Genetic and Morphological Variation of the Forkbeard, Phycis phycis (Pisces, Phycidae): Evidence of Panmixia and Recent Population Expansion along Its Distribution Area

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Abstract

The knowledge of population structure of a species is essential to effectively assess and manage fisheries. In the present study, genetics, by mitochondrial DNA cytochrome b sequence analysis, and body geometric morphometrics were used to evaluate the existence of distinct populations of the forkbeard ( Phycis phycis), an important commercial species in several European countries, especially Portugal and Spain. For geometric morphometric analysis, specimens were collected in the Northeast Atlantic Ocean—Azores, Madeira and mainland Portugal, and for genetic analysis, these samples were complemented with samples collected in the Mediterranean Sea—Spain, Italy and Croatia, in order to cover the entire distribution area of the species. Body shape of the forkbeard from the Northeast Atlantic was found to be highly variable. This variation was probably associated with different environmental factors between the study areas. Despite morphological variation, a low genetic differentiation between samples from different areas was found, most likely due to gene flow that occurred in the past or with the demographic history of the species. Moreover, the presence of unique haplotypes in the Northeast Atlantic and in the Mediterranean suggests that recent gene flow between populations from these areas should be limited. Altogether, a high haplotype diversity, a low nucleotide diversity, a “star-like” network and the results of the mismatch distribution, indicate a possible signature of recent population expansions, which probably started during the end of the Last Glacial Maximum and led to the colonization of the Northeast Atlantic and the Mediterranean.

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Most cited references 22

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Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution.

H. Harpending (1994)

A mismatch distribution is a tabulation of the number of pairwise differences among all DNA sequences in a sample. In a population that has been stationary for a long time these distributions from nonrecombinant DNA sequences become ragged and erratic, whereas a population that has been growing generates mismatch distributions that are smooth and have a peak. The position of the peak reflects the time of the population growth. The signature of an ancient population expansion is apparent even in the low-resolution mtDNA typings described by Merriwether et al. (1991). The smoothness of the mismatch distribution, an indicator of population expansion, is hardly affected by population structure, whereas mean sequence divergence increases in a pooled sample from highly isolated subpopulations.

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Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.

M Slatkin, R R Hudson (1991)

We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population that has been growing in size exponentially for a long time. We show that, in a population of constant size, the sample distribution of pairwise differences will typically deviate substantially from the geometric distribution expected, because the history of coalescent events in a single sample of genes imposes a substantial correlation on pairwise differences. Consequently, a goodness-of-fit test of observed pairwise differences to the geometric distribution, which assumes that each pairwise comparison is independent, is not a valid test of the hypothesis that the genes were sampled from a panmictic population of constant size. In an exponentially growing population in which the product of the current population size and the growth rate is substantially larger than one, our analytical and simulation results show that most coalescent events occur relatively early and in a restricted range of times. Hence, the "gene tree" will be nearly a "star phylogeny" and the distribution of pairwise differences will be nearly a Poisson distribution. In that case, it is possible to estimate r, the population growth rate, if the mutation rate, mu, and current population size, N0, are assumed known. The estimate of r is the solution to ri/mu = ln(N0r) - gamma, where i is the average pairwise difference and gamma approximately 0.577 is Euler's constant.

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Dispersal, gene flow, and population structure.

Andrew Bohonak (1999)

The accuracy of gene flow estimates is unknown in most natural populations because direct estimates of dispersal are often not possible. These estimates can be highly imprecise or even biased because population genetic structure reflects more than a simple balance between genetic drift and gene flow. Most of the models used to estimate gene flow also assume very simple patterns of movement. As a result, multiple interpretations of population structure involving contemporary gene flow, departures from equilibrium, and other factors are almost always possible. One way to isolate the relative contribution of gene flow to population genetic differentiation is to utilize comparative methods. Population genetic statistics such as FST, heterozygosity and Nei's D can be compared between species with differing dispersal abilities if these species are otherwise phylogenetically, geographically and demographically comparable. Accordingly, the available literature was searched for all groups that meet these criteria to determine whether broad conclusions regarding the relationships between dispersal, population genetic structure, and gene flow estimates are possible. Allozyme and mtDNA data were summarized for 27 animal groups in which dispersal differences can be characterized. In total, genetic data were obtained for 333 species of vertebrates and invertebrates from terrestrial, freshwater and marine habitats. Across these groups, dispersal ability was consistently related to population structure, with a mean rank correlation of -0.72 between ranked dispersal ability and FST. Gene flow estimates derived from private alleles were also correlated with dispersal ability, but were less widely available. Direct-count heterozygosity and average values of Nei's D showed moderate degrees of correlation with dispersal ability. Thus, despite regional, taxonomic and methodological differences among the groups of species surveyed, available data demonstrate that dispersal makes a measurable contribution to population genetic differentiation in the majority of animal species in nature, and that gene flow estimates are rarely so overwhelmed by population history, departures from equilibrium, or other microevolutionary forces as to be uninformative.

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Author and article information

Contributors

Wolfgang Arthofer: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, CA USA )

ISSN (Electronic): 1932-6203

Publication date (Electronic): 12 December 2016

Publication date Collection: 2016

Volume: 11

Issue: 12

Electronic Location Identifier: e0167045

Affiliations

[1 ]MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal

[2 ]Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal

[3 ]cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal

University of Innsbruck, AUSTRIA

Author notes

Competing Interests: The authors have declared that no competing interests exist.

Conceptualization: ARV OSP LSG.
Formal analysis: ARV VS OSP.
Funding acquisition: ARV ASBR VS AN RBP OSP LSG.
Investigation: ARV.
Methodology: ARV ASBR VS OSP LSG.
Project administration: ARV OSP LSG.
Resources: ARV OSP LSG.
Supervision: OSP LSG.
Writing – original draft: ARV.
Writing – review & editing: ARV ASBR VS AN RBP OSP LSG.

* E-mail: arivieira@ 123456fc.ul.pt

Author information

Ana Rita Vieira http://orcid.org/0000-0002-5640-7999

Article

Publisher ID: PONE-D-16-18932

DOI: 10.1371/journal.pone.0167045

PMC ID: 5152830

PubMed ID: 27941988

SO-VID: cbbe351e-9c96-46bf-8a75-c03e7f07dc89

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 17 May 2016

Date accepted : 11 October 2016