scholarly journals Asymmetrical dispersal and putative isolation-by-distance of an intertidal blenniid across the Atlantic–Mediterranean divide

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3195 ◽  
Author(s):  
Rita Castilho ◽  
Regina L. Cunha ◽  
Cláudia Faria ◽  
Eva M. Velasco ◽  
Joana I. Robalo
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Secondary Contact ◽  
Transition Zones ◽  
Phylogeographic Break ◽  
Distance Model ◽  
The Mediterranean ◽  
Rocky Habitats ◽  
Salaria Pavo ◽  
Peacock Blenny

Transition zones are of high evolutionary interest because unique patterns of spatial variation are often retained. Here, we investigated the phylogeography of the peacock blenny, Salaria pavo, a small marine intertidal fish that inhabits rocky habitats of the Mediterranean and the adjacent Atlantic Ocean. We screened 170 individuals using mitochondrial and nuclear sequence data from eight locations. Four models of genetic structure were tested: panmixia, isolation-by-distance, secondary contact and phylogeographic break. Results indicated clear asymmetric migration from the Mediterranean to the Atlantic but only marginally supported the isolation-by-distance model. Additionally, the species displays an imprint of demographic expansion compatible with the last glacial maximum. Although the existence of a refugium in the Mediterranean cannot be discarded, the ancestral lineage most likely originated in the Atlantic, where most of the genetic diversity occurs.

scholarly journals Can secondary contact following range expansion be distinguished from barriers to gene flow?

2016 ◽  
Author(s):  
Johanna Bertl ◽  
Harald Ringbauer ◽  
Michael G. B. Blum
Keyword(s):  
Gene Flow ◽  
Range Expansion ◽  
Isolation By Distance ◽  
Molecular Data ◽  
Secondary Contact ◽  
Evolutionary Scenario ◽  
Coalescent Simulations ◽  
Distance Model ◽  
Northward Expansion ◽  
Spatio Temporal

AbstractSecondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of Linkage Disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index Ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.

scholarly journals Can secondary contact following range expansion be distinguished from barriers to gene flow?

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5325 ◽  
Author(s):  
Johanna Bertl ◽  
Harald Ringbauer ◽  
Michael G.B. Blum
Keyword(s):  
Gene Flow ◽  
Range Expansion ◽  
Isolation By Distance ◽  
Molecular Data ◽  
Secondary Contact ◽  
Evolutionary Scenario ◽  
Coalescent Simulations ◽  
Distance Model ◽  
Northward Expansion ◽  
Spatio Temporal

Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.

scholarly journals Phylogeography and population genetics of Macronycteris commersonii s.s. (Chiroptera: Hipposideridae), an endemic Malagasy bat

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Steven M Goodman ◽  
M Corrie Schoeman ◽  
Sandi Willows-Munro
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Recent Common Ancestor ◽  
Climate Conditions ◽  
Most Recent Common Ancestor ◽  
Pleistocene Climate ◽  
Clade C ◽  
Distance Model ◽  
Forested Areas

Macronycteris commersonii (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island, utilising open woodland, degraded habitats, and forested areas from sea level to 1325 m. We investigated the fine-scale phylogeographic history and relationships of populations occurring in the western half of the island using sequence data from two mitochondrial DNA regions and extensive geographical sampling. Our results indicated a highly supported monophyletic group of M. commersonii, in which the Northern Madagascar Clade C formed a single monophyletic clade. The most recent common ancestor of M. commersonii was dated to 0.82 million years ago (mid-Pleistocene). Population expansion events were inferred for Clade B from approximately 130,000 to 70,000 years BP. Bayesian clustering and AMOVA analyses inferred week population genetic structure and sequence data indicated that genetic subdivisions do not support an isolation-by-distance model. Lineage dispersal, genetic divergence, and expansion events of M. commersonii were likely to be associated with Pleistocene climate fluctuations. Our data suggested that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

scholarly journals Phylogeography and population genetics of Macronycteris commersonii s.s. (Chiroptera: Hipposideridae), an endemic Malagasy bat

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Steven M Goodman ◽  
M Corrie Schoeman ◽  
Sandi Willows-Munro
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Recent Common Ancestor ◽  
Climate Conditions ◽  
Most Recent Common Ancestor ◽  
Pleistocene Climate ◽  
Clade C ◽  
Distance Model ◽  
Forested Areas

Macronycteris commersonii (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island, utilising open woodland, degraded habitats, and forested areas from sea level to 1325 m. We investigated the fine-scale phylogeographic history and relationships of populations occurring in the western half of the island using sequence data from two mitochondrial DNA regions and extensive geographical sampling. Our results indicated a highly supported monophyletic group of M. commersonii, in which the Northern Madagascar Clade C formed a single monophyletic clade. The most recent common ancestor of M. commersonii was dated to 0.82 million years ago (mid-Pleistocene). Population expansion events were inferred for Clade B from approximately 130,000 to 70,000 years BP. Bayesian clustering and AMOVA analyses inferred week population genetic structure and sequence data indicated that genetic subdivisions do not support an isolation-by-distance model. Lineage dispersal, genetic divergence, and expansion events of M. commersonii were likely to be associated with Pleistocene climate fluctuations. Our data suggested that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

Phylogenetic relationships of Mediterranean black corals (Cnidaria : Anthozoa : Hexacorallia) and implications for classification within the order Antipatharia

2018 ◽  
Vol 32 (5) ◽  
pp. 1102 ◽  
Author(s):  
M. Bo ◽  
M. Barucca ◽  
M. A. Biscotti ◽  
M. R. Brugler ◽  
A. Canapa ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Data ◽  
Coral Fauna ◽  
Black Coral ◽  
Phylogenetic Studies ◽  
Black Corals ◽  
The Family ◽  
The Mediterranean ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

The Mediterranean black coral fauna includes type species of four antipatharian genera belonging to four different families, therefore phylogenetic studies hold great potential for enhancing systematics within the order. The analysis of six Mediterranean antipatharian species by means of nuclear sequence data of internal transcribed spacer (ITS1 and ITS2) rDNA confirms the separation into different families, as was previously noted on a morphological basis, with a clear distinction of the family Leiopathidae, whose position is supported by a unique number of mesenteries and lack of spines on thicker ramifications. The position of a newly recorded black coral species for the Mediterranean basin belonging to the genus Phanopathes is discussed. Antipathes dichotoma, the type species of the genus Antipathes, on which the order Antipatharia was based, does not group with other members of the family Antipathidae. Supporting a recent finding based on mitochondrial markers, this suggests a critical need for revision of the families that will be impacted by reassignment of this nomenclaturally important taxon.

Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

2012 ◽  
Vol 60 (1) ◽  
pp. 32 ◽  
Author(s):  
Laurence J. Clarke ◽  
Duncan I. Jardine ◽  
Margaret Byrne ◽  
Kelly Shepherd ◽  
Andrew J. Lowe
Keyword(s):  
Genetic Variation ◽  
New Species ◽  
Genetic Structure ◽  
Western Australia ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Conservation Strategies ◽  
New Taxon ◽  
Near Surface ◽  
Two Populations

Atriplex sp. Yeelirrie Station (L. Trotter & A. Douglas LCH 25025) is a highly restricted, potentially new species of saltbush, known from only two sites ~30 km apart in central Western Australia. Knowledge of genetic structure within the species is required to inform conservation strategies as both populations occur within a palaeovalley that contains significant near-surface uranium mineralisation. We investigate the structure of genetic variation within populations and subpopulations of this taxon using nuclear microsatellites. Internal transcribed spacer sequence data places this new taxon within a clade of polyploid Atriplex species, and the maximum number of alleles per locus suggests it is hexaploid. The two populations possessed similar levels of genetic diversity, but exhibited a surprising level of genetic differentiation given their proximity. Significant isolation by distance over scales of less than 5 km suggests dispersal is highly restricted. In addition, the proportion of variation between the populations (12%) is similar to that among A. nummularia populations sampled at a continent-wide scale (several thousand kilometres), and only marginally less than that between distinct A. nummularia subspecies. Additional work is required to further clarify the exact taxonomic status of the two populations. We propose management recommendations for this potentially new species in light of its highly structured genetic variation.

scholarly journals Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus

2021 ◽  
Author(s):  
Julia M. Kreiner ◽  
Amalia Caballero ◽  
Stephen I. Wright ◽  
John R. Stinchcombe
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Sex Differentiation ◽  
Common Garden ◽  
Whole Genome Sequence ◽  
Secondary Contact ◽  
Natural Environments ◽  
Relative Role ◽  
Standing Variation ◽  
Amaranthus Tuberculatus

The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated subspecies. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of subspecies divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry-based inference. The transition into agricultural environments has favoured southwestern var. rudis ancestry that leads to higher biomass and environment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation to agricultural habitats independent of ancestry effects, including marginally higher biomass and later flowering in agricultural populations, and a time to germination home advantage. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales—through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.

Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer

2008 ◽  
Vol 38 (6) ◽  
pp. 1576-1589 ◽  
Author(s):  
Catherine M. Clark ◽  
Ignazio Carbone
Keyword(s):  
Nucleotide Diversity ◽  
Isolation By Distance ◽  
Population Bottlenecks ◽  
Base Pairs ◽  
Distance Model ◽  
History Of ◽  
Lagarostrobos Franklinii ◽  
Tasmanian Endemic ◽  
Western Portion

Genealogy based methods were used to estimate phylogeographic history for a Tasmanian endemic conifer, Huon pine ( Lagarostrobos franklinii (Hook. f.) Quinn). DNA from trees in eight populations was sequenced using three chloroplast primers (trnS–trnT, trnD–trnT, and psbC–trnS). Mean nucleotide diversity was low (π = 0.000 93 ± 0.000 06) from 892 base pairs of sequence, but varied in stands from 0.0 to 0.001 15. Two of the five haplotypes were widely distributed, but the most frequently occurring haplotype was found only in the western portion of the range. Population structure was highly significant among populations overall (GST = 0.261, where GST is the coefficient of gene differentiation, and p ≤ 0.0001), and there were indications of significant isolation by distance (p ≤ 0.022). Populations exhibited the highest levels of differentiation between the southeastern and northwestern watersheds. Estimates of migration between populations obtained using both parametric and nonparametric methods indicated levels of gene flow consistent with an isolation by distance model. Nested clade analysis demonstrated a pattern of genetic diversity in Huon pine that is consistent with a history of range expansion. The exceptionally low level of nucleotide diversity, haplotype distribution, and paleoecological data are congruent with a history of long-term range reduction, population bottlenecks, and subsequent colonization events from refugial areas.

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