A multilocus phylogeny of the fish genus Poeciliopsis: Solving taxonomic uncertainties and preliminary evidence of reticulation

The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, that is, concatenated (also known as super‐matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously considered of undetermined taxonomic status could be unequivocally assigned to P. scarlli; revealing a relatively recent dispersal event across the Trans‐Mexican Volcanic Belt (TMVB) or Pacific Ocean, which constitute a strong barrier to north–south dispersal of many terrestrial and freshwater taxa. The closest relatives of P. balsas, a species distributed south of the TMVB, are distributed in the north; representing an additional north–south split in the genus. An undescribed species of Poeciliopsis, with a highly restricted distribution (i.e., a short stretch of the Rio Concepcion; just south of the US‐Mexico border), falls within the Leptorhaphis species complex. Our results are inconsistent with the hypothesis that this species originated by “breakdown” of an asexual hybrid lineage. On the other hand, network analyses suggest one or more possible cases of reticulation within the genus that require further evaluation with genome‐wide marker representation and additional analytical tools. The most strongly supported case of reticulation occurred within the subgenus Aulophallus (restricted to Central America), and implies a hybrid origin for P. retropinna (i.e., between P. paucimaculata and P. elongata). We consider that P. balsas and P. new species are of conservation concern.     

Craniid brachiopods: aspects of clade structure and distribution reflect continental drift (Brachiopoda: Craniiformea)

We present maximum likelihood and Bayesian inference relative time‐tree analyses of aligned gene sequences from a worldwide collection of craniiform brachiopods belonging to two genera, Novocrania and Neoancistrocrania. Sequences were obtained from one mitochondrial and three nuclear‐encoded ribosomal RNA genes from varying numbers of specimens. Data‐exploration by network (splits) analyses indicates that each gene identifies the same divergent clades and (with one minor exception) the same inter‐clade relationships. Neoancistrocrania specimens were found only in the Pacific Ocean, near Japan, on the Norfolk and Chesterfield Ridges, and near the Solomon Islands. The Novocrania clades, in approximate order of increasing distance from the root comprise 1. a ‘Northern’ clade of animals collected in the NE. Atlantic, W. Mediterranean and Adriatic; 2. a ‘Tethyan’ clade comprising animals from the E. Mediterranean, Cape Verde islands and the Caribbean (Belize and Jamaica); 3. a ‘NE. Pacific’ clade containing animals from Vancouver Island and from localities near Japan and south of Taiwan; 4. a ‘Southern’ clade that contains two widely separated subclades, one from New Zealand and the other with an extraordinarily wide distribution, ranging from near Japan in the north to the Chesterfield Ridge and Solomon Islands in the West, and in the East to the Galapagos Islands, the coast of South America (Chile) and Richardson seamount (off South Africa) in the South Atlantic. To the South, members of this clade were found in the Weddell, Scotia and Bellinghausen Antarctic Seas. The root of the extant craniid radiation was previously found (by relaxed‐clock analysis) to lie on the branch connecting the two genera so that, in effect, the one clade of Neoancistrocrania serves to polarise evolutionary relationships within the several clades of Novocrania. As previously suggested, all results confirm that Neoancistrocrania is sister to the ‘Northern’ Novocrania clade, and this leads to a proposal that Neoancistrocrania represents one extreme of a wide range of variation in ancestral ventral valve mineralisation, speciation (～90 Ma) resulting from competitive exclusion in rapidly‐growing reef environments. To the extent possible, the identified molecular clades are correlated with named species of Novocrania. The reproductive and population biology of craniid brachiopods is not well known, but from available evidence they are considered to have low‐dispersal potential and, except in enclosed localities such as cold‐water fjords, to have small effective population sizes, features which are consistent with the observed divergent populations in well‐separated localities. Exceptionally slow craniid molecular (rDNA) evolution is suggested by the short branch of Novocrania where it has been used as an outgroup for large‐scale analyses of metazoans. Slow molecular evolution is also indicated by the existence of a distinct Tethyan clade, reflecting restricted dispersal at former times, and by the uniform, short, genetic distances and exceptionally wide geographical distribution of the Southern clade. Thus, the geographical distribution and phylogenetic divergence of craniid brachiopods is an example of phylotectonics, in which relationships revealed by phylogenetic analyses reflect opportunities for dispersal and settlement that were created by tectonic plate movements associated, in this case, with opening and closure of Tethys and the breakup of Gondwana. Molecular dating of craniid divergences and radiochemical dating of tectonic events thus illuminate one another. © 2014 The Linnean Society of London     

