Secondary Contact Zone Research Articles

Genetic diversity and phylogeographic analysis of Pinus leiophylla: a post‐glacial range expansion

AbstractAim Mexico is a centre of diversity for species of the genus Pinus, most of which have restricted geographical distributions. An exception is Pinus leiophylla Schiede and Deppe, which is widely distributed throughout most of Mexico’s mountainous regions. We attempt to reconstruct the phylogeographic history of this species, in order to determine if its current broad distribution is associated with major events of environmental change that occurred during the Quaternary.Location Coniferous forests in Sierra Madre Occidental, Eje Volcánico Transversal and Sierra Montañosa del Norte de Oaxaca, Mexico.Methods A total of 323 individuals of both P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana sampled from 22 populations were screened for variation at six paternally inherited chloroplast DNA microsatellite markers (cpSSR). In addition to haplotypic diversity estimates and neutrality tests, the following clustering methods were employed: principal components analysis (PCA), analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), haplotype network and a technique similar to Croizat’s panbiogeographical method of individual and generalized tracks.Results The combination of mutations at the six microsatellites yielded a total of 92 different haplotypes. The percentage of shared haplotypes between varieties (P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana) was only 2.2%. The average haplotypic diversity for the species was H = 0.760. PCA and SAMOVA indicate the presence of four main genetic clusters. The estimated divergence time between the two most frequent haplotypes was between 75,000 and 110,000 years. Significantly large negative Fs values suggest that most of the sampled populations are currently expanding. Individual and generalized tracks identified three potential zones that may have harboured ancestral populations of P. leiophylla and from which the expansion of this species started, as well as two secondary contact zones between the two varieties.Main conclusions The results indicate that one of the three potential areas hypothesized to have harboured ancestral populations of P. leiophylla may be related to the origin of P. leiophylla var. chihuahuana, while the other two may be related to the origin of P. leiophylla var. leiophylla. The current broad distribution of P. leiophylla is probably associated with its strong colonization ability.

Nuclear and Mitochondrial Patterns of Introgression between the Parapatric European TreefrogsHyla arboreaandH. intermedia

Postglacial northward expansions from distinct southern European refugia have lead to the formation of several secondary contact zones between species. These zones are providing growing insights into the relevance of introgressive hybridization in shaping patterns of genetic diversity, and into the evolutionary processes involved in the completion of reproductive isolation barriers. Using both nuclear (9 allozyme loci) and mitochondrial (PCR-RFLP of a cytochrome b gene fragment) diagnostic markers we investigated the genetic patterns of variation across a zone of parapatry between the two European treefrogs Hyla arborea and H. intermedia. Neither F1 and F2 hybrids nor backcrosses were identified, indicating the lack of current gene exchange between the two species. However, introgressed alleles were observed in both species and in all markers analysed, which testifies to the occurrence of past events of introgressive hybridization. A wide variation in the frequencies of introgressed alleles was observed b...

Drainage-independent genetic structure and high genetic diversity of endangered freshwater pearl mussels (Margaritifera margaritifera) in northern Europe

Freshwater pearl mussels (Margaritifera margaritifera) are among the most critically threatened bivalve molluscs worldwide. An understanding of spatial patterns of genetic diversity is crucial for the development of integrative conservation strategies. We used microsatellites to study the genetic diversity and differentiation of 14 populations of M. margaritifera in central Sweden, an area which was described as a major secondary contact zone in postglacial colonisation for other species. Genetic diversity of Swedish pearl mussel populations was much greater than in central and southern Europe but similar to the genetic diversity observed in the northeastern portion of their European range. Genetic differentiation among populations was pronounced but to a large extent independent from present-day drainage systems. The complex patterns of genetic diversity and differentiation in pearl mussel seem to be strongly influenced by the species’ high degree of specialisation and extraordinary life history strategy which involves facultative hermaphrodism and an obligatory encystment stage on a host fish. Genetic drift effects and anthropogenic disturbances resulting in reduction of population size and loss of connectivity are less pronounced in northern pearl mussel populations compared to those in central and southern Europe.

Distribution and diversity of cytotypes in Dianthus broteri as evidenced by genome size variations

Studying the spatial distribution of cytotypes and genome size in plants can provide valuable information about the evolution of polyploid complexes. Here, the spatial distribution of cytological races and the amount of DNA in Dianthus broteri, an Iberian carnation with several ploidy levels, is investigated. Sample chromosome counts and flow cytometry (using propidium iodide) were used to determine overall genome size (2C value) and ploidy level in 244 individuals of 25 populations. Both fresh and dried samples were investigated. Differences in 2C and 1Cx values among ploidy levels within biogeographical provinces were tested using ANOVA. Geographical correlations of genome size were also explored. Extensive variation in chromosomes numbers (2n = 2x = 30, 2n = 4x = 60, 2n = 6x = 90 and 2n = 12x =180) was detected, and the dodecaploid cytotype is reported for the first time in this genus. As regards cytotype distribution, six populations were diploid, 11 were tetraploid, three were hexaploid and five were dodecaploid. Except for one diploid population containing some triploid plants (2n = 45), the remaining populations showed a single cytotype. Diploids appeared in two disjunct areas (south-east and south-west), and so did tetraploids (although with a considerably wider geographic range). Dehydrated leaf samples provided reliable measurements of DNA content. Genome size varied significantly among some cytotypes, and also extensively within diploid (up to 1.17-fold) and tetraploid (1.22-fold) populations. Nevertheless, variations were not straightforwardly congruent with ecology and geographical distribution. Dianthus broteri shows the highest diversity of cytotypes known to date in the genus Dianthus. Moreover, some cytotypes present remarkable internal genome size variation. The evolution of the complex is discussed in terms of autopolyploidy, with primary and secondary contact zones.

Phylogeographic history of the New Zealand stick insect Niveaphasma annulata (Phasmatodea) estimated from mitochondrial and nuclear loci

We have assessed the utility of a single-copy nuclear locus and mitochondrial DNA (mtDNA) in a phylogeographic study of the New Zealand stick insect Niveaphasma annulata (Hutton). We amplified sequences from the mitochondrial cytochrome oxidase subunit I (COI) gene and the single-copy nuclear gene elongation factor-1α (EF1α) from 97 individuals. Allelic phase at the EF1α locus was determined using Denaturing Gradient Gel Electrophoresis. Phylogenetic analyses showed broad congruence between the geographic distribution of three major COI clades and EF1α alleles, which suggested that the phylogenetic patterns reflect population history rather than lineage sorting. However, the geographic boundaries of these clades were not always in exact agreement between the two loci. Our data indicate that Niveaphasma annulata was most likely separated into a number of refugia during Pleistocene glacial advances. Subsequent to glacial retreat these refugial populations have expanded and now form a number of zones of secondary contact. We contrast these patterns with those observed from other New Zealand taxa. Our study offers compelling evidence for the use of nuclear genes alongside mtDNA for future phylogeographic studies.

Genetic, morphological, and feather isotope variation of migratory willow warblers show gradual divergence in a ring

The circular distribution of the willow warbler Phylloscopus trochilus around the Baltic Sea shares many features with the classic examples of ring species; however, the system is much younger. It has previously been shown that a secondary contact zone is located in central Scandinavia, where there are narrow clines for several morphological traits coincident with a migratory divide. Here we analyse multiple traits and genes from > 1700 males captured on breeding territories at 77 sites spread around the Baltic Sea to test the following hypothesis. If the secondary contact zone in Scandinavia is a result of divergence in two allopatric refuge populations during the last glaciation, we expect to find a similar secondary contact zone somewhere else around the circular distribution. Our results show that the trait clines were wider and displaced from each other along the eastern side of the Baltic Sea. Analyses of 12 microsatellite loci confirmed that the genome is very similar between the terminal forms (F(ST) = 0). Two AFLP-derived markers filtered out from a genomic scan instead appear to be maintained by selection. These markers exhibited steep clines at the secondary contact zone in Scandinavia, but as for the phenotypic traits, had vastly different cline centres east of the Baltic Sea. The trait clines along the ring distribution outside the Scandinavian secondary contact zone thus seem to have been shaped by independent action of selection or drift during the process of postglacial colonization.

TESTING PHYLOGEOGRAPHIC HYPOTHESES IN A EURO-SIBERIAN COLD-ADAPTED LEAF BEETLE WITH COALESCENT SIMULATIONS

Few studies to date have investigated the impact of Pleistocene climatic oscillations on the genetic diversity of cold-adapted species. We focus on the geographic distribution of genetic diversity in a Euro-Siberian boreo-montane leaf beetle, Gonioctena pallida. We present the molecular variation from three independent gene fragments over the entire geographic range of this insect. The observed sequence variation identifies a genetic diversity hot spot in the Carpathian Mountains, in central Europe, which reveals the presence of (1) an ancestral refuge population or (2) a secondary contact zone in this area. Modeling of population evolution in a coalescent framework allowed us to favor the ancestral refuge hypothesis. These analyses suggest that the Carpathian Mountains served as a refuge for G. pallida, whereas the rest of the species distribution, that spans a large portion of Europe and Asia, experienced a dramatic reduction in genetic variation probably associated to bottlenecks and/or founder events. We estimated the time of isolation of the ancestral refuge population, using an approximate Bayesian method, to be larger than 90,000 years. If true, the current pattern of genetic variation in this cold-adapted organism was shaped by a climatic event predating by far the end of the last ice age.

Spatial Inference of Admixture Proportions and Secondary Contact Zones

Genetic admixture of distinct gene pools is the consequence of complex spatiotemporal processes that could have involved massive migration and local mating during the history of a species. However, current methods for estimating individual admixture proportions lack the incorporation of such a piece of information. Here, we extend Bayesian clustering algorithms by including global trend surfaces and spatial autocorrelation in the prior distribution on individual admixture coefficients. We test our algorithm by using spatially explicit and realistic coalescent simulations of colonization followed by secondary contact. By coupling our multiscale spatial analyses with a Bayesian evaluation of model complexity and fit, we show that the algorithm provides a correct description of smooth clinal variation, while still detecting zones of sharp variation when they are present in the data. We also apply our approach to understand the population structure of the killifish, Fundulus heteroclitus, for which the algorithm uncovers a presumed contact zone in the Atlantic coast of North America.

Assortative Mating without Complete Reproductive Isolation in a Zone of Recent Secondary Contact between Herring Gulls (Larus argentatus) and Caspian Gulls (L. cachinnans)

ABSTRACT. The zone of secondary contact between Herring Gulls (Larus argentatus) and Caspian Gulls (L. cachinnans) in central Poland is characterized by high levels of introgreeRzemyscular mars several phenotypic characters, with the exception of bare-parts coloration. These patterns suggest a role for coloration as a premating isolating barrier between these species. We investigated the degree of reproductive isolation in this zone of secondary contact by testing three hypotheses: (1) postmating isolation is weak or absent, (2) a partial premating isolation is present, and (3) orbital-ring color or another closely correlated trait is involved in premating isolation, which explains the signal of disruptive selection previously observed (a lower degree of introgression). We also investigated whether differences in breeding phenology could contribute to premating isolation. We found no evidence of postmating isolation, but premating isolation occurred: heterospecific pairs were significantly scarcer than ex...

Genetic population structure of European sprat Sprattus sprattus: differentiation across a steep environmental gradient in a small pelagic fish

Factors such as oceanographic retention, isolation by distance and secondary contact zones have, among others, been suggested to explain the low, but statistically significant, neutral pop- ulation structure observed in many marine fishes. European sprat Sprattus sprattus L. is not known to display philopatric spawning behaviour or to exhibit local retention of eggs and larvae. It thus consti- tutes a good model for studying population structure in a characteristic small pelagic fish with high dis- persal potential and an opportunistic life history. We analysed 931 specimens of sprat from 9 spawning locations in and around the North Sea and Baltic Sea area and from a geographically distant popula- tion from the Adriatic Sea. Analyses of 9 microsatellite loci revealed a sharp genetic division separat- ing samples from the northeastern Atlantic Ocean and the Baltic Sea (pairwise θ = 0.019 to 0.035), con- curring with a steep salinity gradient. We found, at most, weak structure among samples within the northeastern Atlantic region and within the Baltic Sea (pairwise θ = 0.001 to 0.009). The Adriatic Sea population was highly differentiated from all northern samples (pairwise θ = 0.071 to 0.092). Overall, the observed population structure resembles that of most other marine fishes studied in the North and Baltic Sea areas. Nevertheless, spatially explicit differences are observed among species, probably reflecting specific life histories. Such fine-scale population structures should be taken into account when considering complex ecosystem functions, e.g. in multispecies stock management.

Towards resolving the Knautia arvensis agg. (Dipsacaceae) puzzle: primary and secondary contact zones and ploidy segregation at landscape and microgeographic scales.

Detailed knowledge of variations in ploidy levels and their geographic distributions is one of the key tasks faced in polyploid research in natural systems. Flow cytometry has greatly facilitated the field of cytogeography by allowing characterization of ploidy levels at both the regional and population scale, and at multiple stages of the life cycle. In the present study, flow cytometry was employed to investigate the patterns and dynamics of ploidy variation in the taxonomically challenging complex Knautia arvensis (Dipsacaceae) and some of its allies (K. dipsacifolia, K. slovaca) in Central Europe. DNA ploidy levels were estimated by DAPI flow cytometry in 5205 adult plants, 228 seedlings and 400 seeds collected from 292 Knautia populations in seven European countries. The flow cytometric data were supplemented with conventional chromosome counts. A subset of 79 accessions was subjected to estimation of the absolute genome size using propidium iodide flow cytometry. Five different ploidy levels (from 2x to 6x) were found, with triploids of K. arvensis being recorded for the first time. The species also exhibited variation in the monoploid genome size, corresponding to the types of habitats occupied (grassland diploid populations had larger genome sizes than relict and subalpine diploid populations). Disregarding relict populations, the distribution of 2x and 4x cytotypes was largely parapatric, with a diffuse secondary contact zone running along the north-west margin of the Pannonian basin. Spatial segregation of the cytotypes was also observed on regional and microgeographic scales. The newly detected sympatric growth of diploids and tetraploids in isolated relict habitats most likely represents the primary zone of cytotype contact. Ploidy level was found to be a major determinant of the strength of inter-cytotype reproductive barriers. While mixed 2x + 4x populations virtually lacked the intermediate ploidy level at any ontogenetic stage, pentaploid hybrids were common in 4x +6x populations, despite the cytotypes representing different taxonomic entities.

Chromosomal forms of the Mole Rat, Nannospalax nehringi (Satunin, 1898), from the Van Lake Basin in Eastern Turkey

Two different chromosomal forms of the Mole Rat, Nannospalax nehringi (Satunin, 1898), have been found in the Van Basin, Eastern Turkey: a population around the city of Van with 2n=48, NF=72 and NFa=68, and a population around the city of Bitlis with 2n=54, NF=74 and NFa=70. Both populations are confined to well-defined distribution areas. While both populations are separated in the south by Mt Süphan, an extinct volcano over 4000 m high, there is no geographic barrier between both populations in the north, and there seems to be a secondary contact zone. The Van population constitutes a new chromosomal form of Mole Rat in Turkey, and could be regarded as a sibling species. However, no taxomomic decision is taken until more evidence on the evolution of these forms has become available.

The roles of allopatric divergence and natural selection in quantitative trait variation across a secondary contact zone in the lizard Anolis roquet

Populations of the Caribbean lizard, Anolis roquet, are thought to have experienced long periods of allopatry before recent secondary contact. To elucidate the effects of past allopatry on population divergence in A. roquet, we surveyed parallel transects across a secondary contact zone in northeastern Martinique. We used diagnostic molecular mitochondrial DNA markers to test fine-scale association of mitochondrial DNA lineage and geological region, multivariate statistical techniques to explore quantitative trait pattern, and cline fitting techniques to model trait variation across the zone of secondary contact. We found that lineages were strongly associated with geological regions along both transects, but quantitative trait patterns were remarkably different. Patterns of morphological and mitochondrial DNA variation were consistent with a strong barrier to gene flow on the coast, whereas there were no indications of barriers to gene flow in the transitional forest. Hence, the coastal populations behaved as would be predicted by an allopatric model of divergence in this complex, while those in the transitional forest did not, despite the close proximity of the transects and their shared geological history. Patterns of geographical variation in this species complex, together with environmental data, suggest that on balance, selection regimes on either side of the secondary contact zone in the transitional forest may be more convergent, while those either side of the secondary contact zone on the coast are more divergent. Hence, the evolutionary consequences of allopatry may be strongly influenced by local natural selection regimes.

Across the southern Andes on fin: glacial refugia, drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia

We employed DNA sequence variation at two mitochondrial (control region, COI) regions from 212 individuals of Galaxias platei (Pisces, Galaxiidae) collected throughout Patagonia (25 lakes/rivers) to examine how Andean orogeny and the climatic cycles throughout the Quaternary affected the genetic diversity and phylogeography of this species. Phylogenetic analyses revealed four deep genealogical lineages which likely represent the initial division of G. platei into eastern and western lineages by Andean uplift, followed by further subdivision of each lineage into separate glacial refugia by repeated Pleistocene glacial cycles. West of the Andes, refugia were likely restricted to the northern region of Patagonia with small relicts in the south, whereas eastern refugia appear to have been much larger and widespread, consisting of separate northern and southern regions that collectively spanned most of Argentinean Patagonia. The retreat of glacial ice following the last glacial maximum allowed re-colonization of central Chile from nonlocal refugia from the north and east, representing a region of secondary contact between all four glacial lineages. Northwestern glacial relicts likely followed pro-glacial lakes into central Chilean Patagonia, whereas catastrophic changes in drainage direction (Atlantic --> Pacific) for several eastern palaeolakes were the likely avenues for invasions from the east. These mechanisms, combined with evidence for recent, rapid and widespread population growth could explain the extensive contemporary distribution of G. platei throughout Patagonia.

Secondary contact zones and hybridizations: the case of the lesser white-toothed shrew (Crocidura suaveolens group, Soricidae)

In the present study, we analyzed 58 samples of the lesser white-toothed shrew group (Crocidura suaveolens) from eastern Europe and Turkey, where, according to previous publications, three different mitochondrial and nuclear lineages are present. We sequenced 799 bp of the nuclear BRCA1 gene and 400 bp of the mitochondrial cytochrome b gene to: (1) determine a potential contact zone between the lineages; (2) detect hybridizations and introgressions between them; and (3) comment on the level of reproductive isolation of the different lineages. We revealed two zones of hybridization in Turkey, of which the first occurred west of the Bosphorus Straits (three hybrids) and the second in Anatolia (twelve hybrids). In the latter, the nuclear markers revealed a large zone of hybridization, of approximately 600 km. It also revealed that hybrids of first, second, and later generations are present within the populations, and therefore that the reproductive isolation between the different lineages is weak. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 557–565.

Speciation with gene flow in the large white-headed gulls: does selection counterbalance introgression?

We investigated the role of selection in generating and maintaining species distinctness in spite of ongoing gene flow, using two zones of secondary contact between large gull species in Europe (Larus argentatus and Larus cachinnans) and North America (Larus glaucescens and Larus occidentalis). We used the pattern of neutral genetic differentiation at nine microsatellite loci (F(ST)) as an indicator of expected changes under neutral processes and compared it with phenotypic differentiation (P(ST)) for a large number of traits (size, plumage melanism and coloration of bare parts). Even assuming very low heritability, interspecific divergence between L. glaucescens and L. occidentalis in plumage melanism and orbital ring colour clearly exceeded neutral differentiation. Similarly, melanism of the central primaries was highly divergent between L. argentatus and L. cachinnans. Such divergence is unlikely to have arisen randomly and is therefore attributed to spatially varying selection. Variation in plumage melanism in both transects agrees with Gloger's rule, which suggests that latitude (and associated sun and humidity gradients) could be the selective pressure shaping differentiation in plumage melanism. We suggest that strong species differentiation in orbital ring colour results from sexual selection. We conclude that these large gull species, along with other recently diverged species that hybridize after coming into secondary contact, may differ only in restricted regions of the genome that are undergoing strong disruptive selection because of their phenotypic effects.

COMPARING CLINES ON MOLECULAR AND PHENOTYPIC TRAITS IN HYBRID ZONES: A WINDOW ON TENSION ZONE MODELS

The study of zones of secondary contact provides insight into the maintenance of reproductive isolation. Tension zone theory supplies powerful tools for assessing how dispersal and selection shape hybrid zones. We present a multimodal analysis of phenotypic clines in conjunction with clines at molecular markers in a hybrid zone between Larus glaucescens and Larus occidentalis. We developed a new method to analyze simultaneously clines of quantitative traits and molecular data. Low linkage disequilibrium and the lack of coincidence between clines at six microsatellites, a mitochondrial DNA region, and two phenotypic traits indicated introgression. However, the hypothesis of neutral diffusion was rejected based on evidence that all of the clines were concordant and narrower than expected for neutral clines, indicating some indirect selection. The analysis of phenotypic variance gave evidence of restricted phenotypic introgression and together with the bimodal distribution of phenotypes suggested that disruptive selection is acting across the hybrid zone, especially on the coloration of bare parts. Multimodal analysis of phenotypic clines also highlighted a shift between the peak of intermediates and the cline center, left behind by hybrid zone motion. High-resolution analysis of phenotypes distribution thus proved useful for detecting hybrid zone movement even without temporal data.

Habitat choice precedes host plant choice – niche separation in a species pair of a generalist and a specialist butterfly

The sister species Leptidea reali and L. sinapis have partitioned their niches differently in different parts of their sympatric distribution. In Spain and France L. sinapis is a widespread generalist whereas L. reali is specialized on high altitude open areas. Interestingly, the reverse is true in Ireland and the Czech Republic where L. reali is widespread and L. sinapis specialized on meadows. In Sweden, L. reali is a habitat specialist confined to meadows, whereas L. sinapis is a habitat generalist also inhabiting forests. Ultimately, the geographic mosaic of niche separation is the result of local processes in each contact zone or a secondary effect of the host plant distribution, if L. sinapis and L. reali prefer different legume host plants. Hence, in Sweden L. sinapis might utilize the forest habitat either due to a wider habitat preference or due to a wider host plant preference than L. reali. Studies of wild butterflies showed that L. sinapis laid 26% of their eggs on forest‐associated legumes compared to 6% in L. reali, although laboratory experiments showed that both species had virtually identical host plant preferences strongly preferring the meadow‐associated legume Lathyrus pratensis. Furthermore, flight duration tests in a variety of temperatures demonstrated a between‐species difference; L. sinapis females reached their flight optimum at a lower temperature than L. reali females. The lower L. sinapis flight temperature optimum is most probably a secondary effect due to habitat‐specific selection, and therefore a consequence rather than the cause of the habitat partitioning. The finding that habitat choice precedes host plant choice suggests that the European geographic mosaic of niche separation, with L. sinapis and L. reali shifting habitat specialist/generalist roles, is not caused by rigid between‐species differences in a related niche parameter, but instead is a result of local processes within each secondary contact zone.

Diffusion of nuclear and mitochondrial genes across a zone of secondary contact in the maritime shrew, Sorex maritimensis: implications for the conservation of a Canadian endemic mammal

The maritime shrew, Sorex maritimensis, is a Canadian endemic species with a limited distribution in two provinces in eastern Canada. Phylogeographic analysis of mitochondrial DNA control region and cytochrome b sequences revealed two clades, one found in New Brunswick and the other primarily in Nova Scotia, Canada. We propose that these clades have come back into secondary contact following the Wisconsin glaciation via wetlands on the narrow Isthmus of Chigneto that connects these provinces. Despite evidence of an historic separation of maritime shrew subpopulations in Nova Scotia and New Brunswick, we conclude that shrews in these two regions should be considered a single evolutionary significant unit but separate, semi-isolated management units that should be recognized as such for conservation purposes. The susceptibility of this stenotopic species with limited dispersal capabilities raises concerns about its long-term persistence if climate-change induced habitat fragmentation increases. Maintenance of contiguous wetland habitats is needed to ensure connectivity and gene flow among populations of the maritime shrew.

Genetic differentiation and secondary contact zone in the seagrass Cymodocea nodosa across the Mediterranean–Atlantic transition region

AbstractAim A central question in evolutionary ecology is the nature of environmental barriers that can limit gene flow and induce population genetic divergence, a first step towards speciation. Here we study the geographical barrier constituted by the transition zone between the Atlantic Ocean and the Mediterranean Sea, using as our model Cymodocea nodosa, a seagrass distributed throughout the Mediterranean and in the Atlantic, from central Portugal to Mauritania. We also test predictions about the genetic footprints of Pleistocene glaciations.Location The Atlantic–Mediterranean transition region and adjacent areas in the Atlantic (Mauritania to south‐west Portugal) and the Mediterranean.Methods We used eight microsatellite markers to compare 20 seagrass meadows in the Atlantic and 27 meadows in the Mediterranean, focusing on the transition between these basins.Results Populations from these two regions form coherent groups containing several unique, high‐frequency alleles for the Atlantic and for the Mediterranean, with some admixture west of the Almeria–Oran Front (Portugal, south‐west Spain and Morocco). These are populations where only one or a few genotypes were found, for all but Cadiz, but remarkably still show the footprint of a contact zone. This extremely low genotypic richness at the Atlantic northern edge contrasts with the high values (low clonality) at the Atlantic southern edge and in most of the Mediterranean. The most divergent populations are those at the higher temperature range limits: the southernmost Atlantic populations and the easternmost Mediterranean, both potential footprints of vicariance.Main conclusions A biogeographical transition region occurs close to the Almeria–Oran front. A secondary contact zone in Atlantic Iberia and Morocco results from two distinct dispersal sources: the Mediterranean and southernmost Atlantic populations, possibly during warmer interglacial or post‐glacial periods. The presence of high‐frequency diagnostic alleles in present‐day disjunct populations from the southernmost Atlantic region indicates that their separation from all remaining populations is ancient, and suggests an old, stable rear edge.