Analysis of bovidae genomes: Arrangement of repeated and single copy DNA sequences in bovine,goat and sheep

Approximately 43–60% of the total genome in bovine, goat and sheep consisted of interspersed repeated and single copy DNA sequences. Most of the interspersed repeated DNA sequences were 1500–2400 nucleotide pair long while a minor portion was more than 4000 nucleotide pair long in goat and sheep and 3200 nucleotide pair long in bovine. About 1/3rd of single copy sequence were interspersed and their length was in the range of 1000–1500 nucleotide pairs.     

Nestling coloration is adjusted to parent visual performance in altricial birds irrespective of assumptions on vision system for Laniidae and owls,a reply to Renoult et al.

We have recently published support to the hypothesis that visual systems of parents could affect nestling detectability and, consequently, influences the evolution of nestling colour designs in altricial birds. We provided comparative evidence of an adjustment of nestling colour designs to the visual system of parents that we have found in a comparative study on 22 altricial bird species. In this issue, however, Renoult et al. ( J. Evol. Biol., 2009 ) question some of the assumptions and statistical approaches in our study. Their argumentation relied on two major points: (1) an incorrect assignment of vision system to four out of 22 sampled species in our study; and (2) the use of an incorrect approach for phylogenetic correction of the predicted associations. Here, we discuss in detail re‐assignation of vision systems in that study and propose alternative interpretation for current knowledge on spectrophotometric data of avian pigments. We reanalysed the data by using phylogenetic generalized least squares analyses that account for the alluded limitations of phylogenetically independent contrasts and, in accordance with the hypothesis, confirmed a significant influence of parental visual system on gape coloration. Our results proved to be robust to the assumptions on visual system evolution for Laniidae and nocturnal owls that Renoult et al. ( J. Evol. Biol., 2009 ) study suggested may have flawed our early findings. Thus, the hypothesis that selection has resulted in increased detectability of nestling by adjusting gape coloration to parental visual systems is currently supported by our comparative data.     

A new antelope from Gabon

A new subspecies Cephalophus ogilbyi crusalbum , of Ogilby's duiker, is described from Gabon. It is the only duiker with white legs and is isolated from previously described subspecies of C. ogilbyi.     

“On the Windy Edge of Nothing”: A Historical Human Ecology of the Faroe Islands

In the context of the North Atlantic arena, the histories and landscape evolution of the Faroe Islands are comparatively less known. The position of the archipelago astride cyclonic tracks and the predominantly rugged terrain with meagre woodland and limited high quality agricultural land, conspired to produce an environment which might be thought to have severely challenged early colonizers. Those settlers, whether Norse/Vikings, or earlier Irish monks, had access to the vital resources of bird cliffs, rivers, and the sea to supplement the produce of their domestic animals and crops. The lack of apparent crises is a function both of the richness of the resources provided by the Faroe Islands, and of the development of appropriate land management practices such as outfield grazing and soil augmentation to counteract any detrimental effects arising from, for instance, reductions in the bird population, soil and slope erosion, the lack of naturally fertile soils, and any climatic downturn. From the research contained within this volume, it seems likely that there have always been sufficient resources available for an enterprising human population and that the Faroes did not exceed their carrying capacity during the Norse period.     

Phylogenetic analysis of the tribe Bovini (Mammalia: Artiodactyla)

A matrix of 57 (mainly cranial) characters and 32 taxa of fossil and Recent Bovini (buffaloes, bison and cattle) has been analysed using the parsimony program HENNIG86. Among the best established results are the exclusion of Parabos , polyphyly of Leptobos , monophyly of the Bos sensu lato + buffaloes group (a clade including all Recent Bovini), probable monophyly of the Bubalina and Syncerina, and the close relationship between bison and yak. Some other interesting questions raised include the apparent absence of a close link between Pliocene African bovines (except Leptobos syrticus ) and later African buffaloes, and the possible monophyly of Pelorovis oldowayensis+Bos sensu lato .     

牛科动物HSL基因序列分析及其分子进化研究

在对牛科中4种动物即牦牛、瘤牛、普通牛和水牛HSL基因外显子Ⅰ部分核苷酸序列进行测定的基础上,与Gen-Bank中其他物种相应基因核苷酸序列、氨基酸序列进行了比对分析,并构建了牦牛与其他物种间分子系统进化树。结果表明:牦牛与普通牛、瘤牛、水牛、猪、人、小鼠、大鼠7个物种HSL基因外显子Ⅰ部分核苷酸序列间保守性较高,同源性大小依次为99.8%、99.6%、97.4%、90.6%、88.4%、83.5%、82.3%。相应氨基酸序列间保守性更高,同源性分别为100%、100%、98.2%、94.0%、92.2%、89.8%、89.8%。牦牛与各物种该基因部分核苷酸序列间碱基变异类型主要表现为碱基转换和颠换,无碱基插入和缺失发生,碱基转换的频率高于颠换的频率;在核苷酸水平上的多数碱基替换都是同义替换;序列间单碱基变异位点大多出现在同一位点,多发生在密码子第3位,其次是第1位,最少发生在第2位,符合分子进化的中性学说。HSL基因外显子Ⅰ部分核苷酸序列进行多序列对位排列构建的各物种间分子系统进化树结果表明,普通牛和瘤牛首先聚为一类,再分别与牦牛、水牛、猪、人聚类,最后与大鼠、小鼠聚为一类。该聚类结果与动物学上的分类结果一致,表明HSL基因外显子Ⅰ部分核苷酸序列适合于构建物种间分子系统进化树。研究表明,牦牛、普通牛和瘤牛3个物种间的遗传距离大小相近,牦牛和水牛间的遗传距离与普通牛、瘤牛和水牛间的遗传距离大小相当。牦牛、普通牛和瘤牛3个物种间的遗传距离远小于它们各自与水牛这一物种的遗传距离,它们三者之间的亲缘关系也相对于它们各自与水牛间的亲缘关系都较近,故将牦牛、普通牛和瘤牛划分在同一个属——牛属(Bos)更为合理。     

羚牛生态生物学研究现状

羚牛是介于羊和牛之间分类地位特殊的偶蹄目牛科动物, 共有4 个亚种。中国是羚牛的主要分布区, 拥有世界上绝大多数的羚牛种群。有关羚牛的研究主要由中国的科研人员在中国境内完成。羚牛的生态生物学研究主要涉及到地理分布、种群数量、栖息地、季节性迁移活动、集群行为、家域、日活动规律、采食习性、繁殖和防御行为。对羚牛研究现状的综述性介绍即从这10 个方面进行。     

四川三例疑似偶蹄目动物的分子鉴定

测定了3例来自四川崇州的疑似偶蹄目动物样本细胞色素b基因(Cytb),利用NCBI数据库中的BLAST功能对目标序列进行相似性搜索,发现与所测序列相似性高的分别为偶蹄目鹿科毛冠鹿Elaphodu scephalophus和牛科台湾鬣羚Capricornis swinhoei;联合下载四川有分布偶蹄目动物4科19种以及1条台湾鬣羚Cytb基因序列进行系统发育关系重建分析,结果显示有两例待鉴定样本(4#、5#)以置信度值100与毛冠鹿聚在一起;另一例待鉴定样本(1#)对应序列和鬣羚Capricornis milneedwardii聚在一起后与台湾鬣羚形成姊妹关系,然后以置信度值100和斑羚Naemorhedus griseus又形成姊妹关系。因此,3例疑似偶蹄目动物有2例可能为毛冠鹿,1例可能为鬣羚;在MEGA4.0软件中以Kimura2-parameter模型计算2例疑似为毛冠鹿(4#、5#)的目标序列与GenBank上毛冠鹿及赤麂Mun-tiacus muntjak、小麂Muntiacus reevesi序列间的遗传距离,发现两例疑似为毛冠鹿个体间遗传距离为0,2例疑似为毛冠鹿样本序列和下载的毛冠鹿序列间的遗传距离小(0.017),和赤麂、小麂间遗传距离大(0.119～0.120、0.116～0.119);1例疑似鬣羚(1#)的样本和下载鬣羚序列间遗传距离很小(0.006～0.009),和台湾鬣羚的遗传距离较大(0.043),和斑羚遗传距离更大(0.098)。结合四川有分布偶蹄目状况,认为3例待鉴定样本2例可能为毛冠鹿,1例可能是鬣羚。     

Review of taxonomy,geographic distribution,and paleoenvironments of Azhdarchidae (Pterosauria)

The taxonomy, geographic distribution, and paleoenvironmental context of azhdarchid pterosaurs are reviewed. All purported pteranodontid, tapejarid, and azhdarchid specimens from the Cenomanian Kem Kem beds of Morocco are referred to a single azhdarchid taxon, Alanqa saharica. The four proposed autapomorphies of Eurazhdarcho langendorfensis from the lower Maastrichtian Sebeş Formation of Romania are based on misinterpretations of material and this taxon is likely a subjective junior synonym of Hatzegopteryx thambema. Among 54 currently reported azhdarchid occurrences (51 skeletal remains and 3 tracks) 13% are from lacustrine deposits, 17% from fluvial plain deposits, 17% from coastal plain deposits, 18% from estuarine and lagoonal deposits, and 35% from costal marine deposits. Azhdarchids likely inhabited a variety of environments, but were abundant near large lakes and rivers and most common in nearshore marine paleoenvironments.     

Mitochondrial DNA population structure of roan and sable antelope: implications for the translocation and conservation of the species

Mitochondrial DNA (mtDNA) control region sequences were analysed to determine the geographical genetic structure of Hippotragus niger (sable antelope) and H. equinus (roan antelope). Analyses by AMOVA, minimum evolution networks, parsimony, neighbour joining and maximum likelihood show that the roan antelope populations are geographically partitioned and that their phylogeography corresponds well with subspecific boundaries. In sharp contrast, however, our sequence data group all the sable antelope into two well-delineated maternal clades. One comprising specimens from the strictly east African H.n. roosevelti, and a second geographically diverse group which includes H.n. niger (South Africa, Zimbabwe), H.n. variani (Angola), and H.n. Kirkii (Zambia, Malawi). The differences in the genetic population structure suggest that distinct extrinsic and intrinsic factors have shaped the phylogeography of these two closely related antelope species. In the absence of obvious extrinsic barriers to gene flow, we suggest that behavioural differences may be responsible, at least in part, for the contrasting spatial patterns detected among geographical localities. Although our data reflect only the maternal phylogeny of these important game species, they nonetheless suggest that different management strategies should be applied. We recommend that roan antelope be translocated only within the currently defined subspecies boundaries, while in the case of sable antelope, conservation measures should focus on preserving the genetic integrity of the east African and southern African sable populations. Implicit in this is that translocations of animals between populations comprising these two distinct maternal genetic clades should be actively discouraged.     

Genetically solving a zoological mystery: was the kouprey (Bos sauveli) a feral hybrid?

A famous zoological discovery of the 20th century was that of the kouprey Bos sauveli , a medium-sized ox inhabiting Cambodian forests. The kouprey was suspiciously intermediate between banteng oxen and domestic zebu cattle in its structure. Mitochondrial DNA sequences of mainland banteng are compared here with a published kouprey sequence, and the comparison demonstrates a close relationship. Either the kouprey derives partly from banteng or (less likely) these particular banteng acquired kouprey DNA via recent genetic introgression. The kouprey may have been a feral hybrid form, a descendant of domestic oxen, rather than a natural species.