Phylogeographic Split Research Articles

Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia.

Multiple-island endemics (MIE) are considered ideal natural subjects to study patterns of island colonization that involve recent population-level genetic processes. Kleinia neriifolia is a Canarian MIE widespread across the archipelago, which exhibits a close phylogenetic relationship with species in northwest Africa and at the other side of the Sahara Desert. Here, we used target sequencing with plastid skimming (Hyb-Seq), a dense population-level sampling of K. neriifolia, and representatives of its African-southern Arabian relatives to infer phylogenetic relationships and divergence times at the species and population levels. Using population genetic techniques and machine learning (convolutional neural networks [CNNs]), we reconstructed phylogeographic relationships and patterns of genetic admixture based on a multilocus SNP nuclear dataset. Phylogenomic analysis based on the nuclear dataset identifies the northwestern African Kleinia anteuphorbium as the sister species of K. neriifolia, with divergence starting in the early Pliocene. Divergence from its sister clade, comprising species from the Horn of Africa and southern Arabia, is dated to the arid Messinian period, lending support to the climatic vicariance origin of the Rand Flora. Phylogeographic model testing with CNNs supports an initial colonization of the central island of Tenerife followed by eastward and westward migration across the archipelago, which resulted in the observed east/west phylogeographic split. Subsequent population extinctions linked to aridification events, and recolonization from Tenerife, are proposed to explain the patterns of genetic admixture in the eastern Canary Islands. We demonstrate that CNNs based on SNPs can be used to discriminate among complex scenarios of island migration and colonization.

Genetic variation among populations of, and evidence of deep divergence within, the Rio Grande Chirping Frog, Eleutherodactylus campi (Anura: Eleutherodactylidae)

Herein we report the first molecular assessment of intra-species genetic variation and interrelationships within the Rio Grande Chirping frog, Eleutherodactylus campi. We analyzed 548 base pairs of 16S rRNA gene for 71 ingroup individuals belonging to the genus Eleutherodactylus (including 42 E. campi sampled from 15 localities in the United States and Mexico) and four outgroup samples. By unveiling two highly divergent and geographically structured clades within E. campi this study provides a novel phylogenetic placement of E. campi populations north and south of the Rio Grande Valley as sister groups to each other. The observed level of genetic divergence between these two clades (5.8%) is, on average, comparable to or greater than the levels of divergence found between several currently valid amphibian species pairs. Estimates of Time to Most Common Ancestor (TMRCA) indicate that the phylogeographic split between the two E. campi clades may have occurred 7.6 MYA (i.e., late Miocene), consistent with the geologic history of southwestern North America. The study also confirms that south Texas served as the source population for populations of E. campi in its introduced range (i.e., Alabama, Louisiana, and Texas). Overall, this molecular study indicates that E. campi consists of two deeply divergent lineages corresponding to its populations north and south of Rio Grande Valley. These results suggest that the recovered lineages may represent independent species and thereby highlight the need for further research to clarify their status.

Deep phylogeographic splits and limited mixing by sea surface currents govern genetic population structure in the mangrove genus Lumnitzera (Combretaceae) across the Indonesian Archipelago

AbstractThe Indonesian Archipelago accommodates the largest mangrove area in Southeast Asia and possesses the world's richest composition of mangrove species. The archipelago comprises areas of the biogeographic regions Sunda and Wallacea, separated by Wallace's line. Here, we used the true mangrove species Lumnitzera littorea and Lumnitzera racemosa as a study case for understanding the effects of phylogeographic history, sea surface currents, and geographical distance on genetic diversity and genetic structure. We sampled 14 populations of L. littorea (N = 106) and 21 populations of L. racemosa (N = 152) from Indonesia and used 3122 and 3048 SNP loci, respectively, genotyped using the ddRADseq approach. We assessed genetic diversity, genetic structure, and effective dispersal of the populations and related them to geographical distance and sea surface currents. Our study revealed low levels of genetic variation at the population level in Lumnitzera. Pronounced genetic differentiation between populations indicated two phylogroups in both species. While in L. littorea the two phylogroups were largely separated by Wallace's line, L. racemosa showed a northwest vs. southeast pattern with strong mixture in Wallacea. Our findings provide novel insights into the phylogeography of the mangrove genus Lumnitzera and the role of sea surface currents in the Indonesian Archipelago.

Plant phylogeography of the Balkan Peninsula: spatiotemporal patterns and processes

The Balkan Peninsula is widely acknowledged as one of the centers of European biodiversity and a major glacial refugium for plant species. Its extensive geographic heterogeneity and diverse mosaic of habitats, coupled with relatively high environmental stability over long periods, have enabled the diversification of lineages and simultaneously fostered the long-term survival of diverse species. The increasing number of phylogeographically studied plant species in the region has substantially contributed to a better understanding of the relationships among closely related taxa and provided significant insights into intraspecific lineage differentiation. The present paper reviews the current knowledge on plant phylogeography in the Balkan Peninsula. By providing an updated overview of the most recent studies dealing with the diversity and evolution of Balkan plants, we explore the phylogeographic patterns and roles of refugia in structuring genetic diversity and highlight the crucial evolutionary processes that shaped the diversity of plants in the region. Molecular clock-based estimations highlight the importance of Pleistocene climatic fluctuations across taxonomic groups and lineage distribution patterns corroborate the persistence of multiple glacial refugia. Spatial congruence in phylogeographic splits is determined and discussed. An examination of phylogeographic connections with adjacent regions (i.e., the Alps, Apennine Peninsula, Asia Minor, Carpathians, and central Europe) uncovers several consistent patterns. Additionally, allopatric and ecological speciation, polyploidy, and hybridization are identified as crucial evolutionary mechanisms acting in the Balkan Peninsula and shaping species diversity. Furthermore, the existing research gaps are identified and future approaches with the potential to better understand the unique Balkan flora are highlighted.

The taxonomic status of Palearctic and Nearctic populations of northern goshawk Accipiter gentilis (Aves, Accipitridae): New evidence from vocalisations

The taxonomic status of the North American and Eurasian populations of northern goshawk A. gentilis has been called into question by recent molecular studies, indicating the need for additional taxonomic study. Vocalisations have long played an important role in diagnosing potentially reproductively isolated groups of birds. The chattering-type call of A. gentilis plays a role in advertisement and pair-contact, making this a suitable basis for taxonomic study of vocalisations. The data set consisted of recordings of the calls of 75 individuals of the Eurasian gentilis-group of A. gentilis, 37 of the North American atricapillus-group of A. gentilis and, for comparison, seven of Henst’s goshawk A. henstii. The three groups showed non-overlapping variation in the duration of call-notes and also showed several other highly significant differences. Discriminant Function Analysis resulted in 100% correct classification of recordings into the three groups. It is here argued that the new bioacoustic data, in combination with previous evidence of morphological, mitochondrial DNA and genomic DNA differences between Eurasian and North American A. gentilis, suggests that two species are best recognised: northern goshawk A. gentilis and American goshawk A. atricapillus. A. gentilis / A. atricapillus add to a growing list of Holarctic temperate zone taxa that have recently been recognised as separate species based on a deep phylogeographic split between Eurasian and North American populations in combination with differences in other characters. This is the first quantitative taxonomic study of vocalisations in Accipitridae.

Phylogeography of recent Plesiastrea (Scleractinia: Plesiastreidae) based on an integrated taxonomic approach

Scleractinian corals are a diverse group of ecologically important yet highly threatened marine invertebrates, which can be challenging to identify to the species level. An influx of molecular studies has transformed scleractinian systematics, highlighting that cryptic species may be more common than previously understood. In this study, we test the hypothesis that Plesiastrea versipora (Lamarck, 1816), a species currently considered to occur throughout the Indo-Pacific in tropical, sub-tropical and temperate waters, is a single species. Molecular and morphological analyses were conducted on 80 samples collected from 31 sites spanning the majority of the species putative range and twelve mitogenomes were assembled to identify informative regions for phylogenetic reconstruction. Congruent genetic data across three gene regions supports the existence of two monophyletic clades aligning with distinct tropical and temperate provenances. Multivariate macromorphological analyses based on 13 corallite characters provided additional support for the phylogeographic split, with the number of septa and corallite density varying across this biogeographic divide. Furthermore, micromorphological and microstructural analyses identified that the temperate representatives typically develop sub-cerioid corallites with sparse or absent coenosteal features and smooth septal faces. In contrast, tropical representatives typically develop plocoid corallites separated by a porous dissepimental coenosteum and have granulated septal faces. These data suggest that at least two species exist within the genus PlesiastreaMilne Edwards & Haime, 1848. Based on examination of type material, we retain the name Plesiastrea versipora (Lamarck, 1816) for the temperate representatives of the genus and resurrect the name Plesiastrea peroniMilne Edwards & Haime, 1857 for the tropical members. This study highlights how broadly distributed hard coral taxa still need careful re-examination through an integrated systematics approach to better understand their phylogeographic patterns. Furthermore, it demonstrates the utility of integrating micro-, macro-morphological and genetic datasets, and the importance of type specimens when dealing with taxonomic revisions of scleractinian taxa.

Pronounced mito-nuclear discordance and various Wolbachia infections in the water ringlet Erebia pronoe have resulted in a complex phylogeographic structure

Several morphological and mitochondrial lineages of the alpine ringlet butterfly species Erebia pronoe have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1α, RPS5) gene sequences and compared them with sequences from the sister species Erebia melas. Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with Wolbachia strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the E. pronoe-melas complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in E. melas and E. pronoe glottis can be explained by different ages of Wolbachia infections with different Wolbachia strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of E. pronoe glottis in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.

Molecular epidemiology of yellow fever virus in Africa: A perspective of the phylogeographic split between East/Central African and West African lineages

Yellow fever (YF) is a major public-health problem in Africa. Yellow fever virus (YFV), the etiological agent responsible for the disease, exhibits clear delineation of phylogeography between East/Central Africa and West Africa. In order to decipher the genetic nature of the YFV epidemic between these areas, we performed a genome-wide study on its African isolates using the McDonald-Kreitman (MK) test in combination with the type II functional divergence analysis. The results showed that adaptive genetic diversifications have occurred on viral nonstructural protein 1 (NS1) and NS5, which are essential for viral genome replication and immune antagonism, with the East/Central African–West African epidemic split. On both proteins, a number of amino acid replacements have been favored by functional divergence. These findings could help to bridge the gap between the phylogeographic delineation and niche adaptation underlying the YFV-epidemic across Africa and shed light on viral determinants of this process.

Deep phylogeographic splits but no taxonomic structure in the disjointly distributed Draba pacheri (Brassicaceae), a subendemic of the Eastern Alps

Draba (Brassicaeae), a model group for diversification and evolution in Arctic and mountain habitats, is taxonomically challenging and many of its species are insufficiently investigated. One such species is D. pacheri, an endemic of the eastern European Alps and the western Carpathians (here presumably extinct). Several hypotheses exist with respect to the phylogenetic position and the taxonomy of this species, but none of these has ever been tested using molecular data. In this article we examine (i) DNA sequence data to assess the phylogenetic position of D. pacheri within the genus and (ii) AFLP fingerprint data as well as morphometric data to address whether this species can be divided taxonomically into species or subspecies. DNA sequence data firmly place D. pacheri within the Core Draba Group III, whose internal relationships are, however, insufficiently resolved to precisely identify the closest relative of D. pacheri. AFLP data identify several genetically divergent lineages corresponding to geographically distinct regions. Although these lineages are congruent with hypotheses distinguishing either two species (D. pacheri s. str., D. norica) or one species with several subspecies, the lack of clear morphological separation, both with respect to the entire set of traits and single presumably diagnostic characters such as trichome morphology, renders recognition of a single species D. pacheri, as suggested previously, the best taxonomic solution. The deep and geographically strongly structured splits of D. pacheri likely are the result of isolation in several Pleistocene refugia and warrant that conservation efforts should involve populations from each of the main geographic subgroups.

Phylogeography and taxonomic reassessment of Arabidopsis halleri – a montane species from Central Europe

Evolutionary histories of plants from the mid-elevation (montane) zone of European mountain ranges have only rarely been documented, standing in contrast to those of well-researched inhabitants of (sub-)alpine and foothill zones. To fill this gap, we have reconstructed the phylogeography of Arabidopsis halleri, a species preferring coniferous woodlands and corresponding secondary habitats in the montane zone of the Alps, Carpathians, Hercynian massif and Dinaric Alps. Based on range-wide sampling and finer-scale analyses of multiple multilocus DNA markers, we have addressed phylogeographic patterns among the Carpathian populations and inferred their relationships to A. halleri from neighbouring mountain ranges. We also present a taxonomic re-evaluation of the species in Europe, based on the revealed genetic structure complemented by morphological data. Besides two distinct Alpine groups, we identified a major phylogeographic split between the Western and South-Eastern Carpathians. Interestingly, Western and South-Eastern Carpathian populations were genetically closer to populations from neighbouring mountain ranges (the Hercynian massif and the Dinaric Alps for the Western and South-Eastern Carpathians, respectively) than they were to each other, likely reflecting long-term isolation in different parts of the Carpathians or different (re)colonization pathways during the Holocene. In spite of the considerable environmentally correlated variation, the five major European genetic groups exhibited distinctive morphological characters, and we therefore propose treating them as separate subspecies: A. halleri subsp. halleri (Western Europe, Hercynian massif), A. halleri subsp. tatrica (Western Carpathians), A. halleri subsp. ovirensis (Eastern Alps), A. halleri subsp. occidentalis (Western Alps) and A. halleri subsp. dacica (Eastern and Southern Carpathians and Dinaric Alps).

Both vicariance and dispersal have shaped the genetic structure of Eastern Mediterranean Euphorbia myrsinites (Euphorbiaceae)

The Eastern Mediterranean is considered both a reservoir for plant evolution and a cradle for lineage diversification, but most plant groups from this area remain unstudied. To explore phylogeographic patterns within Eastern Mediterranean Euphorbia myrsinites, covering the area from the Apennines to Central Anatolia, we sequenced nuclear ribosomal ITS and the plastid trnT–trnF region and generated amplified fragment length polymorphism (AFLP) fingerprints, along with relative genome size (RGS) data. Our data reveal a complex evolutionary history of E. myrsinites since its origin at the Pliocene/Pleistocene boundary, resulting in a genetic structure that was shaped by fundamentally different processes acting at different time levels. Despite their weak glaciation in the Pleistocene, the high mountain ranges of the western and southern Balkan Peninsula triggered the initial divergence within this species due to vicariance in the Adriatic-Ionian and the Aegean-Pontic Pleistocene refugia. Subsequent range expansions led to the intriguing situation that both clusters nowadays occur in close spatial proximity. In addition, stronger genetic differentiation in the Aegean-Pontic area probably reflects less severe impacts of glaciations and higher environmental stability throughout the Pleistocene in this area, as compared to the Amphi-Adriatic region. The colonization of the Apennine Peninsula from the Balkan Peninsula took place later in the species’ evolutionary history, probably over land bridges connecting both peninsulas in the Pleistocene. On the western Balkan Peninsula the main phylogeographic split is situated along the Neretva river valley. To the north of this valley we detected no population structure whereas strong genetic differentiation in the southerly adjacent areas confirms the “refugia-within-refugia” hypothesis.

Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis.

Yersinia pseudotuberculosis is a Gram-negative intestinal pathogen of humans and has been responsible for several nationwide gastrointestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic species of the genus Yersinia, Yersinia pestis and Yersinia enterocolitica allowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no purpose-designed large-scale global population genomic analysis of Y. pseudotuberculosis has been performed. Here we present analyses of the genomes of 134 strains of Y. pseudotuberculosis isolated from around the world, from multiple ecosystems since the 1960s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.

Genetic Structure across Broad Spatial and Temporal Scales: Rocky Mountain Tailed Frogs (Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate Rainforest.

Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future changes in the range as a function of changing climate. Genetic structure has a strong spatial signature that is precisely congruent with a deep (~1.8 MY) phylogeographic split in mtDNA when we partition populations into 2 clusters (K = 2), and is congruent with refugia areas inferred from our paleorange reconstructions. There is a hierarchical pattern of geographic structure as we permit additional clusters, with populations clustering following mountain ranges. Nevertheless, genetic diversity is the highest in populations at the center of the range and is attenuated in populations closer to the range edges. Similarly, geographic distance is the single best predictor of pairwise genetic differentiation, but connectivity also is an important predictor. At intermediate and local geographic scales, deviations from isolation-by-distance are more apparent, at least in the northern portion of the distribution. These results indicate that both historical and landscape factors are contributing to the genetic structure and diversity of tailed frogs in the Inland Northwest.

Mitochondrial DNA analysis reveals Holarctic homogeneity and a distinct Mediterranean lineage in the Golden eagle (Aquila chrysaetos)

The Golden eagle (Aquila chrysaetos) is among the most widespread of the birds of prey, covering basically the whole Palaearctic from Europe and North Africa through Asia and Japan, to the North American continent. Only few studies have addressed the species' genetic structure and the consequences of its demographic history so far, and none of them has covered larger areas of the distribution range. Our present study aims at closing this gap. Based on 283 samples (mostly feathers collected in the field or from museum collections) across the species' distribution, but with a focus on Europe, we uncover the phylogeography of the Golden eagle. Results imply a phylogeographic split between mainly Northern Europe, Continental Asia, Japan and North America on the one hand and Central–Southern Europe on the other. The observed pattern is likely to be caused by the Last Ice Age, when the population survived in two reproductively isolated glacial refugia. Repopulation of Northern Europe occurred from a presumed Asian refugium, whereas the Alpine range was probably repopulated from a refugium in the Mediterranean region. In Eastern Europe, the Mediterranean and Alpine region we find a co-occurrence of both lineages that heavily influences the local genetic diversity. This pattern is unlike that in most other large raptors in which usually a western and an eastern Eurasian lineage have been recovered.

Small-scale genetic structure of Gracilaria salicornia and its red algal parasite, G. babae (Gracilariaceae, Rhodophyta), in Malaysia

Abstract The present study compares genetic structure from the plastid rbcL, mitochondrial cox1, and nuclear internal transcribed spacer (ITS) sequences among 13 populations of Gracilaria salicornia and its red algal parasite, G. babae, in Malaysia. Owing to the unique biology of the red algal parasite, identical phylogeographies were inferred from the rbcL and cox1 sequences in both G. babae and its host, G. salicornia. Despite the low genetic variation, rbcL and cox1 showed a concordant phylogeographic split that largely corresponds to Peninsular Malaysia and East Malaysia, except for a sample from East Malaysia that was consistently grouped with samples from the peninsula. On the other hand, G. salicornia was separated from G. babae in the midpoint-rooted phylogeny inferred from ITS data despite the failure to retrieve the two taxa in reciprocal monophyly. Gracilaria salicornia was less diverse and lacked apparent geographic structure. In contrast, the ITS data revealed considerable genetic diversity and fine-scale genetic structuring in G. babae within Malaysian waters, probably as a result of adaptation to the local host population.

