Tube-nosed variations-a new species of the genus Murina (Chiroptera: Vespertilionidae) from China.

Taxonomic recommendations for British birds: seventh report

Cobras are among the most widely known venomous snakes, and yet their taxonomy remains incompletely understood, particularly in Africa. Here, we use a combination of mitochondrial and nuclear gene sequences and morphological data to diagnose species limits within the African forest cobra, Naja (Boulengerina) melanoleuca. Mitochondrial DNA sequences reveal deep divergences within this taxon. Congruent patterns of variation in mtDNA, nuclear genes and morphology support the recognition of five separate species, confirming the species status of N. subfulva and N. peroescobari, and revealing two previously unnamed West African species, which are described as new: Naja (Boulengerina) guineensis sp. nov. Broadley, Trape, Chirio, Ineich Wüster, from the Upper Guinea forest of West Africa, and Naja (Boulengerina) savannula sp. nov. Broadley, Trape, Chirio Wüster, a banded form from the savanna-forest mosaic of the Guinea and Sudanian savannas of West Africa. The discovery of cryptic diversity in this iconic group highlights our limited understanding of tropical African biodiversity, hindering our ability to conserve it effectively.

The value of mitochondrial versus nuclear gene sequence data in phylogenetic analysis has received much attention without yielding definitive conclusions. Theoretical arguments and empirical data suggest a lower phylogenetic utility than equivalent nuclear gene sequences, but there are many examples of important progress made using mitochondrial sequences. We undertook a systematic performance analysis of mitochondrial and nuclear sequence partitions taken from a representative sample of dipteran species. When analysed alone, mitochondrial genes generally performed less well than nuclear genes; however, these genes resolved some branches for which nuclear genes failed. Moreover, the combined use of mitochondrial and nuclear sequences produced superior results without artifacts for nodes where mitochondrial and nuclear gene data generated conflicting topologies. These findings strongly advocate the inclusion of mitochondrial sequences, even in deep phylogeny reconstruction. Comparison of tree support between our and previous analyses identified robustly supported high‐confidence clades in the Diptera, but also revealed problematic groupings in need of further analysis.

Gekkonid geckos, representing more than 85 percent of the gekkotan genera, are found on all major land masses and almost all oceanic islands in the tropics and subtropics. Intergeneric relationships of the Gekkonidae have been far more difficult to resolve than those among other gekkotan families. Our data set consists of a large number of complete mitochondrial 12S rRNA gene sequences and partial nuclear C-mos gene sequences for 33 genera of geckos, two genera of pygopods and two genera of eublepharids. Maximum parsimony (MP) and maximum likelihood (ML) trees were generated based on unweighted analysis using PAUP 4.0b10. Bayesian inference (BI) analyses trees were generated by MrBayes 3.0B4. All phylogenetic trees supported the monophyly of Gekkonidae with great confidence. The 12S data and combined data (12S and C-mos) place Sphaerodactylus deeply within gekkonine geckos, whereas Teratoscincus+Pristurus are the sister group of the remaining gekkonids. However, it is known that 12S may be positively misleading when dealing with older divergences. Therefore, the conflict between the results in this study and the latest conclusions based on C-mos points to the need for future focus on the phylogenetic position of both Sphaerodactylus and Teratoscincus.

In eight Holarctic populations of two typical chironomid sibling species of the plumosus group, Chrionomus entis and Chironomus plumosus, nucleotides sequences of mitochondrial (cytb) and nuclear (gb2b) gene regions were examined. The phylogenetic trees reflecting the evolutionary histories of the nuclear and mitochondrial markers exhibited significant differences. On the tree based on the nuclear gene sequences the populations clustered according to their species affiliation, whereas on the tree based on the mitochondrial gene sequences the populations were grouped according to their geographic position. This discrepancy is probably explained by mitochondrial gene flow between sympatric species with incomplete reproductive isolation (sibling species). Based on our results together with the earlier data on nuclear and mitochondrial gene sequences of some other species from the phylogenetic group plumosus, a scheme of phylogenetic relationships within this group is proposed. This scheme is in many ways different from the traditional view on the evolutionary relationships among species of the plumosus group.

We investigated the species status and intraspecific phylogeography in South Korea of two ground beetle species, Coptolabrus jankowskii and Coptolabrus smaragdinus (Coleoptera: Carabidae), using statistical parsimony networks and nested clade analyses based on sequences from the mitochondrial cytochrome oxidase subunit I (COI) and nuclear phosphoenolpyruvate carboxykinase (PepCK) and wingless (Wg) genes. Although traditional parsimony tree construction generally failed to resolve interspecific relationships and construct biologically meaningful genealogies, analysis using statistical parsimony networks yielded statistically significant inter- and intraspecific genealogical structures. We found that although these two species represent a notable case of trans-species polymorphisms in both mitochondrial and nuclear gene sequences, their status as separate species was evidenced by the nonrandom association between species and nested clades at various nesting levels. The exceptional occurrence of shared identical or very similar COI sequences was considered to be the result of introgressive hybridization. In addition, range expansion and fragmentation events across the Korean Peninsula and adjacent islands were inferred from nested clade phylogeographical analyses. The COI gene revealed the geographical divergence of major eastern and western clades and historical biogeographical events within each major clade, whereas the nuclear PepCK gene, which did not reveal corresponding east-west clades, indicated past fragmentation and range expansion across wide areas that may have been the result of older biogeographical events. Thus, phylogeographical inferences drawn from analyses of mitochondrial and nuclear genes can reveal different and potentially complementary information about phylogeographical processes.

We compared morphology and sequenced nuclear and mitochondrial genes from 11 populations of a previously genetically unstudied “Baja California disjunct” species, the diamond turbot (Hypsopsetta guttulata). This species exhibits very limited adult movement and restriction to soft-bottom habitats but has a moderately long pelagic larval duration. Therefore, if pelagic larval duration is correlated with gene flow between Gulf of California and Pacific populations, we expect a reduced level of genetic and morphological differentiation. However, if adult habitat and ecology have more effect on gene flow, we expect the populations in the two bodies of water to be more highly differentiated. We used logistic regression to compare morphological features and phylogenetic and population genetic analyses to compare nucleotide sequence data. Gulf of California H. guttulata are different from Pacific populations in morphology and both mitochondrial and nuclear gene sequences. MtDNA shows reciprocal monophyly, and nuclear sequences from the Gulf of California formed a monophyletic group. Population genetic analyses also suggest further population subdivision within the Pacific and within the Gulf of California. We argue that adult ecology has a significant effect on migration rates among populations in the Pacific Ocean and the Gulf of California.

Phylogenetic relationships in the genus Cyprinella (Actinopterygii: Cyprinidae) based on mitochondrial and nuclear gene sequences

Multiple mitochondrial and nuclear gene sequences reveal substantial genetic variation within the dasyurid marsupial genus Planigale, suggesting greater taxonomic diversity than is currently recognised. To further investigate planigale relationships 116 new mitochondrial and nuclear gene sequences, including 16 new specimens, were added to our database. We confirm the presence of an unrecognised species (Planigale ‘species 1’) limited to the Pilbara region of Western Australia and suggest that the ‘Mt Tom Price’ animals may be closely related to Planigale ingrami subtilissima. We also confirm that at least four distinct genetic lineages make up what is currently recognised as P. maculata. This complex of closely related taxa represents a radiation of sibling species rather than a single, genetically diverse one. Three of these lineages (M1 + M2, M3 and M4) are distributed sympatrically across the Top End of Australia and one (M5 = P. maculata sensu stricto) is localised to the eastern coast of Australia. Within the Planigale ingrami complex, Planigale ‘Mt Tom Price’ (lineage Ing. 1) occurs in the Pilbara in sympatry with Planigale ‘species 1’ and lineage Ing. 2 is found in the Northern Territory in sympatry with species of the P. maculata complex. There is thus a plethora of northern Australian planigales, many of which are formally undescribed and whose geographic ranges require careful re-evaluation.

