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.     

mtDNA variation and evaluation of phylogenetic relationships among karyotypically polymorphic populations of Microtus (Terricola) thomasi (Arvicolidae, Rodentia) from Greece

The Balkan endemic species Microtus (Terricola) thomasi – Thomas' vole – is widely distributed in the Greek mainland and presents regionally confined karyotypic forms. In order to test the significance of geographical isolation and/or karyological differences in microevolutionary processes at the intraspecific level we used restriction enzymes and partial sequencing to study the polymorphism of the mtDNA d -loop control region in ten Greek populations. An overall high rate of both inter- and intrapopulation polymorphism was observed. The mtDNA diversity was unevenly distributed so that most of the populations studied were very similar and closely related, and only a few of them were clearly differentiated from the others. The mtDNA analysis failed to reveal any clear variation pattern that could be correlated with karyotypic forms or geographical proximity of the populations studied. Instead, the mtDNA phylogeny gave evidence in support of the coexistence of non-polymorphic (2 n  = 44) and polymorphic (2 n  < 44) karyotypic forms within the ancestral Greek M. (T.) thomasi stock. Interestingly, only one population (Agios Stefanos) seemed to significantly diverge from all the others in both methods used, forming a well-supported paraphyletic clade. Allozymic studies have already reported similar results, corroborating the genetic peculiarity of this population.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 55–68.     

Increased molecular divergence of two endemic Trachelipus (Isopoda,Oniscidea) species from Greece reveals patterns not congruent with current taxonomy

In the present study, we employed three mitochondrial DNA genetic markers in a phylogenetic analysis aiming at the delineation of the relationships amongst nominal Trachelipus kytherensis populations, as well as between populations of this species and of Trachelipus aegaeus and a new form, occurring syntopically with the latter. Both the phylogenetic analysis and the genetic distances separating populations, show the presence of several distinct and well differentiated clades that undermine the monophyly of T. kytherensis. On the other hand, despite the insular distribution of T. aegaeus populations, their divergence is low and the monophyly of this taxon can be rescued by the inclusion of two more insular populations previously assigned to T. kytherensis. The patterns of genetic divergence among clades are only partially congruent with the geographic distribution of populations. The validity of taxonomic characters used so far in the genus appears to be questionable; therefore, a more comprehensive phylogenetic study at a population level is deemed necessary for understanding the divergence of Trachelipus lineages. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 361–370.     

Phylogeography and conservation genetics of endangered European Margaritiferidae (Bivalvia: Unionoidea)

Margaritifera margaritifera and M. auricularia are among the most endangered freshwater mussels in the world, and the only species of the genus found in Europe. Our genetic study explores allozymic variability (27 loci) and differentiation at the mitochondrial sequence level (partial COI and 16S rRNA gene sequences). The Spanish M. auricularia population showed genetic parameters of variation that were of the same order as those of other freshwater molluscs (though at the lower end of the range), probably permitting its potential recovery. The difference between this species and M. margaritifera was clearly established (ten diagnostic allozymic loci, Nei = 0.462, and mean nucleotide divergence around 9.4%). The M. margaritifera populations analysed showed a certain degree of population genetic structure (according to allozyme data) that was not, however, related to a geographical cline. Nevertheless, two mitochondrial lineages (albeit very closely related) were identified: a northern lineage extending from Ireland to the Kola Peninsula including the western Atlantic coast, and a second cluster distributed from Ireland to the Iberian Peninsula. The phylogenetic relationships between these two species and other related taxa were established. The putative M. m. durrovensis could be considered an 'ecophenotype'. Palaeobiogeographical scenarios are presented and indicate unexpected 'recent' gene flow between M. margaritifera populations that were theoretically isolated in the early Tertiary.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society 2003, 78, 235–252.     

New data on the distribution and genetic structure of Greek moles of the genus Talpa (Mammalia,Talpidae)

In this work, we employed molecular markers and confirmed the occurrence of two mole species, Talpa stankovici and Talpa europaea in Greece. For the first species, all analyses revealed three major phylogroups, exhibiting great genetic divergence, possibly due to a vicariant event. This event was probably the Peloponnisos’ insulation during the Pliocene and the following sea level fluctuations. A scenario of stable, large‐sized populations for a long period rather than rapid growth from small‐sized populations or founder events is supported. Additionally, T. stankovici’s distribution area is extended to a southernmost limit. For T. europaea there is evidence of low genetic divergence between Greek and Central and North European populations.     

