2009 Vol. 30, No. 3
Proper phylogenetic reconstruction is crucial for understanding many evolutionary phenomena. In spite of the great success of molecular phylogenetics, DNA signal still may be limited by some intrinsic constraints such as codon usage bias. The phylogenetic relationships between the five species subgroups of the Drosophila saltans group are a good example of conflicting molecular phylogenies drawn from different genes due to an ancestral substitutional shift. Here, forty morphological characters were analyzed using the same set of species used in previous molecular studies, with at least a single representative of each subgroup. The cladistic analysis was in disagreement with most of the previous hypotheses in placing the sturtevanti subgroup as an early branch, whereas the four remaining subgroups form a well supported clade that can be further subdivided into two sister clades: one containing the cordata and the elliptica subgroups, whereas the second includes the parasaltans and the saltans subgroups. The molecular evolution (codon usage bias) of the saltans group were revised in light of the present finding. The analysis highlights the important role of morphology in phylogeny reconstruction and in understanding molecular evolutionary phenomena.
Fifteen sequences from the mitochondrial cytochrome c oxidase subunit I gene (COI) were determined for 4 species of the genus Meretrix, with the homologous sequences of M. petechialis obtained from the GenBank data library. The alignment length of the sequences was 574 bp after excluding ambiguous sites, including 93 parsimony informative sites. In the fragments, the percentages of A, T, C and G were 21.15%, 44.71%, 14.05% and 20.09% respectively. There were 12 haplotypes identified: 4 M. meretrix, 2 M. lamarckii, 3 M. lusoria, 1 M. lyrata and 2 M. petechialis. Furthermore, it was revealed that M. meretrix, M. petechialis and M. lusoria shared some haplotypes. Phylogeny trees were reconstructed by Maximum-parsimony (MP) and Bayesian method using Cylina sinensis as the outgroup. Our results indicated that M. lusoria, M. petechialis and M. meretrix are closely related species. This is in accordance with the viewpoint that M. petechialis and M. lusoria should be treated as a junior synonym of M. meretrix.
DNA sequences from the mitochondrial gene cytochrome oxidase subunit I (mtDNA COI) were used to estimate the genetic variability in two wild populations and two cultured populations of the hard shelled mussel, Mytilus coruscus. Thirty haplotypes were identified in the four populations. The cultured populations exhibited a lower number of haplotypes and genetic diversity than those of the wild populations, suggesting that a small number of effective founding breeders contributed to the genetic variation of the cultured populations. No significant differentiation was observed between the cultured population and local wild population, implying that persistent gene flow occurred in these populations. This genetic survey is intended as a baseline for future genetic monitoring of M. coruscus aquaculture stocks.
Genetic variability and divergence among natural populations of Jaculus jaculus and J. orientalis in Tunisia were examined by electrophoretic analysis of 16 enzymatic proteins encoded by 23 genetic loci. Low levels of genetic variability were found among populations of both species in comparison to those of other rodent and mammal species of which data are available. In J. jaculus populations, the mean level of observed heterozygosity (Hobs) ranged from 0.08 to 0.19, while the mean percentage of polymorphic loci (P) ranged from 26.2% to 45.2% and the mean number of alleles per locus (A) ranged from 1.1 to 1.4. Nevertheless, the mean values were 0.10 to 0.15, 29.3% to 44.1% and 1.1 to 1.7, respectively, for J. orientalis. In addition, populations of the two species have revealed a lower degree of genetic differentiation (Fst=0.0017 for J. jaculus and 0.0019 for J. orientalis). Moreover, Fst was 0.607, P<0.05 between populations of the two species, indicating that they were highly genetically diverged from each other. The present data assures the previous results on the validity of the present taxonomic situation of the two species and emphasis on the effect of geographic factors (environments type and bioclimatic stages) on the genetic structure of both species.
