A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic

Cytochrome b and D-loop nucleotide sequences were used to study patterns of molecular evolution and phylogenetic relationships between the pheasants and the partridges, which are thought to form two closely related monophyletic galliform lineages. Our analyses used 34 complete cytochrome b and 22 partial D-loop sequences from the hypervariable domain I of the D-loop, representing 20 pheasant species (15 genera) and 12 partridge species (5 genera). We performed parsimony, maximum likelihood, and distance analyses to resolve these phylogenetic relationships. In this data set, transversion analyses gave results similar to those of global analyses. All of our molecular phylogenetic analyses indicated that the pheasants and partridges arose through a rapid radiation, making it difficult to establish higher level relationships. However, we were able to establish six major lineages containing pheasant and partridge taxa, including one lineage containing both pheasants and partridges (Gallus, Bambusicola and Francolinus). This result, supported by maximum likelihood tests, indicated that the pheasants and partridges do not form independent monophyletic lineages.     

江西武夷山雉科鸟类研究初报

2004年9月～2008年5月对江西武夷山国家级自然保护区的雉类资源进行了调查,查明区内分布有白眉山鹧鸪、灰胸竹鸡、黄腹角雉、白鹇、勺鸡、雉鸡、白颈长尾雉等雉科鸟类,隶属于7属7种,分别占我国雉类属、种数量的33.3%和12.7%.较常见的种类有灰胸竹鸡、白鹇和黄腹角雉.并对有关物种的生境利用特点、生物学特征和灾害性天气对其分布的影响等进行了初步分析.     

两种锦鸡和环颈雉线粒体DNA(mtDNA)的比较研究

本文以10种限制性内切酶分析雉科中环颈雉,红腹锦鸡和白腹锦鸡线粒体DNA（mtDNA）。雉属与锦鸡属之间的遗传距离P为0.076（0.067-0.085）,红腹锦鸡与白腹锦鸡的P为0.012。推算雉属和锦鸡属的分化大约发生在3.8×10[6]年以前,红腹锦鸡与白腹锦鸡的分化大约在6×10[5]年以前。这些结果表明：1.在雉科系统发生中,雉属与锦鸡属是近缘的属;2.红腹锦鸡和白腹锦鸡的分化较晚,关系密切,可能只是两个亚种。     

Reproduction of wild birds via interspecies germ cell transplantation

The present study was conducted to apply an interspecies germ cell transfer technique to wild bird reproduction. Pheasant (Phasianus colchicus) primordial germ cells (PGCs) retrieved from the gonads of 7-day-old embryos were transferred to the bloodstream of 2.5-day-old chicken (Gallus gallus) embryos. Pheasant-to-chicken germline chimeras hatched from the recipient embryos, and 10 pheasants were derived from testcross reproduction of the male chimeras with female pheasants. Gonadal migration of the transferred PGCs, their involvement in spermatogenesis, and production of chimeric semen were confirmed. The phenotype of pheasant progenies derived from the interspecies transfer was identical to that of wild pheasants. The average efficiency of reproduction estimated from the percentage of pheasants to total progenies was 17.5%. In conclusion, interspecies germ cell transfer into a developing embryo can be used for wild bird reproduction, and this reproductive technology may be applicable in conserving endangered bird species.     

基于线粒体细胞色素b基因序列的虹雉属鸟类的系统发育关系

通过雉科虹雉属(Lophophorus)、角雉属(Tragopan)、勺鸡属(Pucrasia)和血雉属(Ithaginis)7种鸟类的细胞色素b(cyt b)基因序列比较,构建的虹雉属及其近缘属的分子系统树表明：①3种虹雉构成一个单系群(monophyletic group),虹雉属与角雉属、勺鸡属构成一个单系群;②虹雉属内分为白尾梢虹雉,以及棕尾虹雉和绿尾虹雉两个演化枝。综合分子系统学、地理分布格局和形态学的证据,推测虹雉属鸟类起源于中国的横断山脉,其中繁衍生活在原地的一枝演化为白尾梢虹雉;另一枝则分别进入喜马拉雅山区(西)和中国西南部(东),向西的演化为棕尾虹雉,向东的则为绿尾虹雉。     

江西官山自然保护区四种雉类的生境选择差异

2009年10月—2010年11月在江西官山国家级自然保护区对白颈长尾雉、白鹇、勺鸡和灰胸竹鸡4种雉类的生境选择进行了研究:共调查了6条样线上的388个样方,选取了与这四种雉类栖息地相关的17个生态因子进行观测和测量。结果显示,4种雉类均偏好阔叶林和针阔混交林、阳坡或半阴半阳坡的生境。Kruskal-Wallistest检验表明,4种雉类在海拔、坡度、乔木盖度、灌木盖度、灌木数量、灌木高度、草本盖度、草本种类、草本数量、落叶层盖度和水源距离11个生态因子上存在极显著差异(P<0.01),乔木种类存在显著差异(P<0.05),其余生态因子无显著差异(P>0.05)。典则判别函数图显示,4种雉类在生境选择上存在一定程度的重叠,又有比较明显的差异。逐步判别表明在区分4种雉类生境选择差异方面有一系列的生态因子发挥作用,依照贡献值的大小依次为海拔、草本数量、灌木高度、水源距离、灌木盖度、乔木盖度、坡度、落叶层盖度、灌木数量、草本盖度。由这10个变量构成的方程对4种雉类生境选择差异的正确区分率为74.7%。     

CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes)

Chicken repeat 1 (CR1) elements, a class of retroposons belonging to non-long-terminal repeats, have been recognized as powerful tools for phylogenetic studies. Here we examine the phylogenetic relationships of 11 Phasianidae species based on CR1 retroposons. Together with 19 loci reported previously, a total of 99 CR1 loci were identified from chicken genome and turkey BAC clone sequences. 75 insertion events were used to address the branching order of 11 species in Phasianidae. The topology of our tree suggests that: 1) Gallus gallus possessed a basal phylogenetic position within Phasianidae and was related to Bambusicola thoracica (BSP=100%); 2) After the split of G. gallus and B. thoracica, Arborophila rufipectus diverged from Phasianidae (BSP=100%). Nine unambiguous insertion events supported a phylogenetic position of A. rufipectus different to previous mitochondrial data suggesting a hybrid origin or an ancient introgression of A. rufipectus; and 3) 22 CR1 insertion events strongly supported the eight phasianids under investigation sharing a common ancestor. Our study has revisited the phylogenetic position of G. gallus and A. rufipectus and provided a new insight into the phylogeny of Phasianidae birds. It showed that a CR1-based methodology has a great potential to be informative within Phasianidae in resolving relationships of closely related species whose radiation and speciation have occurred very recently.     

The distribution of endogenous chicken retrovirus sequences in the DNA of galliform birds does not coincide with avian phylogenetic relationships.

The chicken is a domesticated form of Red Jungle-fowl (Gallus gallus), which belongs to the Pheasant family (Phasianidae) within the order Galliformes. Domestic chickens carry the genome of the endogenous retrovirus RAV-O as DNA sequences integrated into host chromosomes transmitted through the germ line. We have examined the presence and distribution of RAV-O-related sequences in the DNA of Red Junglefowl and other closely related species of Junglefowl, as well as more distantly related Pheasants and Quail. DNA sequences homologous to RAV-O were analyzed by molecular hybridization in liquid and after electrophoresis of restriction endonuclease fragments. The presence of RAV-O-related sequences in avian DNA does not correlate with phylogenetic relationships. Under stringent conditions of hybridization in liquid, DNA sequences homologous to RAV-O cDNA were detected at high levels (greater than 80% homology( only in the genomes of the domestic chicken and its phylogenetic ancestor, the Red Junglefowl (Gallus gallus). The DNA of two other species of Gallus (G. sonnerati, Sonnerat's Junglefowl and G. varius, Green Junglefowl), of Ring-necked Pheasant and of Japanese Quail contained sequences with less than 10% homology to RAV-O cDNA. Under conditions permitting mismatching, however, Ring-necked Pheasant DNA hybridized up to 50% of the RAV-O cDNA, and Quail DNA 24%, whereas the extent of hybridization to Sonnerat's and Green Junglefowl DNA was not markedly increased. Analysis of restriction enzyme digests revealed several distinct fragments of DNA hybridizing to chick retrovirus cDNA in both Red Junglefowl and domestic chicken, and multiple fragments in DNA from two species of Phasianus. No fragments with sequences related to chicken retroviruses were found, however, in digests of DNA prepared from Sonnerat's, Ceylonese and Green Junglefowl, from two other Pheasant genera (Chrysolophus and Lophura), or from one Quail genus (Coturnix). Thus the DNA of three Junglefowl species closely related to Gallus gallus lacked RAV-O sequences while the DNA of more distantly related Phasianus species showed significant homology. These results show that RAV-O-related sequences have not diverged together with the normal host genes during the evolution of the Phasianidae. Although RAV-O sequences are endogenous in all domestic chickens and Red Junglefowl studied thus far, it appears that the RAV-O genome has been introduced relatively recently into the germ line of Gallus gallus, following speciation but before domestication, and independently of the related sequences found in members of the genus Phasianus.     

角雉属分类地位的探讨

角雉属Tragopan两性羽色不同,雄性具有艳丽的装饰性羽毛,这与一般雉族Phasianini相似;而尾较翅为短,尾羽的换羽从中央到外侧,这些特征又与鹑族Perdicini各属相同,形态特征上角雉属被划为鹑族.通过PCR扩增鸡形目Galliformes黄腹角雉Tragopan caboti等10个属19个个体的线粒体DNA细胞色素b的部分基因,获取片段长度为828bp,以及从GenBank获取22种样本的相应序列,以角叫鸭Anhima cornuta和海龟Kachuga dhongoka为外群,分别用邻接法(Neighbor-joining,NJ)和最小进化法(Minimum-evolution,ME),对鸡形目和将雉科的15个属分为5个属及雉族和鹑族构建分子系统树,NJ和ME系统树中,都是角雉与雉类相聚.角雉出现形态解剖与基因分析分类地位的不一致,说明雉和鹑可能不是单系群.同时我们认为雌雄的色泽区别比尾羽的长短和换羽方式在对雉和鹑形态特征分类时更为重要.从分子水平分析的结果都是角雉属与雉聚类.因此角雉归为雉族更合理.     

鸡形目鸟类系统发生研究现状

综合形态学、行为学、分子系统发生等方面研究成果,对世界鸡形目鸟类科的系统关系以及属、种间系统发生的研究进展进行了阐述,侧重介绍与我国鸡形目鸟类相关类群的系统发生研究现状。与传统的系统关系比较,新的研究结果主要有:凤冠雉科和冢雉科不再是互为姊妹群;传统分类中的雉族和鹑族被证明并非单源而是多源的;雉族的原鸡属与鹑族的竹鸡属有很近的亲缘关系;灰山鹑、火鸡和松鸡类的系统发生关系可能很近。分子进化的研究表明雉科各属的起源主要集中在上新世。     

Phylogenetic distribution of the novel avian endogenous provirus family EAV-0

A new family of related endogenous proviruses, existing at 50 to 100 copies per haploid genome and distinguishable by remarkably short long terminal repeats, has been described for domestic chickens (Gallus gallus subsp domesticus). In this communication, by using Southern blot analysis and probes derived from both internal viral sequences and locus-specific, cellular flanking sequences, we studied the genetic distribution of this family of moderately repetitive avian endogenous retroviruses within the genomes of four Gallus species. Eight inbred lines of domestic chickens, the evolutionary progenitor to the domestic chicken (red jungle fowl), and two more distantly related species (grey and green jungle fowl) were studied. All Gallus species harbored this class of elements, although the different lines of domestic chickens and different species of jungle fowl bore distinguishable complements of the proviral loci. Jungle fowl appeared to have fewer copies than domestic chickens. For three randomly isolated proviral loci, domestic chickens (G. gallus subsp. domesticus) and red jungle fowl (G. gallus subsp. gallus) showed only a proviral state, whereas the most primitive and divergent of the jungle fowl, the green jungle fowl (G. varius), consistently demonstrated only preintegration states or disparate alleles. The presence of this family in all Gallus species and of related sequences in other genera suggests that a primordial founding integration event occurred prior to the evolutionary separation of Gallus species and possibly related genera. Additionally, at least one proviral locus has been acquired subsequent to speciation, indicating that this family was actively infectious after the primary founding event. This conserved, repetitive proviral family appears to represent the vestigial remnant of an avian retrovirus class related to and evolutionarily more ancient than the Rous-associated virus-0 family of avian endogenous retroviruses.     

Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspe- cies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86±6.36. The overall expected heterozygosity of all population was 0.6708±0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds' distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds' genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds→primitive breeds (Chahua chicken and Tibetan)→red jungle fowl in China (G. gallus spadiceus)→red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin.     

