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.     

Phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the boreal island of Hokkaido,Japan

To test postglacial population expansion in small arboreal mammals dependent on boreal and subboreal forests, we used complete mitochondrial cytochrome b gene sequences (1140 bases) to investigate the phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the Hokkaido Island of Japan. This subspecies is common in the boreal and subboreal forests of Hokkaido. We examined 61 specimens from 27 localities in Hokkaido. Phylogenetic relationships among 29 haplotypes found in the Hokkaido populations were not associated with geographic distribution of sampling localities. There were four mitochondrial DNA phylogroups. Phylogeographic analyses support sudden expansion of S. vulgaris orientis from restricted refugium in the southern part of Hokkaido during the last glacial period. The phylogeographic structure of this subspecies directly reflects the boreal and subboreal forest dynamics occurring in Hokkaido.     

Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis,the spot-tailed earless lizards of Texas

ABSTRACT

We examined genetic relationships among individuals and populations of the species Holbrookia lacerata, the spot-tailed earless lizard, using whole mitochondrial genomes. Lizards were collected from south, central and west Texas. We found significant amounts of genetic structure among populations and evidence of two major reciprocally monophyletic groups of spot-tailed earless lizards in Texas. Holbrookia lacerata lacerata occurs on the Edwards Plateau and adjacent regions of West Texas north of the Balcones Escarpment, while Holbrookia lacerata subcaudalis occurs in South Texas and adjacent Mexico south of the Balcones Escarpment. These two recognised subspecies correspond to the two clades we discovered. Holbrookia l. lacerata occupies much of its historical range at sometimes high population densities, while populations of H. l. subcaudalis appear to be highly fragmented based on recent observations compared to their historical range.     

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 West Palaearctic species of Fidiobia Ashmead, 1894 (Hymenoptera: Platygastroidea)

One new genus Songmachilis and six new species in family Machilidae are described from China: Songmachilis xinxiangensis gen. sp. nov., Coreamachilis songi sp. nov., Pedetontinus jiuzhaiensis sp. nov., Pedetontinus maijiensis sp. nov., Pedetontinus taishanensis sp. nov. and. Pedetontinus wudangensis sp. nov. A key to all Chinese species of Pedetontinus is given. We also examined the relationships among Chinese machilids based on partial sequences of mitochondrial cytochrome c oxidase subunit I (COI). The molecular study further supported the species status of the six new taxa.     

Geographical variation in the golden‐striped salamander,Chioglossa lusitanica Bocage, 1864 and the description of a newly recognized subspecies

Morphological and genetic data for the Iberian golden‐striped salamander, Chioglossa lusitanica, demonstrate the existence of two groups with southern and northern ranges, connected by a zone of intergradation in central Portugal. Because reproductive isolation between them is incomplete we consider the groups to be subspecies. The type locality of C. lusitanica (Buçaco near Lousã) is situated inside the mixed zone. This necessitates identification of the nominotypical subspecies. We sequenced a fragment of mitochondrial DNA from one of the species' syntypes and we determined what position over a latitudinal transect maximizes the morphological discrimination between the groups. Both approaches indicate that C. lusitanica from Buçaco represents the southern subspecies. A new subspecies of C. lusitanica is described from a northern locality (Valongo near Porto in north‐western Portugal). A lectotype is designated for Chioglossa lusitanica.     

Diet similarity between elk and deer in Utah

Growing numbers of elk ( Cervus elaphus ) on winter ranges might adversely affect sympatric wintering mule deer ( Odoeoileus hemionus ) if diets of the two species are similar. Diets of elk and deer on a northern Utah range were analyzed for overlap in winter with microhistological analysis of fecal samples. Diets overlapped 71%. No significant difference was found in use of grasses or shrubs between elk and deer; however, use of forbs was significantly different. Shrubs comprised the largest proportion of the diets of both elk and deer. Deer might be under more severe dietary stress than elk on poor winter ranges.     

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.     

Age-related body weight,fecundity and population change in a south Dorset sika population (Cervus nippon); 1985–1993

Density-related changes in performance have been documented for a number of different ungulate species, with recorded decline in body weight, fecundity and both juvenile and adult survival as population densities increase. While density-dependent responses of this kind have been explored in some detail in red, roe and fallow deer, little published information is available on demographic responses to density in European populations of sika deer (Cervus nippon). This paper offers an analysis of the dynamics of two populations of sika from the south of England from 1985–1993. Data on age-related body weights for males and females and pregnancy rates of females are taken from analysis of cull records of 321 males and 534 females culled during that 8-year period. We describe trends in body mass of adult and juvenile sika of both sexes, and consider changes in pregnancy rates of both mature and yearling females in relation to changes in relative abundance. Despite steadily increasing population density between 1985 and 1991/1992, no consistent decline was recorded in body weight or condition (as measured by % cover of kidney fat) for calves or yearlings of either sex, or for mature females. A decline in recorded body weight of adult males was not significantly correlated to ranked relative abundance. Fecundity was high (with > 90% of mature females sampled found pregnant). Most mature females found pregnant were also lactating. The proportion of animals that conceived as yearlings (72%) was lower than that recorded for more mature hinds; however there is some indication that the difference recorded may simply reflect the fact that yearlings may conceive later in the season than older animals. No significant differences were apparent in the proportion of either adult or yearling females found pregnant in different years.     

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.     

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.     

Bythinella Moquin-Tandon, 1856 (Gastropoda: Rissooidea: Bythinellidae) in Romania: species richness in a glacial refugium

The buff-throated partridge, Tetraophasis szechenyii Madarász, 1885, is a species endemic to west China. The complete mitochondrial genome of this species was sequenced. It was 16,706 base pairs (bp) in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The phylogenetic relationships of the buff-throated partridge and 19 other Phasianidae species were inferred by Bayesian inference and maximum likelihood analyses based on 12 protein-coding genes. With the exception of a few nodes, most internal branches were supported by a high Bayesian posterior probability (BPP?=?1.0). The resulting trees clarified the phylogenetic position of T. szechenyii within Phasianidae. The genetic diversity and population structure of the Pamulin population of T. szechenyii were examined based on the mitochondrial DNA CR. Nucleotide sequence analysis defined 18 haplotypes in 24 individuals. Haplotype diversity (h) was 0.953 and nucleotide diversity (π) was 0.0044. The results revealed that the genetic diversity of this population was not particularly low. Combined with the field work conducted by our lab, we found that members of the Pamuling population are cooperative breeders and the population may contain individuals from neighbouring groups. Our work provided genetic background information for the conservation and management of this species.     

Wintering mule deer preference for 21 accessions of big sagebrush

Wintering mule deer showed differential browsing preference among 21 accessions of big sagebrush ( Artemisia tridentata ) grown on gardens on three different mule deer herd ranges. The Hobble Creek accession of big sagebrush was significantly preferred over the other 20 accessions across all three sites and for all three years. Accessional preference means for the study period for all sites combined ranged from 28.3 to 57.5%. The data collected support the planned release of the Hobble Creek accession as a superior cultivar of big sagebrush for use on mule deer winter ranges. Plant coumarin content was primarily under genetic control, but site factors also had an effect. Assay for coumarin compounds is useful in determining subspecies of A. tridentata but not for precise prediction of mule deer browsing preference.     

New species of the cicada genus Semia Matsumura (Hemiptera: Cicadidae) from China and a phylogeny of Semia spp. and their relatives based on molecular data

Two new cicada species, Semia brevidilata, sp. nov. and Semia tibetensis, sp. nov., are described from China. Semia majuscula, a newly recorded species to China, is re-described, as some new characteristics are recognised which may be useful for further taxonomic and phylogenetic analysis of this genus and its allies. Partial mitochondrial cytochrome oxidase subunit I (COI) sequences of five Semia species and relatives belonging to the genera Pomponia Stål and Psithyristria Stål are further analysed to confirm the validity of related new species and to provide a useful reference for the identification of Semia. A key to all species of Semia is provided, and the phylogenetic relationships among species of Semia and their relatives are discussed.

http://zoobank.org/urn:lsid:zoobank.org:pub:64144283-8CCE-4687-9D07-2033939165E7     

Revision and biogeographical analysis of the black-chinned tilapia Sarotherodon melanotheron (Teleostei,Cichlidae): results of morphometric,allozyme, globin chain and mtDNA studies

Morphometric, allozyme, globin chain and cytochrome b analyses were used for a revision of the subspecies complex of the black-chinned tilapia, Sarotherodon melanotheron Rüppell, 1852. Three out of four subspecies are recognized as valid: S. m. melanotheron (Ivory Coast to Benin), S. m. heudelotii (Senegal to Guinea) and S. m. leonensis (Sierra Leone to Liberia). The fourth subspecies, S. m. nigripinnis, is raised to the species level S. nigripinnis and is composed of the nominate subspecies S. n. nigripinnis known from Gabon and a newly introduced subspecies, S. n. dolloi, originally described as Tilapia dolloi and previously synonymized with S. m. nigripinnis. It is presently known from the mouth of the Congo to the Lower Kouilou. Phylogenetically, populations from the most eastern range, e.g. Gabon/Congo, are considered to represent the most ancient populations. From this area of origin, the western range of West Africa (Senegal to Benin) was colonized. Two independent colonization events are indicated by allozyme and mtDNA analyses. The initial invasion of the western range of West Africa could be dated back to about 2.5 million years ago.     

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.