Mitochondrial phylogeography of a Beringian relict: the endemic freshwater genus of blackfish Dallia (Esociformes)

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median‐joining haplotype networks, Bayesian skyline plots, mismatch analysis and spatial analysis of molecular variance (SAMOVA) to infer genealogical relationships and to assess patterns of phylogeography among extant mitochondrial lineages in populations of species of Dallia. The observed variation includes extensive standing mitochondrial genetic diversity and patterns of distinct spatial segregation corresponding to historical and contemporary barriers with minimal or no mixing of mitochondrial haplotypes between geographic areas. Mitochondrial diversity is highest in the common delta formed by the Yukon and Kuskokwim Rivers where they meet the Bering Sea. Other regions sampled in this study host comparatively low levels of mitochondrial diversity. The observed levels of mitochondrial diversity and the spatial distribution of that diversity are consistent with persistence of mitochondrial lineages in multiple refugia through the last glacial maximum.     

Cryptic divergent lineages of Pultenaea pauciflora M.B. Scott (Fabaceae: Mirbelieae) exhibit different evolutionary history

Genetic structure among disjunct population groups of Pultenaea pauciflora was assessed to determine the evolutionary history of this species as a basis for conservation management strategies. Analysis of individuals from all extant populations using 1737 amplified length polymorphism markers revealed two highly divergent genetic entities with strong geographical structuring. Populations located at Narrogin and Brookton clustered together in Bayesian assignment analysis with every individual optimally placed in a single cluster with complete membership. Genetic differentiation between populations in these two areas was very low. Populations at Boddington were highly divergent from those located at Narrogin and Brookton. All individuals from Boddington populations were optimally placed into a second cluster with complete membership. Populations located at Boddington maintain lower levels of allelic diversity, yet greater levels of mean heterozygosity than populations located at Narrogin and Brookton. The degree of genetic differentiation and different patterns of genetic diversity strongly suggest historical divergence and separate evolutionary influences on the two lineages that occur in different ecological habitat. These Evolutionary Significant Units are likely to represent two cryptic sister taxa in the extant populations currently recognized as P. pauciflora, and the reassessment of taxonomic and conservation status of both lineages is required. © 2013 State of Western Australia. Biological Journal of the Linnean Society © 2013 The Linnean Society of London     

Phylogeography of the Petunia integrifolia complex in southern Brazil

In this study, we evaluated the genetic diversity of the Petunia integrifolia species group using a phylogeographical approach, and attempted to understand better its diversification and taxonomy. Plants from five morphological groups were collected, covering a large part of the geographical distribution of most of the species. Two major clades were found in the phylogenetic tree, and an additional lineage, corresponding to P. inflata, was found in the haplotype network obtained for plastid markers. All three lineages are clearly delimited geographically, but, with the exception of P. inflata, the morphological groups were not genetically distinct. Our results suggest that a population expansion after a size reduction resulted in the establishment of two distinct and allopatric groups c. 0.5 Mya, one group occurring in a geologically ancient area, and the other occurring in areas that were under the influence of a series of marine transgressions/regressions at the end of the Pleistocene. These two clades are evolutionarily significant units with significantly different allele frequencies in their nuclear genome and reciprocal monophyly in maternal, uniparentally inherited markers. All our results suggest that the morphology‐based taxonomy in this group does not reflect its evolutionary history, and revision of its species limits should incorporate the distribution of the genetic diversity. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 199–213.     

Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard

The evolutionary history of the Mexican sierras has been shaped by various geological and climatic events over the past several million years. The relative impacts of these historical events on diversification in highland taxa, however, remain largely uncertain owing to a paucity of studies on broadly‐distributed montane species. We investigated the origins of genetic diversification in widely‐distributed endemic alligator lizards in the genus Barisia to help develop a better understanding of the complex processes structuring biological diversity in the Mexican highlands. We estimated lineage divergence dates and the diversification rate from mitochondrial DNA sequences, and combined divergence dates with reconstructions of ancestral geographical ranges to track lineage diversification across geography through time. Based on our results, we inferred ten geographically structured, well supported mitochondrial lineages within Barisia. Diversification of a widely‐distributed ancestor appears tied to the formation of the Trans‐Mexican Volcanic Belt across central Mexico during the Miocene and Pliocene. The formation of filter barriers such as major river drainages may have later subdivided lineages. The results of the present study provide additional support for the increasing number of studies that suggest Neogene events heavily impacted genetic diversification in widespread montane taxa. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 382–394.     

Colonization of the Aeolian Islands by Pimelia rugulosa rugulosa Germar, 1824 (Coleoptera: Tenebrionidae) inferred from the genetic structure of populations: geological and environmental relations

The darkling beetle Pimelia rugulosa rugulosa Germar, 1824 was selected to investigate the process of colonization in a volcanic archipelago and the role of volcanism in determining spatial patterns of genetic variability. Analyses were conducted in the Aeolian Islands, located in the central Mediterranean directly off the Sicilian coast. Genetic variability and geographic structure were studied in individuals from each island of the archipelago based on sequences of the cytochrome c oxidase subunit 2 mitochondrial gene; a network approach was employed to identify haplotype lineages. A strong genetic structure, with no haplotype sharing among islands, was observed. Six separate lineages were identified that independently colonized different islands of the archipelago from the mainland and differentiated locally to form small haplogroups. Variability of observed haplogroups is correlated with island age and a positive correlation between tenebrionid diversity and mitotype diversity is reported. Some, yet undescribed, catastrophic event is hypothesized to explain the depletion of a substantial part of the genetic, as well as biological diversity in the island of Filicudi. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 29–37.     

Differences in population structure estimated within maternally‐ and paternally‐inherited forms of mitochondria in Lampsilis siliquoidea (Bivalvia: Unionidae)

Mussels in several orders possess two separate mitochondrial lineages: a standard female‐inherited form and one inherited only through males. This system of doubly uniparental inheritance (DUI) for mitochondrial genes provides an opportunity to compare the population structure of gene‐lineages passed either mother‐to‐daughter or father‐to‐son. In the present study, we contrast variation in the male and female haplotype lineages of the American freshwater mussel species, Lampsilis siliquoidea (sometimes called Lampsilis radiata luteola), throughout the Lake Erie, Ohio River, and upper Mississippi River watersheds, and contrast variation with the sequences obtained for the related species/subspecies Lampsilis radiata radiata from Maine. The genetic markers were fragments of the cytochrome c oxidase subunit I gene (COI), which occurs in both mitochondrial types, F (female) and M (male). High haplotype diversity was found in the two independent lineages, although purifying selection against amino acid change appeared to be stronger in the female than the male lineage. Phylogeographical patterns also varied between mitochondria passing through females and males. The female lineage exhibited more population structure, with the occurrence of private or nearly‐private haplotypes within two streams, and three others showed restricted haplotype distributions. By contrast to the F‐haplotypes, complex phylogenetic structure occurred for M‐haplotypes, yet this phylogenetic variation coincided with almost no geographical pattern within haplotypes. Basically, F‐haplotypes showed isolation, especially above physical barriers, whereas M‐haplotypes did not. A few individuals in the eastern Lake Erie watershed even possessed M‐haplotypes of an Atlantic Slope (L. radiata radiata) origin, although their F‐haplotypes were typical of Midwestern L. siliquoidea. The finding that mussels package sperm as spermatozuegmata, which float downstream, may underlie greater gene mobility in male‐inherited mitochondria. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 229–240.     

Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study

Many single‐species freshwater phylogeographic studies have been carried out in south‐east Queensland; however comparative phylogeography requires multiple lines of evidence to infer deep, significant relationships between landscape and biota. The present study aimed to test conclusions resulting from single taxon studies in a multispecies comparative framework: (1) how influential are river basins in the genetic structure of freshwater species; (2) are there biogeographic frontiers between groups of basins; and (3) could deep intraspecific lineages be explained by a single event? New and existing data from 33 freshwater species (23 fishes and 10 crustaceans) were combined, and both standard single‐species analyses (haplotype networks, genetic distances, Φ_ST) and multispecies methods (hierarchical ABC) were carried out for 1814 sequences from eight basins. More than half of the species displayed a high phylogeographic structure and contained at least two distinct lineages. Almost all of the lineage divergences displayed an element of north/south geographic breaks, with the most influential boundary being between the Mary and Brisbane rivers. Of the 11 basin‐pair multispecies coalescent analyses, four implied a single divergence as being most likely. A regional analysis of deep lineages within 16 taxon‐pairs resulted in a strongly supported inference of a single divergence, probably dating to the Pleistocene. Basin boundaries are a key determinant of phylogeographic patterns for most of these freshwater species, although the specific biogeographic relationship between basins often varies depending on the species. There are a number of influential biogeographic frontiers, with the Brisbane‐Mary being the most important. The finding that a single event may be responsible for multiple deep lineages across the region implies that a highly influential climate change event may have been detected. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 554–569.     

On glacial refugia,genetic diversity,and microevolutionary processes: deep phylogeographical structure in the endemic newt Lissotriton italicus1

We investigated the phylogeographical patterns of Lissotriton italcus, a newt endemic to the Italian peninsula, aiming to determine why hotspots of intraspecific diversity so ‘hot’. We found two main mitochindrial DNA lineages (net sequence divergence of 6.8% at two fragments of total length of 1897 bp): one restricted to part of the Calabrian peninsula (i.e the southernmost portion of the species range) and the other widespread throughout the rest of the species range. Both lineages, which had a parapatric distribution, showed evidence of further subdivisions, with an overall number of eight terminal haplogroups, most of whose times to the most recent common ancestors were estimated at the Late Pleistocene. Analysis of molecular variance suggested that partitioning populations according to the geographical distribution of these haplogroups can explain 97% of the observed genetic variation. These results suggest that L. italicus underwent repeated cycles of allopatric fragmentation throughout the Pleistocene, and that it likely survived the Late Pleistocene paleoenvironmental changes within eight separate refugia. Thus, the current hotspot of intraspecific diversity of L. italicus (within the Calabrian peninsula) has not been moulded by long‐term stability of large populations but rather by multiple events of allopatric fragmentation and divergence. When compared with the patterns recently identified in other species, these results suggest that the occurrence of phases of allopatric divergence (eventually followed by secondary admixture) could be a common, albeit probably underrated feature in the history of formation of hotspots of intraspecific diversity. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 42–55.     

Genetic patterns in the Lathyrus pannonicus complex (Fabaceae) reflect ecological differentiation rather than biogeography and traditional subspecific division

The endangered European relict species complex Lathyrus pannonicus shows distinct morphological variation, reflected by the number of subspecies recognized, and complicated patterns of genetic variation. The traditionally recognized subspecies appear to possess different ecological preferences and disjunct distributions, particularly in the western range of the species. In this study, L. pannonicus was investigated by the correlation of distance matrices based on phytosociological, ecological, molecular and morphological data. Ecological characteristics of selected stands of L. pannonicus throughout Europe were assessed using ‘Ellenberg values’ of all the constituent taxa in phytosociological relevés. Genetic distances were calculated using recently developed methods to analyse high degrees of intra‐individual nuclear‐encoded internal transcribed spacer variability. We found that the remarkable genetic (and morphological) diversity in L. pannonicus could not be explained solely by the fragmentation of the distributional range. Instead, patterns of morphological and genetic differentiation were a reflection of the moisture regime in the sampled stands. Two major lineages could be identified: (1) a lineage adapted to dry conditions (Ellenberg indicator F‐value ≤ 3.5) and (2) a lineage preferring moist conditions (F‐value ≥ 4.5). Although both lineages occurred in close proximity in the Pannonian area, they appeared to be reproductively isolated in general. Further data are needed to determine whether these genetically and ecologically defined lineages, or ecospecies, within the L. pannonicus species complex can be formalized as (Linnaean) species or subspecies. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 402–421.     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

Cryptic diversity in a widespread live‐bearing fish (Poeciliidae: Belonesox)

Belonesox belizanus Kner (Teleostei: Poeciliidae) is a wide‐spread livebearing species that occurs on the Atlantic Slope of Central America from southern Mexico to northern Costa Rica. Previous work has noted morphological variation within the species, and recognized two subspecies: Belonesox belizanus belizanus and Belonesox belizanus maxillosus. We used 1122 bp of cytochrome b and 617 bp of S7‐1 DNA to conduct a phylogeographical study of Belonesox, aiming to examine the genetic distinctiveness of these taxa and other populations of Belonesox throughout the range. Bayesian phylogenetic and haplotype analyses indicated that B. b. maxillosus is not distinctive from other northern populations of Belonesox. However, a distinct phylogeographical break is evident near the Rio Grande in southern Belize. One clade comprises the putative B. b. maxillosus and all populations sampled north of the Rio Grande. The other clade comprises the Rio Grande and all populations south thereof. Fossil‐calibrated divergence time estimates suggest that isolation of the northern and southern lineages of Belonesox occurred approximately 14.1 Mya. The phylogeographical structure recovered in the present study is interesting, considering that relatively few studies have examined molecular variation across this portion of Middle America in a time‐calibrated framework. Furthermore, the present study suggests that more work is needed to adequately understand the factors that have shaped diversity of this region. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 848–860.     

Current and historic gene flow of the sand goby Pomatoschistus minutus on the European Continental Shelf and in the Mediterranean Sea

Phylogeographical patterns of the sand goby Pomatoschistus minutus (Gobiidae, Teleostei) were studied by means of sequence and single-stranded conformational polymorphism analysis of a 283-bp fragment of the cytochrome b locus of the mtDNA. A total of 228 individuals sampled at 13 sites throughout the species's distributional range revealed a moderate level of diversity and a low but significant level of overall genetic differentiation at all but one site. The goby sample from the Adriatic Sea differed in sequence by approximately 10% from the Atlantic P. minutus and is thought to belong to a cryptic species of the genus Pomatoschistus . Limited genetic differentiation with a weak pattern of isolation-by-distance was recorded throughout the distributional range of the typical P. minutus . Phylogeographical analysis suggested a contiguous range expansion in the Atlantic and Baltic basins during the Eemian and evidence for a glacial refugium in the southern North Sea during the Weichselian. In P. minutus from the western Mediterranean Sea a high number of endemic haplotypes as well as the most common Atlantic haplotype were recorded in appreciable frequencies. This might be explained by secondary contact between different mitochondrial lineages, which evolved in allopatry.   © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 561–576.     

Ontogenetic shifts in phenotype–environment associations in Nile perch,Lates niloticus (Perciformes: Latidae) from Lake Nabugabo,Uganda

Habitat‐associated trait divergence may vary across ontogeny if there are strong size‐related shifts in selection pressures. We quantified patterns of phenotypic divergence in Nile perch (Lates niloticus) from ecologically distinct wetland edge and forest edge habitats in Lake Nabugabo, Uganda, and we compared patterns of divergence across three size classes to determine whether trends are consistent through Nile perch ontogeny. We predicted that inter‐habitat variation in biotic (e.g. vegetation structure) and abiotic (e.g. dissolved oxygen concentration) variables may create divergent selective regimes. We compared body morphology using geometric morphometrics and found substantial differences between habitats, although not all trends were consistent across size classes. The most striking aspects of divergence in small Nile perch were in mouth orientation, head size, and development of the caudal region. Medium‐sized Nile perch also showed differences in mouth orientation. Differences in large individuals were related to eye size and orientation, as well as caudal length. The observed patterns of divergence are consistent with functional morphological predictions for fish across divergent trophic regimes, high and low predation environments, and complex and simple habitats. Although this suggests adaptive divergence, the source of phenotypic variation is unknown and may reflect phenotypic plasticity and/or genetic differences. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 449–465.     

Phylogeography of the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico

We quantify the population divergence processes that shaped population genetic structure in the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis into three populations: (1) a southern population in Oaxaca and southern Puebla; (2) a population in western Puebla; and (3) a northern population with a broad distribution across Hidalgo, Puebla, and Veracruz. The multilocus nuclear data and mtDNA both supported a Late Pleistocene increase in effective population size, and the nuclear data revealed low levels of unidirectional gene flow from the widespread northern population into the southern and western populations. Populations of S. bicanthalis experienced different demographic histories during the Pleistocene, and phylogeographical patterns were similar to those observed in many co‐distributed highland taxa. Although we recommend continuing to recognize S. bicanthalis as a single species, future research on the evolution of viviparity could gain novel insights by contrasting physiological and genomic patterns among the different populations located across the highlands of south‐eastern Mexico. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 852–865.     

Phylogeography of two cryptic species of African desert jerboas (Dipodidae: Jaculus)

The lesser Egyptian jerboa Jaculus jaculus is a desert dwelling rodent that inhabits a broad Arabian–Saharan arid zone. Recently, two distant sympatric lineages were described in North‐West Africa, based on morphometric and molecular data, which may correspond to two cryptic species. In the current study, phylogenetic relationships and phylogeographical structure among those lineages and geographical populations from North Africa and the Middle East were investigated. The phylogeographical patterns and genetic diversity of the cytochrome b gene (1110 bp) were addressed on 111 jerboas from 41 localities. We found that the variation in Africa is partitioned into two divergent mitochondrial clades (10.5% divergence relating to 1.65–4.92 Mya) that corresponds to the two cryptic species: J. jaculus and J. deserti. Diversifications within those cryptic species/clades were dated to 0.23–1.13 Mya, suggesting that the Middle Pleistocene climatic change and its environmental consequences affected the evolutionary history of African jerboas. The third distant clade detected, found in the Middle East region, most likely represents a distinct evolutionary unit, independent of the two African lineages. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Congeneric phylogeography: hypothesizing species limits and evolutionary processes in Patagonian lizards of the Liolaemus boulengeri group (Squamata: Liolaemini)

In poorly known groups for which data are insufficient to develop biologically plausible model‐based approaches to phylogeographical analyses, a ‘first hypotheses’ protocol is suggested as offering the best way to generate hypotheses for subsequent model‐based tests. Preliminary hypotheses are formulated about species boundaries and population processes in three species complexes of the Liolaemus boulengeri group in the context of mtDNA ‘congeneric phylogeography’. The temperate South American Liolaemus provides a model with ancient and recent allopatric divergence across ecologically and geologically complex landscapes, incipient speciation, secondary contact, and discordance between molecular and morphological patterns of variation. Moderately dense sampling of widely distributed ‘inertial’ species in the Patagonian Steppe has revealed hidden genetic and probably species diversity, and also hinted at demographic and historical processes that may have shaped the histories of these taxa. Five of the seven focal species of the present study were paraphyletic for mtDNA genealogies, suggesting that they represent complexes of species, and nested clade phylogeographical analysis (NCPA) analyses suggest that different historical and demographic processes have shaped the observed patterns. Introgression and incomplete lineage sorting are hypothesized as being the cause of some of the observed paraphyly. Provisional delimitations of species are proposed and NCPA is used to generate hypotheses of population history, all of which are subject to further testing. Multi‐faceted studies, involving phylogenetic assessments of independent molecular markers and morphological variation across codistributed taxa with estimates of niche breadths in a landscape context, will likely yield the most promising returns for cross‐validation of hypotheses of population and speciation histories. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 241–275.     

Phylogeography of Troglophilus (Orthoptera: Troglophilinae) based on Anatolian members of the genus: radiation of an old lineage following the Messinian

Active tectonic history of the Eastern Mediterranean, especially around Aegean area, through the Neogene led to interesting radiation patterns of animal lineages, allowing intriguing biogeographical hypotheses to be tested. Descendants of the ancestral stock in the Miocene Aegean Plate presently occur in the Anatolia, Aegean islands and the Balkan Penninsula. Troglophilus (Orthoptera, Rhaphidophoridae, Troglophilinae) is such a genus represented in these areas with approximately 15 species. The present study addresses the phylogeography of the genus, with a special emphasis on its Anatolian members, aiming to test the biogeographical patterns suggested for this area using mitochondrial [cytochome oxidase I (COI)] and nuclear (ITS1‐5.8S–ITS2) markers. Data matrices obtained from sequences of COI and ITS1‐5.8S–ITS2 were used for phylogenetic analyses using Dolichopoda lycia and Dolichopoda sbordonii as outgroups. All sets of the analyses suggested monophyly of the Anatolian haplotypes, although they are not congruent in revealing their relationships. Anatolian haplotypes constituted three main phylogroups in trees calculated from a matrix of short COI sequences: the ECMA (corresponding to the Eastern part of coastal Mediterranean Anatolia); the CWMA (from the Central and Western part of Mediterranean Anatolia); and NA (from Northern Anatolia). Trees obtained using longer sequences resulted in only two phylogroups, namely ECMA and CWMA + NA. The trees based on the ITS1‐5.8S–ITS2 data matrix supported monophyly of Anatolian phylogroups. BEAST analysis of the COI estimated the time to most recent common ancestor for Dolichopoda and Troglophilus as 10.8 Mya, to that for the Anatolian + Balkan Troglophilus as 7.2 Mya, and to that for the Anatolian Troglophilus as 6.3 Mya. BEAST analysis of ITS1–ITS2 intron regions is largely congruent with that of COI. From these results, several conclusions were drawn. First, the divergence of Dolichopoda and Troglophilus possibly started with the opening of the Mid‐Aegean Trench in the Tortonian. Second, Troglophilus possibly originated from an ancestral stock in the old Aegean Plate. It later diverged as Anatolian and Balkan lineages and, possibly, the Cretan population may be regarded the third lineage. Divergence within the Anatolian lineage is estimated to have occurred through the Pliocene and Pleistocene, although before the last four glacial periods in the late Pleistocene. Additionally, the northern Anatolian Troglophilus appears to originate from the dispersal of an ancestral stock from a mountainous lineage through the Taurus Way. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108 , 335–348.     

DNA‐based species delimitation separates highly divergent populations within morphologically coherent clades of poorly dispersing beetles

We compared species‐level entities recovered using distance, tree‐based, and DNA‐character based methods with morphologically defined species in poorly dispersing lyponiine net‐winged beetles. The phylogenetic relationships were investigated using the cytochrome c oxidase 1–2 mtDNA fragment. We identified 31 species using a morphology‐based concept and additional candidate species were delimited by the general mixed Yule‐coalescent method and barcoding threshold within the morphologically coherent lineages owing to high genetic divergence (up to 10.97% within morphologically defined species, highest density 2.5–6.5%). Genetic divergence was positively correlated with geographical distance: lower in continental China where no apparent dispersal barriers are present (r² = 0.172, P ≤ 0.001, average increase of genetic distance of 0.32% per 100 km) and much higher in Japan (r² = 0.490, P ≤ 0.001, 1.81% per 100 km). We hypothesize that low dispersal propensity contributed to the high level of intraspecific, geographically structured divergence. DNA‐based methods suggested a high number of morphologically undistinguishable species. The observed patterns agree with the model of neutral evolution. The poor dispersers produce gradually divergent populations across the range of the morphologically coherent lineages. We pose the question of what size of range and level of genetic difference justify formal acceptance of a species without morphological divergence from both the taxonomical and conservation management view points. © 2015 The Linnean Society of London     

The phylogeographical and population genetic approach to the investigation of the genetic diversity patterns in self‐incompatible clonal and polyploid Linnaea borealis subsp. borealis

Surveys of genetic diversity patterns of self‐incompatible clonal polyploid plant species are still scarcer than those of diploid plant species. Therefore, I studied the phylogeographical history of Linnaea borealis subsp. borealis to shed light on the colonization history of this clonal self‐incompatible polyploid plant in Eurasia using selected regions of plastid DNA and genetic diversity patterns of 22 populations of this species employing AFLP markers. I also addressed the question of whether the genetic diversity patterns in L. borealis subsp. borealis in Eurasia are similar to those of earlier published studies of clonal self‐incompatible diploid or polyploid plants. This survey revealed that the shallow phylogeographical history (six plastid haplotypes forming one haplogroup, 100% bootstrap support) and moderate genome‐wide diversity estimated using AFLP markers (Frag_poly = 10.8–38.9%, I = 0.060–0.180, F_ST = 0.289) were general characteristics of L. borealis subsp. borealis in its Eurasian range. The sampling strategy, in most cases at 1–2‐m or even 3–5‐m intervals, showed that a balance between vegetative and sexual reproduction and limited pollen dispersal among compatible mates can be important for genetic diversity patterns in populations of this taxon. Despite the fact that one‐half of the investigated populations were strongly isolated, they still preserved similar levels of genetic diversity across the geographical range. I found no support for the hypothesis that a bottleneck and/or inbreeding had accompanied habitat fragmentation as factors shaping genetic diversity. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 64–76.     

Phylogeography and population structure of European sea bass in the north‐east Atlantic

The European sea bass Dicentrarchus labrax represents a historically and commercially valuable species in the north‐east Atlantic, although the demographic history and the patterns of geographical structure of the species in the north‐east Atlantic remain poorly understood. The present study investigates the population genetic structure of sea bass in north‐western European waters, employing different genetic markers [a portion of the mitochondrial (mt)DNA control region and 13 nuclear microsatellites] aiming to unravel demographic history and population connectivity. The results obtained show a previously unrecognized pattern of population divergence at mtDNA, with three strikingly different lineages identified. Extant sea bass populations, including the Mediterranean lineage, derive from an Atlantic ancestor. A much increased number of nuclear microsatellite loci (comparatively to previous studies) still fail to detect biologically meaningful patterns of spatial genetic structuring in the North Atlantic. Past Pleistocene glacial and interglacial events and some degree of female philopatry might be at the basis of the current geographical separation of the Atlantic lineages that has been identified. Signatures of sudden demographic expansions are more evident in the most recent mitochondrial lineages, and their slight, yet significant, geographical segregation leads to the hypothesis that present‐day spawning grounds for European sea bass may still to some extent be linked to their most recent glacial refugia. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 364–377.