The freshwater turtle genus Mauremys (Testudines,Geoemydidae) — a textbook example of an east–west disjunction or a taxonomic misconcept?

Barth, D. Bernhard, D. Fritzsch, G. & Fritz, U. (2004): The freshwater turtle genus Mauremys— a textbook example of an east–west disjunction or a taxonomic misconcept? —Zoologica Scripta, 33, 213–221. We compare 1036 bp of the mitochondrial cytochrome b gene (cyt b) from all six Mauremys species with 16 other taxa, representing both currently recognized subfamilies of the Geoemydidae (Geoemydinae and Batagurinae) to contribute a comprehensive dataset towards resolving the conflicting Mauremys taxonomy and phylogeography. Mauremys, a representative of the Geoemydinae, is thought to be an example of a taxon with an east–west disjunction due to Pleistocene glacial extinction, with species occurring in the western Palearctic and species in the eastern Palearctic and Oriental regions. Our results contradict this traditional zoogeographical scheme and the current taxonomy of the Geoemydidae. Mauremys is paraphyletic with respect to two East Asian genera belonging to the Batagurinae: Chinemys and Ocadia. Therefore, Mauremys, as currently understood, clearly represents a taxonomic misconcept. Mauremys+Chinemys+Ocadia contains four well supported clades, two of which —M. japonica+Chinemys+Ocadia and M. annamensis+M. mutica— are confined to eastern Asia. The other two —M. caspica+M. rivulata and M. leprosa— occur in the western Palearctic. Mauremys leprosa may represent an ancient lineage which differentiated before the split between the other western and eastern species occurred. The patchy distribution of the four clades is likely the result of several ancient radiations rather than of a Pleistocene extinction. The sister‐group of Mauremys+Chinemys+Ocadia is Cuora, a morphologically highly specialized genus with a complicated shell hinging mechanism.     

Molecular Evidence for Multiple Origins of the European Spined Loaches (Teleostei,Cobitidae)

We present a phylogenetic investigation of the Northern Clade, the major monophyletic clade within the freshwater fish family Cobitidae, one of the most prominent families of freshwater fishes found in Asian and European waters. Phylogenetic reconstructions based on the cytochrome b and RAG-1 genes show the genera Microcobitis, Sabanejewia, Koreocobitis and Kichulchoia as monophyletic groups. These reconstructions also show a Cobitis sensu lato and a Misgurnus sensu lato group. The Cobitis sensu lato group includes all species of Cobitis, Iksookimia, Niwaella and Kichulchoia, while the Misgurnus sensu lato group includes Misgurnus, Paramisgurnus and Koreocobitis. Although the monophyly of both the Cobitis sensu lato and Misgurnus sensu lato groups is supported, relationships within the groups are incongruent with current generic definitions. The absence of monophyly of most genera included in the Cobitis sensu lato group (Cobitis, Iksookimia and Niwaella) or their low genetic differentiation (Kichuchoia) supports their consideration as synonyms of Cobitis. Molecular phylogenies indicate that the Asian species of Misgurnus experienced a mitochondrial introgression from a lineage of Cobitis. We also find two nuclear haplotypes in the same Cobitis species from the Adriatic area that, in the absence of morphological differentiation, may indicate molecular introgression. Most lineages within the Northern Clade consist of species found in East Asia. However, some lineages also contain species from Europe and Asia Minor. The phylogenetic relationships presented here are consistent with previous studies suggesting an East Asian origin of the Northern Clade. According to the current distributions and phylogenetic relationships of the Misgurnus sensu lato and Cobitis clade lineages, particularly of M. fossilis and C. melanoleuca, the range expansion of East Asian species into Europe was most likely via Siberia into Northern and Central Europe. Phylogenetic analyses also show that the Cobitis sensu lato group consists of two clear subgroups (I and II), each presenting geographical differences. Subgroup I is distributed exclusively in East Asian drainages with an Eastern European offshoot (C. melanoleuca), whereas Subgroup II includes species widespread throughout Europe (including the Mediterranean), Asia Minor, the Black Sea and the Caucasus, with some lineages related to species restricted to East Asia.     