Gymncypris eckloni, being distributed mainly in the upper reaches of Yellow River and lakes in the Qinghai-Tibetan Plateau, plays significant roles in the trophic web of plateau freshwater communities. In the present study, the complete sequences of the mitochondrial Cyt b gene (1 140 bp) from sixty eight individuals representing five populations from the upper Yellow River were obtained to assess the genetic variation and diversity. Within the aligned 1140 bp bases, 30 (2.63%) nucleotides were variable, and a total of 18 haplotypes were identified. The results showed that the haplotype diversity and nucleotide diversity of Gymncypris eckloni populations were low by comparison with the other species of family Cyprinidae, which maybe related to tectonic movements and paleoenvironmental fluctuations of the Qinghai-Tibetan Plateau, and that the populations have experienced bottleneck events in history. The AMOVA analysis indicated that the genetic variation mainly occurred within populations instead of among different geographic groups or among populations within among different geographical groups. There is no geographic clustering observed in the phylogenetic tree and the TCS network, which suggest that the natural populations of Gymncypris eckloni should be managed and conserved as a whole. The unimodal mismatch distribution of haplotypes, together with the selective neutrality test of Fu’s Fs (−15.3400, P<0.001) and Tajima’s D (−0.6254, P =0.3080), suggest that a recent population expansion of Gymncypris eckloni have been occurred.
The transition protein-2 gene (tnp2) have been reported as the round spermatid-specific marker gene. However, the DNA sequence of tnp2 gene in Ovis aries have not been reported. In order to study the sheep round spermatid-specific marker gene, we designed primers according to the reported Bos taurus tnp2 gene cDNA sequences in the GenBank. The partial CDS was amplified by RT-PCR. The PCR fragment was inserted into the T-A cloning vector pMD19-T. The partial nucleotide sequences of Mongolia sheep tnp2 gene were compared with the counterpart sequences of Bos taurus, and the nucleotide homology was 95.3%. Using the primers designed according to the tnp2 cDNA sequence, the tnp2 gene transcription expression in the co-cultured cells derived from four-months old sheep testis was assessed by RT-PCR. The results demonstrate that the round spermatid cells are generated in the co-culture system until ten weeks in vitro. The cDNA cloning and sequencing lay down a foundation for further study on spermatogenesis of sheep.
2009, 30(3): 267-275. doi: 10.3724/SP.J.1141.2009.03267
To finely map and identify the mutant gene of snthr-1Bao mouse whose mutation gene showing single gene recessive heredity was mapped on the terminal side of chromosome 9，F2 mice bred through (C57BL/6J ×snthr-1Bao )F1 mice intercrossing and the polymorphisms of 2 microsetallites, 35 SSRs presumed by computer and 3 SNPs chosen and tested were for fine mapping. RT-PCR amplifying cDNA combined with genomic sequence to identify mutation after affirming candidate gene. Based on genomic markers D9Mit151, a new SSR，two SNPs (rs8 254 361 and rs30 195 705) and 1 100 F2 scant hair mice selected from over 4 400 F2 mice, the mutant gene was narrowed down to a 1.367 Mb region between 117.762 kb and 119.129 kb from the centromere on the chromosome 9 and Plcd1was the primary candidate gene. Genomic sequence revealed there was a 14 883 bp deletion and such deletion destructed the Plcd1 and Vill. The 14 883 bp genomic deletion covering subtotal Plcd1and Vill, more likely the Plcd1, is responsible for the abnormal phenotype of snthr-1Bao mouse.
Between December 2007 and December 2008, we studied the avian guilds structure of the secondary broad-leaved forests in Yaoluoping, Dabieshan Mountain, Anhui Province. We used focal sampling method to observe feeding behaviors of the bird community, and collected food resource utilization data. PC-ORD was used in Cluster Analysis for the guild structures in the two seasons, and Detrended Correspondence Analysis (DCA) for the feeding patterns of the 32 birds in both the breeding/non-breeding seasons. Results indicated that during the non-breeding season, the bird community could be divided into four guilds: ground forager, shrub forager, tree trunk (branches) forager, and canopy forager. In addition to the four listed guilds, there was an air foraging guild during the breeding season. The first axis of DCA represented the information of the foraging height, the second axis represented the information of the foraging position, and the third axis represented the information of the foraging pattern and the foraging matrix. The ordination for the 32 birds by the first two DCA axes indicated the behavior of 6 birds mainly changed along the first DCA axis, which represented the change information of the foraging height. Additionally, behavior of 4 birds mainly changed along the second DCA axis, which represented the change information of the foraging position.
