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.     

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.     

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.     

Cedar Hollow, an early Holocene faunal site From Whidbey Island, Washington

Coastal erosion at central Whidbey Island reveals a cross-section view of dune sands that contain the only known record of animals that inhabited the Pacific Northwest coast during the early Holocene. Mammal fossils include bones and teeth of deer, wolf, brown bear, and several species of rodents. A deer vertebra from basal beds yielded a 14 C age of 8840 ± 50 yr BP. The faunal diversity suggests that the region was repopulated relatively quickly following the final retreat of the Cordilleran sheet. This paleofauna was quite different from that of the late Pleistocene, when the region was inhabited by mammoth, musk oxen, giant sloth, and other large mammals. Avian remains include hawks, geese, and seabirds, 3 groups that occupied quite different ecological niches. Early Holocene bird fossils from Whidbey Island are dissimilar to late Pleistocene avifaunas from inland sites in California and Oregon, evidence that the coastal environment offered habitat conditions quite unlike those of interior wetlands.     

A herpetological survey of the Kathmandu Valley,Nepal, and phylogenetic identification of Megophrys (Xenophrys) zhangi

ABSTRACT

The herpetofauna of Nepal have been historically understudied, and although previous studies have reported on bioinventory surveys of the Kathmandu Valley, few have surveyed widely during the peak monsoon season. In addition, past studies largely neglected to survey intact forest habitats. Here we conduct a comprehensive field survey of the herpetofauna of the Kathmandu Valley, Nepal, with an emphasis on the surrounding foothills containing intact forest habitat. We record natural history and distribution data for seven species of amphibians and four species of reptiles. We also use mitochondrial sequence data to confirm the phylogenetic placement of two frog species, Megophrys (Xenophrys) parva and Duttaphrynus melanostictus. Using phylogenetic and morphological data we assign Megophrys parva from the Kathmandu Valley to Megophrys zhangi. We find that while this species shares a haplotype with its sister species, Megophrys monticola, morphological data align the individuals from the Kathmandu Valley with M. zhangi from Tibet. We find that M. zhangi exhibits no phylogenetic structure within the Kathmandu Valley, and wider sampling is needed throughout the Himalayas to determine its full range. These findings support the hypothesis that molecular sequence data will lead to the discovery of cryptic species in Nepal and facilitate the revision of species taxonomy.     

Activity patterns and habitat use of pudu deer (Pudu puda) in a mountain forest of south-central Chile

The pudu (Pudu puda) is a small, endemic deer, and the only native ungulate found in Chilean and Argentinean temperate forests. Its ecology, including its double role as an herbivore and as a prey, is poorly known. Therefore, it is pressing to gain a better understanding of the pudu given that its habitat is being transformed rapidly by anthropogenic causes. On a coastal mountain range in south-central Chile, we conducted a habitat use study and examined the activity patterns of the pudu using camera traps. The study area was a large native forest patch, surrounded by commercial plantations which would not constitute a habitat for this deer. Using a sampling effort of 7559 camera days, we found that this deer was largely nocturnal with little activity during daytime. The pudu selected Araucaria forests, and avoided Nothofagus forests. These behaviours suggest that the pudu traded off habitat use patterns and activity time to avoid predation, mainly by puma which is the top predator in the rich local community of carnivores occurring in the latter habitat.     

Terellia fuscicornis (Diptera: Tephritidae): biological and morphological adaptation on artichoke and milk thistle

The biology, morphology, and genetics of Terellia fuscicornis on cultivated artichoke and its new recorded host, Silybum marianum, are examined. Morphometrically, the two host‐associated populations were distinct. Except for egg length, all immature stages of the artichoke‐associated population were larger. Principal component analysis, based on head and wing measurements, showed that the adults from both populations clustered into two groups, with the adults reared from artichoke being larger. The ovipositor was significantly longer and blunter in the artichoke‐associated females, reflecting the larger flower heads exploited. Male terminalia measurements showed significant differences between the two populations. Several differences in courtship behaviour were detected between the two populations. Although the two populations show allochronic isolation, sequencing of two mitochondrial genes, ND1 and COI, and one nuclear gene, 18S, revealed no genetic differences between the two populations.     

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.     

A new lycaenid butterfly exclusively associated with the subalpine sclerophyllous oak forests in Taiwan (Lepidoptera,Lycaenidae, Theclinae)

Subalpine sclerophyllous oak forest grows at high elevation in Taiwan, distantly separated from similar forest communities found in western China, Tibet and India. An investigation on bud‐breaking phenology of oaks and associated phytophagous insects in this community revealed an undescribed species of Teratozephyrus lycaenid. This and other oak‐associated insects suggest that the presence of this oak community in Taiwan resulted from a more widely distributed community. The newly discovered Teratozephyrus turned out to be most closely related to T. nuwaii, described from western China, and is described below as T. elatus sp. nov. Two other species of Teratozephyrus also inhabit Taiwan, but both are associated with broad‐leaved oak forests. Of them, T. arisanus is widespread both in China and Taiwan, is morphologically distinct from the other Teratozephyrus species and is exclusively associated with broad‐leaved oaks. The other, T. yugaii, probably gained its broad‐leaved oak association secondarily as no similar species is found in the broad‐leaved oak communities on continental Asia, and it favours cool, higher‐elevation environments even though its host plant ranges into far lower elevations.     

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.     

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.     

Reproductive ecology and behaviour of a species of Adenomera (Anura,Leptodactylinae) with endotrophic tadpoles: Systematic implications

The species of the Leptodactylus fuscus group and those of the genus Adenomera lay their eggs in underground chambers. According to current systematic arrangement of these genera, this behaviour is convergent. Here we describe reproduction, courtship, tadpole morphology, calls, chamber structure, and populational phenology of an Adenomera species, and compare some of these features with those of other species of the genus and with species of Leptodactylus of the fuscus and pentadactylus groups. We tested the tadpoles of the Adenomera sp. and those of Leptodactylus labyrinthicus (pentadactylus group) for their foam‐making abilities. There was sexual dimorphism in size; males averaged 22.0?mm and females 24.3?mm in snout–vent length. Males called from late September to late February; calling often began about 2–3?h before sunset. Males called exclusively in open (non‐forest) areas. Egg clutches were found around male calling sites. Males excavated spherical chambers which had a direct entrance. During mating, the male led the female towards a previously excavated chamber. Territorial interactions (aggressive calls and fights) occurred when an intruder male approached a calling male. Late‐stage tadpoles and newly metamorphosed juveniles were found within underground chambers. Clutch size averaged 10.6; eggs averaged 3.7?mm in diameter and were cream coloured. Tadpoles had horny beaks, but no labial tooth; spiracle was present. All tested groups of tadpoles generated foam within 10?h. As we report for Adenomera sp., the males of Leptodactylus species of the fuscus group lead the female to a previously excavated chamber. Tadpole foam‐making behaviour was reported in Leptodactylus of the fuscus group and was previously unknown for any species of Adenomera or for Leptodactylus of the pentadactylus group. The way in which the tadpoles of Adenomera sp., Leptodactylus spp. (of the fuscus group) and L. labyrinthicus made foam was quite similar. The foam‐making behaviour of the studied tadpoles may act to avoid compaction of the tadpoles at the bottom of the basin or underground chamber, avoiding overcrowding and increasing respiratory and excretory efficiency. As presently recognized, the phylogenetic position of Adenomera suggests that reproductive major behavioural features are convergent with some Leptodactylus species. Alternatively, our data point to close phylogenetic relationships between Adenomera and Leptodactylus of the fuscus and pentadactylus groups, reinforcing the paraphyletic nature of the genus Leptodactylus.     

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.     

Molecular and morphological identification of two new African species of Dugesia (Platyhelminthes,Tricladida, Dugesiidae) from Cameroon

The paper describes two new Dugesia species collected from the rivers Messassi and Ntsetsensooh in Cameroon, representing the first planarian flatworms documented from this country. Based on morphological data, the new species Dugesia bijuga Harrath & Sluys, sp. nov. is characterized mainly by the presence of two diaphragms, a barrel-shaped penis that is traversed by numerous ducts of penis glands and is provided with a short nozzle, and the presence of two atrial folds. The other new species, Dugesia pustulata Harrath & Sluys, sp. nov., is characterized mainly by absence of a penis bulb, presence of a large, elongated and weakly muscular seminal vesicle, and by the ventroposterior section of the bursal canal being thrown into distinct folds. The phylogenetic position of the two new species was determined through a molecular phylogenetic tree, based on a mitochondrial and a nuclear gene, including species from the major geographical range of distribution of the genus Dugesia. The phylogenetic tree revealed that the Cameroon lineage does not constitute a monophyletic group with the other Afrotropical species; it also showed that the African continent may house a great diversity of Dugesia species that still remains to be discovered.

urn:lsid:zoobank.org:pub:007441A5-F037-4950-9F5B-AD6ED12A40ED     

Patterns of artificial avian nest predation by introduced rats in a fragmented laurel forest (Tenerife,Canary Islands)

The importance of introduced rats as damaging factors on island biotas is globally recognized. The predation of artificial avian nests by Ship rats (Rattus rattus) in fragmented laurel forests in Tenerife (Canary Islands) was explored. The influence of road edge, patch type, and position (ground versus tree) on nest survival in two forest remnants differing in conservation degree, were assessed using failure‐time analysis. Overall, nest predation was greater in the preserved than in the disturbed remnant. Nest predation also differed among and within patches, variation being greater within the disturbed remnant. The probability of nest failure was higher at the interior than along the road edge in both remnants, but the road edge effect on nest predation was more intense in the disturbed remnant. Predation pressure was higher in patches of mature, closed canopy or dense understorey with stump sprouting. Ground nests were predated at higher rates than tree nests at any location. These results contrast with other nest predation studies in fragmented landscapes where forest edges rather than the interior are more frequently used by predators. Predatory activity by rats seems negatively affected by forest disturbance and road edge effect. Overall, artificial nest predation patterns by rats confirm a potential predation risk for the avifauna of the Canarian laurel forest. This should be considered in implementing conservation management programmes.     

Reclassification of Bracon mendocinus,a gall‐associated doryctine wasp,and description of a new closely related species of Allorhogas (Hymenoptera: Braconidae)

One of the first reported gall‐associated braconids, from 1910, Bracon mendocinus Kieffer and Jörgensen, is removed from the subfamily Braconinae and transferred to the doryctine genus Allorhogas, A. mendocinus (Kieffer and Jörgensen) comb. nov. A new species morphologically similar to A. mendocinus, A. joergenseni Martinez and Zaldivar‐Riverón sp. nov., is also described. Additionally a neotype is designated for B. mendocinus Kieffer and Jörgensen. We base our conclusions on the morphological examination of recently collected specimens from central Argentina associated with galls on Lycium chilense (Solanaceae), as well as on the DNA variation at 28S ribosomal RNA and cytochrome oxidase subunit I (COI) mitochondrial DNA genes.     

A new species of Fabricinuda Fitzhugh, 1990 (Fabriciinae: Sabellidae: Polychaeta) from the Caribbean,with an emendation of the genus

During a survey of the infauna of seagrass meadows in Venezuela, several specimens of an unknown species of Fabriciinae were collected. The species could not be assigned to any genus of the subfamily, although it was most closely allied to Fabricinuda Fitzhugh, 1990. However, the absence of pseudospatulate inferior notochaetae on chaetiger 8 prevented assignment of the specimens to this genus since their presence on chaetigers 3 to 8 is one of its diagnostic apomorphies. In order to decide whether to establish a new genus for the species or to redefine Fabricinuda, a phylogenetic analysis of the subfamily was made on the basis of a pre‐existing character matrix. Twenty‐two anatomical characters were analysed for 59 species including the new one, and from the resulting consensus tree it was clear that the new species must be included within Fabricinuda and consequently an emendation of the genus is provided herein.