A Mitochondrial Phylogeny and Biogeographical Scenario for Asiatic Water Shrews of the Genus Chimarrogale: Implications for Taxonomy and Low-Latitude Migration Routes

The six species and three subspecies in the genus Chimarrogale (Soricomorpha: Soricidae) are commonly referred to as Asiatic water shrews. The Chimarrogale are the most widely distributed group of Nectogaline shrews, extending throughout the Oriental region and Japan. Because of the limited numbers of specimens available for study, the phylogenetic relationships and biogeographical history of this genus have not been comprehensively discussed. We used mitochondrial cytochrome b gene sequences to estimate phylogenetic relationships and divergence times among four Chimarrogale species, including all three subspecies of Chimarrogale himalayica. We also conducted a species delimitation analysis and tested two alternative migration scenarios in Asia through species distribution modeling and a reconstruction of the ancestral distribution. Here, we present the first proposed hypothesis regarding the Asiatic water shrew phylogeny and reveal ten putative species within the four recognized species. Distinct phylogenetic statuses of Chimarrogale phaeura, Chimarrogale platycephala, and Chimarrogale styani were confirmed. Chimarrogale himalayica was strongly supported as paraphyletic. We suggest that three subspecies of Chimarrogale himalayica should be reconsidered as distinct species. However, these suggestions must be considered with caution because only a single locus of a mtDNA gene was used. Four additional putative species, possibly distributed in central southwestern China and Taiwan, are currently undescribed; therefore, comprehensive morphological analyses are warranted to test their taxonomic statuses. The estimated molecular divergence times indicated that rapid speciation occurred during the early Pliocene, and current distribution patterns may have been affected by global cooling during the Pliocene/Pleistocene boundary. Reconstruction of the ancestral distribution and species distribution modeling for Asiatic water shrews revealed a low-latitude migration route over which ancestral Chimarrogale migrated from Europe via Central Asia to their current distribution. Our results demonstrated that Asiatic water shrews could have evolved throughout the low-latitude migration route from Europe to East and Southeast Asia.     

Molecular taxonomy and subgeneric classification of tapeworms of the genus Moniezia Blanchard, 1891 (Cestoda,Anoplocephalidae) in northern cervids (Alces and Rangifer)

Phylogenetic relationships of tapeworms of the genus Moniezia Blanchard, 1891 (Cestoda, Anoplocephalidae) parasitizing the Eurasian elk Alces alces, the moose A. americanus and the reindeer/caribou Rangifer tarandus (Cervidae) were studied using DNA sequences of two mitochondrial genes (cox1 and nad1). Several isolates from domestic ruminants, representing Moniezia expansa (Rudolphi, 1810) sensu lato and M. benedeni (Moniez, 1879) sensu lato, and one unidentified isolate from an African antelope, were also included in the analysis.Both genes identified the same six species of Moniezia, but interspecific phylogenetic relationships were better resolved by the nad1 data. The six species of Moniezia comprised two main clades: clade 1 that originates in bovids, with subsequent colonization of northern cervids in Eurasia, and clade 2 that originates in northern cervids, with subsequent specific divergence within these hosts. Clade 2 has a Holarctic distribution.None of the Moniezia specimens in Alces and Rangifer was conspecific with the species in domestic ruminants, suggesting that the custom of identifying Moniezia spp. in northern cervids either as M. expansa or M. benedeni is incorrect. At least two of the species parasitizing Alces and Rangifer have not been previously recognized. These findings challenge the results of all previous studies concerning the diversity and ecology of Moniezia spp. in northern cervids.The traditional classification into three subgenera (Moniezia Blanchard, 1891, Blanchariezia Skrjabin & Schultz, 1937 and Baeriezia Skrjabin & Schultz, 1937), based on the presence and type of interproglottidal glands, conflicts with the currently observed molecular phylogenetic relationships within the genus Moniezia.     

Phylogeny and biogeography of wild roses with specific attention to polyploids

Background and Aims The genus Rosa (150–200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus.Methods Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas.Key Results Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa.Conclusions The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.     

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37–0.47 and 0.14–0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.     

Revision of <Emphasis Type="Italic">Protohydnum</Emphasis> (Auriculariales,Basidiomycota)

Three species currently addressed to Protohydnum (Auriculariales) are studied with morphological and DNA methods. The genus Protohydnum is retained for the type species only, P. cartilagineum, recently re-collected in Brazil. The European species, P. piceicola, is not congeneric with P. cartilagineum and, therefore, placed in its own genus, Hyalodon, gen. nov. Another Hyalodon species, H. antui, is described from East Asia. The third member of Protohydnum sensu lato, P. sclerodontium from South-East Asia, is transferred to Elmerina.     

西北太平洋海岸带大弹涂鱼复合体的隐存种与进化历史

大弹涂鱼Boleophthalmus pectinirostris间断分布于西太平洋海岸带东亚与马来西亚马六甲海峡,但马来西亚种群的分类地位尚存争议。研究使用线粒体ND5基因序列（718 bp）与核位点Rag1基因序列（1395 bp）对西北太平洋海岸带11个地点的45尾大弹涂鱼属鱼类进行系统发育关系重建,结果表明大弹涂鱼包括东亚与马来西亚两个单系群,两者形成姊妹群关系。GMYC分析、*BEAST物种树支持大弹涂鱼东亚谱系和马来西亚谱系是不同种。分子测定年龄分析表明大弹涂鱼东亚谱系与马来西亚谱系之间的分化时间为2.73百万年。因此,西北太平洋海岸带大弹涂鱼是复合体,包括两个物种:东亚种群是大弹涂鱼Boleophthalmus pectinirostris sensu stricto,而马来西亚种群是隐存种Boleophthalmus sp.。大弹涂鱼与隐存种之间的物种分化可能是晚上新世冰期海平面下降产生的地理隔离以及间冰期洋流对基因交流的阻碍两方面相互作用的结果。       

Phylogenetic position of the genus Ferula (Apiaceae) and its placement in tribe Scandiceae as inferred from nrDNA ITS sequence variation

Recent molecular systematic investigations suggested that Ferula, an umbellifer genus of about 170 species, is polyphyletic, with its members placed in the apioid superclade and within tribe Scandiceae. We analyzed ITS sequence variation from 134 accessions of Apiaceae, including 83 accessions (74 species) of Ferula to ascertain the phylogenetic position of the genus within the family. Phylogenetic analyses of these data using maximum parsimony, Bayesian, and neighbor-joining methods support the monophyly of Ferula upon the addition of Dorema and Leutea (as Ferula sensu lato) and its placement in tribe Scandiceae. Ferula sensu is closely allied with other major lineages of Scandiceae, corresponding to subtribes Scandicinae, Daucinae, and Torilidinae. Therefore, we recognize the Ferula clade as subtribe Ferulinae. Another addition to tribe Scandiceae is a clade composed of genera Glaucosciadium and Mozaffariania. The three accessions of Ferula misplaced in the apioid superclade represent a species of Silaum.     

Repeated landmass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo‐Oriental Region

Southeast Asia harbours abundant biodiversity, hypothesized to have been generated by Pliocene and Pleistocene climatic and environmental change. Vicariance between the island of Borneo, the remaining Indonesian archipelago and mainland Southeast Asia caused by elevated sea levels during interglacial periods has been proposed to lead to diversification in the littoral zone mosquito Anopheles (Cellia) sundaicus (Rodenwaldt) sensu lato. To test this biogeographical hypothesis, we inferred the population history and assessed gene flow of A. sundaicus s.l. sampled from 18 populations across its pan‐Asian species range, using sequences from mitochondrial cytochrome c oxidase subunit 1 (CO1), the internal transcribed spacer 2 (ITS2) and the mannose phosphate isomerase (Mpi) gene. A hypothesis of ecological speciation for A. sundaicus involving divergent adaptation to brackish and freshwater larval habitats was also previously proposed, based on a deficiency of heterozygotes for Mpi allozyme alleles in sympatry. This hypothesis was not supported by Mpi sequence data, which exhibited no fixed differences between brackish and freshwater larval habitats. Mpi and CO1 supported the presence of up to eight genetically distinct population groupings. Counter to the hypothesis of three allopatric species, divergence was often no greater between Borneo, Sumatra/Java and the Southeast Asian mainland than it was between genetic groupings within these landmasses. An isolation‐with‐migration (IM) model indicates recurrent gene flow between the current major landmasses. Such gene flow would have been possible during glacial periods when the current landmasses merged, presenting opportunities for dispersal along expanding and contracting coastlines. Consequently, Pleistocene climatic variation has proved a homogenizing, rather than diversifying, force for A. sundaicus diversity.     

Introgressive Hybridization between Anciently Diverged Lineages of Silene (Caryophyllaceae)

Hybridization has played a major role during the evolution of angiosperms, mediating both gene flow between already distinct species and the formation of new species. Newly formed hybrids between distantly related taxa are often sterile. For this reason, interspecific crosses resulting in fertile hybrids have rarely been described to take place after more than a few million years after divergence. We describe here the traces of a reproductively successful hybrid between two ancestral species of Silene, diverged for about six million years prior to hybridization. No extant hybrids between the two parental lineages are currently known, but introgression of the RNA polymerase gene NRPA2 provides clear evidence of a temporary and fertile hybrid. Parsimony reconciliation between gene trees and the species tree, as well as consideration of clade ages, help exclude gene paralogy and lineage sorting as alternative hypotheses. This may represent one of the most extreme cases of divergence between species prior to introgressive hybridization discovered yet, notably at a homoploid level. Although species boundaries are generally believed to be stable after millions of years of divergence, we believe that this finding may indicate that gene flow between distantly related species is merely largely undetected at present.     

Systématique du groupe « Palaeochelys sensu lato – Mauremys » (Chelonii,Testudinoidea) du Tertiaire d’Europe occidentale : principaux résultats

Among fossil chelonians from the Tertiary of Western Europe, freshwater Testudinoidea (sensu Hirayama, 1985, Gaffney et Meylan, 1988) are abundant, and more particularly the “Palaeochelys sensu lato—Mauremys” group. This group has never been studied as a whole. Taxa of this group were before referred to extinct genera such as Ocadia, Clemmys, Emys or to the fossil genera Palaeochelys, Borkenia and Palaeoemys. These taxa are redefined, new taxa are described and a hypothesis of phylogenetic relationships is given.     

Identification of a New Borrelia Species among Small Mammals in Areas of Northern Spain Where Lyme Disease Is Endemic

The role of small mammals as reservoir hosts for Borrelia burgdorferi was investigated in several areas where Lyme disease is endemic in northern Spain. A low rate of infestation by Ixodes ricinus nymphs was found in the small mammal populations studied that correlated with the near-absence of B. burgdorferi sensu lato in 184 animals tested and with the lack of transmission of B. burgdorferi sensu lato to I. ricinus larvae that fed on them. In contrast, questing ticks collected at the same time and in the same areas were found to carry a highly variable B. burgdorferi sensu lato repertoire (B. burgdorferi sensu stricto, Borrelia garinii, Borrelia valaisiana, and Borrelia afzelii). Interestingly, the only isolate obtained from small mammals (R57, isolated from a bank vole) grouped by phylogenetic analyses with other Borrelia species but in a separate clade from the Lyme disease and relapsing fever organisms, suggesting that it is a new species. This new agent was widely distributed among small mammals, with infection rates of 8.5 to 12% by PCR. Moreover, a high seroprevalence to B. burgdorferi sensu lato was found in the animal sera, suggesting cross-reactivity between B. burgdorferi sensu lato and R57. Although small mammals do not seem to play an important role as reservoirs for B. burgdorferi sensu lato in the study area, they seem to be implicated in the maintenance of spirochetes similar to R57.     