2009, 30(3): 288-294. doi: 10.3724/SP.J.1141.2009.03288
Lanius schach is typical of species with color polymorphism. The black morph has been regarded as an independent species by some authors. We compared the breeding ecology of the black morph and brown morph of L. schach to explore the classification position of the black morph. From February to June in 2008, observations were made on the breeding ecology of the two morphs. Trials, including of interchanging their eggs and nestlings, were carried out in Haifeng Natural Reserve, Guangdong Province, China. Logistic equations were used to describe growth of the body morphological characters of the nestlings. The results showed: 1) There were no significant differences of egg figures between two types (P>0.05). 2) The growth of the body mass, wing length and other morphological characters of >15-day-old nestlings could be described accurately by the Logistic equation. 3) There were no significant difference between the body morphological characters of the 14-day-old nestlings，but there was significant difference on the asymptotic value of the ninth primary. 4) The experiments of interchanging eggs and nestlings showed that during the process of sitting and fostering, eggs and nestlings of the same period from the two color morphs were accepted, but eggs of different periods were rejected. 5) Nestling behaviors did not differ between the nestlings from different patterns. We concluded that black morph is not an independent species but a color morph of L. schach.
2009, 30(3): 295-302. doi: 10.3724/SP.J.1141.2009.03295
We investigated the avian nesting guilds in Hangzhou across an urban gradient from March 2007 to August 2007. This gradient includes different urbanization level habitats of urban areas, rural-urban continuum areas, farmland areas, forestland mixed areas, and forestland areas, in order to recognize the effects of urbanization on avian nesting guilds. There were 18 strip transects (3 km×100 m) in each type of habitats, totaling 90 transects. Ninety-six bird species and 9 nesting guilds were recorded. Based on the locations of the nest sites, these were classified as canopy nesters, shrubs nesters, canopy/ shrub nesters, natural cavity nesters, buildings nesters, natural cavity/ buildings nesters, ground nesters, water surface nesters and parasite nesters. The results showed that the urbanization could decrease both the numbers of the nesting guilds and the species in nesting guilds. We found that the urbanization had different impact patterns for different nesting guilds. For example, the number of canopy nesters, shrub nesters, ground nesters and natural cavity nesters declined with increased urbanization. Shrub nesters and ground nesters were particularly more sensitive to urbanization. For the natural cavity/build nesters, numbers were increased with urbanization. The affecting patterns of urbanization were different with different nesting guilds as they using different nest-sites. Additionally, we found that although all of variables of habitat measured in our survey, the vegetation coverage, areas of buildings, distance to the city center and human disturbance could influence the avian community structure of nesting guilds, each variable had a specific pattern of the effect on the nesting guilds separately.
The composition of nocturnal migratory birds was investigated by light trapping at Jinshan yakou in Ailao Mountain, Xinping County, Yunnan Province from September 5th to November 5th 2007 and from September 3rd to November 7th 2008. Totally, 7943 individuals of 129 species, which belong to 23 families, 14 orders, were caught. Passerines were the main species at 58.9% of all birds captured. Lanius cristatus, Cuculus poliocephalus, Luscinia calliope were predominant and every one was more than 5%. The number of birds captured was highest from 20:00 to 22:00 and from 04:00 to 06:00 every day. During 2007 and 2008，Both of Shannon-Wiener diversity index and Pielou evenness index were lowest, and C index was highest in early period. However, both of the Shannon-Wiener diversity index and Pielou evenness index were highest, and C index was lowest in the middle stage. C index and G-F index were higher in 2007 than in 2008. But Shannon-Wiener diversity index and Pielou evenness index were higher in 2008 than in 2007. There were differences with the number and species of the birds captured at night between various birds migration localities. Geography and climate were important factors that affect the differences.