Speciation by polyploidization has been documented to have independently occurred in 12 families of anuran amphibians. Tomopterna tandyi was described as a South African allotetraploid species of sand frogs in the family Pyxicephalidae. Recent taxonomic revisions and new species descriptions in the genus present problems with respect to the evolution of this tetraploid species. Chromosomes, mitochondrial and nuclear gene sequences, isozymes, and male mating calls were examined for T. tandyi and for diploid species of Tomopterna. Mitochondrial sequences confirmed the diploid species, T. adiastola, to be the maternal ancestor that gave rise to the tetraploid about 5 mya. Nuclear sequences and isozymes reveal a complex reticulation of paternal ancestry that may be explained by occasional hybridization of T. tandyi with diploid species of Tompoterna at various times in sympatric populations. Interspecific diploid to tetraploid gene introgression is suspected to have also occurred in Australian and North American tetraploid species of frogs. Diploid to tetraploid introgression is facilitated through triploid hybrids that are more viable than diploid hybrids and produce unreduced triploid eggs.

We assessed dispersal and vicariant events in four species of Japanese moles in the genera Mogera and Euroscaptor to better understand the factors shaping intra- and interspecific differentiation in Japanese moles. We used the combined viewpoints of molecular phylogeny and historical geology using nucleotide sequences of mitochondrial (cytochrome b; Cytb) and nuclear (A2ab, Bmp4, Tcf25, vWf) genes. The divergence times estimated from the molecular data were verified with available geological data on the chronology of fluctuations in sea level in the Korea Strait, assuming sequential migration and speciation events. This produced possible migration times of 5.6, 3.5, 2.4, and 1.3 million years ago for four species of Japanese moles, Euroscaptor mizura, Mogera tokudae, M. imaizumii, and M. wogura, respectively. For the western Japanese mole M. wogura, Cytb sequences revealed four major phylogroups with strong geographic affinities in southwestern Central Honshu (I), western Honshu/Shikoku (II), Kyushu/westernmost Honshu (III), and Korea/Russian Primorye (IV). The nuclear gene sequences supported the distinctiveness of phylogroups I and IV, indicating long, independent evolutionary histories. In contrast, phylogroups II and III were merged into a single geographic group based on the nuclear gene data. Intraspecific divergences in M. imaizumii and M. tokudae were rather apparent in Cytb but not in nuclear gene sequences. The results suggest that repeated dispersal events have occurred between the Asian continent and the Japanese Islands, and intensive vicariant events associated with abiotic and biotic factors have created higher levels of species and genetic diversities in moles occurring on the Japanese Islands.

Phylogeny of the Neotropical genus Acestrorhynchus (Ostariophysi: Characiformes) based on nuclear and mitochondrial gene sequences and morphology: A total evidence approach

Phylogeny and character evolution of endemic Australian carabid beetles of the genus Pamborus based on mitochondrial and nuclear gene sequences

Buzan, E. V., Pagès, M., Michaux, J. & Krystufek, B. (2011). Phylogenetic position of the Ohiya rat (Srilankamys ohiensis) based on mitochondrial and nuclear gene sequence analysis. —Zoologica Scripta, 40, 545–553.We investigated the phylogenetic position the Ohiya rat, endemic to Sri Lanka, Srilankamys (Rodentia, Murinae), within the tribe Rattini based on the combined analysis of three independent genes (a mitochondrial one and two nuclear exons). Three major lineages (the Maxomys, the Dacnomys and the Rattus divisions) were retrieved as monophyletic groups within the tribe Rattini. Srilankamys was not affiliated to any of the representatives of the Dacnomys division as it was supposed based on morphological characters, but clearly appeared as the first genus to diverge among the Rattus division. The Mindanao Shrew Mouse, Crunomys melanius, emerged as a part of the Maxomys division raising questions about the validity of the Crunomys and the Maxomys divisions as currently defined. Molecular date of divergence between Srilankamys and the other representatives of the Rattus division falls within the interval 6.7 ± 0.74 Mya, coinciding with the time of the isolation of Sri Lanka from the Deccan peninsula and the aridification period owing to the climate change at the end of the Miocene epoch. We suggest that the isolation of Sri Lanka from the continent, reinforced by the action of a seasonal monsoon‐dominated climate, would have led to the isolation of some ancestral rodents of the Rattus division, which would have differentiated later into the Ohiya rat by a vicariant process. In a more general point of view, our study supports the previous results obtained on other organisms and evidence that Sri Lanka appears to be characterized by a particular fauna as compared to the Indian mainland. This island would therefore be considered as a specific distinct hotspot of biodiversity.

Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes