Molecular phylogeny of major lineages of the avian family Phasianidae inferred from complete mitochondrial genome sequences

Phasianidae is a large family of birds which contains most of the gallinaceous birds of the world. So far, the taxonomic status of many genera within Phasianidae has been controversial. The complete mitochondrial genome sequence of the white-eared pheasant (Crossoption crossoptilon) was determined in this study. Combining this with other previously published mitochondrial genome sequences, we reconstructed the phylogenetic relationships of Phasianidae and related species using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All analyses yielded a similar and well-supported topology, in which Crossoptilon grouped with Lophura. Perdix dauurica was sister taxon to the gallopheasants with high support, and Pucrasia was sister to this clade and separate from the other tragopans. Tetraophasis and Lophophorus grouped together, with Tragopan as the sister taxon. In addition, our results indicated that Meleagris clustered with Bonasa forming a monophyletic clade embedded in the pheasant‐partridge clade and the turkey–grouse lineage should be considered a part of the pheasant–partridge radiation.     

The complete mitochondrial genome of the Chinese Sika deer (Cervus nippon Temminck, 1838), and phylogenetic analysis among Cervidae,Moschidae and Bovidae

The complete mitochondrial genomes of the Sichuan Sika deer (Cervus nippon sichuanicus) and the South China Sika deer (Cervus nippon kopschi) were determined. Their sizes were 16,429 and 16,428 base pairs, respectively. The similarity of the mitochondrial DNA genome among subspecies of the Chinese Sika deer was calculated, and the values estimated from complete nucleotide sequences and entire amino-acid sequences were 98.4–99.9% and 99.7–99.9%, respectively. Molecular phylogenetic analyses were conducted using maximum parsimony and Bayesian inference methods based on the sequences of 12 concatenated heavy-strand encoded protein-coding genes. The consensus of phylogenetic trees supported the monophyly of Moschidae, Cervidae and Bovidae, and placed Moschidae as a sister group to Cervidae/Bovidae. The relationships among Chinese Sika deer inferred from the phylogenetic analysis were inconsistent with subspecies designations and the present geographic distribution. Our complete mitochondrial genomes will be available as important and basic data for phylogenetics, breeding, genetics and conservation in Cervidae.     

The complete mitochondrial genome and phylogenetic analysis of forest musk deer (Moschus berezovskii)

The complete mitochondrial genome sequence of the forest musk deer (Moschus berezovskii) was determined. Sequence analysis revealed that the organization of the mitochondrial genome in the forest musk deer was consistent with that of other reported mammals. Molecular phylogenetic analysis of the forest musk deer and 22 other species of the order Cetartiodactyla was conducted using maximum parsimony and Bayesian inference methods based on the 12 heavy‐strand protein‐coding genes, RNA genes and their combination. Both the consensus phylogenetic trees and the topologies test supported the monophyly of Cervidae, Bovidae and Cetancodonta, and placed Moschidae as a sister group to Cervidae/Bovidae.     

Preliminary report on the genetic structure of Glyphoglossus molossus (Anura: Microhylidae) from the Khorat Plateau,north-eastern Thailand

Glyphoglossus molossus, is one of the most economically important amphibians in the Khorat Plateau, north-eastern Thailand. It is categorised as a near-threatened species by IUCN due to over-exploitation. Here, we examined the genetic structure of G. molossus using partial mitochondrial cytochrome-b gene sequences from specimens collected at 11 localities. The sequence analysis revealed the presence of 15 haplotypes, 5 of which are shared by 2 or more populations, and 10 haplotypes that are confined to a single population. The relatively low haplotype (h) and nucleotide (π) diversities suggest that the Phu Phan Mountain Range is not high enough to act as an effective dispersal barrier between the Sakon Nakhon and Khorat Basins. However, AMOVA and phylogenetic analyses based on Maximum likelihood (ML) and Bayesian inference (BI) strongly supported the presence of two genetically divergent clades, Sakon Nakhon Basin and the northern part of the Khorat Basin (clade A) and the southern part of the Khorat Basin (clade B). These two lineages are separated by substantial geographical distance, which has putatively resulted in a reduction of gene flow. Further studies, with more extensive genetic sampling, especially from throughout the species range will aid in better interpreting our results.     

The phylogenetic position of Thermophis (Serpentes: Colubridae), an endemic snake from the Qinghai‐Xizang Plateau,China

The snakes of the genus Thermophis, including two species (Thermophis baileyi and Thermophis zhaoermii), which are found only on the Qinghai‐Xizang Plateau, were studied to determine the phylogenetic position of the genus within the broad superfamily Colubroidea. In this study, T. baileyi from two different localities in Xizang and T. zhaoermii from western Sichuan formed a monophyletic group as determined using Bayesian and likelihood methods of phylogenetic inference. Based on the nucleotide sequence of the cyt b and c‐mos genes, Thermophis appeared to be a member of the subfamily Xenodontinae, which prior to this finding had been confined to a New World distribution. The molecular data also indicate a large genetic distance between T. baileyi and T. zhaoermii, which strengthens the validity of the new species: T. zhaoermii.     

A new species of arboreal salamander (Caudata: Plethodontidae: Pseudoeurycea) from the mountains of Oaxaca,Mexico

Recent surveys of the plethodontid salamander fauna of Oaxaca, Mexico, disclosed the existence of a new, morphologically distinct arboreal species of the genus Pseudoeurycea. The new species, described here, is from the Sierra Mazateca in northern Oaxaca. Sequences of 1833 base pairs of the 16S, cytochrome b and ND4 mitochondrial DNA (mtDNA) genes from the new taxon were used to assess its phylogenetic position. Previous phylogenetic analyses based on mtDNA supported recognition of four clades within Pseudoeurycea: P. bellii, P. gadovii, P. juarezi and P. leprosa-Lineatriton species groups. One additional species, P. unguidentis, was not closely allied to any of the four groups. Re-analysis including the additional sequences reported here establishes a sister-group relationship between the new species and P. unguidentis. Moreover, it supports this clade as part of the P. juarezi species group.     

Synopsis and taxonomic revision of three genera in the snake tribe Sonorini

ABSTRACT

Delimiting species is a crucial goal of integrative biology, and yet can be misled by homoplasy and high levels of morphological variation. The snake tribe Sonorini contains three genera that have long confounded taxonomists: Chilomeniscus, Chionactis and Sonora. Dynamic colour evolution in this group, including rampant geographic variation in colour and colour polymorphism, has led to a chaotic taxonomy. We used mitochondrial and high-throughput nuclear data (ddRADseq) and complete taxonomic sampling of each genus to reconstruct phylogenetic relationships and systematically revise the genus. Our research revealed that Sonora is paraphyletic with regards to Chilomeniscus and Chionactis and that at least one species (S. semiannulata) is paraphyletic with respect to at least one other recognized species. Additionally, we found substantial undescribed genetic diversity within multiple species which is incongruent with morphological variation in coloration. Accordingly, we proposed synonymizing Chionactis and Chilomeniscus with Sonora, which has taxonomic priority over both genera. As we found genetic evidence that supported some of the historically delimited diversity within multiple taxa, we revised species-level taxonomy accordingly. This new taxonomy recognizes a revised genus of Sonora that contains 15 species of diminutive and often brightly coloured snakes that are distributed from central Mexico to north-western USA.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:45A553D8-6435-4E0A-84ED-DF31E2CCD872     

Traditional and geometric morphometric analyses reveal homogeneity in European Scutacarus acarorum Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)

The mite Scutacarus acarorum (Scutacaridae, Heterostigmatina) is one of the dominant bumblebee inquilines in the Holarctic. The wide distribution and the host generalist behaviour of S. acarorum suggest that it could be a group of multiple cryptic species. European S. acarorum populations and a small population from New York were studied using traditional and geometric morphometric methods to detect possible geographical or host-dependent variation. The analyses revealed homogeneity of all populations, suggesting that the species experienced a bottleneck during the last ice age and that gene flow between the populations is maintained. High variability within populations indicates a high genetic diversity. No host-related morphological differences were detected, suggesting that S. acarorum is a true generalist. Fresh mite samples from locations all over the Holarctic are needed to draw further conclusions on the species’ phylogeography and also on its population genetic structure.     

Sequence variation of mitochondrial DNA ND5 in captive South China tigers (Panthera tigris amoyensis)

This paper represents the first study of the genetic diversity of captive South China tigers Panthera tigris amoyensis by sequence variation in a fragment of mitochondrial DNA (mtDNA) NADH dehydrogenase subunit 5 (ND5) gene. Two haplotypes (haplotype I and haplotype II) were identified and the captive population had a bias towards haplotype I. This subspecies as a whole demonstrated an extremely low level of genetic diversity with the nucleotide diversity of 0.057±0.021%. The mtDNA ND5 variations detected in the present study could provide significant information to the studbook data of the South China tiger.     

Two new Andean species of Anolis lizard (Iguanidae: Dactyloinae) from southern Ecuador

ABSTRACT

We describe two new species of Anolis lizard that are sympatric on the Amazonian slopes of the Andes of southern Ecuador at elevations between 1440 and 1970 m. The new species may be distinguished from other Anolis by external anatomy, mitochondrial divergence and dewlap colour. We estimate the phylogenetic positions of the new species using Bayesian analysis of DNA sequence data including all species of Dactyloa-clade Anolis for which DNA data are available. Anolis hyacintogularis sp. nov. is sister to Anolis calimae, whereas Anolis lososi sp. nov. is sister to Anolis williamsmittermeierorum, herein reported for Ecuador for the first time. Individuals of both new species were collected within a protected area in southern Ecuador, Podocarpus National Park, which suggests that at least some populations of these species are well protected.

www.zoobank.org/urn:lsid:zoobank.org:pub:E55FA804-E3FD-4412-8FEB-5234E29E272D     

Effects of fragmentation on genetic variation in populations of the terrestrial earthworm Drawida japonica Michaelsen, 1892 (Oligochaeta,Moniligastridae) in Shandong and Liaodong peninsulas,China

Earthworms are excellent indicators of landscape fragmentation due to their widespread distribution and poor dispersal abilities over water. Based on field studies conducted in the Shandong and Liaodong peninsulas and their associated islands during summer 2009, we analysed the genetic variation of Drawida japonica Michaelsen, 1892 (Oligochaeta, Moniligastridae) using DNA sequences of the 16S and 28S ribosomal genes in samples obtained from 13 localities, 12 of which were islands, one artificially connected to the mainland by man (Yangma SC). We identified 55 haplotypes among 79 samples, based on 1094 bp, including 47 unique haplotypes. The phylogenetic tree topologies showed two distinct clades. A multiple-apex Poisson distribution using a mismatch analysis of nucleotides was also detected. Results of a Tajima D neutral test were not significant (p > 0.05). Genetic divergence among populations was much larger than within populations. A positive relationship between genetic diversity and island area was revealed, but no significant correlation between genetic diversity and distance to the nearest larger landmass was found. These results indicate that the intraspecific genetic diversity of D. japonica has been influenced by geographic isolation (i.e. island habitat). Passive transport via anthropogenic activities or nonhuman vertebrates (birds or mammals) may also play a key role in dispersal.     

Genus Baseodiscus (Nemertea: Heteronemertea): Molecular identification of a new species in a phylogenetic context

A new heteronemertean, Baseodiscus jonasii sp. nov., is described from Guadalcanal, Solomon Islands. It resembles B. delineatus in inner morphology but can be distinguished from this species by its different colour pattern and differences in the nucleotide sequence of the mitochondrial 16S rRNA gene. The monophyletic status of the genus is investigated by reconstructing the phylogeny of six specimens from four species assigned to this genus, together with 22 specimens from nine other heteronemertean genera, using parsimony and Bayesian analysis. The results imply that Baseodiscus is a monophyletic group while several other heteronemertean genera are non‐monophyletic.     

A new species of Allorhogas (Hymenoptera: Braconidae: Doryctinae) inducing ovule galls on Miconia chamissois Naudin,a potentially invasive shrub in the Brazilian cerrado

ABSTRACT

Allorhogas Gahan (Hymenoptera: Braconidae) is a mainly Neotropical doryctine wasp genus whose species have been associated with 11 vascular plant families. All species of Allorhogas whose feeding habits are known are confirmed or presumed to be phytophagous, either by being gall inducers on seeds, seeds predators or by inquilinism of other gall former taxa. Here we describe a new species of Allorhogas from Brazil and assess its phylogenetic affinities using one mitochondrial (COI) and one nuclear (28S) marker. Different from other described species of Allorhogas that induce galls on fruits/seeds of Melastomataceae, the new species attacks floral bud ovules of Miconia chamissois Naudin (Melastomataceae), forming ‘fruit-like’ galls. We recovered a clade exclusively composed of species of Allorhogas that attack Melastomataceae species. The new species could potentially be used as a biological control of M. chamissois populations to prevent the imbalance of the plant diversity of cerrado, which is one of the most endangered biomes in Brazil.

http://www.zoobnk.org/urn:lsid:zoobank.org:act:27ADE2CD-6C55-4712-92EC-B0F209FEFD10     

Revisiting the saproxylic beetle ‘Propomacrus cypriacus Alexis & Makris, 2002’ (Coleoptera: Euchiridae) using molecular,morphological and ecological data

Propomacrus cypriacus a saproxylic beetle endemic to Cyprus, was described as a species distinct from P. bimucronatus on the basis of a few morphological characters and has been evaluated as Critically Endangered by IUCN, as it depends on veteran trees and has a restricted distribution. Herein we explored the distribution, ecology, morphology and genetic variation of the populations from Cyprus, and we attempted a phylogenetic analysis including related species based on two mitochondrial and one nuclear DNA markers. We also used published mtDNA divergence rates to date cladogenetic events. Despite extensive sampling, we found only a small number of individuals, adding a few additional localities to the known distribution of the species, and we identified two more host species to those previously reported. Morphological examination showed that only the form of male protibiae differs consistently in Cyprus populations compared to those of P. bimucronatus from Turkey and the Lebanon. Nevertheless, genetic analyses do not support a distinct species status for populations from Cyprus, which should instead be considered as a subspecies of P. bimucronatus. Morphological and ecological data further support this conclusion. Cyprus populations have diverged from nearby continental ones in mid to late Pleistocene.     

Repeated sampling adds to the genetic diversity of Lepidochelys olivacea (Eschscholtz 1829) olive ridley sea turtle

ABSTRACT

First sampled in the late 1990s, Campamento Tortuguero La Gloria, in Jalisco, Mexico, was resampled for olive ridley sea turtle (Lepidochyles olivacea Eschscholtz) diversity 10 years later. A comparison with all previously reported mitochondrial sequences revealed that these new samples added to the known genetic diversity for this species, and revealed unexpectedly high genetic diversity among turtles nesting on this beach. The results highlight the importance of systematic resampling in known nesting rookeries to verify the genetic diversity of study populations. Three new olive ridley haplotypes are reported, all more closely related to Baja Californian haplotypes than to Australian haplotypes. Significant genetic divergence is reported within populations, within ocean basins (Atlantic, Pacific, Indian and Indo-Pacific), and between ocean basins. Furthermore, this is the first study that integrates satellite tagging data to demonstrate diverse post-nesting migration patterns of turtles with identical haplotypes, and it demonstrates flexibility in post-nesting migratory behaviour for olive ridley sea turtles of the same genetic provenance.     

Integrative taxonomic analysis reveals a new species of Leptobrachium (Anura: Megophryidae) from north-eastern Cambodia and central Vietnam

ABSTRACT

Species boundaries within the red-eyed Leptobrachium of southern Indochina have been uncertain. Leptobrachium pullum and L. mouhoti from upper and lower elevations, respectively, of the Langbian Plateau of southern Vietnam and eastern Cambodia differ in body size but have relatively low interspecific mitochondrial DNA divergence, leading to speculation that these might represent a single species with an elevational cline in body size. The recent discovery of an allopatric high-elevation population of red-eyed Leptobrachium on the Kon Tum Plateau (= Central Highlands) of north-eastern Cambodia and central Vietnam has been referred to both species, and to a putatively undescribed species. We examine variation in morphology of adults and tadpoles, mitochondrial DNA, 11 nuclear genes and advertisement calls, and show corroborating lines of evidence for the existence of three species of red-eyed Leptobrachium in southern Indochina. Although the three species are reciprocally monophyletic in mitochondrial DNA, their shallow mitochondrial DNA divergences are not mirrored by morphology, advertisement calls, or – in part – nuclear DNA, and probably reflect past mitochondrial introgression rather than recent speciation. The Central Highlands taxon is described herein as a new species.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:CE6650AF-D9FB-40F4-8A2E-9B4E23AAC205     

Molecular phylogenetic analysis of three groups of Asian epilachnine ladybird beetles recognized by the female internal reproductive organs and modes of sperm transfer

We determined partial sequences of the nuclear 28S ribosomal RNA gene (717 base pairs) and mitochondrial DNA NADH-dehydrogenase subunit 2 gene (535 base pairs) of 25 species of phytophagous ladybird beetles from Asia that comprise 16 species of the genus Henosepilachna and nine species of the genus Epilachna, and reconstructed the phylogenetic trees for each gene by the maximum parsimony and maximum likelihood methods. The estimated phylogenetic relationships were consistent with those obtained by the mode of sperm transfer and female internal reproductive system, and supported an earlier assumption that very similar elytral spot patterns of some sympatric members of epilachnine beetles evolved independently.     

Genetic differentiation and gene flow of Porcellionides pruinosus (Crustacea: Isopoda: Oniscidea) in Tunisia

Iso-enzymatic polymorphism analysis was carried out on Tunisian populations of Porcellionides pruinosus to clarify their confused taxonomic status, previously revealed by reproductive and morphological approaches. Seventeen allozyme loci were studied, using horizontal starch gel electrophoresis, in 230 adult specimens belonging to nine populations of P. pruinosus located in north, central and south Tunisia, to assess the levels of their intra-genetic and inter-genetic diversity, and to analyse their genetic structure. Our results indicate a low genetic variability with a polymorphism ratio ranging from 29.4% in Tabarka to 47.1% in the Garat Nâam and Raccada populations, and the mean number of alleles per locus was estimated at 1.51 ± 0.15. The direct-count of heterozygosity ranged between 8.1% and 15%. Substantial estimates of demic structuring were found at the total population (F_ST = 0.198), with a generalized and significant heterozygote deficiency detected in every population (with a mean value for all populations of F_IS = 0.372). Genetic distances between the studied populations were low, indicating that they belong to the same species. Nevertheless, the genetic analyses showed the divergence of the population of Tabarka from all the other studied populations, with the lowest mean gene flow, 0.58, and the highest mean genetic distance, (0.182) obtained also by the morphological and reproductive approaches.     

Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach

The genera Cratera Carbayo et al., 2013 and Obama Carbayo et al., 2013, belonging to the subfamily Geoplaninae, were recently proposed to encompass some of the species that belonged to the genus Geoplana Stimpson, 1857. Herein we describe two new species of Geoplaninae, occurring in areas of ombrophilous forest which belong to the southern portion of the Brazilian Atlantic Rain Forest. The species are sympatric in their type-locality. In general, both new species herein described match the diagnostic characteristics of their genera. However, some of these features are noteworthy when characters of the new species are taken into consideration, especially the pattern of the sensory pits and the morphology of the prostatic vesicle. Both species are differentiated from their congeners by a combination of morphological characteristics, corroborated by phylogenetic analyses of the cytochrome c oxidase subunit I gene, using maximum likelihood and Bayesian inference, as well as the Automatic Barcode Gap tool.     

Cryptic and non-cryptic diversity in New Guinea ground snakes of the genus Stegonotus Duméril,Bibron and Duméril, 1854: a description of four new species (Squamata: Colubridae)

ABSTRACT

The island of New Guinea has been identified as biologically megadiverse but many taxa are still poorly known. This is especially the case for many of the island’s snakes, which by their very nature can be difficult to collect and study. Here we examine the phylogenetic and phylogeographic structure of a poorly studied snake genus, Stegonotus, focusing on the species of New Guinea; until now, Stegonotus has never been examined using modern phylogenetic methods. Using molecular data from 49 individuals representing eight of the ten described species, and including all New Guinea taxa, we estimate a multilocus phylogeny and examine population structure to help identify undescribed taxa. We use morphological data from the corresponding museum vouchered specimens (where available) and also examine additional specimens for taxa not included in the molecular data set to determine morphological differences among putative taxa. We find molecular evidence for four new species of Stegonotus, both morphologically obvious and cryptic, and describe them herein. The recognition of these four species indicates that Stegonotus diversity has been previously underestimated and also suggests that there are likely additional undescribed taxa within the genus. These four taxa increase the number of described species by 40% and further confirm New Guinea as the centre of diversity for the genus.

www.zoobank.org/urn:lsid:zoobank.org:pub:9E21390E-3FD4-40EB-9442-31BC92A76B4F