Molecular and morphological boundaries of the predatory mite Neoseiulus californicus (McGregor) (Acari: Phytoseiidae)

Neoseiulus californicus (McGregor) is a natural enemy of pest mites used worldwide in many crops. Its correct identification is thus essential to ensure biological control success. The present study aimed to characterize molecular and morphological intraspecific variations for assisting in the diagnosis of the species and to build baseline information about expected variations within a commercially important phytoseiid species. Morphological and molecular [12S rRNA, cytochrome b mitochondrial (mt)DNA, and internal transcribed spacer] analyses were carried out on fourteen populations collected worldwide and on one mass‐reared strain. The genetic distances between the specimens of N. californicus and another related species were high and no overlap was observed, sustaining the reliability of such molecular methods for assisting a specific diagnosis. Furthermore, the genetic distances between populations of N. californicus were very low and overlap between intra‐ and interpopulations distances was observed, except for two populations collected in France (Marsillargues and Midi‐Pyrénées). The high mitochondrial differentiation between these two latter populations and the others questions their specific status: do they belong to the species N. californicus or to another cryptic species? However, using nuclear DNA marker analyses, no distinct differences were observed. Furthermore, even if significant morphological differences were observed between the populations, these differences were very small and the standard errors within each population were very low. We thus concluded that all the populations studied belong to the species N. californicus, despite unexpected high mitochondrial variations. The present study thus displays the importance of an integrative taxonomic approach for avoiding misidentifications. A discussion on morphological and mtDNA variations in relation to diagnostic reliability is developped. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 393–406.     

Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers

The genetic variation of the critically endangered Corfu killifish (Valencia letourneuxi), an endemic freshwater fish species of the western Balkans, was assessed for nine populations sampled in eight water systems in western continental Greece, the Peloponnese and the Ionian Island of Corfu, using mitochondrial and microsatellite markers. The analyses were based on data from three mtDNA regions (D‐loop, COI and 16S rRNA sequences) and 14 microsatellite loci. Samples from the congeneric species Valencia hispanica and the phylogenetically closely related species Aphanius fasciatus were also used in the study as outgroups. Both the mitochondrial and the microsatellite analyses revealed three distinct population groupings associated with the geographical distribution of the populations: one southern group occupying rivers draining to the Patraikos Gulf, the second one including the populations flowing into the Amvrakikos Gulf and the third, more northern group, including the other populations from rivers in Corfu Island and Epirus flowing into the Ionian Sea. Within these groupings there is limited genetic differentiation between populations; in addition, there is reduced intrapopulation genetic variation, evidenced by low heterozygosity values, number of alleles and haplotype diversity. In terms of taxonomic implications and appropriate management actions for conservation, our data suggest that the major population groups should be regarded at least as three distinct conservation units (CUs), with translocation and restocking actions to take place only within the geographical range of the CU concerned. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 334–349.     

Mitochondrial DNA variation and the evolutionary history of the Mediterranean species of Cicada L. (Hemiptera,Cicadoidea)

Cicadas are widely distributed in the Mediterranean area and are mainly distinguished by male acoustic signals, which act as specific mate recognition systems. Within the genus Cicada L. several species have diverged in their calling songs without showing external morphological differences, so acoustic recordings and genetic studies are particularly useful for systematic, biogeography and evolutionary studies. This study assesses sequence variation in closely related species of Cicada from the Mediterranean area, using domain III of the 12S rRNA mitochondrial gene in order to determine the phylogenetic relationships and the evolutionary history of this group, as well as the population structure of the two most common species, C. orni and C. barbara. Five distinct haplogroups were identified, C. orni, C. barbara, C. mordoganensis, C. cretensis and C. lodosi, each corresponding to a distinct evolutionary group. C. barbara was the most divergent species within this group, while C. orni and C. mordoganensis were the most similar. The population structure and demographic parameters of the species were not completely resolved. However, there is evidence for the separation of the C. orni Greek populations from the rest of Europe and also for demographic expansions probably related to Pleistocene climate changes. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 266–288.     

