a software for choosing the appropriate number of markers and samples

  2013cited by this paper
• The interplay between habitat availability and population differentiation

  2012cited by this paper
• Reliability of genetic bottleneck tests for detecting recent population declines

  2012cited by this paper
• GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update

  2012influential reference
• STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

  2012cited by this paper
• From archives to conservation: why historical data are needed to set baselines for marine animals and ecosystems

  2012cited by this paper
• Genetic Substructure of Pacific Harbor Seal (Phoca vitulina richardsi) Populations Along the Coasts of Oregon and Washington

  2011cited by this paper
• Long‐term patterns in harbour seal site‐use and the consequences for managing protected areas

  2011cited by this paper
• A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

  2011cited by this paper
• Genetically effective population sizes of Antarctic seals estimated from nuclear genes

  2011influential reference
• Inferring Population Decline and Expansion From Microsatellite Data: A Simulation-Based Evaluation of the Msvar Method

  2011cited by this paper
• Estimating Contemporary Effective Population Size on the Basis of Linkage Disequilibrium in the Face of Migration

  2011cited by this paper
• adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

  2011cited by this paper
• Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

  2010cited by this paper
• Low Microsatellite Variation in Spotted Seal (Phoca largha) Shows a Decrease in Population Size in the Liaodong Gulf Colony

  2010cited by this paper
• The distribution of coalescence times and distances between microsatellite alleles with changing effective population size.

  2010influential reference
• Last nine-thousand years of temperature variability in Northern Europe

  2009cited by this paper
• METHODOLOGY ARTICLE Open Access

  2009cited by this paper
• Historical baselines for large marine animals.

  2009cited by this paper
• Asymmetrical male-mediated gene flow between harbor seal (Phoca vitulina) populations in Alaska

  2009cited by this paper
• An examination of genetic diversity and effective population size in Atlantic salmon populations.

  2009influential reference
• Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change

  2009cited by this paper
• Pleistocene population expansions of Antarctic seals

  2009cited by this paper
• Simultaneous estimation of null alleles and inbreeding coefficients.

  2009cited by this paper
• genepop’007: a complete re‐implementation of the genepop software for Windows and Linux

  2008cited by this paper
• False sex‐linked microsatellite primer for Phoca vitulina

  2008cited by this paper
• Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence?

  2008cited by this paper
• adegenet: a R package for the multivariate analysis of genetic markers

  2008influential reference
• Ice caps existed throughout the Lateglacial Interstadial in northern Scotland

  2008cited by this paper
• Zooarchaeology and Arctic marine mammal biogeography, conservation, and management.

  2008cited by this paper
• Maximum-Likelihood Estimation of Allelic Dropout and False Allele Error Rates From Microsatellite Genotypes in the Absence of Reference Data

  2007cited by this paper
• Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions

  2007cited by this paper
• Recent demographic bottlenecks are not accompanied by a genetic signature in banner‐tailed kangaroo rats (Dipodomys spectabilis)

  2007cited by this paper
• Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates

  2007influential reference
• Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment

  2007cited by this paper
• Using sparse survey data to investigate the declining abundance of British harbour seals

  2007cited by this paper
• genalex 6: genetic analysis in Excel. Population genetic software for teaching and research

  2006cited by this paper
• Mating system and reproductive success in eastern Pacific harbour seals

  2006cited by this paper
• The 1988 and 2002 phocine distemper virus epidemics in European harbour seals.

  2006cited by this paper
• Limits to the adaptive potential of small populations

  2006cited by this paper
• LARGE VARIANCE IN REPRODUCTIVE SUCCESS AND THE Ne/N RATIO

  2005influential reference
• Arlequin (version 3.0): An integrated software package for population genetics data analysis

  2005cited by this paper
• DIFFERENTIAL MOVEMENTS BY HARBOR SEAL PUPS IN CONTRASTING ALASKA ENVIRONMENTS

  2005cited by this paper
• Drafting a Conservation Blueprint – a practitioner’s guide to planning for biodiversity

  2005cited by this paper
• Detecting the number of clusters of individuals using the software structure: a simulation study

  2005cited by this paper
• Quantifying the extinction vortex.

  2005cited by this paper
• COLONIZATION HISTORY OF THE BALTIC HARBOR SEALS: INTEGRATING ARCHAEOLOGICAL, BEHAVIORAL, AND GENETIC DATA

  2005cited by this paper
• Genetic assignment methods for the direct, real‐time estimation of migration rate: a simulation‐based exploration of accuracy and power

  2004cited by this paper
• Book Review - Drafting a conservation blueprint. A Practitioner's Guide to Planning for Biodiversity Craig R. Groves. Island Press, Washington, DC, 2003, cloth $70, ISBN 1-55963-938-5; paper $35, ISBN 1-55963-939-3

  2004cited by this paper
• Low genetic variability in the highly endangered mediterranean monk seal.

  2004cited by this paper
• GENECLASS2: a software for genetic assignment and first-generation migrant detection.

  2004cited by this paper
• Micro-Checker: Software for identifying and correcting genotyping errors in microsatellite data

  2004influential reference
• Estimates of minimum viable population sizes for vertebrates and factors influencing those estimates

  2003cited by this paper
• Bayesian inference of recent migration rates using multilocus genotypes.

  2003cited by this paper
• Trends and status of harbor seals in Washington State: 1978-1999

  2003cited by this paper
• Whales Before Whaling in the North Atlantic

  2003cited by this paper
• Postglacial loss of microsatellite variation in the landlocked Lake Saimaa ringed seal

  2003cited by this paper
• THE ABUNDANCE OF HARBOR SEALS IN THE GULF OF ALASKA

  2003cited by this paper
• Maternal and newborn life‐history traits during periods of contrasting population trends: implications for explaining the decline of harbour seals (Phoca vitulina), on Sable Island

  2003cited by this paper
• Dinucleotide microsatellite markers from the Antarctic seals and their use in other Pinnipeds

  2002cited by this paper
• Contribution of inbreeding to extinction risk in threatened species

  2002influential reference
• Geographical and temporal variation in levels of organochlorine contaminants in marine mammals.

  2002cited by this paper
• Marine mammal biology : an evolutionary approach

  2002cited by this paper
• The role of genetics in population viability analysis

  2002cited by this paper
• Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach.

  2002cited by this paper
• Spatial structure of harbour seal populations and the implications thereof

  2001cited by this paper
• Microsatellite variation in ringed seals (Phoca hispida): genetic structure and history of the Baltic Sea population

  2001cited by this paper
• Establishing management schemes on marine Special Areas of Conservation in Scotland

  2001cited by this paper
• Population structure of Atlantic salmon (Salmo salar L.): a range‐wide perspective from microsatellite DNA variation

  2001cited by this paper
• MOLECULAR EVIDENCE FOR TWINNING IN WEDDELL SEALS (LEPTONYCHOTES WEDDELLII)

  2001cited by this paper
• Local declines in the abundance of harbour seals: implications for the designation and monitoring of protected areas

  2001cited by this paper
• Inference of population structure using multilocus genotype data.

  2000influential reference
• Primer3 on the WWW for general users and for biologist programmers.

  2000cited by this paper
• Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality

  2000cited by this paper
• Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data

  1999cited by this paper
• Mitochondrial and microsatellite DNA analyses of harbour seal population structure in the northeast Pacific Ocean

  1999cited by this paper
• Genetic detection of sex‐biased dispersal

  1999influential reference
• Detecting population expansion and decline using microsatellites.

  1999cited by this paper
• Primer Notes

  1998cited by this paper
• Empirical Evaluation of a Test for Identifying Recently Bottlenecked Populations from Allele Frequency Data

  1998cited by this paper
• Distortion of allele frequency distributions provides a test for recent population bottlenecks.

  1998cited by this paper
• Cultural selection and genetic diversity in matrilineal whales.

  1998cited by this paper
• Patterns of extensive genetic differentiation and variation among European harbor seals (Phoca vitulina vitulina) revealed using microsatellite DNA polymorphisms.

  1998cited by this paper
• Changes in haematological parameters in relation to prey switching in a wild population of harbour seals

  1997influential reference

• Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

  2023cites this paper
• The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution

  2023influential citation
• Population structure and genetic connectivity reveals distinctiveness of Irish harbour seals ( Phoca vitulina ) and implications for conservation management

  2022cites this paper