Patterns and processes in plant phylogeography in the Mediterranean Basin. A review

Phylogeography, born to bridge population genetics and phylogenetics in an explicit geographic context, has provided a successful platform for unveiling species evolutionary histories. The Mediterranean Basin, one of the earth's 25 biodiversity hotspots, is known for its complex geological and palaeoclimatic history. Aiming to throw light on the causes and circumstances that underlie such a rich biota, a review of the phylogeographic literature on plant lineages from the Mediterranean Basin is presented focusing on two levels. First, phylogeographic patterns are examined, arranged by potential driving forces such as longitude, latitude – and its interaction with altitude –, straits or glacial refugia. Spatial coincidences in phylogeographic splits are found but, in comparison to other regions such as the Alps or North America, no largely common phylogeographic patterns across species are found in this region. Factors contributing to phylogeographic complexity and scarcity of common patterns include less drastic effects of Pleistocene glaciations than other temperate regions, environmental heterogeneity, the blurring of genetic footprints via admixing over time and, for older lineages, possibly a greater stochasticity due to the accumulation of responses to palaeoclimatic changes. At a second level, processes inferred in phylogeographically framed studies that are potential drivers of evolution are examined. These include gradual range expansion, vicariance, long-distance dispersal, radiations, hybridization and introgression, changes in reproductive system, and determinants of successful colonization. Future phylogeographic studies have a great potential to help explaining biodiversity patterns of plant groups and understanding why the Basin has come to be one of the biodiversity hotspots on earth. This potential is based on the crucial questions that can be addressed when geographic gaps are adequately filled (mainly northern Africa and the eastern part of the region), on the important contribution of younger lineages – for which phylogeographic approaches are most useful – to the whole diversity of the Basin, and on the integration of new methods, particularly those that allow refining the search for spatio-temporal concordance across genealogies.

Reproductive isolation between phylogeographic lineages scales with divergence

Phylogeographic studies frequently reveal multiple morphologically cryptic lineages within species. What is not yet clear is whether such lineages represent nascent species or evolutionary ephemera. To address this question, we compare five contact zones, each of which occurs between ecomorphologically cryptic lineages of skinks from the rainforests of the Australian Wet Tropics. Although the contacts probably formed concurrently in response to Holocene expansion from glacial refugia, we estimate that the divergence times (τ) of the lineage pairs range from 3.1 to 11.5 Ma. Multi-locus analyses of the contact zones yielded estimates of reproductive isolation that are tightly correlated with divergence time and, for lineages with older divergence times (τ > 5 Myr), substantial. These results show that phylogeographic splits of increasing depth represent stages along the speciation continuum, even in the absence of overt change in ecologically relevant morphology.

Genetic Diversity of Northeastern Palaearctic Bats as Revealed by DNA Barcodes

Sequences of the DNA barcode region of the cytochrome oxidase subunit I gene were obtained from 3 8 species of northeastern Palaearctic bats to assess patterns of genetic diversity. These results confirmed earlier findings of deep phylogeographic splits in four pairs of vicariant species (Myotis daubentoniilpetax, M. nattererilbombinus, Plecotus aurituslognevi and Miniopterus schreibersiil fuliginosus) and suggested previously unreported splits within Eptesicus nilssoni and Myotis aurascens. DNA barcodes support all taxa raised to species rank in the past 25 years and suggest that an additional species — Myotis sibiricus — should be separated from Myotis brandtii. Major phylogeographic splits occur between European and Asian populations of Myotis aurascens, Rhinolophus ferrumequinum and Myotis frater; smaller scale splits are observed between insular and mainland populations in the Far East (M. frater, Myotis ikonnikovi and Murina ussuriensis) and also between southeastern Europe and Ciscaucasia (Myotis daubentonii, Plecotus auritus, and Pipistrellus pipistrellus). One confirmed case of sequence sharing was observed in our dataset — Eptesicus nilssoni/serotinus. This study corroborates the utility of DNA barcodes as a taxonomic assessment tool for bats.

Patterns of Genetic Differentiation Among Populations of Smilisca fodiens

The Trans-Mexican Volcanic Belt and surrounding areas contain substantial biological diversity. The mountains that make up the Trans-Mexican Volcanic Belt are a hypothesized biogeographic barrier for the terrestrial fauna found in the region. Several phylogeographic studies have provided genetic evidence in support of this historical narrative; however, the species examined represent a small percentage of the diversity found in this part of Mexico. Thus, additional studies are needed to identify concordant phylogeographic patterns and infer the historic species composition of particular ecoregions. In this study we investigated genetic variation in the Lowland Burrowing Treefrog, Smilisca fodiens, a species that occurs on both sides of the Trans-Mexican Volcanic Belt. We used mitochondrial (12S and 16S ribosomal subunits; 1039 base pairs [bp]) and nuclear (tyrosinase precursor; 513 bp) DNA to perform phylogenetic analyses on frogs from several localities in Mexico. Mitochondrial DNA supported two well-defined clades that correspond to populations found north and south of the Trans-Mexican Volcanic Belt, respectively. These analyses of matrilineal lineages also found higher levels of genetic diversity south of the Trans-Mexican Volcanic Belt. Although our nuclear DNA analysis did not reveal a phylogeographic split at the Trans-Mexican Volcanic Belt, we observed higher genetic variation among our southern samples, similar to the mitochondrial analyses. Our results are consistent with studies in other sympatric taxa that propose the Trans-Mexican Volcanic Belt as a biogeographic barrier. Additionally, our results suggest recent northern range expansion of S. fodiens. We suggest retaining S. fodiens as a single species until future work can clarify the amount and direction of gene flow between the mitochondrial clades.

Complex genetic population structure of the bivalve Cerastoderma glaucum in a highly fragmented lagoon habitat

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 406:173-184 (2010) - DOI: https://doi.org/10.3354/meps08549 Complex genetic population structure of the bivalve Cerastoderma glaucum in a highly fragmented lagoon habitat K. Tarnowska1,2, A. Chenuil2,*, R. Nikula3,4, J.-P. Féral2, M. Wołowicz1 1Laboratory of Estuarine Ecology, Institute of Oceanography, University of Gdańsk, Al. Piłsudskiego 46, 81-378 Gdynia, Poland 2UMR 6540 CNRS DIMAR, Centre d’Océanologie de Marseille, Université de la Méditerranée, Station Marine d’Endoume, Rue de la Batterie des Lions, 13007 Marseille, France 3Finnish Museum of Natural History, PO Box 26, FI-00014 University of Helsinki, Finland 4Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand *Corresponding author. Email: anne.chenuil-maurel@univmed.fr ABSTRACT: The genetic structure of a lagoon specialist, the bivalve Cerastoderma glaucum, was studied from 4 nuclear microsatellite loci and sequences from a 514 bp mitochondrial DNA region. Both marker types revealed strong differentiation among populations that is likely due to the highly fragmented distribution of this species. The geographic location and strength of the major divisions were different between the genomes. The deepest phylogeographic split in mtDNA grouped Aegean Sea and Ponto-Caspian region populations against the more western populations, whereas nuclear data singled out Ionian Sea populations or indicated a Ponto-Caspian character of nuclear DNA from the Ionian Sea. In agreement with their presumably rapid post-glacial establishment, the northern populations showed evidence of founder effects and strong genetic drift in their genetic structuring. Two unexpected geographic disjunctions were detected in the mtDNA, but not in the microsatellite characteristics, of the studied populations. We suspect long-distance dispersal via migrating birds to be a probable dispersal means among isolated lagoon habitats and to have generated the disjunctions by contributing to the post-glacial spread of C. glaucum to its northern distribution area. The discrepancies between the nuclear and mitochondrial genetic characteristics of the populations could be a result of selective sweeps in mtDNA, sex-biased dispersal, biased effective sex ratio or differential introgression of the genomes. The high level of differentiation found between the main genetic groups led us to conclude that the taxonomy of Cerastoderma needs revision, but we acknowledge that due to hybridization the taxa can be occasionally impossible to delineate. KEY WORDS: Microsatellites · mtDNA · Lagoon · Glacial refuge Full text in pdf format Supplementary material PreviousNextCite this article as: Tarnowska K, Chenuil A, Nikula R, Féral JP, Wołowicz M (2010) Complex genetic population structure of the bivalve Cerastoderma glaucum in a highly fragmented lagoon habitat. Mar Ecol Prog Ser 406:173-184. https://doi.org/10.3354/meps08549Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 406. Online publication date: May 10, 2010 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2010 Inter-Research.