Morphological and molecular taxonomy of a new Daptonema (Nematoda,Xyalidae) with comments on the systematics of some related taxa

A new species of Daptonema is described based upon morphological characters and 18S rRNA sequence. Daptonema matrona sp. nov. was collected in Pina Basin (north‐eastern Brazil). It differs from all other species of the genus by the presence of reduced cephalic setae and straight spicules. These features require an adaptation of the generic diagnosis. Moreover, the females are characterized by intra‐uterine development of the offspring, considered herein as their major autapomorphic feature. Molecular systematic analyses supported Daptonema matrona sp. nov. as a distinct genetic and evolutionary lineage. The data also indicate hypotheses of taxonomic synonymies amongst some related taxa from Xyalidae as well as the paraphyly of Daptonema. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 1–15.     

Molecular and morphometric data demonstrate the presence of cryptic lineages among freshwater crabs (Decapoda: Potamonautidae: Potamonautes) from the Drakensberg Mountains, South Africa

The evolutionary importance of cryptic taxa is well documented, yet few studies have examined them with a view to conservation. In the present study, the significance of cryptic speciation in freshwater crabs is examined. Allozyme and 16S rRNA sequence data were used to explore the degree of population differentiation between mountain stream populations of two distinct freshwater crab species. Marked patterns of differentiation were evident among populations; those in close geographical proximity were characterized by the fixation of alternate alleles at certain loci, indicating that currently there is no gene flow among populations. Both allozyme and sequence data provide evidence for the recognition of at least five distinct evolutionary lineages with pronounced levels of genetic differentiation. Morphometric data failed to detect any distinct geographically intermediate population groupings. Our findings indicate the presence of five phylogeographical units, all worthy of conservation, three of which are evolutionarily significant.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78 , 129–147.     

Differentiation patterns in the E. MediterraneanScutellaria rubicunda group (Lamiaceae)

Strict sterility barriers where found between theScutellaria populations on Sicily and the Greek populations. The material from Samos is separated by a strict sterility barrier from the other Greek populations. In contrast, the populations on mainland Greece and adjacent islands are all ± interfertile. Three species are recognized,S. rubicunda Hornem., endemic to Sicily, andS. brevibracteata subsp.icarica, endemic to Samos and Ikaria. All other populations are referred toS. rupestris with eight subspecies, most of which are endemic to one island or to one mountain. Three new subspecies are described, viz. subsp.rechingeri and subsp.olympica, endemic to mt Vourinos and mt Olympus in North Greece, respectively, and subsp.caroli-henrici, native to the Malea peninsula of Peloponnisos. The phytogeographical connections and genetic differentiation within and between populations are discussed.Dedicated to Prof. DrK. H. Rechinger on the occasion of his 80th birthday.     

Microevolutionary relationships between phylogeographical history,climate change and morphological variability in the common vole (Microtus arvalis) across France

Aim In this study, we analyse microevolutionary processes in common voles (Microtus arvalis) through the investigation of tooth morphological structure, in order to assess the relative impact of climate and phylogeographical history. Microevolutionary studies have shown that climate change may play a role in both population phylogeography and phenotypic differentiation. However, relatively little is known about the precise relationship between phylogeography and phenotypic variability and about how organisms respond to climate change. Location France, from sea level to the Alps (5 to > 2300 m a.s.l.). Methods This morphological analysis is based on first lower molar measurements from 16 geographically distinct common vole populations. Size and shape components are assessed separately. Population structure patterns are characterized using canonical variate analysis. We use phylogenetic analyses of two regions of mitochondrial DNA (the control region and the cytochrome b gene) to infer genetic structure. We calculate climate parameters from temperature and precipitation data. We investigate the influence of climate, geography and phylogeographical history on the phenotype using (1) multiple regression tests, (2) pairwise comparison of observation‐by‐variable matrices, and (3) a correlation method designed to compare three matrices. Results All populations were clearly structured, whatever the dataset. Neither size nor shape variation was correlated with climate parameters, but tooth shape was strongly correlated with both genetic structure and geographical distance. Main conclusions In French Microtus arvalis populations, molar shape differentiation is clearly associated with both phylogeographical history and geographical distance. Population phylogeographical history has a greater relevance than climate in accounting for variation in tooth morphology.     

A karyosystematic study of the genus Bellevalia Lapeyr. (Hyacinthaceae) in Greece

The genus Bellevalia is represented in Greece by eight taxa, three of which are endemic. Bellevalia brevipedicellata (2n = 8) and B. sitiaca (2n = 16) are restricted to the island of Kriti, while B. hyacinthoides (2n = 8, 12) is distributed in the Kiklades Islands, the central and southern mainland and the Ionian Islands. Four taxa, i.e. B. dubia subsp. boissieri (2n = 8), B. trifoliata (2n = 8), B. romana (2n = 8) and B. ciliata (2n = 8, 16) are Mediterranean elements. The presence of B. edirnensis (2n = 24) is reported as new for the Greek flora. New ploidy levels of three Bellevalia species (triplo‐, tetra‐ and hexaploids) are reported for the first time. The main morphological features, the chromosome numbers, the karyotype morphology, as well as the geographical distribution and further issues of taxonomy and conservation of all Bellevalia taxa in Greece are presented and discussed. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 723–739.     

Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences

The Persian racerunner Eremias persica Blanford, 1875 is confined to the Iranian plateau, and forms one of the most widespread but rarely studied species of the family Lacertidae. With many local populations inhabiting a variety of habitats, and exhibiting considerable morphological, genetic, and ecological variations, it represents a species complex. We analysed sequences of mitochondrial cytochrome b and 12S ribosomal RNA (rRNA) genes derived from 13 geographically distant populations belonging to the E. persica complex. Using our knowledge of palaeogeographical events, a molecular clock was calibrated to assess the major events in fragmentation, radiation, and intraspecific variation. The sequence data strongly support a basal separation of the highland populations of western Iran from those of the open steppes and deserts, occurring in the east. The subsequent radiation, fragmentation, and evolution of these major assemblages have led to several discernable geographical lineages across the wide area of the Iranian plateau. The results indicate a middle‐Miocene origin for the clade as a whole. The first split, isolating the western and eastern clades, appears to have occurred 11–10 Mya. Further fragmentations and divergence within the major clades began about 8 Mya, with an evolutionary rate of 1.6% sequence divergence per million years among the lineages in the genes studied (combined data set). Molecular and morphological data strongly support a taxonomic revision of this species complex. At least four of the discovered clades should be raised to species, and two to subspecies, rank. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 641–660.     

Biochemical genetic variability in brown hares (Lepus europaeus) from Greece

Allozyme variability of 91 brown hares (Lepus europaeus) from seven regions in Greece was compared to existing data of Bulgarian populations to test the hypothesis of the occurrence of specific alleles in Greece, likely stemming from an isolated Late Pleistocene refugial population in the southern Balkans. This hypothesis is particularly suggested by some subfossil Late Pleistocene hare remains in Greece and the reported high mtDNA diversity in Greek hares. Allozymic diversity could be higher in Greek hares than in hares from neighboring regions as a result of the accumulation of variants in a long-lasting Pleistocene refugium. Conversely, Greek hares could exhibit reduced genetic diversity because of long-lasting low effective population sizes during the Late Glacial Maximum and a lower chance of postglacial gene flow from other populations into this rather marginal part in the southern Balkans. Horizontal starch gel electrophoresis of proteins from 35~loci revealed three alleles (Es-1 ^–162, Pep-2 ¹¹⁴, Mpi ⁸⁸) at low frequencies, which were not found in Bulgarian or any other brown hare population. In contrast, some alleles from the populations from Bulgaria and other regions of Europe were absent in the Greek samples. Population genetic statistics indicated only a slight tendency of increased gene pool diversity in Greek hares, little substructuring in Greek and Bulgarian populations, respectively, as well as an only slightly lower level of gene flow between the two neighboring regions, as compared to the gene flow within each region. The results conform to the hypothesis of a Late Pleistocene refugial population in the southern Balkans, with some few specific nuclear gene pool characteristics, but little effect on the overall genetic differentiation between Greek and Bulgarian hares.     

Molecular phylogeny of the Greek populations of the genus Ligidium (Isopoda, Oniscidea) using three mtDNA gene segments

The phylogeny of Greek populations of the terrestrial isopod genus Ligidium is reconstructed based on three mtDNA gene segments: 12S rRNA, 16S rRNA and COI. Two widely distributed European species, as well as three outgroups belonging to different isopod genera, were also included in the analyses. The samples used represent almost all Ligidium species known to occur in Greece, as well as several populations of unknown specific status plus some new records. Phylogenetic analyses of the combined data set were performed using Bayesian inference and maximum parsimony. The two main sister clades with good support indicate the sympatric differentiation of two lineages in southern continental Greece (Peloponnisos), where Ligidium populations exhibit a mosaic distribution of sibling species. The insular populations of the Aegean Islands show increased genetic divergence and form separate clades. The presence of a third lineage of Asiatic origin is strongly suggested by both the molecular phylogeny and morphology. The only presumably valid diagnostic morphological character exhibits only partial correspondence to well supported clades of the molecular phylogeny. Genetic differentiation between populations is very high, a fact that can be attributed to the strict ecological specialization of these animals that leads to increased levels of isolation even between populations that are in close proximity. As a consequence, Greek Ligidium populations, especially those present on islands, are unique genetic pools and extremely vulnerable to extinction.     

Phylogenetic relationships and rate of early diversification of Australian Sphenomorphus group scincids (Scincoidea, Squamata)

The Australian Sphenomorphus group is a morphologically and ecologically diverse clade of lygosomine scincids, collectively comprising more than one‐half of the Australian scincid fauna. A previous phylogenetic analysis of mitochondrial 12S and 16S rRNA, and ND4 and adjacent tRNA sequences for a series of Australian Sphenomorphus group scincids recovered several well‐supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage‐level polytomies, I employ ATP synthetase‐β subunit intron sequences and the existing mitochondrial (mt)DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mtDNA and intron sequence data reveal a number of congruent clades, including Anomalopus, Calyptotis, Ctenotus, Lerista, the Eulamprus quoyii group, the Glaphyromorphus crassicaudis group (including Glaphyromorphus cracens, Glaphyromorphus darwiniensis, and Glaphyromorphus fuscicaudis), Glaphyromorphus gracilipes + Hemiergis, Coeranoscincus reticulatus + Ophioscincus truncatus + Saiphos, and Eulamprus amplus + Eulamprus tenuis + Gnypetoscincus + Nangura. The relationships among these clades indicated by the two data sets, however, are generally incongruent. Although this may be partially ascribed to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mtDNA and intron fragments considered, if not essentially simultaneous. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92 , 347–366.     

Leaf morphological variation in beech (Fagus sylvatica L.) populations in Greece and its relation to their post‐glacial origin

Diversity in leaf morphological traits was assessed in 38 Greek Fagus sylvatica populations, covering the distribution of the species in the country. The relationship between the post‐glacial origin of these populations and leaf morphology was investigated. The results showed a complex and geographically continuous morphological diversity pattern, influenced mainly by traits expressing leaf size, leaf shape and petiole length. Two simultaneous trends appeared to be responsible for the existing diversity pattern. One was geographical, with leaf types resembling F. sylvatica subsp. sylvatica occurring in the western part of the distribution of beech in Greece and types resembling F. sylvatica subsp. orientalis being dominant in the eastern part. A second trend seemed to be connected with the post‐glacial origin of the populations, as described by previous plastid DNA haplotype studies of the same trees. The genetic background and the possible adaptation of beech populations to different environmental conditions have resulted in a complex morphological pattern, especially in areas in which different post‐glacial lineages appear to meet. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 422–436.     

MITOCHONDRIAL DNA VARIATION IN THE FIELD VOLE (MICROTUS AGRESTIS): REGIONAL POPULATION STRUCTURE AND COLONIZATION HISTORY

Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.     

Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia

The evolutionary history and biogeography of freshwater-dependent taxa in Australia is of intrinsic interest given the present-day aridity of this continent. Cherax is the most widespread and one of the most species-rich of Australia's nine freshwater crayfish genera. The phylogenetic relationships amongst 19 of the 23 Australian Cherax were established from mitochondrial DNA sequences representing the 12S rRNA and 16S rRNA gene regions. The relationships among species support an initial east–west separation, followed by a north–south divergence in eastern Australia. Molecular clock estimations suggest that these divergences date back to the Miocene. The phylogenetic relationships support endemic speciation within geographical regions and indicate that long-distance dispersal has not led to recent speciation as previously hypothesized. This new evolutionary scenario is consistent with the climatic history of Australia and the evolutionary history of other similarly distributed freshwater-dependent organisms in Australia.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 553–563.