We studied summer and winter bed-site selection by goitred gazelle (G. s. sairensis) using transect method from June to August in 2007, and November, 2007 to January, 2008 in Mt. Kalamaili Ungulate Nature Reserve, Xinjiang, China. In summer, we measured 49 bed-site quadrants used by goitred gazelle and 36 control quadrants during 26 transect surveys. While in winter, we measured 75 bed-site quadrants used by goitred gazelle and 75 control quadrants during 30 transect surveys. Through comparing the characteristics of bed site quadrants and control quadrants, we found summer bed sites of goitred gazelles were characterized by plains, lower or no slope position, over 900 m of altitude, far from permanent water source, main road and human community, of higher plant density, higher herb density and higher canopy cover. In winter, goitred gazelles preferred to bed on hill, or on half-sunny slope and sunny slope, steep slope position, of 901−1 000 m of altitude, with distance of 501 to 1 000 m or over 2 000 m to main road and, near human residence, lower and middle canopy cover, snow depth of 1.1-3cm, higher plant density and herbage density. Principal Component Analysis (PCA) showed that 4 principal components explained 86.57% of the total variance in the bed site selection by goitred gazelle in summer. First principal component in summer was positively related to plant density, herbage density, density of Stipa spp., distance to nearest human residence, distance to permanent water source and altitude. PCA also showed that 4 principal components explained 73.88% of total variance the bed site selection by goitred gazelle in winter. First principal component in winter was positively related to plant density, herbage density, density of Stipa spp. and altitude.
Three new Tenthredinidae species are reported from Gansu and three from Qinghai Provinces of China. Tenthredo (Tenthredo) sinotemula sp. nov., Tenthredo (Tenthredella) labrangensis sp. nov. and Tenthredo (Tenthredella) sinosimplex sp. nov. are described from Gansu, Tenthredo (Tenthredella) rolleri sp. nov., Tenthredo (Tenthredella) qinghaiensis sp. nov. and Tenthredo (Tenthredella) yunningsiensis sp. nov. from Qinghai Province.
A new freshwater goby, Rhinogobius zhoui sp. nov., was found in the stream of Lianhua Mountain（23º01'N，115º17'E）in Haifeng County, Guangdong Province, China. The new species can be distinguished from related species by combination of characters: second dorsal fin rays I, 8-9; anal fin rays I, 7-8; pectoral fin rays 16—18; longitudinal scale series 29-31; predorsal scales 10-12; vertebral count 10+16=26; In adult male, first dorsal fin without black spot, each median fin with broad white band, cheek and branchiostegal membrane unpigmented, 6-;8 red blotches on body side.
Field surveys of Nanla River, located on the southwest border between China and Myanmar, were conducted in January and from May to June of 2008. Based on field surveys and historical records, there are a total of 42 species belonging to 4 orders, 14 families, and 34 genera in Nanla River. The species of Cypriniformes are dominant, including 27 species, accounting for 64.3% of the total number of species. Siluriformes and Perciformes both have 6 species, accounting for 14.3% of the total. The number of species of Synbranchiformes is 2, 4.8% of the total. Hemibagrus wyckioides is listed in the China Species Red List. Pangasius sanitwangsei, with a suspected distribution through the Nanla River, is listed in the China Red Data Book of Endangered Animals and China Species Red List. Fish fauna taxa of the Nanla River is dominated by ‘old Tertiary groups’, which mainly occur in tropical rivers and flood plains, and is the typical group of fishes in tropical Southeast Asia. Based on the ecology type, bottom-dwelling and omnivorous fishes are dominant. Finally, the causes for the listed statuses are briefly summarized as water pollution, overfishing and impacts of introduced species.
The synaptonemal complex protein 3 (Scp3) plays a crucial role in synaptonemal complex formation and male germ cells meiosis. Until now, no studies on goat Scp3 have been reported. In present study, we cloned the Cashmere goat Scp3 cDNA using RT-PCR and molecular cloning techniques. The Scp3 sequence of Cashmere goat showed 98% identity with that of bovine. Primers were designed according to the sequence we got and RT-PCR was performed to analyze the expression of Scp3 in prepubertal Cashmere goat testes. The results showed that the testes development in prepubertal goat varies in different animals, and the first round of meiosis in analyzed Cashmere goat testes occurs mostly after 73 days after birth.