Pleistocene effects on the European freshwater fish fauna: double origin of the cobitid genus Sabanejewia in the Danube basin (Osteichthyes: Cobitidae)

Biogeographical hypotheses of European freshwater fishes were inferred using phylogeographic analysis of the complete cytochrome b and ATP synthase 8 and 6 mitochondrial genes (1982bp). To test the relative importance of drainage origin versus Pleistocene glaciations in the origin of primary freshwater fishes in Europe, we reconstructed the phylogenetic relationships of the genus Sabanejewia which is distributed in European waters. The phylogenetic relationships recovered for the genus Sabanejewia (n=75) provide support for the monophyly of six main evolutionary mtDNA lineages: Sabanejewia larvata, Sabanejewia romanica, Sabanejewia aurata/Sabanejewia caucasica, Sabanejewia kubanica, Sabanejewia baltica, and the Danubian-Balkanian complex. The Caucasian-Caspian mtDNA lineages, S. kubanica, S. aurata/S. caucasica, and the Northern European S. baltica represents the sister group of the Danubian-Balkanian complex mtDNAclade, supporting a Caucasian-Northern European origin of most of mtDNA lineages of the Central European freshwater fish fauna. The mtDNA divergence observed between the Danubian Sabanejewia species is too dissimilar to support their contemporary origin. Rather, the mtDNA data suggest that the Danubian Sabanejewia lineages most likely have a double origin, indicating that the European Sabanejewia lineages have experienced different historical processes for the following reasons. First, the origin of the S. larvata and S. romanica mtDNA clades predates the origin of the Danubian-Balkanian complex, and our results showed that the completion of the Alps and the origin of the Danube drainage seem to have promoted the speciation of the earliest Sabanejewia clades in the Miocene. Second, small genetic distances and the geographical pattern found within the Danubian-Balkanian complex clade indicate that the lineages included in this clade spread recently across the Danube and Greek river drainages. The inclusion of the S. balcanica species within all mtDNA lineages suggests that cyclical cold periods during the Pleistocene glaciations have favoured its rapid expansion and genetic homogenisation across Central European and Greek waters.     

Evolutionary systematics in African gerbilline rodents of the genus Gerbilliscus: inference from mitochondrial genes

Gerbilliscus has recently been proposed as an endemic African rodent genus distinct from the Asian Tatera. A molecular phylogeny of the genus, including nine species from southern, western and eastern Africa, is presented here based on the analysis of the cytochrome b and 16S mitochondrial genes. With an adequate taxonomic sampling over a wide geographic range, we here provide a clear picture of the phylogenetic relationships between species and species groups in this genus. Three distinct clades were resolved, corresponding to major geographical subdivisions: an eastern clade that possibly diverged first, then a southern and a western clades which appeared later. We suggest two possible hypotheses concerning the dispersal of the genus across Africa, considering also the patterns of karyotypic variation. Finally, we discuss the taxonomic status of G. gambianus and the relationships between Gerbillurus and Gerbilliscus, as previous studies have suggested that the former should be included in the latter. Our data seem to support the synonymy of the two taxa and suggest that Gerbillurus and Gerbilliscus lineages diverged from a common ancestor appeared in eastern Africa.     

Molecules and morphology suggest cryptic species diversity and an overall complex taxonomy of fish scale geckos, genus Geckolepis

The current classification of the Malagasy-Comoroan geckos of the genus Geckolepis recognizes three valid species and is based on morphological differences only. Species allocation of individuals is difficult, mainly because of the insufficiently known degree of variation and the frequent partial loss of the integument in preserved specimens. Here we study Geckolepis specimens from almost their entire known range. We combine molecular and morphological data to estimate species richness in the genus, and to assess the taxonomic validity of the morphological differences proposed. Analyses of mitochondrial (12S, ND4) and nuclear (RAG1, CMOS) gene sequences support three major clades in addition to the morphologically distinct G. polylepis (included for 12S only), and the presence of various divergent lineages within these clades, some occurring in sympatry. Among lineages, the external morphology seems to be comparatively conservative, and differences are faint in many cases. For each major lineage, we summarize the most diagnostic morphological characters that distinguish it from other lineages. The combined molecular and morphological data strongly indicate the presence of highly divergent lineages, three of which are tentatively referred to the names Geckolepis maculata, G. polylepis and G. typica, whereas three other major lineages are considered Confirmed Candidate Species. Among the remaining lineages, differentiation is shallower, and these may qualify for Deep Conspecific Lineages. In conclusion, our analysis provides evidence for an underestimation of species richness in the genus and a complex evolutionary history, not reflected by current Geckolepis species-level taxonomy.     

Barcoding Fauna Bavarica: Myriapoda - a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda)

We give a first account of our ongoing barcoding activities on Bavarian myriapods in the framework of the Barcoding Fauna Bavarica project and IBOL, the International Barcode of Life. Having analyzed 126 taxa (including 122 species) belonging to all major German chilopod and diplopod lineages, often using four or more specimens each, at the moment our species stock includes 82% of the diplopods and 65% of the chilopods found in Bavaria, southern Germany. The partial COI sequences allow correct identification of more than 95% of the current set of Bavarian species. Moreover, most of the myriapod orders and families appear as distinct clades in neighbour-joining trees, although the phylogenetic relationships between them are not always depicted correctly. We give examples of (1) high interspecific sequence variability among closely related species; (2) low interspecific variability in some chordeumatidan genera, indicating that recent speciations cannot be resolved with certainty using COI DNA barcodes; (3) high intraspecific variation in some genera, suggesting the existence of cryptic lineages; and (4) the possible polyphyly of some taxa, i.e. the chordeumatidan genus Ochogona. This shows that, in addition to species identification, our data may be useful in various ways in the context of species delimitations, taxonomic revisions and analyses of ongoing speciation processes.     

Cryptic diversity in the lizard genus Plica (Squamata): phylogenetic diversity and Amazonian biogeography

Intra‐ and interspecific genetic diversity of the lizard species Plica plica (9 localities) and Plica umbra (19 localities) from the Brazilian Amazon was analysed using two mitochondrial (16S rDNA and CO1) and one nuclear (prolactin receptor – PRLR) genes. We generated a maximum‐likelihood and Bayesian hypotheses of phylogenetic relationships, and using the bPTP and ABGD lineage delimiting methods inferred the most likely number of lineages within each species. Both methods delimited five distinct lineages in Plica plica and six lineages within Plica umbra. The nominal subspecies of Plica umbra was comprised of one lineage, while Plica umbra ochrocollaris was comprised of five lineages. In majority of the cases, lineages were restricted to the interfluves of major Amazonian rivers, and different lineages occupied distinct areas of endemism. Phylogenetic relationships of the lineages are largely concordant with the hypothesized formation of the areas of endemism. The geographic structuring of the clades and the delimitation of these clades as distinct lineages suggest the possibility that these lineages represent species. If the observed diversity of lineages within the genus Plica is characteristic of squamate reptiles of the Amazon region, the diversity of squamates is grossly underestimated.     

Evolution of ant-cultivar specialization and cultivar switching in Apterostigma fungus-growing ants

Almost all of the more than 200 species of fungus-growing ants (Formicidae: Attini) cultivate litter-decomposing fungi in the family Lepiotaceae (Basidiomycota: Agaricales). The single exception to this rule is a subgroup of ant species within the lower attine genus Apterostigma, which cultivate pterulaceous fungi distantly related to the Lepiotaceae. Comparison of cultivar and ant phylogenies suggests that a switch from lepiotaceous to pterulaceous fungiculture occurred only once in the history of the fungus-growing ants. This unique switch occurred after the origin of the genus Apterostigma, such that the basal Apterostigma lineages retained the ancestral attine condition of lepiotaceous fungiculture, and none of the Apterostigma lineages in the monophyletic group of pterulaceous fungiculturists are known to have reverted back to lepiotaceous fungiculture. The origin of pterulaceous fungiculture in attine ants may have involved a unique transition from the ancestral cultivation of litter-decomposing lepiotaceous fungi to the cultivation of wood-decomposing pterulaceous fungi. Phylogenetic analyses further indicate that distantly related Apterostigma ant species sometimes cultivate the same cultivar lineage, indicating evolutionarily frequent, and possibly ongoing, exchanges of fungal cultivars between Apterostigma ant species. The pterulaceous cultivars form two sister clades, and different Apterostigma ant lineages are invariably associated with, and thus specialized on, only one of the two cultivar clades. However, within clades Apterostigma ant species are able to switch between fungi. This pattern of broad specialization by attine ants on defined cultivar clades, coupled with flexible switching between fungi within cultivar clades, is also found in other attine lineages and appears to be a general phenomenon of fungicultural evolution in all fungus-growing ants.     

Phylogenetic relationships of Oriental torrent frogs in the genus Amolops and its allies (Amphibia, Anura, Ranidae)

We investigated the phylogenetic relationships among 20 species of Oriental torrent frogs in the genus Amolops and its allies from China and Southeast Asia based on 1346-bp sequences of the mitochondrial 12S and 16S rRNA genes. Oriental species of the tribe Ranini form a monophyletic group containing 11 clades (Rana temporaria + Pseudoamolops, R. chalconota, four clades of Amolops, Meristogenys, three clades of Huia species, and Staurois) for which the phylogenetic relationships are unresolved. The genus Amolops consists of southern Chinese, southwestern Chinese, Thai, and Vietnamese-Malaysian lineages, but their relationships are also unresolved. The separation of southern and southwestern lineages within China conforms to previous morphological and karyological results. Species of Huia do not form a monophyletic group, whereas those of Meristogenys are monophyletic. Because P. sauteri is a sister species of R. temporaria, distinct generic status of Pseudoamolops is unwarranted.     

Evolutionary relationships and biogeography of Biomphalaria (Gastropoda: Planorbidae) with implications regarding its role as host of the human bloodfluke, Schistosoma mansoni.

The wide geographic distribution of Schistosoma mansoni, a digenetic trematode and parasite of humans, is determined by the occurrence of its intermediate hosts, freshwater snails of the genus Biomphalaria (Preston 1910). We present phylogenetic analyses of 23 species of Biomphalaria, 16 Neotropical and seven African, including the most important schistosome hosts, using partial mitochondrial ribosomal 16S and complete nuclear ribosomal ITS1 and ITS2 nucleotide sequences. A dramatically better resolution was obtained by combining the data sets as opposed to analyzing each separately, indicating that there is additive congruent signal in each data set. Neotropical species are basal, and all African species are derived, suggesting an American origin for the genus. We confirm that a proto-Biomphalaria glabrata gave rise to all African species through a trans-Atlantic colonization of Africa. In addition, genetic distances among African species are smaller compared with those among Neotropical species, indicating a more recent origin. There are two species-rich clades, one African with B. glabrata as its base, and the other Neotropical. Within the African clade, a wide-ranging tropical savannah species, B. pfeifferi, and a Nilotic species complex, have both colonized Rift Valley lakes and produced endemic lacustrine forms. Within the Neotropical clade, two newly acquired natural hosts for S. mansoni (B. straminea and B. tenagophila) are not the closest relatives of each other, suggesting two separate acquisition events. Basal to these two species-rich clades are several Neotropical lineages with large genetic distances between them, indicating multiple lineages within the genus. Interesting patterns occur regarding schistosome susceptibility: (1) the most susceptible hosts belong to a single clade, comprising B. glabrata and the African species, (2) several susceptible Neotropical species are sister groups to apparently refractory species, and (3) some basal lineages are susceptible. These patterns suggest the existence of both inherent susceptibility and resistance, but also underscore the ability of S. mansoni to adapt to and acquire previously unsusceptible species as hosts. Biomphalaria schrammi appears to be distantly related to other Biomphalaria as well as to Helisoma, and may represent a separate or intermediate lineage.     

Phylogeography, geographic structure, genetic variation, and potential species boundaries in Philippine slender toads

We investigated phylogeography of Philippine slender toads (genus Ansonia) and used a temporal framework for diversification, statistical tests of alternate topologies, and Bayesian approaches to test previous hypotheses concerning dispersal to, and colonization routes within, the southern Philippine island of Mindanao. Two species of Ansonia previously have been documented, with ranges separated by an east–west split corresponding to the approximate boundaries of Mindanao’s paleoisland precursors. We present new mtDNA sequence data (1946 bp from genes encoding ND1, 16S rRNA and tRNA^Leu) for 105 Ansonia specimens sampled from 20 localities on Mindanao Island. Our data suggest that Philippine Ansonia is composed of at least eight, well-supported population lineages, structured into a minimum of four highly divergent mtDNA clades. One clade corresponds to Ansonia mcgregori, a range-restricted species apparently limited to the distal portion of the Zamboanga Peninsula of western Mindanao. Two morphologically indistinguishable, but genetically divergent, lineages possibly are undescribed cryptic species from western Mindanao. We recognize the five remaining lineages as Ansonia muelleri pending data from morphology or bioacoustics that might diagnose separate species among these lineages. Regardless of their species status, the five allopatric lineages of A. muelleri should be viewed as important genetic units for future genetic conservation planning.     

Phylogeographic Analyses Strongly Suggest Cryptic Speciation in the Giant Spiny Frog (Dicroglossidae: Paa spinosa) and Interspecies Hybridization in Paa

Species identification is one of the most basic yet crucial issues in biology with potentially far-reaching implications for fields such as conservation, population ecology, and epidemiology. The widely distributed but threatened frog Paa spinosa has been speculated to represent a complex of multiple species. In this study, 254 individuals representing species of the genus Paa were investigated along the entire range of P. spinosa: 196 specimens of P. spinosa, 8 specimens of P. jiulongensis, 5 specimens of P. boulengeri, 20 specimens of P. exilispinosa, and 25 specimens of P. shini. Approximately 1333 bp of mtDNA sequence data (genes 12S rRNA and 16S rRNA) were used. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood and Bayesian inference. BEAST was used to estimate divergence dates of major clades. Results suggest that P. spinosa can be divided into three distinct major lineages. Each major lineage totally corresponds to geographical regions, revealing the presence of three candidate cryptic species. Isolation and differentiation among lineages are further supported by the great genetic distances between the lineages. The bifurcating phylogenetic pattern also suggests an east–west dispersal trend during historic cryptic speciation. Dating analysis estimates that P. spinosa from Western China split from the remaining P. spinosa populations in the Miocene and that P. spinosa from Eastern China diverged from Central China in the Pliocene. We also found that P. exilispinosa from Mainland China and Hong Kong might have a complex of multiple species. After identifying cryptic lineages, we then determine the discrepancy between the mtDNA and the morphotypes in several individuals. This discrepancy may have been caused by introgressive hybridization between P. spinosa and P. shini.     

A preliminary revision of the genus Plecotus (Chiroptera, Vespertilionidae) based on genetic and morphological results

The phylogenetic relationships within the genus Plecotus were assessed using molecular as well as morphological methods. With only three species missing, our study is based on an almost comprehensive taxonomic sampling. The genetic analysis comprised 151 individuals from throughout the range. Sequences of two mitochondrial sections, parts of the 16S rRNA gene (16S) and of the control region (CR) were analysed. The morphological analysis of cranial and external characters comprised 697 individuals, including 10 holotypes and one lectotype. Data from 15 craniometric characters of 442 specimens were used in the multivariate analyses. The molecular data identified nine primary clades representing 11 species, 10 of which could be assigned to described taxa, whereas one was described as a new species, Plecotus strelkovi Spitzenberger sp. nov. The tree based on 16S revealed two major lineages, one consisting of only one primary clade restricted to the Mediterranean, the other consisting of eight primary clades representing Eurasian taxa. The morphological analysis revealed five additional species, two of them not described. Together with the recently described P. taivanus, P. sardus and P. balensis, which were not included in our analysis, the genus Plecotus comprises at least 19 more or less cryptic species. Phylogenetic and phenetic analyses resulted in similar but not completely concordant arrangements of the species. The proposed classification relies mainly on the tree based on 16S sequences. The current distribution indicates that 16 species can be linked to arboreal refugia, three to eremial refugia. We assume that speciation within the gleaning, rather slow flying long‐eared bats is due to a multitude of disruption and isolation processes within a formerly continuous range of the broad‐leaved Arcto‐Tertiary forest in which Plecotus probably originated. An exact calibrated molecular dating of the splits is not possible. The Early Oligocene age of the presumed ancestor of the Plecotini and a correlation of the molecular diversifications with palaeogeographic reconstructions suggest that the divergence of the two major lineages may have occurred already during the Middle Miocene, 14.5 Mya.     