Complex phylogeography in the Southern Smooth Snake (Coronella girondica) supported by mtDNA sequences

Palearctic reptiles with wide distribution through the Western Mediterranean are expected to display genetic substructuring because of the combining effects of current or past geographic barriers and climate fluctuations. We have examined this issue by sequencing cytochrome b and 16S rRNA mitochondrial fragments of 80 individuals of the snake Coronella girondica from 71 localities, covering the range of the species across Tunisia, Algeria, Morocco, Spain, Portugal, southern France and north‐western Italy. According to the obtained genealogy, C. girondica is structured into three divergent and well‐supported clades (north‐western Africa, Betic range and Iberia–France–Italy), which greatly match other phylogeographies already published for this region. Our estimations suggest that the divergence among the three clades took place approximately 1.4‐2.0 Ma, which roughly coincides with the Plio‐Pleistocene transition, characterized by an increase in climate variability. The existence of a clade in a narrow belt of south‐eastern Iberia represents another example of the high endemism rate of the region, with a key geographical situation and an important role in vicariant processes. Since the split among the three major lineages would be take place after the opening of the Strait of Gibraltar, overwater dispersal is here suggested. The subsequent genetic substructuring of these clades during the Pleistocene fits within the refugia‐within‐refugia model, highlighting the importance of the region as a scenario for multiple vicariant events.     

Biogeographic history of geminate cirrhitoids (Perciformes: Cirrhitoidea) with east–west allopatric distributions across southern Australia, based on molecular data

The biogeographic history of three cirrhitoid species pairs with east–west allopatric distributions across southern Australia was examined by determining levels of mitochondrial DNA sequence divergence and applying molecular clock calibrations. Similar levels of genetic divergence were observed for Aplodactylus Valenciennes and Goniistius Gill species pairs, but these were more than twice that observed for a Nemadactylus Richardson pair. Molecular clock calibrations suggested divergences occurred during the late Miocene and mid Pliocene, respectively. Given evidence of high dispersal capabilities, the habitat and climatic barriers of the Australian south coast appear too small to have facilitated speciation of the cirrhitoids examined. A mechanism is proposed by which ancestral cirrhitoids were vicariantly isolated into east and west coast populations during periods of climate change. Although Aplodactylus and Goniistius divergences occurred during the same period, separate vicariant events across the Australian north and south coasts are invoked.     

Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences

Aim To test a vicariant speciation hypothesis derived from geological evidence of large‐scale changes in drainage patterns in the late Miocene that affected the drainages in the south‐eastern Tibetan Plateau. Location The Tibetan Plateau and adjacent areas. Methods The cytochrome b DNA sequences of 30 species of the genus Schizothorax from nine different river systems were analysed. These DNA sequences were analysed using parsimony, maximum likelihood and Bayesian methods. The approximately unbiased and Shimodaira–Hasegawa tests were applied to evaluate the statistical significance of the shortest trees relative to alternative hypotheses. Dates of divergences between lineages were estimated using the nonparametric rate smoothing method, and confidence intervals of dates were obtained by parametric bootstrapping. Results The phylogenetic relationships recovered from molecular data were inconsistent with traditional taxonomy, but apparently reflected geographical associations with rivers. Within the genus Schizothorax, we observed a divergence between the lineages from the Irrawaddy–Lhuit and Tsangpo–Parlung rivers, and tentatively dated this vicariant event back to the late Miocene (7.3–6.8 Ma). We also observed approximately simultaneous geographical splits within drainages of the south‐eastern Tibetan Plateau, the Irrawaddy, the Yangtze and the Mekong–Salween rivers in the late Miocene (7.1–6.2 Ma). Main conclusions Our molecular evidence tentatively highlights the importance of palaeoriver connections and the uplift of the Tibetan Plateau in understanding the evolution of the genus Schizothorax. Molecular estimates of divergence times allowed us to date these vicariant scenarios back to the late Miocene, which agrees with geological suggestions for the separation of these drainages caused by tectonic uplift in south‐eastern Tibet. Our results indicated the substantial role of vicariant‐based speciation in shaping the current distribution pattern of the genus Schizothorax.     

Differential regional response of the bushy‐tailed woodrat (Neotoma cinerea) to late Quaternary climate change

Aim To reconstruct the regional biogeographical history of the bushy‐tailed woodrat, Neotoma cinerea (Rodentia: Cricetidae), across its distribution using multiple sources of information, including genetic data, ecological niche models and the palaeorecord. Location Western North America. Methods We analysed complete cytochrome b gene (1143 bp) sequences from 182 specimens of N. cinerea using Bayesian and coalescent methods to infer phylogenetic relationships, time of major divergences, and recent demographic trends. For comparison, we developed clade‐specific ecological niche models for groups of interest and analysed spatial trends of N. cinerea in the palaeorecord as well as temporal frequency trends across strata of individual palaeomiddens. Results We found two largely allopatric clades within N. cinerea, with several regionally distinct subclades showing contrasting recent population dynamics. Niche models showed consistent habitat at the Last Glacial Maximum (LGM) and modern times in the Rocky Mountains and northern United States, while the Great Basin may have been markedly less suitable at the LGM than today. The palaeorecord showed great spatio‐temporal variability in the presence of N. cinerea, but documents broad‐scale patterns of occupancy and regional population trends. Main conclusions The Quaternary dynamics and evolutionary history of N. cinerea appear to have been shaped by both vicariant events associated with geographical barriers and the availability of suitable habitat through time. Divergence of the two major clades dates to the Pliocene–Pleistocene transition, with clades separated by the Green and Colorado rivers and northern Rocky Mountain Pleistocene glaciations. We found largely concordant genetic, niche model and palaeorecord patterns suggesting long‐term population stability in the Rocky Mountains, while extant clades in the Great Basin and far north appear to have expanded or re‐expanded into these regions relatively recently. Furthermore, disjunct haplotype distributions, regional demographic history, and historical distribution of suitable habitat suggest that the Great Basin has been a particularly dynamic region.     

Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the existence of the ancient Teays River

Aim To assess the roles of dispersal and vicariance in shaping the present distribution and diversity within Hypentelium nigricans, the northern hogsucker (Teleostei: Cypriniformes). Location Eastern United States. Methods Parsimony analyses, Bayesian analyses, pairwise genetic divergence and mismatch plots are used to examine patterns of genetic variation across H. nigricans. Results Species relationships within the genus Hypentelium were consistent with previous hypotheses. However, relationships between haplotypes within H. nigricans revealed two deeply divergent groups, a clade containing haplotypes from the New and Roanoke rivers (Atlantic Slope) plus Interior Highlands and upper Mississippi River and a clade containing haplotypes from the Eastern Highlands, previously glaciated regions of the Ohio and Wabash rivers, and the Amite and Homochitto rivers of south‐western Mississippi. Main conclusions The phylogenetic history of Hypentelium was shaped by old vicariant events associated with erosion of the Blue Ridge and separation of the Mobile and Mississippi river basins. Within H. nigricans two clades existed prior to the Pleistocene; a widespread clade in the pre‐glacial Teays‐Mississippi River system and a clade in Cumberland and Tennessee rivers. Pleistocene events fragmented the Teays‐Mississippi fauna. Following the retreat of the glaciers H. nigricans dispersed northward into previously glaciated regions. These patterns are replicated in other clades of fishes and are consistent with some of the predictions of Mayden's (Systematic Zoology, 37, 329, 1988) pre‐Pleistocene vicariance hypothesis.     

Impact of mountain chains, sea straits and peripheral populations on genetic and taxonomic structure of a freshwater turtle, Mauremys leprosa (Reptilia, Testudines, Geoemydidae)

Mauremys leprosa, distributed in Iberia and North‐west Africa, contains two major clades of mtDNA haplotypes. Clade A occurs in Portugal, Spain and Morocco north of the Atlas Mountains. Clade B occurs south of the Atlas Mountains in Morocco and north of the Atlas Mountains in eastern Algeria and Tunisia. However, we recorded a single individual containing a clade B haplotype in Morocco from north of the Atlas Mountains. This could indicate gene flow between both clades. The phylogenetically most distinct clade A haplotypes are confined to Morocco, suggesting both clades originated in North Africa. Extensive diversity within clade A in south‐western Iberia argues for a glacial refuge located there. Other regions of the Iberian Peninsula, displaying distinctly lower haplotype diversities, were recolonized from within south‐western Iberia. Most populations in Portugal, Spain and northern Morocco contain the most common clade A haplotype, indicating dispersal from the south‐western Iberian refuge, gene flow across the Strait of Gibraltar, and reinvasion of Morocco by terrapins originating in south‐western Iberia. This hypothesis is consistent with demographic analyses, suggesting rapid clade A population increase while clade B is represented by stationary, fragmented populations. We recommend the eight, morphologically weakly diagnosable, subspecies of M. leprosa be reduced to two, reflecting major mtDNA clades: Mauremys l. leprosa (Iberian Peninsula and northern Morocco) and M. l. saharica (southern Morocco, eastern Algeria and Tunisia). Peripheral populations could play an important role in evolution of M. leprosa because we found endemic haplotypes in populations along the northern and southern range borders. Previous investigations in another western Palearctic freshwater turtle (Emys orbicularis) discovered similar differentiation of peripheral populations, and phylogeographies of Emys orbicularis and Mauremys rivulata underline the barrier status of mountain chains, in contrast to sea straits, suggesting common patterns for western Palearctic freshwater turtles.     

Australian biogeographical connections and the phylogeny of large genera in the plant family Myrtaceae

Aim To compare the phylogeny of the eucalypt and melaleuca groups with geological events and ages of fossils to discover the time frame of clade divergences. Location Australia, New Caledonia, New Guinea, Indonesian Archipelago. Methods We compare published molecular phylogenies of the eucalypt and melaleuca groups of the plant family Myrtaceae with geological history and known fossil records from the Cretaceous and Cenozoic. Results The Australasian eucalypt group includes seven genera, of which some are relictual rain forest taxa of restricted distribution and others are species‐rich and widespread in drier environments. Based on molecular and morphological data, phylogenetic analyses of the eucalypt group have identified two major clades. The monotypic Arillastrum endemic to New Caledonia is related in one clade to the more species‐rich Angophora, Corymbia and Eucalyptus that dominate the sclerophyll vegetation of Australia. Based on the time of rifting of New Caledonia from eastern Gondwana and the age of fossil eucalypt pollen, we argue that this clade extends back to the Late Cretaceous. The second clade includes three relictual rain forest taxa, with Allosyncarpia from Arnhem Land the sister taxon to Eucalyptopsis of New Guinea and the eastern Indonesian archipelago, and Stockwellia from the Atherton Tableland in north‐east Queensland. As monsoonal, drier conditions evolved in northern Australia, Arnhem Land was isolated from the wet tropics to the east and north during the Oligocene, segregating ancestral rain forest biota. It is argued also that the distribution of species in Eucalyptopsis and Eucalyptus subgenus Symphyomyrtus endemic in areas north of the stable edge of the Australian continent, as far as Sulawesi and the southern Philippines, is related to the geological history of south‐east Asia‐Australasia. Colonization (dispersal) may have been aided by rafting on micro‐continental fragments, by accretion of arc terranes onto New Guinea and by land brought into closer proximity during periods of low sea‐level, from the Late Miocene and Pliocene. The phylogenetic position of the few northern, non‐Australian species of Eucalyptus subgenus Symphyomyrtus suggests rapid radiation in the large Australian sister group(s) during this time frame. A similar pattern, connecting Australia and New Caledonia, is emerging from phylogenetic analysis of the Melaleuca group (Beaufortia suballiance) within Myrtaceae, with Melaleuca being polyphyletic. Main conclusion The eucalypt group is an old lineage extending back to the Late Cretaceous. Differentiation of clades is related to major geological and climatic events, including rifting of New Caledonia from eastern Gondwana, development of monsoonal and drier climates, collision of the northern edge of the Australian craton with island arcs and periods of low sea level. Vicariance events involve dispersal of biota.     

Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri?

We examined historical patterns of gene flow in the freshwater fish Poecilia butleri in western Mexico. We tested the hypothesis that the boundaries between four freshwater ecological communities (ecoregions) might have limited the movement of P. butleri because changes in species compositions might restrict establishment between adjacent ecoregions, even in situations where a physical barrier is absent. Hence, we predicted that boundaries between ecoregions should correspond to phylogeographical breaks in P. butleri. We also tested the hypothesis that the width of the continental shelf affected historical gene flow in P. butleri because a broad continental shelf provides a greater opportunity for rivers to coalesce during historical episodes of low sea levels as opposed to a narrow continental shelf that should restrict the potential for gene flow among adjacent rivers. Hence, we predicted greater amounts of historical gene flow among neighbouring river basins in the region of western Mexico where the continental shelf is wider, whereas, in the region where the continental shelf is narrower, we expected to detect limited levels of historical gene flow. We analyzed mitochondrial DNA sequence data (cytochrome b) taken from 264 individuals of P. butleri collected from 34 locations distributed across four different ecoregions in western Mexico. To examine patterns of phylogenetic diversification and historical gene flow in P. butleri, we employed several analytical approaches, including traditional tree‐based phylogenetic analyses (likelihood and parsimony), haplotype network reconstruction, analyses of molecular variance, and spatial analysis of molecular variance. We found genetic breaks coinciding with two out of three different ecoregion boundaries, suggesting limited historical gene flow. In addition to different species compositions between these adjacent ecoregions, geological features such as the Trans‐Mexican Volcanic Belt and the mountainous topography in south‐western Mexico, likely contributed to these observed genetic breaks. By contrast, no genetic break was evident between two other ecoregions, a result that partially rejects our first hypothesis. Several results were consistent with our second hypothesis. Changes in the width of the continental shelf in western Mexico are associated with the observed patterns of historical gene flow. Our results indicate that the interactions among multiple geological and biological factors affect the spatial patterns of genetic diversity of widespread freshwater species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 399–416.     

Phylogeographic structure in the gilgie (Decapoda: Parastacidae: Cherax quinquecarinatus): a south‐western Australian freshwater crayfish

The gilgie (Cherax quinquecarinatus) is among the more widespread of the six endemic south‐western Australian freshwater crayfish species. In the present study, the phylogeographic structure of the gilgie was investigated across its distribution to determine whether patterns reflected those identified earlier in a co‐distributed congeneric, the koonac (Cherax preissii). Gilgies were sampled from 20 localities, a 412‐bp fragment of the cytochrome c oxidase subunit I mitochondrial DNA gene was amplified from 75 individuals, and allozyme variation was assayed at nine loci. As in the koonac, three geographically‐restricted lineages were identified: from the north‐western, southern coastal, and intermediate/south‐western regions. Phylogeographic breaks appeared to be congruent with those in the koonac. The extent of genetic differentiation among lineages was comparable to that in the koonac, suggesting temporal congruence of the historical events responsible for the observed structure. A relaxed Bayesian molecular clock suggested that the major clades and lineages in each species diverged in the Late Miocene–Early Pliocene (4.0–9.6 Myr ago), possibly resulting from increasing pulses of aridity. The retrieval of almost‐identical phylogeographic structure in two co‐distributed species suggests that biogeographic regions can be more accurately defined in south‐western Australia. With the geographic fidelity of these lineages, the present data also provide evidence of the translocation of a single individual from the north‐west to the south coast. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 385–402.     

Phylogeny and diversification of the cloud forest Morpho sulkowskyi group (Lepidoptera,Nymphalidae) in the evolving Andes

The monophyletic Morpho sulkowskyi butterfly group, endemic of Andean cloud forests, was studied to test the respective contributions of Mio‐Pliocene intense uplift period and Pleistocene glacial cycles on Andean biodiversity. We sampled nine taxa covering the whole geographical range of the group. Two mitochondrial and two nuclear genes were analysed using a Bayesian method. We established a dated phylogeny of the group using a relaxed clock method and a wide‐outgroup approach. To discriminate between two hypotheses, we used a biogeographical probabilistic method. Results suggest that the ancestor of the M. sulkowskyi group originated during the Middle–Late Miocene uplift of the Eastern Cordillera in northern Peru. Biogeographical inference suggests that the M. sulkowskyi and Morpho lympharis clades diverged in the northern Peruvian Andes. The subsequent divergences, from the Late Miocene to the Late Pliocene, should have resulted from a dispersal towards the Northern Andes (M. sulkowskyi clade), after the closure of the West Andean Portal separating the Central and Northern Andes, and a southwards dispersal along the Peruvian and Bolivian Eastern Cordilleras (M. lympharis clade). Only a few divergences occurred at the very end of the Pliocene or during the Pleistocene, a period when the more recent uplifts interfered with Pleistocene glacial cycles.     

The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Praomys misonnei and to document whether or not rain forest refugia and rivers structure patterns of diversity within this species. Location Tropical Africa, from Ghana to Kenya. Methods Patterns of genetic structure and signatures of population history (cytochrome b gene) were assessed in a survey of 229 individuals from 54 localities. Using maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intra‐specific relationships and tested hypotheses for historical patterns of gene flow within P. misonnei. Results Our phylogenetic analyses reveal a strong phylogeographical structure. We identified four major geographical clades within P. misonnei: one clade in Ghana and Benin, a Nigerian clade, a West Central African clade and a Central and East African clade. Several subclades were identified within these four major clades. A signal of population expansion was detected in most clades or subclades. Coalescence within all of the major clades of P. misonnei occurred during the Middle Pleistocene and/or the beginning of Late Pleistocene. Main conclusions Our results suggest a role for both Pleistocene refugia and rivers in structuring genetic diversity in P. misonnei. This forest‐dwelling rodent may have been isolated in a number of forest fragments during arid periods and expanded its range during wetter periods. Potential forest refugia may have been localized in Benin–Ghana, south‐western Cameroon, southern Gabon, northern Gabon and eastern Democratic Republic of Congo–western Uganda. The Niger and/or the Cross Rivers, the Oubangui‐Congo, Sanaga, Ogooue and/or Ivindo Rivers probably stopped the re‐expansion of the species from relict areas.     

Mitochondrial differentiation and biogeography of Hyla meridionalis (Anura: Hylidae): an unusual phylogeographical pattern

Aim To study the patterns of genetic variation and the historical events and processes that influenced the distribution and intraspecific diversity in Hyla meridionalis Boettger, 1874. Location Hyla meridionalis is restricted to the western part of the Mediterranean region. In northern Africa it is present in Tunisia, Algeria and Morocco. In south‐western Europe it is found in the south of France, north‐western Italy and north‐eastern and south‐western Iberian Peninsula. There are also insular populations, as in the Canaries and Menorca. Methods Sampling included 112 individuals from 36 populations covering the range of the species. We used sequences of mitochondrial DNA Cytochrome Oxidase I (COI) for the phylogeographical analysis (841 bp) and COI plus a fragment including part of tRNA lysine, ATP synthase subunits 6 and 8 and part of Cytochrome Oxidase III for phylogenetic analyses (2441 bp). Phylogenetic analyses were performed with paup *4.0b10 (maximum likelihood, maximum parsimony) and Mr Bayes 3.0 (Bayesian analysis). Nested clade analysis was performed using tcs 1.18 and Geo Dis 2.2. A dispersal‐vicariant analysis was performed with diva 1.0 to generate hypotheses about the geographical distribution of ancestors. Results We found little genetic diversity within samples from Morocco, south‐western Europe and the Canary Islands, with three well‐differentiated clades. One is distributed in south‐western Iberia and the High Atlas, Anti‐Atlas and Massa River in Morocco. The second is restricted to the Medium Atlas Mountains. The third one is present in northern Morocco, north‐eastern Iberia, southern France and the Canaries. These three groups are also represented in the nested clade analysis. Sequences from Tunisian specimens are highly divergent from sequences of all other populations, suggesting that the split between the two lineages is ancient. diva analysis suggests that the ancestral distribution of the different lineages was restricted to Africa, and that an explanation of current distribution of the species requires three different dispersal events. Main conclusions Our results support the idea of a very recent colonization of south‐western Europe and the Canary Islands from Morocco. South‐western Europe has been colonized at least twice: once from northern Morocco probably to the Mediterranean coast of France and once from the western coast of Morocco to southern Iberia. Human transport is a likely explanation for at least one of these events. Within Morocco, the pattern of diversity is consistent with a model of mountain refugia during hyperarid periods within the Pleistocene. Evaluation of the phylogenetic relationships of Tunisian haplotypes will require an approach involving the other related hylid taxa in the area.     

Mitochondrial DNA sequences suggest unexpected phylogenetic position of Corso-Sardinian grass snakes (<Emphasis Type="Italic">Natrix cetti</Emphasis>) and do not support their species status,with notes on phylogeography and subspecies delineation of grass snakes

We supplement a previously published mitochondrial DNA data set of grass snake sequences (ND1, ND2, ND4, cyt b, in total 3,806 bp) with sequences of Corso-Sardinian and Tuscan specimens and infer their phylogeny using Bayesian, maximum likelihood and maximum parsimony methods. In addition, we estimate divergence times of grass snake clades using a relaxed molecular clock calibrated with fossil evidence, and, in a second approach, the post-Messinian reopening of the Strait of Gibraltar. Recently it was suggested that Corso-Sardinian grass snakes represent a distinct species: Natrix cetti. All tree-building methods revealed well-supported branching patterns and deep divergences among grass snakes. However, sequences of N. natrix were consistently paraphyletic with respect to Corso-Sardinian sequences. The sister group of Corso-Sardinian grass snakes is a clade embracing N. n. helvetica and N. n. lanzai. Extensive gene flow between N. n. helvetica and a more distantly related subspecies (N. n. natrix) is well known, which is why we conclude that the status of Corso-Sardinian grass snakes as subspecies of N. natrix should be reinstated. Many currently recognized grass snake subspecies conflict with mitochondrial clades, suggestive of inappropriate morphological taxon delineation and mitochondrial introgression. Divergences among grass snakes are old, and the results of the two independent dating approaches are largely congruent. Accordingly, the Alpine orogenesis seems to have caused the origin of the oldest clade, corresponding to Iberian N. n. astreptophora. The formation of Corso-Sardinian grass snakes was dated to the Early Pliocene and could result from post-Messinian flooding of the Mediterranean Basin. Another deeply divergent clade of approximately the same age, endemic in central and northern Europe, suggests the Pleistocene survival of grass snakes north of the Alps. At least one glacial refuge in which old lineages survived Pleistocene cold periods was located on each of the three major southern European peninsulas and in Anatolia. Due to pronounced sequence divergences among Italian and southern Swiss grass snakes, we hypothesize multiple refugia south of the Alps and in the Apennine Peninsula, and there is evidence for two refuges on the Balkan Peninsula.     

Phylogeographic analysis detects congruent biogeographic patterns between a woodland agamid and Australian wet tropics taxa despite disparate evolutionary trajectories

Aim To test the congruence of phylogeographic patterns and processes between a woodland agamid lizard (Diporiphora australis) and well‐studied Australian wet tropics fauna. Specifically, to determine whether the biogeographic history of D. australis is more consistent with a history of vicariance, which is common in wet tropics fauna, or with a history of dispersal with expansion, which would be expected for species occupying woodland habitats that expanded with the increasingly drier conditions in eastern Australia during the Miocene–Pleistocene. Location North‐eastern Australia. Methods Field‐collected and museum tissue samples from across the entire distribution of D. australis were used to compile a comprehensive phylo‐geographic dataset based on c. 1400 bp of mitochondrial DNA (mtDNA), incorporating the ND2 protein‐coding gene. We used phylogenetic methods to assess biogeographic patterns within D. australis and relaxed molecular clock analyses were conducted to estimate divergence times. Hierarchical Shimodaira–Hasegawa tests were used to test alternative topologies representing vicariant, dispersal and mixed dispersal/vicariant biogeographic hypotheses. Phylogenetic analyses were combined with phylogeographic analyses to gain an insight into the evolutionary processes operating within D. australis. Results Phylogenetic analyses identified six major mtDNA clades within D. australis, with phylogeographic patterns closely matching those seen in many wet tropics taxa. Congruent phylogeographic breaks were observed across the Black Mountain Corridor, Burdekin and St Lawrence Gaps. Divergence amongst clades was found to decrease in a north–south direction, with a trend of increasing population expansion in the south. Main conclusions While phylogeographic patterns in D australis reflect those seen in many rain forest fauna of the wet tropics, the evolutionary processes underlying these patterns appear to be very different. Our results support a history of sequential colonization of D. australis from north to south across major biogeographic barriers from the late Miocene–Pleistocene. These patterns are most likely in response to expanding woodland habitats. Our results strengthen the data available for this iconic region in Australia by exploring the understudied woodland habitats. In addition, our study shows the importance of thorough investigations of not only the biogeographic patterns displayed by species but also the evolutionary processes underlying such patterns.     

