基于生物信息学对部分鸡形目鸟类系统发生关系的研究

本研究从GenBank下载了31种鸡形目鸟类、2种雁形目鸟类、1种戴胜目鸟类、1种佛法僧目鸟类和1种犀鸟目鸟类的线粒体16SrRNA基因的部分序列。经比对后序列长度为1384bp,其中有400个变异位点。A+T平均含量为54.2%,C+G平均含量为45.8%。贝叶斯系统发生分析揭示出鸡形目和雁形目分别形成单系。研究表明:(1)珠鸡科是鸡形目中较为原始的一个类群;(2)传统分类中的雉亚科和鹑亚科并非分别形成单系;(3)吐绶鸡科和松鸡科与雉科的亲缘关系较近;(4)孔雀属、Francolinus和Bambusicola之间的亲缘关系较近;山鹑属与多个雉亚科的亲缘关系较近;(5)雉科内各个属的属内分化主要发生于后中新世-更新世期间。     

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.     

雪鸡属分类地位探讨

以5种鸡形目鸟类,包括4个藏雪鸡Tetraogallus tibetanus、12个喜玛拉雅雪鸡T.himalayensis、1个阿尔泰雪鸡T.altaicus、1个石鸡Alectoris chuckar和1个斑翅山鹑Perdix dauurica为材料.通过P(永扩增线粒体细胞色素6基因513个碱基,同时从GenBank下载25种鸡形目鸟类细胞色素b基因序列.通过对鸡形目24个属线粒体细胞色素b基因序列的分析,结果表明共有214个变异位点,简约信息位点184个.以鸿雁 Anser cygnoides为外群,在运用不同分析方法得到的拓扑结构基础上,构建了最大简约树(MP)和最大似然树(ML),结果表明鸡形目鸟类鹑族和雉族基本上是多系发生的.结合分子钟和遗传信息分析,可以得出雪鸡属在鹑族中形成的时间相对较晚,约在14.6Myr出现石鸡属的祖先种群;而在约12.6Myr属和鹌鹑属开始出现.雪鸡属的祖先足起源于低海拔环境,后来伴随着青藏高原的逐渐降起和更新世冰期事件的发生各自演化形成现今各个种.     

世界鸡形目鸟类

介绍了世界上鸡形目鸟类的分布、分类、形态特点、栖地类型及生活习性。世界鸡形目鸟类分为７个科,共计２８１种。中国鸡形目鸟类包括松鸡科８种和雉科５２种。介绍了中国鸡形目鸟类种的分类等方面的一些最新进展。     

从c-mos和12S rRNA基因序列探讨现生鸟类早期历史和三趾鹑类的系统地位

通常认为古腭型鸟类处在现生鸟类系统进化树的基部,最近的分子水平研究则认为今腭型鸟类中雀形目种类构成了现生鸟类中一个最古老的支系.本研究通过对现生鸟类中21目39种核c-mos基因和线粒体12S rRNA基因部分序列的分析,从分子角度对现生鸟类的早期进化及三趾鹑鸟类的系统发生进行了探讨.研究结果表明,鸡雁类是现生鸟类最古老的一个支系,现生鸟类的祖先并不是经白垩纪到第三纪大灭绝后残留下来的一些过渡性水鸟(transitional shorebirds).在现生鸟类中,今腭型鸟类为并系发生,古腭型鸟类为单系发生.三趾鹑类在系统发生中晚于鸡雁类和古腭型鸟类,早于今腭型鸟类中非鸡雁类鸟类与鹤形目鸟类的亲缘关系较远.建议将现生鸟类分为初鸟下纲和新鸟下纲2个下纲,三趾鹑类属新鸟下纲的三趾鹑目(Turniciformes).     

信息与动态

[本刊讯]据中国动物学会鸟类学分会秘书处消息,今年10月,“中国动物学会鸟类学分会第九届学术研讨会”和“第四届国际鸡形目鸟类学术研讨会”(World Pheasant Association)将相继在四川召开。第四届国际鸡形目鸟类学术研讨会由世界雉类协会、IUCN雉类专家组、鹑类专家组主办,中     

石鸡属鸟类研究现状

石鸡属(Alectoris,Kaup 1829)鸟类隶属鸟纲,鸡形目(Galliformes),雉科(Phasianidae),全世界共有7种石鸡属鸟类。综合分类、生理生化、生态学、系统地理学和遗传学等方面的内容对石鸡属鸟类的研究历史进行了回顾和总结,侧重介绍了我国学者在石鸡属鸟类方面的研究。提出了石鸡属鸟类今后研究的方向。     

以mtDNA细胞色素b基因探讨斑翅山鹑的分类地位

以线粒体DNA细胞色素b(mtDNA Cytb)基因作为分子标记,提取鸡形目雉科10个属18个样本的DNA,PCR扩增自动测序,获得序列长度828bp。将山鹑属中的斑翅山鹑(Perdix dauuricae)与其近缘属排序对比,分别以角叫鸭(Anhima cornuta)和海龟(Kachuga dhongoka)为外群,用邻接法、最大简约法和最小进化法构建分子系统发生树。邻接法构建的系统树显示斑翅山鹑与雉聚类,核苷酸序列差异值斑翅山鹑与环颈雉为15．2％,与石鸡为16．1％。分析认为在雉科中斑翅山鹑与雉类更接近,而与真正的鹑亲缘关系较远。同时以mtDNA分析鸟类系统发生时海龟更适合作为外群。以角叫鸭为外群加入西方松鸡(Tetrao urogallus)时,则斑翅山鹑的分类地位不能确定,这可能与鸡形目的适应辐射有关。     

四川卧龙国家级自然保护区三种高山同域鸡形目鸟类的时空生态位比较

高海拔山区气候条件恶劣, 资源匮乏, 探究同域分布的近缘物种如何利用有限的资源以实现稳定共存, 对于了解高山生态系统生物多样性格局的形成和维持机制具有重要意义。鸡形目鸟类飞行能力弱, 属于典型的地栖物种, 生态位空间相对狭窄, 可能面临更高的种间竞争压力。本研究旨在比较几种同域分布的鸡形目鸟类的时空生态位, 为了解高山生态系统同域物种的共存机制提供新的研究案例。2020年4-9月, 研究人员在四川卧龙国家级自然保护区海拔3,300-4,200 m的高山区域进行了野外调查, 通过样线法和样方法对鸡形目鸟类群落优势物种绿尾虹雉(Lophophorus lhuysii)、雉鹑(Tetraophasis obscurus)和雪鹑(Lerwa lerwa)繁殖期的微生境进行调查, 使用红外相机对其活动节律进行监测, 并运用核密度估计法从微生境利用和日活动节律两个生态维度进行了种间生态位比较。结果显示, 雪鹑在微生境利用和日活动节律上均与其他两个物种存在显著差异。绿尾虹雉与雉鹑在微生境的利用上具有相似偏好; 但绿尾虹雉的早活动高峰晚于雉鹑, 晚活动高峰早于雉鹑, 表现出显著的种间日活动节律差异; 然而, 整合两个维度后, 绿尾虹雉和雉鹑的整体生态位仍然高度重叠, 没有显著分化。本研究表明高山鸡形目物种间的生态位分化体现于多个不同的生态维度, 并且不同物种之间的分化方式有所差异。在空间和时间生态位上的显著分化使雪鹑与同域物种间的竞争压力相对较小, 有利于其实现稳定共存。而绿尾虹雉与雉鹑的整体生态位高度重叠, 建议进一步对其食性开展研究, 探讨营养生态位上的潜在种间分化。     

白眉山鹧鸪在福建的分布

白眉山鹧鸪(Arborophila gingica),以往曾称为白额山鹧鸪[1,2],属鸡形目(Galliformes)雉科(Phasianidae),为我国南方山地特有鹑族(Perdicini)鸟类,被视为全球易危物种(VU)[3～5].     

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.     

<Emphasis Type="Italic">Gallus gallus</Emphasis> aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups

Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGC1) for phylogenetic analysis of the main groups of Galliformes including Phasianidae, Numididae, and Odontophoridae. We also included species from Cracidae and Megapodiidae which are considered by some as Craciformes and others, including here as Galliformes. The uncorrected sequence divergence of the G3 fragments ranges from 1 among the grouses to 36% between some of the distant groups within Galliformes. These sequences contain 39–48% AT nucleotides and the ratios of transition versus transversion are above 1.5 in majority of the comparisons. Using G3 sequences from an Anseriform, Oxyura jamaicensis, as out-groups, phylogenetic trees were obtained using maximum parsimony and distance algorithms and bootstrap analyses. These trees were consistent with those described using Avian sarcoma and leucosis virus gag genes and those from amino acid sequences of hemoglobin and lysozyme c. Our data also support relationships among Galliformes which were defined using mtDNA sequences. In addition to the general support of the five main families of Galliformes, our data are also consistent with previous work that showed Francolinus africanus and Gallus gallus are in the same clade and that Tetraoninae is a well-supported monophyletic subfamily within Phasianidae. The results presented here suggest that the AGC1 sequences meet the criterion of novel nuclear DNA sequences that can be used to help resolve the relationships among Galliformes.     