The origin and genetic diversity of Chinese native chicken breeds

The first 539 bases of mitochondrial DNA D-loop region of six Chinese native chicken breeds (Gallus gallus domesticus) were sequenced and compared to those of the red junglefowl (Gallus gallus), the gray junglefowl (Gallus sonneratii), the green junglefowl (Gallus varius) and Lafayette's junglefowl (Gallus lafayettei) reported in GenBank, and the phylogenetic trees for the chickens were constructed based on the D-loop sequences. The results showed that the four species of the genus Gallus had great differences among each other, the G. g. domesticus was closest to the red junglefowl in Thailand and its adjacent regions, suggesting the Chinese domestic fowl probably originated from the red junglefowl in these regions. The two subs pecies of Thailand, G. g. gallus and G. g. spadiceus, should belong to one subspecies because of their resemblance. In the case of native breeds, there existed a great difference between the egg breeds and general purpose breeds, which suggested different maternal origins of the two types.     

运用红外相机对太行山猕猴国家级自然保护区（济源）鸟兽多样性的调查

河南太行山猕猴国家级自然保护区（济源）内野生动物种类非常丰富,但已多年未进行过野生动物本底资源调查。于2015年1月至7月,在保护区4个林场内设置了51个2km×2km网格,采用红外相机技术对保护区内兽类和地栖性鸟类资源进行调查。经过6,014个捕获日的调查,共记录到野生兽类5目13科17种,鸟类6目12科28种,其中东北刺猬（Erinaceus amurensis）、红腹锦鸡（Chrysolophus pictus）、灰林鸮（Strix aluco）、宝兴歌鸫（Turdus mupinensis）、虎斑地鸫（Zoothera dauma）、紫啸鸫（Myophonus caeruleus）、普通（Sitta europaea）、黄腹山雀（Parus venustulus）、斑胸钩嘴鹛（Pomatorhinus gravivox）、画眉（Garrulax canorus）等10个种类为保护区新记录种。首次在该保护区拍摄到国家Ⅰ级重点保护动物——豹（Panthera pardus）和林麝（Moschus berezovskii）,以及国家Ⅱ级重点保护动物猕猴（Macaques mulatta）、黄喉貂（Martes flavigula）、勺鸡（Pucrasia macrolopha）、红腹锦鸡和灰林鸮。兽类以猪獾（Arctonyx collaris）的相对丰富度指数最高为4.57;鸟类以红腹锦鸡的相对丰富度指数最高为2.03。调查结果显示保护区仍保存较为完整的大中型兽类群落,但顶级捕食者数量稀少,应加大对其栖息地及猎物的保护恢复力度。此外,相机拍摄到大量放牧活动照片,说明当地人为干扰严重,应加强管理。本次调查初步掌握了太行山猕猴国家级自然保护区（济源）内兽类和地栖性鸟类的资源现状,为保护区开展红外相机野生动物长期监测积累了基础资料。     

Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species

Coturnix chinensis (blue-breasted quail) has been classically grouped in Galliformes Phasianidae Coturnix, based on morphologic features and biochemical evidence. Since the blue-breasted quail has the smallest body size among the species of Galliformes, in addition to a short generation time and an excellent reproductive performance, it is a possible model fowl for breeding and physiological studies of the Coturnix japonica (Japanese quail) and Gallus gallus domesticus (chicken), which are classified in the same family as blue-breasted quail. However, since its phylogenetic position in the family Phasianidae has not been determined conclusively, the sequence of the entire blue-breasted quail mitochondria (mt) genome was obtained to provide genetic information for phylogenetic analysis in the present study. The blue-breasted quail mtDNA was found to be a circular DNA of 16,687 base pairs (bp) with the same genomic structure as the mtDNAs of Japanese quail and chicken, though it is smaller than Japanese quail and chicken mtDNAs by 10 bp and 88 bp, respectively. The sequence identity of all mitochondrial genes, including those for 12S and 16S ribosomal RNAs, between blue-breasted quail and Japanese quail ranged from 84.5% to 93.5%; between blue-breasted quail and chicken, sequence identity ranged from 78.0% to 89.6%. In order to obtain information on the phylogenetic position of blue-breasted quail in Galliformes Phasianidae, the 2,184 bp sequence comprising NADH dehydrogenase subunit 2 and cytochrome b genes available for eight species in Galliformes [Japanese quail, chicken, Gallus varius (green junglefowl), Bambusicola thoracica (Chinese bamboo partridge), Pavo cristatus (Indian peafowl), Perdix perdix (gray partridge), Phasianus colchicus (ring-neck pheasant), and Tympanchus phasianellus (sharp-tailed grouse)] together with that of Aythya americana (redhead) were examined using a maximum likelihood (ML) method. The ML analyses on the first/second codon positions, the third codon positions, and amino acid sequence consistently demonstrated that blue-breasted quail and Japanese quail are in the same phylogenetic cluster.     

勺鸡的生态研究

1984－1990年作者在安徽大别山北坡对勺鸡安徽亚种进行了系统观察,本文就其栖息地,垂直分布,活动规律,食性,繁殖习性及数量等报道于下。     

Induction of cytochrome P4501A by highly purified hexachlorobenzene in primary cultures of ring-necked pheasant and Japanese quail embryo hepatocytes

Primary cultures of ring-necked pheasant (Phasianus colchicus) and Japanese quail (Coturnix japonica) embryo hepatocytes were used to compare the potencies of highly purified hexachlorobenzne (HCB-P), reagent-grade HCB (RG-HCB) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) as inducers of ethoxyresorufin O-deethylase (EROD) activity, cytochrome P4501A (CYP1A4) messenger ribonucleic acid (mRNA) and CYP1A5 mRNA. HCB-P, RG-HCB and TCDD all induced EROD activity and up-regulated CYP1A4 and CYP1A5 mRNA. Induction was not caused by contamination of HCB with polychlorinated dibenzo-p-dioxins, dibenzofurans or biphenyls. Based upon a comparison of the EC(50) and EC(threshold) values for EROD and CYP1A4/5 concentration-response curves, the potency of HCB relative to TCDD was 0.001 in ring-necked pheasant and 0.01 in Japanese quail embryo hepatocytes. Differences in species sensitivity to HCB were found to be mainly dictated by differences in species sensitivity to TCDD rather than differences in the absolute potency of HCB. Consequently, ring-necked pheasant and Japanese quail embryo hepatocytes were found to be equally sensitive to HCB exposure. Species sensitivity comparisons were also made with chicken (Gallus gallus domesticus) and revealed that chicken embryo hepatocytes were less responsive to EROD induction (lower maximal response) by HCB compared to the embryo hepatocytes of pheasant and quail.     

The mitochondrial genome of Cygnus columbianus, the Whistling Swan.

The nucleotide sequence of the mitochondrial genome of the Whistling Swan, Cygnus columbianus, is reported. Many of the features common to avian mitochondrial genomes are present in C. columbianus and are described here. The gene order is the same as in Gallus gallus. The sequence of this mitochondrial genome allows relationships within the family Anatidae (swans, geese and ducks) to be reconsidered in the light of a large suite of mitochondrial characters. Protein-coding gene sequences of C. columbianus were concatenated to form a supergene, which was analyzed phylogenetically with similar constructs from previously published avian genomes. Relationships within Anatidae and between the Anatidae and the galliform birds were addressed. Three independent phylogenetic methods confirmed traditional classifications and the existence of the Galloanseres clade.     

Polymorphic microsatellites developed by cross-species amplifications in common pheasant breeds

Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross-species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty-six primers (25 specific for chicken and 11 for turkey) amplified pheasant DNA. Fifteen markers yielded specific products and were tested for polymorphism. Eight of them (55%) were polymorphic, with an average polymorphism of two alleles per locus. Specific polymerase chain reaction (PCR) products were sequenced; repeats were found in 11 of the 15 markers, although only two loci showed the same repeat and could be homologous to chicken ones.     

Metagenomics analysis of the fecal microbiota in Ring-necked pheasants (Phasianus colchicus) and Green pheasants (Phasianus versicolor) using next generation sequencing

Pheasant reintroduction and conservation efforts have been in place in Pakistan since the 1980 s, yet there is still a scarcity of data on pheasant microbiome and zoonosis. Instead of growing vast numbers of bacteria in the laboratory, to investigate the fecal microbiome, pheasants (green and ring neck pheasant) were analyzed using 16S rRNA metagenomics and using IonS5TMXL sequencing from two flocks more than 10 birds. Operational taxonomic unit (OTU) cluster analysis and phylogenetic tree analysis was performed using Mothur software against the SSUrRNA database of SILVA and the MUSCLE (Version 3.8.31) software. Results of the analysis showed that firmicutes were the most abundant phylum among the top ten phyla, in both pheasant species, followed by other phyla such as actinobacteria and proteobacteria in ring necked pheasant and bacteroidetes in green necked pheasant. Bacillus was the most relatively abundant genus in both pheasants followed by Oceanobacillus and Teribacillus for ring necked pheasant and Lactobacillus for green necked pheasant. Because of their well-known beneficial characteristics, these genus warrants special attention. Bird droppings comprise germs from the urinary system, gut, and reproductive sites, making it difficult to research each anatomical site at the same time. We conclude that metagenomic analysis and classification provides baseline information of the pheasant fecal microbiome that plays a role in disease and health.