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PubMed2003

Partitioned likelihood support and the evaluation of data set conflict.

In simultaneous analyses of multiple data partitions, the trees relevant when measuring support for a clade are the optimal tree, and the best tree lacking the clade (i.e., the most reasonable alternative). The parsimony-based method of partitioned branch support (PBS) "forces" each data set to arbitrate between the two relevant trees. This value is the amount each data set contributes to clade support in the combined analysis, and can be very different to support apparent in separate analyses. The approach used in PBS can also be employed in likelihood: a simultaneous analysis of all data retrieves the maximum likelihood tree, and the best tree without the clade of interest is also found. Each data set is fitted to the two trees and the log-likelihood difference calculated, giving "partitioned likelihood support" (PLS) for each data set. These calculations can be performed regardless of the complexity of the ML model adopted. The significance of PLS can be evaluated using a variety of resampling methods, such as the Kishino-Hasegawa test, the Shimodiara-Hasegawa test, or likelihood weights, although the appropriateness and assumptions of these tests remains debated.

Animals↗
PubMed1967

The serologic specificity of tropocollagen telopeptides.

Tropocollagen preparations from carp, buffalo fish, rats, calves, sheep, and humans have been studied by electron microscopy and serologic methods. Tropocollagens from each species appeared identical by electron microscopy but they were readily distinguished (except between sheep and calves) by C'-fixation tests with rabbit antisera against the various tropocollagens. Tests with calf tropocollagen antiserum showed no distinction between tropocollagen isolated from different tissues nor between individuals of the same or different strains. The major immunogenic sites in native tropocollagen are the telopeptides, and these are present on both alpha1- and alpha2-chains. The C'-fixing activity was lost with heat denaturation of the tropocollagen, but could be recovered in a concentration-dependent process on cooling. The fact that pure and enzyme-treated collagen can provoke serologic reaction implies that collagenous sutures and prostheses used in surgery may lead to sensitization and rejection, a fact which may merit clinical concern.

Animals↗
PubMed2004

Maternal dominance, maternal condition, and offspring sex ratio in ungulate mammals.

Trivers and Willard's suggestion that natural selection favors maternal control of offspring sex ratio in relation to maternal condition has been much debated. The theoretical plausibility of the idea, under some conditions, is firmly established, and there is strong empirical support for conditional sex allocation in some taxa. However, the extent to which this hypothesis can be applied to mammals, particularly ungulates, has been more controversial. We used meta-analysis to review published studies of the Trivers-Willard hypothesis within ungulates and to assess the overall level of empirical support for the hypothesis. Overall, data from 37 studies of 18 species suggested a weak but significant positive correlation between maternal condition and sex ratio (r=+0.09). However, average effect size differed markedly between different categories of studies. Studies using measures of maternal condition that were taken preconception and on the basis of behavioral dominance provided strong evidence for a relationship between maternal condition and the sex ratio (r=+0.17-0.25). In contrast, studies that used morphological or physiological measures of condition that were measured postconception provided little or no evidence for a relationship between maternal condition and sex ratio (r=+0.05-0.06). There are several reasons to suggest that data collected postconception and relying on morphological measures of condition are less likely to capture variables that cause selection for biased sex allocation. In addition, we found that the relationship between sex ratio and maternal condition depended on life-history characteristics; relationships were stronger when sexual size dimorphism was more male biased and when gestation periods were longer. Overall, our analyses suggest that data from ungulates are consistent with the Trivers-Willard hypothesis but only when appropriate measures are used.

Animals↗
PubMed2005

Ontogenetic patterns in heritable variation for body size: using random regression models in a wild ungulate population.

Body size is an important determinant of fitness in many organisms. While size will typically change over the lifetime of an individual, heritable components of phenotypic variance may also show ontogenetic variation. We estimated genetic (additive and maternal) and environmental covariance structures for a size trait (June weight) measured over the first 5 years of life in a natural population of bighorn sheep Ovis canadensis. We also assessed the utility of random regression models for estimating these structures. Additive genetic variance was found for June weight, with heritability increasing over ontogeny because of declining environmental variance. This pattern, mirrored at the phenotypic level, likely reflects viability selection acting on early size traits. Maternal genetic effects were significant at ages 0 and 1, having important evolutionary implications for early weight, but declined with age being negligible by age 2. Strong positive genetic correlations between age-specific traits suggest that selection on June weight at any age will likely induce positively correlated responses across ontogeny. Random regression modeling yielded similar results to traditional methods. However, by facilitating more efficient data use where phenotypic sampling is incomplete, random regression should allow better estimation of genetic (co)variances for size and growth traits in natural populations.

Aging↗
PubMedDate not supplied

Rabies in the kudu antelope (Tragelaphus strepsiceros).

An epizootic of rabies in the greater kudu (Tragelaphus strepsiceros) occurred in Namibia during 1977-1983. The virus strain involved in the epizootic proved to be identical to rabies strains found in infected dogs in many African countries. Such a sudden and large outbreak of rabies could not be explained on the basis of the etiologic agent. A thorough investigation into kudu characteristics revealed that the kudu population had increased disproportionally before the epizootic in response to favorable conditions. The social behavior of the kudu, i.e., group browsing on acacia trees, whose thorns cause lesions in the kudu's oral cavity, as well as the excretion of relatively high titers of virus in the saliva of infected animals provide suitable conditions for transmission in the kudu population after initial infection through the jackal or other species. These factors offer an explanation for this epizootic.

Animals↗
PubMed1997

Evolution of T-cell receptor gamma and delta constant region and other T-cell-related proteins in the human-rodent-artiodactyl triplet.

In this paper we report a detailed comparative and evolutionary analysis of the sequences of constant T-cell receptor (Tcr) C gamma delta genes of artiodactyls compared to the homologous sequences of rodents and primates. Because of the frequency and physiological distribution of gamma delta T-cells in different animals, rodents and humans are defined as "gamma delta low" species and ruminants as "gamma delta high" species. Such a characteristic seems to be due to an adaptive role of gamma delta T-cell function. By analyzing the ruminant gene phylogeny of Tcr C gamma we were able to estimate the distance between cattle and sheep at 18 million years ago, a time that is in agreement with other nonmolecular estimates. For Tcr C gamma delta genes a peculiar phylogenetic relationship was found, with human and mouse clustering together and leaving artiodactyls apart. By using appropriate outgroups, the same phylogenetic pattern was obtained with other T-cell related sequences: namely, Tcr C alpha chain, CD3 gamma and delta invariant subunits. Interleukin-2. Interleukin-2 receptor alpha chain and Interleukin-1 beta with the exception of Tcr C beta chain and Interleukin-1 alpha. In contrast, the analysis of all other T-cell nonrelated genes, available in primary databases reveals a different tree, where primates and artiodactyls are sister taxa and rodents are apart in accordance with the current view of mammalian phylogeny. These data are relevant to important evolutionary issues. They show how misleading a phylogeny based on a single or on a few homologous genes may be. In addition they demonstrate that genes with correlated functions may evolve in a lineage specific manner probably in relation to environmental conditions.

Amino Acid Sequence↗
PubMed2002

Vanishing GC-rich isochores in mammalian genomes.

To understand the origin and evolution of isochores-the peculiar spatial distribution of GC content within mammalian genomes-we analyzed the synonymous substitution pattern in coding sequences from closely related species in different mammalian orders. In primate and cetartiodactyls, GC-rich genes are undergoing a large excess of GC --> AT substitutions over AT --> GC substitutions: GC-rich isochores are slowly disappearing from the genome of these two mammalian orders. In rodents, our analyses suggest both a decrease in GC content of GC-rich isochores and an increase in GC-poor isochores, but more data will be necessary to assess the significance of this pattern. These observations question the conclusions of previous works that assumed that base composition was at equilibrium. Analysis of allele frequency in human polymorphism data, however, confirmed that in the GC-rich parts of the genome, GC alleles have a higher probability of fixation than AT alleles. This fixation bias appears not strong enough to overcome the large excess of GC --> AT mutations. