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 Complex population structure of the Atlantic puffin revealed by whole genome analyses

2020 ◽  
Author(s):  
Oliver Kersten ◽  
Bastiaan Star ◽  
Deborah M. Leigh ◽  
Tycho Anker-Nilssen ◽  
Hallvard Strøm ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Secondary Contact ◽  
Whole Genome ◽  
Genome Data ◽  
Complex Population ◽  
Genome Analyses ◽  
Atlantic Puffin

AbstractThe factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

scholarly journals Isolation and endemism in subterranean aquatic snails: unexpected case of Montenegrospeum bogici (Pešić et Glöer, 2012) (Gastropoda: Truncatelloidea: Hydrobiidae)

Hydrobiologia ◽  
2021 ◽  
Author(s):  
Andrzej Falniowski ◽  
Vladimir Pešić ◽  
Brian Lewarne ◽  
Jozef Grego ◽  
Aleksandra Rysiewska ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Karst Region ◽  
Aquatic Species ◽  
Isolated Populations ◽  
Dinaric Karst ◽  
Distance Model ◽  
Single Locality

AbstractThe subterranean aquatic snails may serve as a model of endemism and isolation vs. migration in subterranean habitats. The aim of the present paper is to verify the hypothesis that subterranean aquatic snails can migrate through diverse subterranean habitats, applying four molecular markers as well as a RAPD technique and shell morphometry. They were used to estimate the differences and gene flow between populations of the hydrobiid subterranean aquatic species Montenegrospeum bogici, collected in the Dinaric karst region. Three molecularly distinct taxonomic units were distinguished. The mOTU B was found at single locality, mOTU C at two, but the mOTU A at ten localities, scattered along 236 km distance, at two of them in sympatry with either mOTU B or C. Within mOTU A, the estimated levels of the gene flow were high. The pairwise measures of genetic differentiation were statistically significantly associated with geographic distances between the populations. In general, neither the infinite-island model of interpopulation differentiation, expected for isolated populations, nor the stepping-stone one, but rather the isolation-by-distance model explained the observed pattern. Our results suggest that interstitial habitats provide ways of migration for the stygobiont M. bogici, as has been already suggested for other subterranean gastropods.

scholarly journals Limited long-distance dispersal success in a Western European fairy shrimp evidenced by nuclear and mitochondrial lineage structuring

2019 ◽  
Vol 66 (3) ◽  
pp. 227-237
Author(s):  
Paula C Rodríguez-Flores ◽  
Ernesto Recuero ◽  
Yolanda Jiménez-Ruiz ◽  
Mario García-París
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Iberian Peninsula ◽  
Isolation By Distance ◽  
Local Scale ◽  
Long Distance Dispersal ◽  
Evolutionary Potential ◽  
Long Distance ◽  
Widespread Species ◽  
Spatio Temporal

Abstract Anostraca are known by their ability for long-distance dispersal, but the existence in several species of deep, geographically structured mtDNA lineages suggests their populations are subjected to allopatric differentiation, isolation, and prevalence of local scale dispersion. Tanymastix stagnalis is one of the most widespread species of Anostraca and previous studies revealed an unclear geographical pattern of mtDNA genetic diversity. Here, we analyze populations from the Iberian and Italian Peninsulas, Central Europe, and Scandinavia, with the aim to characterize the patterns of genetic diversity in a spatio-temporal framework using mtDNA and nuclear markers to test gene flow among close populations. For these aims we built a time-calibrated phylogeny and carried out Bayesian phylogeographic analyses using a continuous diffusion model. Our results indicated that T. stagnalis presents a deeply structured genetic diversity, including 7 ancient lineages, some of them even predating the Pleistocene. The Iberian Peninsula harbors high diversity of lineages, with strong isolation and recent absence of gene flow between populations. Dispersal at local scale seems to be the prevailing dispersal mode of T. stagnalis, which exhibits a pattern of isolation-by-distance in the Iberian Peninsula. We remark the vulnerability of most of these lineages, given the limited known geographic distribution of some of them, and the high risk of losing important evolutionary potential for the species.

scholarly journals Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

2014 ◽  
Author(s):  
Jared A Grummer ◽  
Martha L. Calderón ◽  
Adrián Nieto Montes-de Oca ◽  
Eric N Smith ◽  
Fausto Méndez-de la Cruz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Ancestral Population ◽  
Secondary Contact ◽  
Sympatric Populations ◽  
Interspecific Gene Flow ◽  
Ancestral Gene ◽  
Mixed Support ◽  
Coalescent Simulations ◽  
Range Overlap ◽  
Analytical Approaches

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.

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.

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