Patterns of gene flow in two species of eel-tailed catfish, Neosilurus hyrtlii and Porochilus argenteus (Siluriformes: Plotosidae), in western Queensland's dryland rivers

Using genetic techniques (mtDNA, microsatellites and allozymes), this study investigated patterns of gene flow in two plotosid catfish species ( Neosilurus hyrtlii and Porochilus argenteus ), at various hierarchical scales in the dryland rivers of western Queensland, Australia. The study area constituted two major catchments, Cooper and Darling, representing arid and semiarid systems, respectively. Results generally conformed to expectations, with high levels of gene flow observed within catchments and limited contemporary gene flow evident across catchment boundaries. However, the isolation between catchments was more recent than expected, occurring approximately 40 000–72 000 years ago. Also contrary to predictions, genetic structure within the Cooper catchment did not fit the stream hierarchy model of genetic differentiation, which there was evidence of in the Darling catchment. This was hypothesized to relate to the different climatic regimes and hydrological inputs in each system, leading to a more genetically homogeneous system in the Cooper than in the Darling system.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 457–467.     

Population structure of Macrobrachium australiense (Decapoda: Palaemonidae) in Western Queensland, Australia: the role of contemporary and historical processes

Rivers of Western Queensland, Australia, represent a discontinuous and variable aquatic habitat for the freshwater fauna of the region. Rivers periodically fluctuate between being highly fragmented, with numerous disconnected waterholes and ephemeral channels, and being highly connected by a dominant system of anastomosing channels. We used mitochondrial sequences to investigate the genetic structure and inferred patterns of dispersal associated with this flow regime for the freshwater prawn, Macrobrachium australiense (Decapoda: Palaemonidae), sampling 28 localities throughout eight catchments. Based on a 505 base pair fragment of mitochondrial cytochrome c oxidase subunit I, we identified 98 haplotypes in a sample of 402 individuals. The haplotypes clustered into two main clades corresponding geographically to the major drainages: the Lake Eyre and Murray-Darling basins. Populations of M. australiense inhabiting the two basins appear to have diverged around 800,000 years ago (estimated sequence divergence of 1.6%). Analysis of population differentiation indicated contemporary high levels of genetic subdivision and restricted gene flow among populations within and among catchments. Phylogenetic analysis detected a series of historical range expansions in the region and we suggest that climate fluctuations during the Pleistocene have resulted in extensive floods that have promoted historical movements of aquatic organisms across catchment boundaries.     

The molecular systematics of Leiopotherapon unicolor (Günther, 1859): testing for cryptic speciation in Australia's most widespread freshwater fish

Leiopotherapon unicolor is the most widespread freshwater fish species in Australia. A comprehensive allozyme and mitochondrial DNA 16S rRNA data set was assembled from 141 specimens of L. unicolor collected Australia-wide in order to test for cryptic speciation in this far-ranging species. Surprisingly, little genetic diversity was observed within L. unicolor and provided no evidence for the existence of cryptic species within this lineage. In contrast, a small sample set of L. aheneus used as the outgroup showed two highly divergent haplotypes strongly suggestive of cryptic speciation. L. unicolor has a number of ecological and life history attributes that may explain the lack of significant genetic divergence over substantial geographical distances. The occurrence of other widespread fish and crustacean species that also display only limited genetic diversity indicate that climate conditions more favourable to dispersal across central and northern Australia than is suggested by the extent of present-day aridity have occurred in the relatively recent geological past.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 537–552.     

Lineage diversification on an evolving landscape: phylogeography of the California newt, Taricha torosa (Caudata: Salamandridae)

We used mitochondrial cytochrome  b sequences (up to 778 bp) and starch gel electrophoresis (45 loci) to examine the phylogeographical history of 39 populations of the California newt, Taricha torosa . Phylogenetic and population genetic methods were integrated to infer history at deep and shallow time depths. Using a molecular clock, the subspecies T. t. torosa and T. t. sierrae were estimated to have diverged 7–13 Mya. Within T. t. torosa, genetically differentiated groups were identified along coastal California, in southern California, and in the southern Sierra Nevada. The coastal group exhibited isolation by distance, but a lack of genetic variation north of present-day Monterey was indicative of a recent range expansion. In southern California, a disjunct population in central San Diego County was genetically diverged from coastal populations to the north (Nei's genetic distance of 0.113). However, mtDNA and protein data were geographically discordant regarding the boundary between the coastal and southern Californian groups, and a biogeographical scenario was developed to account for this discordance. The southern Sierran clade of T. t. torosa was weakly diverged from coastal populations for mtDNA sequence variation, yet was strongly differentiated for allozyme variation (Nei's genetic distance of 0.17–0.20). Populations of T. t. sierrae exhibited substantial population structure, and showed a steeper pattern of isolation by distance than did coastal populations of T. t. torosa . These results are interpreted in consideration of the known geomorphological history of California.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 213–239.     

Mitochondrial gene diversity in Cepaea– population structure, history and positive selection

Previous studies on the geographical distributions of both shell polymorphisms and mitochondrial haplotypes in Cepaea land snails have suggested varying contributions of natural selection, random genetic drift and population history to the origin and persistence of variation. We combine previous studies of polymorphism within two species of Cepaea , with new molecular data from two mitochondrial genes. The distributions of mitochondrial variants suggest that elements of population history may have been influential in creating patterns of diversity. However, some patterns of amino acid substitution that are found in a protein coding gene are also consistent with the action of diversifying selection. This suggests the possibility that in addition to stochastic processes such as repeated founder events, local extinctions and random genetic drift within a structured population, adaptive molecular change may have affected mitochondrial diversity.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 167–184.     

Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene

The phylogeography of Atlantic brown trout ( Salmo trutta ) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 904–917.     

Contrasting levels of genetic diversity between the common, self-compatible Liparis kumokiri and rare, self-incompatible Liparis makinoana (Orchidaceae) in South Korea

Levels of allozyme variation and intrapopulation spatial genetic structure of the two terrestrial clonal orchids Liparis kumokiri , a self-compatible relatively common species, and L. makinoana , a self-incompatible rare species, were examined for 17 ( N  = 1875) and four ( N  = 425) populations, respectively, in South Korea. Populations of L. makinoana harboured high levels of genetic variation ( H _e = 0.319) across 15 loci. In contrast, L. kumokiri exhibited a complete lack of allozyme variation ( H _e = 0.000). Considering the lack of genetic variability, it is suggested that current populations of L. kumokiri in South Korea originated from a genetically depauperate ancestral population. For L. makinoana , a significant deficit of heterozygosity (mean F _IS = 0.198) was found in population samples excluding clonal ramets, suggesting that pollen dispersal is localized, generating biparental inbreeding. The significant fine-scale genetic structuring (≤ 2 m) found in a previous study, in addition to the moderate levels of population differentiation ( F _ST = 0.107) and the significant relationship between genetic and geographical distances ( r  = 0.680) found here, suggests a leptokurtic distribution of seed dispersal for L. makinoana . Although populations of L. makinoana harbour high levels of genetic variation, they are affected by a recent genetic bottleneck. This information suggests that genetic drift and limited gene flow could be the main evolutionary forces for speciation of a species-rich genus such as Liparis .  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 41–48.     

Genetic relationships of the western Mediterranean painted frogs based on allozymes and mitochondrial markers: evolutionary and taxonomic inferences (Amphibia, Anura, Discoglossidae)

Allozymes and sequencing of mitochondrial cytochrome  b (cyt  b ) and 12S genes were used to reconstruct the genetic structure and phylogenetic relationships of all Discoglossus taxa described so far (except the probably extinct D. nigriventer ). This is the first time that a comprehensive study on the Discoglossus painted frogs has used nuclear and mitochondrial markers, evidencing a discordant pattern between the two datasets. Comparison of these discrepancies suggests a role of stochastic sorting of ancestral polymorphisms, possibly associated with male-biased dispersal and present or past secondary contact. The genetic relationships between taxa with intermediate levels of divergence were well defined by allozyme data, but showed short internodes and low bootstrap values for mitochondrial data, suggesting a rapid radiation of their lineages during the Messinian Lago Mare phase. The results provide information about the taxonomic status of D. galganoi and D. jeanneae , considered as subspecies, and indicate D. pictus as nonmonophyletic, confirming D. scovazzi as a distinct species.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 515–536.     

Multiple levels of allopatric divergence in the endemic Philippine fruit bat Haplonycteris fischeri (Pteropodidae)

As part of a larger comparative phylogeographical study of Philippine fruit bats, I used fragments of the mitochondrial genes cytochrome  b and ND2 to investigate phylogeography and diversification in Haplonycteris fischeri , a pteropodid bat endemic to the Philippines but widespread within the archipelago. Genetic diversity in H. fischeri was extremely high in these commonly studied genes, with 101 unique haplotypes in 123 sequenced individuals, although small, continuously isolated islands had less diversity than had large island complexes. Seven monophyletic groups and one paraphyletic group were restricted to individual islands, groups of islands, or parts of islands. Each Pleistocene island complex had a single resident monophyletic lineage; these five groups were separated by approximately 6–8% sequence divergence and apparently have been diverging for 4–6 Myr. Within island groups, monophyletic lineages on some individual islands suggest that current ocean channels have also been barriers to gene flow; in some cases, multiple allopatric clades were present on single islands. Basal divergence dates were estimated to be in the early Pliocene, and most diversification was apparently connected to the ongoing geological evolution of the Philippines. Geological history and current geography interact with ecology to cause substantial genetic differentiation within this primary forest-specialist species.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 329–349.     

Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae)

Phylogeographical and population genetics methods are used to reconstruct the diversification history of two species of the genus Xiphorhynchus (Aves: Dendrocolaptidae) associated with seasonally flooded forest types in Amazonia. Sequences of the mitochondrial gene cytochrome b were assessed for 21 and 30 individuals, belonging to eight and ten populations, of Xiphorhynchus kienerii and Xiphorhynchus obsoletus , respectively. Uncorrected genetic distances among unique haplotypes recovered ranged only from 0.01% to 0.4% for both species. Over 90% of the genetic variation detected in both species was partitioned within populations, and therefore was not structured geographically. Mismatch distributions and values of Tajima's D -tests indicate that both X. kienerii and X. obsoletus have had small evolutionary effective population sizes, but experienced a recent demographic expansion. These demographic expansions are tentatively dated as occurring over the last 18 000 years BP, a time frame which coincides with the establishment of the early and mid-Holocene age floodplain forest in most of central and eastern Amazonia, following a period of increased river stages throughout the basin. Based on phylogenetic, phylogeographical, and populations genetics data obtained for X. kienerii and X. obsoletus , an evolutionary scenario is proposed to account for the historical diversification of floodplain specialist species in Amazonia.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 383–395.     

Distribution and genetic divergence of two parapatric sibling ant species in Central Europe

The two sibling ant species Temnothorax nylanderi and Temnothorax crassispinus are widely distributed throughout deciduous forests in Europe. Their resemblance in morphology and similar ecological requirements suggest that they evolved from the same ancestral species in different glacial refugia and re-immigrated into Central Europe after the last ice age. Here, we show that the two species are parapatrically distributed in south-eastern Germany and hybridize along a narrow contact zone close to the continental divide. Phylogeographical data based on the mitochondrial genes cytochrome oxidase subunit I and cytochrome b suggest that the dominant haplotypes for T. nylanderi and T. crassispinus might have diverged already 1.5–2 Mya. Intraspecific variability is extremely low in both species, which might be explained by severe bottlenecks during rapid postglacial expansion into Central Europe.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 223–234.     

Evolution and phylogeny of the genus Natrix (Serpentes: Colubridae)

Some aspects of the natural history of snakes of the colubrid genus Natrix have been well studied. With their extensive European distribution and relative abundance, their ecology, reproduction and behaviour are well known. Yet other facets of their biology remain poorly understood. These include knowledge of Natrix phylogeny, hypotheses explaining the current distribution of the three extant members of the genus, and their evolution and relationships. In this study we used molecular data, the nucleotide sequences of four protein-coding mitochondrial genes (3806 bp total), to provide a well-supported phylogeny for the genus Natrix . With these molecular data, evidence from the fossil record, and knowledge of palaeogeological events, we used two approaches in designing a time scale which we used to date the major events in Natrix speciation and intraspecific variation. Our data strongly support a phylogeny for the genus in which N. maura is basal with N. natrix and N. tessellata being sister species. The calibrated molecular clock suggests that N. maura diverged from the common ancestor of the three species 18–27 mya and that N. natrix and N. tessellata diverged 13–22 mya. Although the ranges of these estimates are large they support an early Miocene to late Oligocene origin for the three species. Intraspecific divergence is estimated to have commenced 5.3, 6.0 and 6.7 mya with evolutionary rates of 1 : 1.25 : 1.35% per million years for N. maura, N. natrix and N. tessellata , respectively.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 127–143.     

The phylogeographical and management implications of genetic population structure in the imperiled snuffbox mussel, Epioblasma triquetra (Bivalvia: Unionidae)

Seven populations of the imperiled snuffbox mussel, Epioblasma triquetra , were sampled from across the central basin of North America. Samples were genotyped using 15 microsatellite DNA loci, and maternal history was inferred using mitochondrial DNA (mtDNA) cytochrome  c oxidase subunit-I (COI) sequences. Populations in the Clinch and St Francis rivers were quite distinct in their mtDNA. The population in the St Francis River had a unique, fixed haplotype. Among a suite of haplotypes, the population in the Clinch River had two unique haplotypes of common ancestry. The other populations were dominated by a common haplotype, which also occurred in the Clinch River population. Analysis of DNA microsatellites revealed much greater divergences and showed significant genetic structure between populations in the formerly glaciated regions. Divergence has occurred between the populations, as evidenced by moderate to high fixation indices ( F _ST and R _ST values) and nearly perfect assignment tests. These results indicate the occurrence of three glacial refugia for E. triquetra : the Tennessee River, rivers south of the Ozark Crest, and the lower Ohio River drainage near the confluence with the Mississippi. Populations in the lower Ohio River were likely to be responsible for the postglacial reinvasion into formerly glaciated regions, and into the upper Tennessee River drainage. The population of the St Francis River may constitute a distinct taxonomic entity. Conservation efforts, if necessary for this imperiled species, should not mix populations.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 371–384.     

Phylogeography of a host-specific insect: genetic structure of Ips typographus in Europe does not reflect past fragmentation of its host

The phylogeography of the bark beetle Ips typographus was assessed using five microsatellite markers. Twenty-eight populations were sampled throughout Europe on the host tree Picea abies . I. typographus showed very low levels of genetic diversity, and the study revealed a lack of genetic structure across Europe. No significant barrier to gene flow was found, even though P. abies has a fragmented distribution. A weak but significant effect of isolation by distance was found. These results suggest a high dispersal capacity of I. typographus , which leads to low genetic differentiation between populations. Its high dispersal capacity is likely to have prevented I. typographus from developing important local adaptations to its host, which would have influenced its genetic structure. The nuclear data was compared to previously published mitochondrial data that showed strong differentiation between Central–Northern European populations and Russian–Baltic populations, and a founder effect in Scandinavia, probably reflecting the postglacial history of I. typographus . Discrepancies between nuclear and mitochondrial markers could be due to the maternal inheritance of mitochondrial DNA, and to sex-biased dispersal in I. typographus . The overall low genetic diversity observed on both markers on a large geographical scale is discussed. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 239–246.     

Subtle population genetic structure in the Hawaiian grouper, Epinephelus quernus (Serranidae) as revealed by mitochondrial DNA analyses

The endemic Hawaiian grouper, Epinephelus quernus , is a commercially important species experiencing intense fishing pressure in part of its distributional range. We examined population genetic structure with 398 base pairs of the mitochondrial control region across a large portion of the range of E. quernus , spanning approximately 2000 km of the Hawaiian archipelago. Examination of genetic diversity shows that Gardner Island, situated midway along the island chain, harbours the most diverse haplotypes. F -statistics and Bayesian estimates of migration also reveal the mid-archipelago as genetically differentiated, where the first significant break among adjacent pairs of populations lies between the islands of Nihoa and Necker. Most island comparisons beyond Necker and Gardner to the north-west and among the lower five islands to the south-east show little to no genetic differences. Evidence of historical population expansion across the islands was also found by Maximum Likelihood analyses. The results suggest that management should be structured to reflect the genetic differentiation and diversity in the mid-archipelago, the patterns of which may be associated with oceanic current patterns.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 449–468.     

Intraspecific vicariant history and the evolution of adaptive morphological diversity in a fish species (Osmerus mordax)

Vicariant geographic isolation and resource partitioning have long been independently identified as processes contributing to the morphological divergence of closely-related species. However, little is known about the extent to which vicariant history influences the adaptive ecological divergence associated with resource partitioning and trophic specialization within species. The present study thus quantified the contribution of vicariant historical genetic divergence to the adaptive contemporary morphological divergence of intraspecific feeding specialists in the Rainbow smelt (Pisces: Osmerus mordax ). This species is characterized by the polyphyletic origin of two lacustrine feeding specialists originating in two intraspecific lineages associated with independent glacial refuges. The historical genetic segregation was initiated approximately 350 000 years ago, whereas the lacustrine trophic segregation arose within the past 10 000 years. Wild caught lacustrine smelt populations were grouped a priori based on known historical genetic identities (Acadian and Atlantic mitochondrial DNA clades) and contemporary feeding specializations (microphageous and macrophageous morphotypes). The present study demonstrated that independent suites of correlated morphological traits are associated with either vicariant history or contemporary feeding specializations. Second, functionally-similar feeding specialists exhibit distinct morphologies resulting largely from vicariant historical processes. Although, the evolutionary processes producing historical phenotypes remains unknown, the results obtained demonstrate how adaptive radiation associated with ecological resource partitioning and feeding specializations can be strongly influenced by intraspecific phenotypic diversification resulting from relatively recent vicariant histories.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 140–151.     

Phylogeographical analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deeply divergent mitochondrial lineages

Isopods of the species Ligia oceanica are typical inhabitants of the rocky intertidal of the northern European coastline. The aim of this study was to assess the genetic structure of this species using mitochondrial and nuclear sequence data. We analysed partial mitochondrial cytochrome c oxidase subunit I (CO1) and 16S rRNA gene sequence data of 161 specimens collected from ten sites ranging from Spain to Norway. For selected specimens, we also sequenced the hypervariable V7 expansion segment of the nuclear 18S rRNA gene as a supplementary marker. Furthermore, we studied the infection rate of all analysed specimens by the alphaproteobacterium Wolbachia. Our analyses revealed two deeply divergent mitochondrial lineages for Ligia oceanica that probably diverged in the late Pliocene to mid Pleistocene. One lineage comprised specimens from northern populations (‘lineage N’) and one primarily those from France and Spain (‘lineage S’). Distribution patterns of the haplotypes and the genetic distances between both lineages revealed two populations that diverged before the Last Glacial Maximum. Given that we found no homogenization of mitochondrial haplotypes, our present results also reject any influence of Wolbachia on the observed mtDNA variability. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 16–30.     

Sympatric occurrence of diverged mtDNA lineages of Pityogenes chalcographus (Coleoptera, Scolytinae) in Europe

Differentiation among the European populations of the six-toothed spruce bark beetle Pityogenes chalcographus was observed for the first time in the 1970s as mating males from Northern Europe with females from Central Europe led to a significant decline in fecundity. Morphological examination revealed that P. chalcographus can be separated into two European races. Here, we investigated the genetic background of this separation by analysing 39 populations ( n  = 695), sequencing almost the complete cytochrome oxidase I gene (1543 bp) and applying single-strand conformation polymorphism. Phylogenetic analysis of 58 haplotypes yielded three major clades with a maximum sequence divergence of 2.33%, indicating that the demographic events took place in the late Pleistocene. These results support the hypothesis of allopatric divergence of the mtDNA lineages, which postglacially came into sympatric existence in Europe. However, as a result of partial crossing incompatibility the diverged lineages retained their genetic identity during postglacial times.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 331–340.     

Galápagos' Opuntia (prickly pear) cacti: extensive morphological diversity, low genetic variability

Due to the pronounced morphological variation and geographical distribution of Galápagos' Opuntia cacti, numerous hypotheses have been advanced regarding their radiation, diversification, and classification. The currently accepted classification is based on morphology and recognizes six species and fourteen varieties, but the plasticity of many of the characteristics renders any morphological taxonomy problematic. Our analysis of previously published morphological data agrees only partially with the current classification. We present the first molecular phylogeny of these plants. Multiple DNA sequences indicate little genetic distinction among the currently identified species, despite restricted gene flow and limited long distance dispersal within the archipelago. No clear relationship exists between morphological and genetic differences. These results suggest that both molecular and morphological data should be used in conservation planning.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 451–461.     

A role for nonphysical barriers to gene flow in the diversification of a highly vagile seabird, the masked booby (Sula dactylatra)

To test the hypothesis that nonphysical barriers to gene flow play a role in the divergence of low-latitude seabird populations, we applied phylogeographic methods to mitochondrial control region sequence variation in a global sample of masked boobies (Sula dactylatra). In accord with previous studies, we found that Indo-Pacific and Atlantic haplotypes form two divergent lineages, excluding one haplotype previously attributed to secondary contact between the Indian Ocean and the Caribbean Sea. Within the Indo-Pacific and the Atlantic, we found a relatively large number of haplotypes, many of which were unique to a single population. Although haplotypes from most populations were found in more than one higher-level clade, nested clade analysis revealed a significant association between clades and geography for the majority of higher-level clades, most often interpreted as a consequence of isolation by distance. We found low levels of gene flow within Indo-Pacific and Atlantic populations, and a significant correlation between gene flow and geographical distance among Indo-Pacific populations. We estimate that Indo-Pacific masked boobies experienced rapid population growth approximately 180,000 years ago and that the majority of Indo-Pacific and Atlantic populations diverged within the last approximately 115,000 years. These combined data suggest that the predominant pattern between Indo-Pacific and Atlantic populations is long-term isolation by physical barriers to gene flow. In contrast, populations within these regions appear to have diverged despite few obvious physical barriers to gene flow, perhaps as a consequence of limited natal dispersal combined with local adaptation and/or genetic drift.