Towards robust evolutionary inference with integral projection models

Integral projection models (IPMs) are extremely flexible tools for ecological and evolutionary inference. IPMs track the distribution of phenotype in populations through time, using functions describing phenotype‐dependent development, inheritance, survival and fecundity. For evolutionary inference, two important features of any model are the ability to (i) characterize relationships among traits (including values of the same traits across ages) within individuals, and (ii) characterize similarity between individuals and their descendants. In IPM analyses, the former depends on regressions of observed trait values at each age on values at the previous age (development functions), and the latter on regressions of offspring values at birth on parent values as adults (inheritance functions). We show analytically that development functions, characterized this way, will typically underestimate covariances of trait values across ages, due to compounding of regression to the mean across projection steps. Similarly, we show that inheritance, characterized this way, is inconsistent with a modern understanding of inheritance, and underestimates the degree to which relatives are phenotypically similar. Additionally, we show that the use of a constant biometric inheritance function, particularly with a constant intercept, is incompatible with evolution. Consequently, current implementations of IPMs will predict little or no phenotypic evolution, purely as artefacts of their construction. We present alternative approaches to constructing development and inheritance functions, based on a quantitative genetic approach, and show analytically and through an empirical example on a population of bighorn sheep how they can potentially recover patterns that are critical to evolutionary inference.     

绵羊X染色体59383635位点多态性与脂尾性状的相关性分析

脂尾(臀)性状是绵羊逆境生存的必要性状, 其脂肪在尾臀部大量沉积的遗传特性与分子机制仍不明晰。为此, 文章以筛选的X染色体59383635位点SNP为候选分子标记, 利用PCR-SSCP技术检测该位点在我国尾型极端差异的阿勒泰羊、小尾寒羊、湖羊、中国美利奴细毛羊以及引入品种萨福克羊群体中的多态性, 并采用模型分析其与尾(臀)性状的相关性。结果表明, X染色体59383635位点T等位基因高频出现在表型分值较高的阿勒泰群体中, 而C等位基因则在瘦尾型绵羊品种中高频出现; 等位基因频率T/C的比值与尾臀表型分值相关性模型表明T/C比值随着尾臀表型分值增加呈指数倍增长。以上结果提示, 绵羊X染色体59383635位点多态性在脂尾(臀)与瘦尾绵羊群体中分布存在较大差异, 该SNP可作为一个理想的分子标记应用于高、低脂绵羊品种选育, 但其生物功能仍有待进一步深入研究。     

中国美利奴(新疆军垦型)绵羊9个微卫星基因座多态性研究

利用PCR技术和复合电泳银染技术检测中国美利奴(新疆军垦型)绵羊第1号染色体上BM6506,BM1824,BM6438, ILSTS004和OarDB6 等5个基因座和第6号染色体上 BM4621,OarHH55,BM143和OarJMP8 等4个基因座,共9个基因座的基因频率（Pi）、个体鉴别力（DP）、杂合度（H）、多态信息含量（PIC）、和非父排除概率（PE）。结果显示：9个微卫星基因座的基因型分布符合Hardy-Weinberg平衡,绵羊中9个微卫星基因座中BM4621 基因座的DP、H、PIC和PE都为最高。9个微卫星基因座的累积个体鉴别力(CDP)为0.99999,累积非父排除能力(CPE)为0.99915。结果显示9个微卫星基因座适用于中国美利奴(新疆军垦型)绵羊的遗传连锁分析、个体识别和亲权鉴定等研究领域。     

凉山半细毛羊1号染色体微卫星遗传连锁图谱的构建

实验选择绵羊1号条染色体上的9个微卫星标记,采用父系半同胞家系群体（共387个个体）构建凉山半细毛羊1号染色体遗传连锁图。建立的资源参考家系通过20个微卫星标记进行了系谱确证。试验结果表明,9个标记的等位基因数变化范围为5~15个,杂合度在0.202~0.831之间,平均杂合度为0.617,各标记的平均多态信息含量PIC=0.604。构建的凉山半细毛羊1号条染色体遗传连锁图总长度311.0 cM,与美国肉畜中心（USDA）和国际绵羊作图中心（IMF）构建的绵羊1号条染色遗传连锁图结果基本一致。可用于下一步的QTL定位研究。     

贺兰山保护区冬季岩羊集群特征的初步分析

Group size and composition of blue sheep （Pseudois nayaur) were studied in the Helan Mountains, Ningxia Autonomous Region from November to December 2003. We scanned mountain slopes with binoculars and observed with 20 - 60 x spotting-scope. A total of 310 herds of blue sheep and 1 336 individuals were observed during the study period. Blue sheep were frequently seen in small herds of 2 to 8 individuals, which represent 94.8% of total herds observed. Herds consisting of 9 individuals or more represented 5.2%. The largest herd we observed numbered 51 individuals. Mean group size was 4.2 individuals. Blue sheep herds can be divided into three types: male herds （composed solely of males), female herds (consisting of females with or without juveniles of both sexes), and mixed herds （including adult males, females, and subadults). Among the 310 herds, female herds were counted 150 times (48.4%}, mixed herds 154 times (49.7%), and male berds 6 times (1.9%) . Of 1 336 blue sheep classified by sex and age, adults, subadults and juveniles composed 64.1%, 20.8%, and 15.1% respectively. The female: male ratio of adults was 1:0.73. The ratio of adult females to juveniles was 1:0.56, which is higher than the ratio recorded in spring （ 1:0.43) or summer （ 1:0.44). The results showed that the Helan Mountains State Nature Reserve has succeed in protecting blue sheep.     

A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genome

Ovis aries chromosome one (OAR1) is the largest submetacentric chromosome in the sheep genome and is homologous to regions on human chromosomes 1, 2, 3 and 21. Using the USUoRH5000 ovine whole-genome radiation hybrid (RH) panel, we have constructed a RH map of OAR1 comprising 102 framework and 75 placed/binned markers across five linkage groups spanning 3759.43 cR5000, with an average marker density of 21.2 cR5000/marker. The alignment of our OAR1 RH map shows good concordance with the recently developed virtual sheep genome, with fewer than 1.86% discrepancies. A comparative map of OAR1 was constructed by examining the location of RH-mapped orthologues in sheep within the genomes of cow, human, horse and dog. Analysis of the comparative map indicates that conserved syntenies within the five ovine RH linkage groups underwent internal chromosomal rearrangements which, in general, reflect the evolutionary distances between sheep and each of these four species. The ovine RH map presented here integrates all available mapping data and includes new genomic information for ovine chromosome 1.     

Mining activity and habitat use by mountain sheep (<Emphasis Type="Italic">Ovis canadensis</Emphasis>)

We studied mountain sheep in the vicinity of three high-wall limestone mines in San Bernardino County, CA, USA to evaluate factors that influenced habitat use and, specifically, to investigate the influence of mining activity on distribution of those specialized ungulates. We used aerial telemetry data to estimate a resource selection function by fitting a logistic regression model and then comparing environmental characteristics at observed sheep locations to those at random locations. Distribution of mountain sheep was most influenced by a fire in 1999 that resulted in an area they avoided. Mountain sheep used steeper slopes, areas of lower terrain roughness, higher elevations, and areas closer to escape terrain than were random points. In contrast, sheep avoided areas near roads (federal and state highways, local roads, and off-road vehicle trails) but used areas near hiking trails and a railway. Water sources had the smallest effect of the factors considered, with sheep being associated with areas further from water points than were random locations. The disturbed area associated with the mines had a moderate influence on distribution, with sheep being associated with areas closer to the mine than were random points. Mining activities can alter terrain features and vegetation structure or composition in a way that promotes occupancy by sheep if they create steep slopes and rugged terrain (escape terrain) or reduce vegetation density or height (i.e., improve visibility). Whether increased occupancy reflects a benefit depends on the demographic responses of those sheep to the resources and conditions available on mine sites; information about those responses remains lacking.     

Assessment of Predictive Habitat Models for Bighorn Sheep in California's Peninsular Ranges

ABSTRACT We developed predictive habitat models for a bighorn sheep (Ovis Canadensis) population in the Peninsular Ranges of southern California, USA, using 2 Geographic Information System modeling techniques, Ecological Niche Factor Analysis (ENFA) and Genetic Algorithm for Rule-set Production (GARP). We used >16,000 Global Positioning System locations from 34 animals in 5 subpopulations to develop and test ENFA and GARP models, and we then compared these models to each other and to the expert-based model presented in the United States Fish and Wildlife Service's Recovery Plan for this population. Based on a suite of evaluation methods, we found both ENFA and GARP to provide useful predictions of habitat; however, models developed with GARP appeared to have higher predictive power. Habitat delineations resulting from GARP models were similar to the expert-based model, affirming that the expert-based model provided a useful delineation of bighorn sheep habitat in the Peninsular Ranges. In addition, all 3 models identified continuous bighorn sheep habitat from the northern to southern extent of our study area, indicating that the Recovery Plan's recommendation of maintaining habitat connectivity throughout the range is an appropriate goal.