Complete mitochondrial genome of ring-necked pheasant Phasianus colchicus alaschanicus from China's Helan Mountains and description of its phylogenetic relationships in Galliformes

Phasianus colchicus alaschanicus, Phasianidae, Galliformes is known only from the Helan Mountains of Ningxia and Inner Mongolia Autonomous Regions, China. Due to few studies on this subspecies, the taxonomic status of Phasianus colchicus alaschanicus in Galliformes is unclear. We sequenced the mitochondrial genome of one P. c. alaschanicus and downloaded 36 species of 22 genera from GeneBank to construct a phylogenetic tree based on the Maximum Likelihood (ML) method. The mitochondrial genome sequence length of P. c. alaschanicus was 16,688 bp with a base composition of 30.6% A, 25.3% T, 30.8% C, and 13.3% G, including two rRNA genes (12S rRNA, 16S rRNA), 22 tRNA genes, 13 protein-coding genes, and a control region. We confirmed the genetic classification status of P. c. alaschanicus in Galliformes. The Phasianidae formed a complex clade, which could be separated into eighteen lineages. P. c. alaschanicus was a sister group of the remaining taxa (posterior probabilities 100% in ML).     

Phylogenetic position of the genus Tetraophasis (Aves, Galliformes, Phasianidae) as inferred from mitochondrial and nuclear sequences

The genus Tetraophasis is endemic to China and the systematic relationships of the genus in Phasianidae based solely on their morphology are not clear. The phylogenetic position of this genus and other genera in Phasianidae was investigated in this study using the mitochondrial genes cytochrome b (CYT B), NADH dehydrogenase subunit 2 (ND2) and nuclear ovomucoid intron G (OVO-G). Maximum parsimony, Bayesian and maximum likelihood analyses were employed. Comparison between the mitochondrial and nuclear findings suggested that our final combined data had higher resolving power than the separate data. Both separate data and combined data yielded a sister relationship between Tetraophasis and Lophophorus with strong support, which provided new evidence that pheasants and partridges were not monophyletic. In addition, our results indicated a basal position of Ithaginis, but the position of Perdix and Pucrasia were still unresolved. The result of this study provided a phylogenetic background for a revised classification of Galliformes.     

Identification of CR1 retroposons in Arborophila rufipectus and their application to Phasianidae phylogeny

Chicken repeat 1 (CR1), a member of non‐LTR retroposon, is an important phylogenetic marker in avian systematics. In this study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254 966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined data set comprising of 22 CR1 loci, mitochondrial genomes and eight unlinked introns was analysed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.     

Amino acid sequences of hemoglobin from guinea fowl (Numida meleagri) and California quail (Lophortyx californica) with phylogenetic analysis of major groups of Galliformes

We determined the complete amino acid sequences of the hemoglobin of two species, guinea fowl and California quail, in Galliformes from intact globin chain and chemical cleavage fragments in order to analyze the molecular evolution of hemoglobin for the classification of Galliformes. Galliformes have two types of hemoglobin components, HbA and HbD, which consist of identical chain and different chains. The sequences are similar to globin chains of Galliformes reported previously. These sequences were compared with those of other Galliformes (Phasianidae, Meleagrididae) using duck and goshawk as out-groups. The phylogenetic tree of major groups of Galliformes based on hemoglobin was similar to the tree model produced based on the amino acid sequence of lysozyme c.     

Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes

The avian subfamily Tetraoninae (grouse and ptarmigan) is a Holarctic group in the order Galliformes distinguished by morphological adaptations to cold environments and behavioral traits associated with elaborate courtship. Here we investigate the relationships of 17 tetraonines and 12 other galliform species using mitochondrial 12S and ND2 sequence data. We found support for the recent phylogenetic classification that separates the genus Dendragapus into two genera, Falcipennis and Dendragapus. In addition, we found support for a tetraonine clade in which the first divergence is between Bonasa umbellus and all others, followed by divergence between a Bonasa bonasia/Bonasa sewerzowi clade and the remaining tetraonines. Falcipennis canadensis is sister to a clade with four Tetrao species, and the genus Centrocercus is sister to a Dendragapus obscurus/Tympanuchus clade. Our data indicate a basal position for Cracidae and Megapodiidae among the five recognized galliform families. We also found strong support for the monophyly of Phasianidae, although the relative positions of Numididae and Odontiphoridae remains unresolved. We use a maximum likelihood approach to infer ages of 37mya for divergence of Numididae and Phasianidae and 28mya for the divergence of Tetraoninae and Meleagris gallopavo. These estimates must be viewed as tentative as they depend on tests of rates of molecular evolution and accurate fossil dates.     

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.