Phylogeographic Break Research Articles

Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster.

Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species' range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction‐site‐associated DNA sequencing; these SNPs were selected to maximize differentiation at a range of both broad and fine scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the north‐east Atlantic was revealed using both putatively neutral and outlier SNPs, but the precise driver(s) of this clinal pattern—isolation by distance, secondary contact, selection across an environmental gradient, or a combination of these factors—remains undetermined. Putatively neutral markers differentiated lobsters from Oosterschelde, an estuary on the Dutch coast, a finding likely explained by past bottlenecks and limited gene flow with adjacent North Sea populations. Building on the findings of our spatial genetic analysis, we were able to test the accuracy of assigning lobsters at various spatial scales, including to basin of origin (Atlantic or Mediterranean), region of origin and sampling location. The predictive model assembled using 79 SNPs correctly assigned 99.7% of lobsters not used to build the model to their basin of origin, but accuracy decreased to region of origin and again to sampling location. These results are of direct relevance to managers of lobster fisheries and hatcheries, and provide the basis for a genetic tool for tracing the origin of European lobsters in the food supply chain.

High genetic differentiation in the edible cannonball jellyfish (cnidaria: Scyphozoa: Stomolophus spp.) from the Gulf of California, Mexico

Studies of population genetic structure in relation to ecological and evolutionary processes are crucial for conservation genetics and particularly for sustainable management of fisheries. However, such knowledge is not always available for the management of fisheries, as is the case of the edible cannonball jellyfish Stomolophus spp. fishery in the Gulf of California, Mexico. The aim of this study is describe the population genetic structure of cannonball jellyfish in the Gulf of California. We used sequences of cytochrome oxidase I (COI) and microsatellite markers in five locations within the Gulf of California and the southern Pacific coast. Both COI and microsatellite markers corroborated the presence of two differentiated genetic lineages in the fishing areas, which diverged around 1.17 Mya: Stomolophus sp.1, distributed in the Golfo de Santa Clara; and Stomolophus sp.2, in the southern region of the Gulf of California and the Pacific coast of the Baja California peninsula. In addition, significant differentiation between the four locations within the lineage Stomolophus sp.2 was found (mean FST: 0.56 and 0.12 for COI and microsatellites respectively). Our results are consistent with the endemism and phylogeographic break hypotheses proposed for the northern region of the Gulf of California. We proposed that the historical geology and complex oceanography of the Gulf of California might be responsible of this species-level differentiation. Conversely, the population structure within Stomolophus sp.2 could be more related to the life cycle, and particularly due the short larval dispersal stage of cannonball jellyfish in the Gulf of California.

Phylogeography of ants from the Brazilian Atlantic Forest

Known for its remarkable biodiversity and high levels of endemism, the Brazilian Atlantic Rainforest has been characterized as one of the most threatened biomes on the planet. Despite strong interest in recent years, we still lack a comprehensive scenario to explain the origin and maintenance of diversity in this region, partially given the relatively low power of analyses involving few independent genetic loci. In this study, we examine a phylogenomic dataset of five ant species to investigate phylogeographical patterns across the Brazilian Atlantic Forest. We sequenced ultraconserved elements to generate hundreds of loci using a bait set developed specifically for hymenopterans. We analyzed the data using Bayesian and maximum likelihood approaches of phylogenetic inference. Results were then integrated with environmental niche modeling of current and past climates, including the Last Glacial Maximum and the last interglacial period. The studied species showed differentiation patterns that were consistent with the north/south division of the Atlantic Rainforest indicated in previous studies for other taxa. However, there were differences among species, both in the location of phylogeographic breaks and in the pattern of genetic variation within these areas. Samples from southern localities tended to show recent genetic structure, although a site in Tapirai (state of Sao Paulo) repeatedly showed an intriguing older history of differentiation. All species experienced shifts in areas of suitability through the time. Our study suggests that distinct groups may have responded idiosyncratically to the climatic changes that took place in the Brazilian Atlantic Forest. The amount of intraspecific genetic structure was related to the inferred geographical distribution of habitat suitability according to current and past times. Also, a parallel between the amount of Quaternary climatic suitability and the level of interspecific differentiation was detected for four species. Finally, despite strong contractions at the northeastern region of the forest, the remaining areas appear to have been able to act as refugia.

A river runs through it: tree frog genomics supports the Dead Sea Rift as a rare phylogeographical break

AbstractPhylogeographical breaks can be viewed as regional hotspots of diversity where the genetic integrity of incipient species is put to the test. We focus on an understudied species transition from the Middle East, namely the Dead Sea Rift in the Levant region, which presumably divided the tree frogs Hyla savignyi and H. felixarabica. Combining multilocus genetic analyses (mitochondrial DNA and RAD-sequencing) with ecological niche modelling, we test whether the rift effectively acts as a biogeographical barrier preventing this pair from admixing and merging. The answer is yes: despite weak signs of introgression, all parapatric populations were assigned to either species without cyto-nuclear discordance. Yet, the projected distributions under present and glacial conditions largely overlapped in the area, meaning their current parapatric ranges do not represent an ecological transition. Instead, we hypothesize that H. savignyi and H. felixarabica are maintained apart by limited opportunities for dispersal across the barren Jordan Valley, combined with advanced reproductive isolation. Therefore, the Dead Sea Rift may represent a rare phylogeographical break, and we encourage international efforts to assess its contribution to the rich biodiversity of the Middle East.

Genetic and morphological divergence at a biogeographic break in the beach-dwelling brooder Excirolana hirsuticauda Menzies (Crustacea, Peracarida)

BackgroundThere is a biogeographic break located at 30°S in the southeast Pacific, in a coastal area of strong environmental discontinuities. Several marine benthic taxa with restricted dispersal have a coincident phylogeographic break at 30°S, indicating that genetic structure is moulded by life history traits that limit gene flow and thereby promote divergence and speciation. In order to evaluate intraspecific divergence at this biogeographic break, we investigated the genetic and morphological variation of the directly developing beach isopod Excirolana hirsuticauda along 1900 km of the southeast Pacific coast, across 30°S.ResultsThe COI sequences and microsatellite data both identified a strong discontinuity between populations of E. hirsuticauda to the north and south of 30°S, and a second weaker phylogeographic break at approximately 35°S. The three genetic groups were evidenced by different past demographic and genetic diversity signatures, and were also clearly distinguished with microsatellite data clustering. The COI sequences established that the genetic divergence of E. hirsuticauda at 30°S started earlier than divergence at 35°. Additionally, the three groups have different past demographic signatures, with probable demographic expansion occurring earlier in the southern group (south of 35°S), associated with Pleistocene interglacial periods. Interestingly, body length, multivariate morphometric analyses, and the morphology of a fertilization-related morphological character in males, the appendix masculina, reinforced the three genetic groups detected with genetic data.ConclusionsThe degree of divergence of COI sequences, microsatellite data, and morphology was concordant and showed two geographic areas in which divergence was promoted at differing historical periods. Variation in the appendix masculina of males has probably promoted reproductive isolation. This variation together with gene flow restrictions promoted by life history traits, small body size, oceanographic discontinuities and sandy-beach habitat continuity, likely influenced species divergence at 30°S in the southeast Pacific coast. The degree of genetic and morphological differentiation of populations to the north and south of 30°S suggests that E. hirsuticauda harbours intraspecific divergence consistent with reproductive isolation and an advanced stage of speciation. The speciation process within E. hirsuticauda has been shaped by both restrictions to gene flow and a prezygotic reproductive barrier.

Comparative phylogeography of five widespread tree species: Insights into the history of western Amazonia.

Various historical processes have been put forth as drivers of patterns in the spatial distribution of Amazonian trees and their population genetic variation. We tested whether five widespread tree species show congruent phylogeographic breaks and similar patterns of demographic expansion, which could be related to proposed Pleistocene refugia or the presence of geological arches in western Amazonia. We sampled Otoba parvifolia/glycycarpa (Myristicaceae), Clarisia biflora, Poulsenia armata, Ficus insipida (all Moraceae), and Jacaratia digitata (Caricaceae) across the western Amazon Basin. Plastid DNA (trnH–psbA; 674 individuals from 34 populations) and nuclear ribosomal internal transcribed spacers (ITS; 214 individuals from 30 populations) were sequenced to assess genetic diversity, genetic differentiation, population genetic structure, and demographic patterns. Overall genetic diversity for both markers varied among species, with higher values in populations of shade‐tolerant species than in pioneer species. Spatial analysis of molecular variance (SAMOVA) identified three genetically differentiated groups for the plastid marker for each species, but the areas of genetic differentiation were not concordant among species. Fewer SAMOVA groups were found for ITS, with no detectable genetic differentiation among populations in pioneers. The lack of spatially congruent phylogeographic breaks across species suggests no common biogeographic history of these Amazonian tree species. The idiosyncratic phylogeographic patterns of species could be due instead to species‐specific responses to geological and climatic changes. Population genetic patterns were similar among species with similar biological features, indicating that the ecological characteristics of species impact large‐scale phylogeography.

Every beach an island—deep population divergence and possible loss of genetic diversity in Tylos granulatus, a sandy shore isopod

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 614:111-123 (2019) - DOI: https://doi.org/10.3354/meps12882 Every beach an island—deep population divergence and possible loss of genetic diversity in Tylos granulatus, a sandy shore isopod Nozibusiso A. Mbongwa1, Cang Hui2, Andrea Pulfrich3, Sophie von der Heyden1,* 1Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa 2Department of Mathematical Sciences, University of Stellenbosch, and African Institute for Mathematical Sciences, Matieland 7602, South Africa 3Pisces Environmental Services (Pty) Ltd, PO Box 302, McGregor 6708, South Africa *Corresponding author: svdh@sun.ac.za ABSTRACT: Biogeographic and phylogeographic patterns of sandy beach species are poorly understood, although these ecosystems are heavily impacted by anthropogenic pressures and are of elevated conservation concern. To contribute towards filling the knowledge gap on sandy beaches, we made use of phylogeographic approaches to determine levels of genetic structuring and diversity for Tylos granulatus, a large isopod with direct development distributed in South Africa and Namibia. Individuals (n = 214) were sampled from 9 locations encompassing the entire distribution range, and sequence data were generated for mtDNA cytochrome c oxidase subunit I (COI) and 16S. Results revealed high levels of population structuring between populations (ΦST = 0.11-0.96, p < 0.05), 2 deeply divergent lineages of T. granulatus and a new phylogeographic break in southern Africa. Northern populations are genetically more diverse, suggesting more stable evolutionary history compared to those in the south. Importantly, the patterns of divergence suggest unique evolutionary signals over short spatial scales (<80 km), with nearly all T. granulatus populations effectively isolated from each other. This, in combination with increasing anthropogenic disturbance throughout their range, leaves this species extremely vulnerable to local, and potentially regional, loss and extinction of genetic diversity. We suggest that T. granulatus serves as a valuable bioindicator, which, if recognised for protection, will broadly capture biological and evolutionary patterns of other sandy beach macrofauna in the region. Our work adds to a growing field of sandy beach science, and contributes towards a better understanding of the significance, vulnerability and complexity of sandy beach ecosystems for conservation and management aims. KEY WORDS: Anthropogenic pressures · Marine isopod · Sandy beach ecosystems · Population differentiation · Evolutionary lineages · Conservation genetics · Population decline Full text in pdf format PreviousNextCite this article as: Mbongwa NA, Hui C, Pulfrich A, von der Heyden S (2019) Every beach an island—deep population divergence and possible loss of genetic diversity in Tylos granulatus, a sandy shore isopod. Mar Ecol Prog Ser 614:111-123. https://doi.org/10.3354/meps12882 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 614. Online publication date: April 04, 2019 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2019 Inter-Research.

Pre‐Pleistocene origin of phylogeographical breaks in African rain forest trees: New insights from Greenwayodendron (Annonaceae) phylogenomics

AbstractAimPalaeoecological records indicate that Pleistocene glaciations affected the African rain forest, probably causing its fragmentation, which could explain phylogeographical breaks documented in many tree species. This refuge hypothesis was further tested through species distribution models, hindcasting persistence during the Last Glacial Maximum. However, previous studies failed to estimate with sufficient precision the divergence time between phylogeographical entities to confirm their Pleistocene origin. Developing genomic tools on a representative tree of mature rain forests, we test if parapatric genetic clusters documented in widespread tree species can be interpreted as the legacy of past population fragmentation during the last glacial period(s).LocationTropical Africa, Guineo‐Congolian forests.TaxonGreenwayodendron (Annonaceae).MethodsTo further test the Pleistocene refuge hypothesis by molecular dating, we sequenced the plastome of 145 individuals of the shade‐tolerant rain forest tree Greenwayodendron suaveolens and congeneric species, and genotyped the same samples using nuclear microsatellites to identify genetic clusters.ResultsFive plastid phylogroups of G. suaveolens occur in parapatry throughout Central Africa, following a spatial pattern generally congruent with genetic clusters. Four of them diverged 3.5–4.5 Ma, whereas the fifth one, located in the Cameroon volcanic line (CVL), diverged 8.3 Ma, in the range of divergence times between Greenwayodendron species, highlighting the key role of the CVL in hosting ancient lineages. Within phylogroups, most nodes were dated from 0.9 to 3.2 Myr and a correlation between haplotype divergence and spatial distance was still perceptible, indicating a slow population dynamic.Main conclusionsThe phylogeographical structures of Central African trees probably established during the Pliocene or early Pleistocene, and while they might have been reinforced during subsequent glacial–interglacial cycles, interglacial phases did not lead to genetic homogenization. Therefore, interpreting phylogeographical patterns of African trees must account for a much deeper past than previously assumed, and cannot be limited to the last glacial period.

Testing Hypotheses of Diversification in Panamanian Frogs and Freshwater Fishes Using Hierarchical Approximate Bayesian Computation with Model Averaging

Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Molecular Ecology 1998, 7, 499–517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.

Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses

BackgroundThe unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs.MethodsThe phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses.ResultsNo spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years.DiscussionThe comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers.

Pleistocene divergence of two disjunct conifers in the eastern Australian temperate zone

The eastern Australian temperate biota harbours many plants with fragmented geographic ranges distributed over 1000s of kilometres, yet the spatial genetic structure of their populations remains largely unstudied. In this study, we investigated genetic variation of the nuclear internal transcribed spacer (ITS) and chloroplast DNA sequences to disentangle the phylogeography of two widely distributed but highly fragmented eastern Australian fire-sensitive temperate conifers: Callitris oblonga (12 populations and 121 individuals) and C. rhomboidea (22 populations and 263 individuals). The three highly disjunct populations of C. oblonga all had unique chloroplast and ITS haplotypes consistent with the classification of these three populations as distinct subspecies. Molecular dating indicates that divergences of these populations occurred pre- to mid- Pleistocene (2.66 to 1.08 mya). Callitris rhomboidea showed greater diversity of chloroplast haplotypes which was strongly phylogeographically structured (Gst = 0.972), with haplotypes unique to specific geographic regions. ITS haplotype diversity was far higher than in C. oblonga with 38 haplotypes displaying high geographic structuring (Gst = 0.387) with many population-specific haplotypes. A phylogeographic break was identified between populations north and south of eastern Victoria dated at 0.43–0.47 mya. In both species, the strong genetic structuring of both chloroplast and ITS haplotypes provides evidence that their widespread ranges have resulted from long term persistence in low fire frequency refugia combined with poor dispersal. Any loss of populations due to increasing fire frequency or habitat loss is likely to result in a reduction of genetic diversity.

Environmental transition zone and rivers shape intraspecific population structure and genetic diversity of an Amazonian rain forest tree frog

Diversification processes acting across geographically continuous populations have been rarely documented in Amazonia, because of the lack of fine-scale sampling over extensive areas. We aimed to determine the geographic effects of an environmental transition zone and large rivers on the intraspecific population structure of the Manaus slender-legged tree frog (Osteocephalus taurinus) along a ~ 900 km transect of tropical rain forest. Using one mitochondrial (16S), two nuclear genes (TYR, POMC) and three microsatellites, we estimated the population structure, phylogenetic relationships and geographic variation of 262 O. taurinus and 5 O. oophagus (a close relative) along the Purus–Madeira interfluve (PMI) and opposite banks of the central Amazon and upper Madeira rivers, at central-southern Amazonia, Brazil. Six genetic clusters were identified: two corresponding to sympatric populations of O. taurinus and O. oophagus from their type locality, north of Amazon river. Within PMI, there were three distinct O. taurinus genetic clusters distributed along the geographic gradient with one main phylogeographic break found (concordant between 16S and TYR), that corresponds to a transition zone (ecotone) between dense and open rain forest ecotypes. The sixth cluster was an O. taurinus population isolated at the east bank of the upper Madeira river. In addition, restricted haplotype sharing was identified from the west to east banks at upper Madeira river. Within PMI, parapatric genetic structure is explained by a potential association of the genetic clusters to the different forest ecotypes they inhabit coupled with isolation by distance, thus supporting the gradient hypothesis for diversification. Differentiation of populations that are external to the PMI is most likely explained by the barrier effect of the Madeira and Amazon rivers. Our findings provide new evidence on diversification processes across continuous Amazonian landscapes; however, the specific mechanisms underlying the origin and maintenance of the identified phylogeographic break need to be further studied.

