Phylogenetic Relationships and Status Quo of Colonies for Gayal Based on Analysis of Cytochrome b Gene Partial Sequences

Thirty-three mutations and four different haplotypes were found when cytochrome b（Cytb） gene partial sequences of 12 gayals were analyzed. Together with sequences of Bos indicus, Bos taurus, Bos grunniens, and Bos gaurus with Bubalus bubalis as the out group, the partial sequences of Cytb gene of gayals were aligned and base composition and nucleotide variation of Cytb gene were analyzed. The phylogenetic trees were constructed by the NJ method and the MP method respectively, both supporting almost the same topology. Gayal is an independent species of Bos from Bos indicus, Bos taurus, and Bos gaurus. The results also indicate that a great proportion of gayal bloodline was invaded by other species, and the protection of gayal is facing a formidable situation.

Phylogenetic Relationships of 11 Bumblebee Species (Hymenoptera:Apidae) Based on Mitochondrial Cytochrome b Gene Sequences

Phylogenetic relationships of 11 bumblebee species,including 5 subgenera:Bombus (5 species),Thoracobombus (3 species),Mendacibombus (1 species),Fervidobombus (1 species) and Pyrobombus (1 species),were analyzed based on the 357?bp mitochondrial cytochrome b gene sequences.There are 65 singleton polymorphic sites and 71 parsimony informative polymorphic sites in this DNA segment,and 45 polymorphic sites within the total 119 translated amino acids segment.Both NJ tree and MP tree show that Mendacibombus (B.avinovielllus) is basal to others,followed by Fervidobombus (B.pensylvanicus);Pyrobombus (B.impatiens) and Bombus are sister subgenera;the subgenus of Bombus is monophyletic,in which B.ignitus diverged first.

Sequence Comparison of Partial Cytochrome b Genes of Two Coilia species

Sequence variation of partial cytochrome b genes between two Coilia species, C. ectenes and C. mystus, was in- vestigated. Of the 402 nucleotides, twenty-seven (6.72%) are polymorphic and all are synonymous substitutions. At the third positions of genetic condon of cytochrome b gene, the two species show an extreme anti-G bias (<4%) and a pronounced bias towards A and C (>68%). There is no amino acid sequence divergence between the partial cytochrome b genes of the two species, indicating a close genetic relationship between them. The k-2p genetic distance of partial cytochrome b segment of the two species is 0.072, suggesting that the species were separated 3.6 Ma ago, in the middle Pliocene. Our result reveals that the cytochrome b gene is an appropriate marker for studies of population genetic structures and phylogeographic pat- terns of the two species.

Molecular Phylogeny of Slow Lorises (Nycticebus) Revealed by D-loop Sequences and Complete Cytochrome b Gene Sequences of Mitochondrial DNA

Partial sequences of the D-loop and the complete sequences of cytochrome b gene (1 140 bp) of the slow lorises (genus Nycticebus) were undertaken to investigate evolutionary relationships among species of Nycticebus.Sequence analysis results consistently provide new taxonomy evidence at the DNA level for supporting Ratajszczak and Groves’ viewpoint that N.intermedus is merely the adult of N.pygmaeus (Ratajszczak,1998;Groves,1971).Phylogenetic analysis was performed by means of the combined data and these two separate sequences data,respectively,by using various methods,supporting the same topology,in which genus Nycticebus was formed of two clusters.The first cluster was composed of N.pygmaeus,and the second cluster of N.coucang.It also could provide a new molecular genetic evidence to support the view that the genus comprises two species:N.coucang and N.pygmaeus.

Intraspecific Relationship of Sheep Based on Mitochondrial Cytochrome b Gene

[ Objective] To preliminarily explore the intraspecific relationship of sheep based on cytochrome b （ Cyt b） gene of mitochondrial DNA （mtDNA）. [Method] The Cyt b gene sequences in 112 sheep individuals of two local sheep breeds were amplified by PCR. Then the amplified products were digested with EcoR I and analyzed by restriction fragment length polymorphism （RFLP）. [ Result] As many as 56 samples from Tan sheep and 56 samples from Wadi sheep were detected. The results showed that the amplified Cyt b gene in 51 individuals of Tan sheep had one EcoR I restriction site and no EcoR I restriction site in other five individuals, thus the Cyt b gene in Tan sheep showed two restriction morphs; the Cyt b gene in all 56 individuals of Wadi sheep had one EcoR I restriction site and showed one restriction morph. [ Conclusion] The polymorphism of mitochondrial Cyt b gene in Tan sheep and Wadi sheep is poor, and the Cyt b gene in sheep breeds is very conservative. Therefore, using Cyt b gene as gene marker to study the intraspecific relationship of sheep has some limitations.

Identification of sika deer and red deer using partial cytochrome b and 12s ribosomal RNA genes

A study was conducted on the identifications of the degraded samples of sika deer （Cervus nippon） and red deer （Cervus elaphus） by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical （0.026±0.006）, which was smaller than the smallest nucleotide distance between eastern red deer and sika deer （0.036）. Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.

Genetic diversity and the biogeographical process of Acheilognathus macropterus revealed by sequence variations of mitochondrial cytochrome b gene

In this study,thirty-six individuals of Acheilognathus macropterus were collected from the Heilongjiang River,the Yangtze River,and the Nandujiang River.Partial mitochondrial cytochrome b gene region(636 base pair)was sequenced to these samples and 22 haplo-types were found.With A.chankaensis and A.tokinensis as outgroups,their relationships were analyzed.The p-distances were calculated with Mega software and a molecular phylogenetic tree was constructed using the neighbor-joining(NJ)method.The proportions of main morphological characters were compared as well.P-distances showed that the genetic differences in A.macropterus samples were far smaller than those between these samples and the outgroups.The molecular phylogenetic tree shows that samples with barbels and those without barbels were intermingled.There was no distinctive difference in proportions of morphological characteristics among them.These results suggested that samples with barbels and those without barbels(formally identified as A.taenianalis)are the same species;A.taenianalis is synonymous with A.macropterus.The thirty-six individuals were grouped into five clades and the positions of the samples in the clades were correspondingly grouped within their geographical distributions.Among the five clades,clades 1 and 5 included samples from the Heilongjiang River and Nandujiang River respectively.The samples from the Yangtze River scattered into clades 2,3,and 4.There were distinctive genetic differences(>5%)among them.Interestingly,the distributions of the 21 samples in these three clades were not correlated to their geographical distributions.It is postulated that these genetic differences were due to the bitterlings’mating choice mechanism,the prozygotic isolation.The genetic differences between the fish from Nandujiang River and those from the mainland indicated that they were separated early.However,the small genetic differences among the samples and the positions of the fish from the Heilonjiang River in the molecular phylogenetic tree indicate that fish in Heilongjiang River might have dispersed from the Yangtze River to that area much later.

Phylogenetic relationships of some Sylviidae species based on complete mtDNA cyt b and partial COI sequence data

Members of the passerine family Sylviidae are distributed widely around the Old World and the phylogenetic relationships of many species still remain controversial.In this study,we investigated the phylogeny and relationships among 37 species of 11 genera by analyzing DNA sequences obtained from the complete mitochondrial cytochrome b (cyt b) and partial cytochrome oxidase I (COI) genes.The data were analyzed by maximum-likelihood analysis and Bayesian inference.The results demonstrate that the current genus Phylloscopus is non-monophyletic,while Seicercus is synonymized with Phylloscopus or is a group within the genus Phylloscopus.We may conclude that within Phylloscopus there are close relations between P.magnirostris and P.borealis;among P.proregulus,P.yunnanensis,P.pulcher and P.maculipennis,as well as among P.occisinensis,P.schwarzi,P.armandii,P.collybita and P.fuscatus.Monophyly of the genus Cettia could not be corroborated;it is closely related to the genera Abroscopus and Tesia.However monophyly of Acrocephalus is supported.Furthermore,the close relationships between Sylvia and Zosterops and among Prinia,Orthotomus and Cisticola are also supported.

Phlebotomus(Adlerius) kabulensis(Diptera: Psychodidae) a new record sand fly species from Iran: Morphological and molecular aspects

Objective: To represent a new geographical record, Phlebotomus(Adlerius) kabulensis(P.kabulensis), which is suspected to be a potential vector of visceral leishmaniasis.Methods: For the first time, P.kabulensis specimens were collected using the sticky paper traps method in outdoor places in mountainous areas with vegetation coverage of three provinces in Iran.Identification of males was based on ecological, morphological, morphometric and molecular(mtDNA cytochrome b gene sequences) criteria.Generally, males have two ascoids on the 8^(th)antennal segment and one ascoid on segments 9^(th)to 15^(th), aedeagus with normal obtuseangled sub-terminal notch and coxite with 27–50 groups of hairs on the distal half of its body.Results: Morphometric measurement revealed that P.kabulensis specimens were the same as compared with seven other morphological characters in three provinces of the country but lengths of the coxite were significantly different.The PCR result of the cytochrome b(Cyt b)-mtDNA fragment shows 550-bp length, with its special nucleotide arrangement.The male and female of P.kabulensis were newly discovered members of the subgenus Adlerius from Iran.Initial DNA analysis indicated how distinct this species is.Conclusions: The results show that the P.kabulensis female will be identified by comparing with other Adlerius female groups regarding its morphometric characters and molecular sequencing.

Mitochondrial DNA Sequences Imply Anhui Musk Deer a Valid Species in Genus Moschus

Anhui musk deer [ Moschus ( moschiferus/berezovskii ) anhuiensis ] has been a taxonomic mystery since its discovery in early 80's.In this paper,with museum samples,we sequenced the complete cytochrome b gene of five Anhui musk deer.When compared with other species in Genus Moschus ,Anhui musk deer showed a rather level of sequence divergence from all the other species in this genus.The phylogenetic trees constructed by multiple methods supported the same topology,in which the monophyly of Anhui musk deer was clearly demonstrated.Therefore,our molecular data suggest a full species status for Anhui musk deer ( Moschus anhuiensis ),rather than a subspecies of either M moschiferus or M berezovskii previously suggested by morphological studies.

Detection of food source by PCR analysis of the gut contents of Aldrichina grahami （Aldrich） （Diptera： Calliphoridae） during post-feeding period

The last meal of sarcophagous maggots may be useful in identifying the species on whose flesh they have fed （the＂host＂species）. The DNA profile of the host species may indeed be detectable in the＂last meal＂. In this paper, mitochondrial DNA analysis of gut contents was used to identify the prior host of post-feeding larvae of Aldrichina grahami （Aldrich） （Diptera： Calliphoridae）. A modified logistic equation was fitted to estimate the probability of identifying the host under five different constant temperatures （16, 20, 24, 28 and 32 ℃）. Our results shows that the detected time ranged from a maximum of 24 h at 32℃ to 42 h at 16℃ and a minimum of 12 h at 32~C to 30 h at 16℃. Furthermore, the host detection time was also calculated to give the maximal time after larval hatching from the egg. These results indicate that, in criminal cases where the maggots stray from the corpse, the last meal of the larvae should not be overlooked as potentially critical evidence.

Ancient DNA sequences from Coelodonta antiquitatis in China reveal its divergence and phylogeny

Ancient DNA data have supported a sister relationship between woolly rhinoceros and extant Sumatran rhinoceros.This relationship has been used to explore the divergent times for the woolly rhinoceros from their relatives.Complete and partial ancient DNA sequences of the mitochondrial cytochrome b(cyt b)gene were retrieved from bones of the late Pleistocene Coelodonta antiquitatis excavated from northern and northeastern China.The newly obtained sequences together with the European and northern Asian Coelodonta antiquitatis sequences from GenBank were used to estimate the evolutionary divergence time.Phylogenetic analyses showed the exchange of genetic information between the Chinese individuals and Coelodonta antiquitatis of north Asia,which also indicated a more recent evolutionary timescale(3.8–4.7 Ma)than previous molecular estimations(17.5–22.8 or 21–26 Ma)for woolly rhinoceros based on the fossil calibration of outgroups.This new timescale was more consistent with the fossil record of the earliest known genus Coelodonta.