A phylogeny of four mitochondrial gene regions suggests a revised taxonomy for Asian pitvipers (Trimeresurus and Ovophis)

We present a phylogeny of the Asian pitvipers, based on 2403 bp of four mitochondrial gene regions. All but six known species of Trimeresurus sensu stricto (s.s.) as currently defined, as well as multiple populations of widespread species, which may yet be described as full species, and representatives of all other Asian pitviper genera, are included. Both the greater sampling and larger dataset provide improved resolution over previous studies and support the existence of distinct species groups within Trimeresurus s.s. Although all but two species currently referred to this genus form a monophyletic group, morphological and molecular analyses identify four subgroups that warrant recognition at the generic level. We propose a new generic arrangement to reflect these findings. We also highlight the non-monophyly of Ovophis, and propose a new genus to accommodate a species formerly assigned to Ovophis.     

Reexamination of relationships, habital evolution, and phylogeography of checker mallows (Sidalcea; Malvaceae) based on molecular phylogenetic data

Phylogenetic analysis of nuclear ribosomal DNA external and internal transcribed spacer region (ETS and ITS) sequences for Sidalcea (Malvaceae) resolved five major, well-supported lineages, three of which represent species groups that have each been noted for complex patterns of morphological variation: the oregana, malviflora, and glaucescens clades. Very low variation within each of the three groups in the sequenced regions is consistent with recent radiation of each clade. We reject the previously suggested hypothesis of monophyly for the annual species of Sidalcea. Based on our findings, the annual habit in Sidalcea arose at least four times, probably as an adaptation to seasonally dry habitats. The hypothesis that the perennial species S. hickmanii and S. malachroides represent basally divergent groups within Sidalcea is supported, but the more recently discovered S. stipularis represents an additional basally divergent lineage. The previous suggestion that the genus spread northward from Mexico along two major routes (through the Rocky Mountains and the Sierra Nevada foothills), with the Rocky Mountain species S. candida and S. neomexicana representing basally divergent lineages, is not supported. Sidalcea neomexicana is nested within the malviflora clade and is likely a lineage of relatively recent descent that originated in California and subsequently spread to the Rocky Mountains.     

Hidden diversity of Euscorpius (Scorpiones: Euscorpiidae) in Greece revealed by multilocus species‐delimitation approaches

Phylogenetic analysis of the genus Euscorpius (Scorpiones: Euscorpiidae) across the Mediterranean region (86 specimens, 77 localities, four DNA markers: 16S rDNA, COI, COII, and ITS1), focusing on Greek fauna, revealed high variation, deep clade divergences, many cryptic lineages, paraphyly at subgenus level, and sympatry of several new and formerly known lineages. Numerous specimens from mainland and insular Greece, undoubtedly the least studied region of the genus' distribution, have been included. The reconstructed phylogeny covers representative taxa and populations across the entire genus of Euscorpius. The deepest clades detected within Euscorpius correspond (partially) to its current subgeneric division, outlining subgenera Tetratrichobothrius and Alpiscorpius. The rest of the genus falls into several clades, including subgenus Polytrichobothrius and a paraphyletic subgenus Euscorpius s.s. Several cryptic lineages are recovered, especially on the islands. The inadequacy of the morphological characters used in the taxonomy of the genus to delineate species is discussed. Finally, the time frame of differentiation of Euscorpius in the study region is estimated and the distributional patterns of the lineages are contrasted with those of other highly diversified invertebrate genera occurring in the study region. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 728–748.     

Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography

Aim Using molecular data and dental features, we investigated the genetic and morphological diversity among species of palm civets in the genus Paradoxurus, with a focus on the common palm civet, Paradoxurus hermaphroditus (Carnivora, Viverridae), in order to address biogeographic scenarios and provide recommendations for a taxonomic revision. Location Asia: Pakistan to the Lesser Sunda Islands. Methods We investigated the genetic diversity within Paradoxurus using two mitochondrial (cytochrome b, control region) and one nuclear (intron 7 of the β‐fibrinogen) markers. We used samples from 85 individuals of P. hermaphroditus (including 20 museum specimens) and one representative of each of the other species in the genus Paradoxurus: Paradoxurus jerdoni and Paradoxurus zeylonensis. DNA sequences were analysed using phylogenetic and haplotype network methods, and divergence dates were estimated for the clades retrieved. Furthermore, we examined dental characters from a large series of specimens and compared the morphological variation with the molecular data. Results Our phylogenetic analyses revealed that P. hermaphroditus is paraphyletic. We identified three major lineages distributed: (1) in the Indian subcontinent, south China, Hainan and in areas above 200 m in Indochina; (2) in Peninsular Malaysia, Java, Sumatra and in areas below 200 m in Indochina; and (3) in Borneo, the Philippines and the Mentawai archipelago. Our morphological observations were congruent with these three molecular lineages. Divergence date estimates inferred a Pliocene origin for Paradoxurus (2.8–5.7 Ma), with the three main clades diversifying from the mid–Early Pliocene to the end of the Pliocene. We suggest that the flooding of the Isthmus of Kra during the Pliocene was a major event shaping the diversification of Paradoxurus palm civets. We also hypothesize that the elevational segregation of the two lineages on the mainland could have resulted from the vegetational changes that were induced by Late Pliocene glacial episodes. Main conclusions The Isthmus of Kra is a major boundary between two major lineages of P. hermaphroditus. There is a need for a taxonomic revision for P. hermaphroditus, and we suggest that this species should be split into at least three species.     

Extreme gender flexibility: using a phylogenetic framework to infer the evolution of variation in sex allocation, phylogeography, and speciation in a genus of bidirectional sex changing fishes(Lythrypnus, Gobiidae)

The genus Lythrypnus is a group of marine gobies that exhibit extreme gender flexibility as bidirectional sex changers. The genus consists of 20 described species and several undescribed species that are distributed in the Americas. Five species have been characterized with respect to sex allocation and gonad morphology. The hormonal, morphological, and behavioral aspects of sex change have been studied extensively for one species, L. dalli. These data, however, have not been interpreted in an evolutionary context because a phylogenetic hypothesis has not previously been proposed for the genus Lythrypnus. We propose the first phylogenetic hypothesis for the genus based on molecular data from three mitochondrial genes (12s, ND2, and Cytb), one nuclear gene (Rag1) and one nuclear intron (S7). We also include three previously undescribed Lythrypnus species. Our results support the monophyly of the genus with L. heterochroma, an Atlantic species, as the basal taxon. After the divergence of L. heterochroma, there are two main clades, one comprised of species distributed in the Atlantic, the other comprised of species distributed in the Pacific. These data indicate an Atlantic origin for the genus, followed by divergence after the closure of the Isthmus of Panama. Our data also support the monophyly of three previously described species complexes, the L. rhizophora complex and L. dalli complex in the Pacific, and the L. mowbrayi complex in the Atlantic. We mapped patterns of sex allocation within this genus onto the fully resolved and supported topology, and found that sexual plasticity and gender flexibility is likely a synapomorphy for the genus. Overall our results create a well-supported framework to understand the phylogeography of the genus, and to interpret the evolution of sex allocation in Lythrypnus gobies.     

Phylogenetics,historical biogeography and molecular species delimitation of Gnaptorina Reitter (Coleoptera: Tenebrionidae: Blaptini)

With 38 described species or subspecies, Gnaptorina Reitter is the second‐most species‐rich genus in the darkling beetle subtribe Gnaptorinina (Tenebrionidae: Tenebrioninae). In this study, we reconstructed a phylogeny of the genus based on one nuclear and three mitochondrial genes and used this phylogeny to explore the historical biography and diversification of Gnaptorina species. We implemented multiple molecular species delimitation approaches to reassess the status of Gnaptorina species and taxonomic subdivisions of the genus. Dating and historical biogeography analyses suggest an early Eocene origin of the genus, with the southeastern regions of the Tibetan Plateau most likely as areas of origin. Based on these results, we propose a new classification for Gnaptorina with three major clades identified. Consequently, the monotypic subgenus Boreoptorina is newly synonymized with the more species‐rich subgenus Hesperoptorina, and G. dongdashanensis Shi is transferred from Hesperoptorina to the subgenus Gnaptorina. In addition, G. minxiana Medvedev, formerly treated as a subspecies of G. potanini Reitter, is elevated to species. Results of molecular species delimitation analyses are largely congruent and confirm the status of most morphological species.     

Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism

The family Cobitidae represents a characteristic element of the Eurasian ichthyofauna. Despite diverse features of sexual dimorphism, comparably few morphological characters have been utilized for taxonomic studies resulting in many unresolved puzzles. Here we present the phylogenetic relationships of Cobitidae as inferred from the mitochondrial cytochrome b gene and the nuclear gene RAG-1. Analyses of both markers show a group of eight nominal genera, which all occur in Europe and eastern, northern and western Asia, forming a monophyletic lineage (northern clade) while all other clades inhabit South and Southeast Asia (southern lineages). While all eight southern lineages correspond to genera as defined by morphological studies, only four lineages were reliably recovered within the northern clade, and of these only one (Sabanejewia) corresponds to a formerly considered genus. The genera Cobitis, Iksookimia and Niwa?lla were polyphyletic. A comparison of the two markers shows several incongruities within the northern clade and mitochondrial introgression at least in the genus Misgurnus. Mapping the characters of sexual dimorphism on our cladogram, we identified five character states that are diagnostic for certain lineages. Estimations of the divergence times dated the separation of the northern clade from the southern lineages to the middle Eocene (46 MYA) and the origin of "Cobitis"misgurnoides, the basal taxon of the northern clade, during early Oligocene (30-35 MYA). The geographic distribution of the major clades supports recently developed hypotheses about the river history of East Asia and further suggests that a range expansion of the northern clade in late Miocene (15 MYA) led to the colonisation of Europe by three already distinct genera.     

Red drifters and dark residents: The phylogeny and ecology of a Plio-Pleistocene dragonfly radiation reflects Africa’s changing environment (Odonata,Libellulidae, Trithemis)

In the last few million years, tropical Africa has experienced pronounced climatic shifts with progressive aridification. Such changes must have had a great impact on freshwater biota, such as Odonata. With about forty species, Trithemis dominates dragonfly communities across Africa, from rain-pools to streams, deserts to rainforests, and lowlands to highlands. Red-bodied species tend to favor exposed, standing and often temporary waters, have strong dispersal capacities, and some of the largest geographic ranges in the genus. Those in cooler habitats, like forest streams, are generally dark-bodied and more sedentary. We combined molecular analyses of ND1, 16S, and ITS (ITSI, 5.8S, and ITSII) with morphological, ecological, and geographical data for 81% of known Trithemis species, including three Asian and two Madagascan endemics. Using molecular clock analyses, the genus’s origin was estimated 6–9 Mya, with multiple lineages arising suddenly around 4 Mya. Open stagnant habitats were inferred to be ancestral and the rise of Trithemis may have coincided with savannah-expansion in the late Miocene. The adaptation of red species to more ephemeral conditions leads to large ranges and limited radiation within those lineages. By contrast, three clades of dark species radiated in the Plio-Pleistocene, each within distinct ecological confines: (1) lowland streams, (2) highland streams, and (3) swampy habitats on alternating sides of the Congo-Zambezi watershed divide; together giving rise to the majority of species diversity in the genus. During Trithemis evolution, multiple shifts from open to more forested habitats and from standing to running waters occurred. Allopatry by habitat fragmentation may be the dominant force in speciation, but possibly genetic divergence across habitat gradients was also involved. The study demonstrates the importance of combining ecological and phylogenetic data to understand the origin of biological diversity under great environmental change.     

Genetic divergences and intraspecific variation in corvids of the genus Corvus (Aves: Passeriformes: Corvidae) – a first survey based on museum specimens

The first comprehensive overview of intra‐ and interspecific variation within the genus Corvus as well as first insights into the phylogenetic relationships of its species is presented. DNA sequences of the mitochondrial control region were obtained from 34 of the 40 described species (including subspecies: 56 taxa). As the study was based mainly on museum material, several specimens did not yield the full length marker sequence. In these cases, only a short section of the control region could be analysed. Nevertheless, even these individuals could be assigned tentatively to clades established on the full length marker sequence. Inclusion of sequences of other corvid genera as available in GenBank clearly confirmed the monophyly of the genus Corvus. Within the Corvus clade several distinct subclades can be distinguished. Some represent lineages of single species or species pairs while other clades are composed of many species. In general, the composition of the clades reflects geographical contiguousness and confirms earlier assumptions of a Palearctic origin of the genus Corvus with several independent colonizations of the Nearctic and the Aethiopis. The Australasian radiation seems to be derived from a single lineage. The distribution of plumage colour in the phylogenetic tree indicates that the pale markings evolved several times independently. The white/grey plumage colour pattern – which is found also in other genera of the family Corvidae, for example, in Pica– occurs already in the species pair representing the first split within the genus Corvus (Corvus monedula, Corvus dauuricus). Thus, reversal to full black colour seems to have occurred as well. The use of colour traits as a phylogenetic marker within Corvus should be considered with severe caution.