Genetic structure of intertidal shimofuri goby in the Zhejiang Coastal Sea, China: implications for management

The shimofuri gobies Tridentiger bifasciatus (Gobiidae: Gobionellinae), are small, benthic fish indigenous to the coastal waters of the West Pacific Ocean. In this study, 582-bp mitochondrial cytochrome C subunit I (COI) and 789-bp nuclear ryanodine receptor 3 (Ryr3) DNA sequence data were employed to evaluate population genetic structure of T. bifasciatus. A total of 14 distinct COI haplotypes and 14 distinct Ryr3 alleles were recovered for 140 samples collected from eight intertidal localities in the Zhejiang Coastal Sea, China. The indices of haplotype and nucleotide diversity within populations are 0.42–0.87 (Hd) and 0.13–0.54% (π) for COI and 0.26–0.59 (Hd) and 0.05–0.09% (π) for Ryr3. FST distances between population pairs are − 0.007–0.768 (COI) and − 0.030–0.311 (Ryr3). The south population of Cangnan exhibits significant divergence from all the north populations (p < 0.01). The median-joining (MJ) network indicates that one COI haplotype and one Ryr3 allele found in Cangnan are absent in all the north populations. This observation of phylogeographic break can be interpreted: (1) the dispersal of T. bifasciatus is driven more by small-scale local currents, including inflows of local rivers than by large-scale oceanographic currents; (2) the recruitment is frequently shared among the geographically proximate populations in the northern areas of Zhejiang Coastal Sea, whereas infrequently shared between Cangnan and geographically distant north populations. Tajima’s D statistics, star-like pattern observed on the MJ network, and mismatch distribution analysis present compelling evidence for pronounced demographic fluctuations for the overall population of T. bifasciatus, and infer that the species along the Zhejiang Coastal Sea has undergone a sudden expansion following bottleneck in the past, probably during the quaternary glaciations. The central components for management efforts should occur with preserving ecological diversity and integrity, especially in areas with strong rates of economic growth and high degrees of artificial disturbance, as well as acknowledging separate management units for Cangnan and the other north populations of T. bifasciatus in the Coastal Sea.

Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean

BackgroundRecently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea. Recently, marked divergence between two highly separated haplogroups (genetic types I and II) of C. aestuarii was discerned across the Siculo-Tunisian Strait, suggesting an Early Pleistocene vicariant event. In order to better identify phylogeographic patterns in this species, a total of 263 individuals from 22 Mediterranean locations were analysed by comparing a 587 basepair region of the mitochondrial gene Cox1 (cytochrome oxidase subunit 1). The examined dataset is composed of both newly generated sequences (76) and previously investigated ones (187).ResultsOur results unveiled the occurrence of a highly divergent haplogroup (genetic type III) in the most north-eastern part of the Mediterranean Sea. Divergence between the most distinct type III and the common ancestor of both types I and II corresponds to the Early Pleistocene and coincides with the historical episode of separation between types I and II. Our results also revealed strong genetic divergence among adjacent regions (separating the Aegean and Marmara seas from the remaining distribution zone) and confirmed a sharp phylogeographic break across the Eastern Mediterranean. The recorded parapatric genetic divergence, with the potential existence of a contact zone between both groups in the Ionian Sea and notable differences in the demographic history, suggest the likely impact of paleoclimatic events, as well as past and contemporary oceanographic processes, in shaping genetic variability of this species.ConclusionsOur findings not only provide further evidence for the complex evolutionary history of the green crab in the Mediterranean Sea, but also stress the importance of investigating peripheral areas in the species’ distribution zone in order to fully understand the distribution of genetic diversity and unravel hidden genetic units and local patterns of endemism.

Multiple Pleistocene refugia and repeated phylogeographic breaks in the southern Caspian Sea region: Insights from the freshwater crab Potamon ibericum

AbstractAimPhylogeographic studies on a number of Western Palaearctic taxa imply that the southern Caspian Sea region served as a refugium during the Last Glacial Maximum (LGM). Nevertheless, the LGM biogeography of the terrestrial and freshwater organisms in this region is poorly understood. By studying phylogeography of a species of freshwater crab, we unravel the location of probable local refugia and colonization patterns across this topographically complex landscape.LocationSouthern Caspian Sea region.TaxonThe freshwater crab Potamon ibericum.MethodsWe inferred the demographic history of Potamon ibericum using 163 mtDNA Cox1 sequences from 16 localities. For a subset of specimens, we amplified mtDNA 16S and four nuclear markers (28S, Histone3, Enolase, NaK) to confirm the phylogeographic structure. We tested Pleistocene expansion–contraction dynamics, using species distribution modelling (SDM) and assessed morphological variability by geometric–morphometric methods.ResultsMitochondrial markers revealed the existence of three parapatrically distributed lineages in the western, central and eastern parts of the region. The more conserved nuclear markers did not reflect this. The SDM revealed the fundamental niche expansion of P. ibericum along the southern Caspian Sea during the LGM, agreeing with results from the Cox1 data of demographic expansions. Despite strong morphological resemblance, geometric–morphometrics elucidated clinal carapace shape variation.Main ConclusionsConsidering the Caspian Sea level fluctuations during the late Pleistocene, we hypothesize a scenario of demographic contraction during interglacial/warmer conditions, due to the Caspian Sea transgression and latitudinal range shift within the narrow distribution of the species between the southern Caspian Sea and northern slopes of the Alborz Mountains. During the glacial periods, the sea regressed and moist and warm conditions, characterizing glacial refugia, became prevalent in the region and caused isolated populations to expand. Our study confirms the deep transverse phylogeographic break, previously identified for Darevskia lizards in the region, and adds support to the presence of several LGM refugia in the southern Caspian Sea region.

Phylogeography of the widespread spider Nephila clavipes (Araneae: Araneidae) in South America indicates geologically and climatically driven lineage diversification

AbstractAimAmazonia and Atlantic Rain Forests share a common biogeographical origin and have an interconnected history that includes the drier biomes between them. It is not clear if the establishment of the South American Dry Diagonal promoted isolation between these forests or if connections between them have occurred after this event. We sought to investigate biotic diversification and geographical evolution in these biomes with a phylogeographical study of Nephila clavipes, a rain forest dwelling spider.LocationSouth America.MethodsWe collected 320 individuals from 49 sites and sequenced one mitochondrial and two nuclear DNA regions. We analysed the genetic diversity, structure and demography, did phylogenetic inferences, estimated divergence times, inferred ancestral areas and applied a model‐based approach to test competitive hypotheses on the species’ evolution.ResultsAn ancient split, coincident with the Central Cordillera final uplift, segregated a Trans‐Andean Colombian lineage from the others. Four lineages occur in Brazil, with a Pleistocene divergence: one in Amazonia, one in the northern and southern Atlantic Forest and two associated with the Dry Diagonal, but also reaching the Southern Atlantic Forest and Amazonia. The biogeographical analysis indicated that some lineages have expanded their ranges along the Pleistocene.Main conclusionsPleistocene connections of Amazonia and Atlantic rain forests through the central part of the Cerrado were supported. No phylogeographical break was detected along the Atlantic Forest. Geological and climatic events contributed to lineage diversification in N. clavipes. Studying widely distributed species is primary in unveiling evolutionary patterns in highly complex regions.

Evidence for panmixia despite barriers to gene flow in the hooked mussel, Ischadium recurvum (Mytilidae; Brachidontinae) along the North American coastline

The discovery of phylogeographic patterns within broadly distributed marine species can be particularly challenging because absolute physical barriers to dispersal can be inconspicuous. Genetic boundaries often lie where ocean currents meet, forming sharp physical and ecological gradients, which may act as barriers to successful migrants. In eastern North America, coastal species often show phylogeographic differentiation associated with two recognized genetic barriers: the Gulf/Atlantic and the Virginia/Carolina discontinuities. We examined 185 specimens of the intertidal hooked mussel Ischadium recurvum collected from 15 locations along the eastern coastline of North America to examine phylogeographic, migration and historical demographic patterns associated climate change associated with Pleistocene glacial patterns. Hypothesis testing using Bayes factors in Migrate-n rejected the presence of phylogeographic breaks consistent with either maritime discontinuity and favoured a panmictic population model. The migration rate from the Gulf to the Atlantic was approximately three times higher than the migration from the Atlantic to the Gulf whereas the Carolina–Virginia migration rates were nearly equal. The summary statistics (Tajima’s D, Fu’s Fs) were significant and the demographic analyses (mismatch distributions, Bayesian skyline plot) were consistent with patterns of population expansion following glacial retreat during the Pleistocene epoch.

Phylogeographic structure in three North American tent caterpillar species (Lepidoptera: Lasiocampidae): Malacosoma americana, M. californica, and M. disstria.

While phylogeographic structure has been examined in many North American vertebrate species, insects have received much less attention despite their central ecological roles. The moth genus Malacosoma (Hübner, 1820), is an important group of forestry pests responsible for large-scale defoliation across much of the Nearctic and Palearctic. The present study uses sequence variation in the mitochondrial cytochrome c oxidase 1 (COI) gene to examine the population genetic structure of the three widespread Malacosoma species (M. americana, M. californica, and M. disstria). Populations of all three species showed highest diversity in the south, suggesting that modern populations derived from southern refugia with loss of variation as these lineages dispersed northwards. However, despite similar life histories and dispersal abilities, the extent of regional variation varied among the taxa. M. americana, a species restricted to eastern North America, showed much less genetic structure than the western M. californica or the widespread M. disstria. The regional differentiation in the latter reflects the likely derivation of modern lineages from several refugia, as well as taxonomic uncertainty in M. californica. In these respects, the three species of Malacosoma share phylogeographic patterns similar to those detected in vertebrates which are characterised by greater phylogeographic breaks in the western half of the continent and limited structure in the east.

Neither barriers nor refugia explain genetic structure in a major biogeographic break: phylogeography of praying mantises in the Brazilian Atlantic Forest

The Atlantic Forest is one of the world’s top biodiversity hotspots, but the diversification processes of its biota are still poorly known, with competing models attributing dominant roles to either Quaternary climatic changes or geographic barriers. Many studies identify the Doce river as a major phylogeographic break, but the reasons for this phenomenon are highly debated. Here we test the predictions of the refugial and barrier models for a common species of praying mantis, Miobantia fuscata, focusing in the areas immediately south and north of the Doce river. Our analyses show high intraspecific genetic diversity, deep coalescence times and no evidence for recent population expansion. Phylogeographic structure is inconsistent with a refugial hypothesis. Significant gene flow between northern and southern populations also conflicts with a strong role for geographic barriers. This study highlights the need for considering invertebrate taxa to infer recent landscape changes, and points towards a more complex picture of genetic diversification in the Atlantic Forest.

Systematics of the combtooth blenny clade Omobranchus (Blenniidae: Omobranchini), with notes on early life history stages

The combtooth blenny (Blenniidae) genus Omobranchus contains small, cryptobenthic fishes common to nearshore habitats throughout the Indo-West Pacific. Recent molecular systematic studies have resolved Omobranchus as monophyletic but little research has been done to resolve species-level relationships. Herein, phylogenetic analyses of one mitochondrial (CO1) and four nuclear (ENC1, myh6, sreb2, and tbr1) genes provide evidence for the monophyly of Omobranchus and support for the elongatus and banditus species group. Sampling of multiple individuals from widespread species (O. ferox, O. punctatus, and O. elongatus) suggested that the Thai-Malay Peninsula is a phylogeographic break that may be a historic barrier to gene flow. Additionally, common meristics and other morphological characters are used to describe an early life history stage of O. ferox and O. punctatus.