Mitochondrial DNA sequence analysis reveals multiple Pleistocene glacial refugia for the Yellow‐spotted mountain newt,Neurergus derjugini (Caudata: Salamandridae) in the mid‐Zagros range in Iran and Iraq

Phylogeography is often used to investigate the effects of glacial cycles on current genetic structure of various plant and animal species. This approach can also identify the number and location of glacial refugia as well as the recolonization routes from those refugia to the current locations. To identify the location of glacial refugia of the Yellow‐spotted mountain newt, Neurergus derjugini, we employed phylogeography patterns and genetic variability of this species by analyzing partial ND4 sequences (867 bp) of 67 specimens from 15 sampling localities from the whole species range in Iran and Iraq. Phylogenetic trees concordant with haplotype networks showed a clear genetic structure among populations as three groups corresponding to the populations in the north, center, and south. Evolutionary ages of clades north and south ranging from 0.15 to 0.17 Myr, while the oldest clade is the central clade, corresponding to 0.32 Myr. Bayesian skyline plots of population size change through time show a relatively slight increase until about 25 kyr (around the last glacial maximum) and a decline of population size about 2.5 kyr. The presence of geographically structured clades in north, center, and south sections of the species range signifies the disjunct populations that have emerged in three different refugium. This study illustrates the importance of the effect of previous glacial cycles in shaping the genetic structure of mountain species in the Zagros range. These areas are important in terms of long‐term species persistence and therefore valuable areas for conservation of biodiversity.     

The Asian Fish Tapeworm Bothriocephalus acheilognathi: a Potential Threat to Native Freshwater Fish Species in Mexico

Introduction of the parasite Bothriocephalus acheilognathi Yamaguti, 1934 with the herbivorous carp Ctenopharyngodon idellus, and other cyprinids, has been documented in almost every continent, except Antarctica. This study presents the current geographical distribution of this cestode in the freshwater fish of Mexico, highlighting infections in autochthonous and endemic species. It compiles existing information and presents original data. B. acheilognathi is widely dispersed among the freshwater fish of Mexico, being recorded to date in 49 fish species from 26 genera, 7 families and 5 orders. B. acheilognathi is reported from Mexico for the first time in Dionda ipni, Notropis celayensis, Yuriria alta, Gambusia vittata, Poecilia butleri, P. mexicana, Poeciliopsis baenschi, Poeciliopsis sp., Cichlasoma cyanoguttatum and C. labridens. The new hosts identified in this study bring the total number of known host species to 102 in 14 families and 7 orders of freshwater fishes around the world. Given its wide distribution among Mexican freshwater fish species, the abundance of the parasite and its high pathogenicity, parasitological data for B. acheilognathi should be considered as an important factor in native fish conservation policies. Biological changes in the freshwater habitats in Mexico caused by the introduction of exotic fish species and their parasites are virtually ubiquitous and extremely difficult to eradicate once established. As such, they should be considered as one of the most serious threats to native fish conservation.     

Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late‐Pleistocene demographic expansion across the Northern Hemisphere

Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.     

Alpine–Himalayan orogeny drove correlated morphological,molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

The Persian dwarf snake Eirenis (Pseudocyclophis) persicus (Anderson, 1872) has a wide distribution range in south‐western Asia. This species group was comprehensively studied here using traditional biometry, geometric morphometrics, ecological niche modelling, and genetics. Our analyses revealed that E. persicus is split into two clades. A western clade, bearing at least two different species: E. persicus, distributed in south‐western Iran, and an undescribed species from south‐eastern Turkey and western Iran. The eastern clade consists of at least three species: Eirenis nigrofasciatus, distributed across north‐eastern Iraq, and western and southern Iran; Eirenis walteri, distributed across eastern Iran, southern Turkmenistan, and western and southern Pakistan, and Eirenis angusticeps, distributed in north‐eastern Pakistan. Ecological niche modelling revealed that the distribution of the species in the western clade are mainly affected by winter precipitation, and those in the eastern clade are mainly affected by the minimum temperature of the coldest month. A molecular clock analysis revealed that the divergence and diversification of the E. persicus species group mainly correspond to Eocene to Pliocene orogeny events subsequent to the Arabia–Eurasia collision. This study confirms that specimens with the unique morphology of having 13 dorsal scale rows on the anterior dorsum, occurring in the Suleiman Mountains in central Pakistan, can be referred to Eirenis mcmahoni (Wall, 1911). However, at this moment we have insufficient data to evaluate the taxonomy of this species.