Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates

Vascular endothelial growth factor (VEGF), known to play an important role in vascular homeostasis, vascular integrity and angiogenesis, is little known about the evolutionary relationship of its five members especially the role of gene duplication and natural selection in the evolution of the VEGF family. In this study, seventy-five full-length cDNA sequences from 33 vertebrate species were extracted from the NCBI's GenBank, UniProt protein database and the Ensembl database. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the VEGFs. Five VEGF family members in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain the relationship of the site-specific evolution in the vertebrate VEGF family. Eleven positive selection sites, one transmembrane region and the active sites were detected in this process.     

卡拉麦里山自然保护区蒙古野驴的食性

蒙古野驴(Equus hemionus hemionus),国家一级保护动物.由于人类活动的加剧,分布范围缩小,加之过度狩猎,目前已处于濒危状态.     

Validating Aerial Photographic Mark-Recapture for Naturally Marked Feral Horses

ABSTRACT Accurately estimating large mammal populations is a difficult challenge because species of interest often occupy vast areas and exhibit low and heterogeneous visibility. Population estimation techniques using aerial surveys and statistical design and analysis methods provide a means for meeting this challenge, yet they have only rarely been validated because wild populations of known size suitable for field tests are rare. Our study presents field validations of a photographic aerial mark-recapture technique that takes advantage of the recognizable natural markings on free-roaming feral horses (Equus caballus) to accurately identify individual animals and groups of animals sighted on multiple occasions. The 3 small populations of feral horses (<400 animals each) in the western United States used in the study were all closely monitored on a weekly basis by local researchers, thus providing test populations of known size. We were able to accurately estimate these population sizes with aerial surveys, despite rugged terrain and dense vegetation that created substantial heterogeneity of sighting probability among horse groups. Our best estimates at the 3 sites were within −6.7%, 2.6%, and −8.6% of known truth (-4.2% mean error, 6.0% mean absolute error). In contrast, we found undercount bias as large as 32% before any statistical corrections. The necessary corrections varied both temporally and spatially, in response to previous sighting history (behavioral response), and by the number of horses in a group. Despite modeling some of the differences in horse-group visibility with sighting covariates, we found substantial residual unmodeled heterogeneity that contributed to underestimation of the true population by as much as 22.7% when we used models that did not fully account for these unmeasured sources. We also found that the cost of the accurate and validated methods presented here is comparable to that of raw count (so called, census) methods commonly employed across feral horse ranges in 10 western states. We believe this technique can assist managers in accurately estimating many feral horse populations and could be applied to other species with sufficiently diverse and distinguishable visible markings.     

Asian horses deepen the MSY phylogeny

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y‐chromosomal phylogeny of modern horses based on 1.46 Mb of the male‐specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.     

Diversity of rickettsial pathogens in Columbian black‐tailed deer and their associated keds (Diptera: Hippoboscidae) and ticks (Acari: Ixodidae)

Cervids host multiple species of ixodid ticks, other ectoparasites, and a variety of rickettsiae. However, diagnostic test cross‐reactivity has precluded understanding the specific role of deer in rickettsial ecology. In our survey of 128 Columbian black‐tailed deer (Odocoileus hemionus columbianus (Richardson)) and their arthropod parasites from two northern Californian herds, combined with reports from the literature, we identified four distinct Anaplasma spp. and one Ehrlichia species. Two keds, Lipoptena depressa (Say) and Neolipoptena ferrisi Bequaert, and two ixodid ticks, Ixodes pacificus Cooley and Kohls and Dermacentor occidentalis Marx, were removed from deer. One D. occidentalis was PCR‐positive for E. chaffeensis; because it was also PCR‐positive for Anaplasma sp., this is an Anaplasma/Ehrlichia co‐infection prevalence of 4.3%. 29% of L. depressa, 23% of D. occidentalis, and 14% of deer were PCR‐positive for Anaplasma spp. DNA sequencing confirmed A. bovis and A. ovis infections in D. occidentalis, A. odocoilei in deer and keds, and Anaplasma phagocytophilum strain WI‐1 in keds and deer. This is the first report of Anaplasma spp. in a North America deer ked, and begs the question whether L. depressa may be a competent vector of Anaplasma spp. or merely acquire such bacteria while feeding on rickettsemic deer.     

Ancient latitudinal gradients of C3/C4 grasses interpreted from stable isotopes of New World Pleistocene horse (Equus) teeth

Carbon and oxygen isotopic data are reported from 116 Pleistocene Equus teeth from sixty-six localities in the New World ranging from 68°N (Alaska, Canada) to 35°S (Argentina). Equus species have been predominantly grazers, and as such, carbon isotopic values of their tooth enamel provide evidence of the Pleistocene distribution of C₃ and C₄ grasses. The carbon data presented here indicate a gradient (δ¹³C range of 10 parts/mil) in the relative proportion of C₃ and C₄ grasses between high latitude and equatorial Equus samples. The largest amount of change from C₃ to C₄ grasses during the Pleistocene occurred in the mid-latitudes between about 30 to 40°. The oxygen data, which vary proportionately with temperature, indicate a latitudinal gradient (δ¹⁸O range of 20 parts/mil) between high-latitude and equatorial Equus samples. The basic pattern of latitudinal gradients of C₃/C₄ grass distribution and temperature as interpreted from these Pleistocene data is similar to the modern-day. The use of stable isotopes of fossil herbivore teeth represents a new means to interpret Pleistocene climates and terrestrial ecology.