Molecular Identification and Analysis of Borrelia burgdorferi Sensu Lato in Lizards in the Southeastern United States

Lyme borreliosis (LB) group spirochetes, collectively known as Borrelia burgdorferi sensu lato, are distributed worldwide. Wild rodents are acknowledged as the most important reservoir hosts. Ixodes scapularis is the primary vector of B. burgdorferi sensu lato in the eastern United States, and in the southeastern United States, the larvae and nymphs mostly parasitize certain species of lizards. The primary aim of the present study was to determine whether wild lizards in the southeastern United States are naturally infected with Lyme borreliae. Blood samples obtained from lizards in Florida and South Carolina were tested for the presence of LB spirochetes primarily by using B. burgdorferi sensu lato-specific PCR assays that amplify portions of the flagellin (flaB), outer surface protein A (ospA), and 66-kDa protein (p66) genes. Attempts to isolate spirochetes from a small number of PCR-positive lizards failed. However, PCR amplification and sequence analysis of partial flaB, ospA, and p66 gene fragments confirmed numerous strains of B. burgdorferi sensu lato, including Borrelia andersonii, Borrelia bissettii, and B. burgdorferi sensu stricto, in blood from lizards from both states. B. burgdorferi sensu lato DNA was identified in 86 of 160 (54%) lizards representing nine species and six genera. The high infection prevalence and broad distribution of infection among different lizard species at different sites and at different times of the year suggest that LB spirochetes are established in lizards in the southeastern United States.     

The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia,a rare,monospecific genus from Mozambique

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.     

Molecular phylogeny and the underestimated species diversity of the endemic white‐bellied rat (Rodentia: Muridae: Niviventer) in Southeast Asia and China

The white‐bellied rat, Niviventer, is a genus endemic to Southeast Asia and China. However, the interspecific phylogenetic relationships and species diversity of this genus remain poorly understood. In the present study, single and multi‐locus analyses were performed. Phylogenetic reconstruction on Cytochrome b (512 individuals, including data from Genbank) revealed five major clades with approximately 35 operational taxonomic units (OTUs), a number twice the existing taxonomy. The first clade (N. langbianis species group) was the earliest diverged. The second clade (N. fulvescens species group) diverged in Southeast Asia, the south and lower altitude regions of the Hengduan Mountains, and Southeast China. The third clade (the N. eha species group) is endemic to high altitudes in Northwest Yunnan and the central region of Himalaya. The fourth clade (the N. andersoni species group), is mainly confined to alpine regions of the Hengduan Mountains. The fifth clade (N. confucianus species group) is mainly distributed in the north and higher altitude regions of eastern Himalaya, the Hengduan Mountains and Taiwan, with the complex also invading central and northern China. Results from the combined dataset of four genes (Cytochrome b, Cytochrome oxidase subunit I, the D‐loop sequence of the mitochondrial genome and the first exon of the nuclear interphotoreceptor retinoid binding protein) for 82 representative individuals from China generally coincide with the result of the single gene, with 12 OTUs identified. These results provide a preliminary framework for the existing classification of this highly diversified genus. The divergence time of Niviventer based on the four gene topology was dated to the late Miocene ~6.41 Ma. Significant differences were detected in the general body form changes among these units based on voucher specimens. Moreover, geometric morphometric analysis of the cranium shape of voucher specimens indicated significant differences among five major species groups. Shape divergence of the cranium among several OTUs within the N. confucinaus complex is also significant. Our results provide further evidence for rapid and highly underestimated diversification of Niviventer both in genetics and morphology.     

Reconstruction of phylogenetic relations of Ponto-Caspian gobies (Gobiidae, Perciformes) based on mitochondrial genome variation and some problems of their taxonomy

Phylogenetic relations of Ponto-Caspian gobies in the context of different taxonomic hypotheses have been studied based on the analysis of variations in cytochrome b gene. Evidence for the paraphyly of the genus Neogobius sensu lato, represented by two independent phyletic lineages that should be treated as separate genera Neogobius s. stricto (includes a species group of N. melanostomus-N. fluviatilis-N. caspius) and Ponticola, has been provided. It has been demonstrated that the Racer goby N. gymnotrachelus refers to the latter genus. It is proved that the Grass goby Gobius ophiocephalus belongs to the genus Gobius s. stricto.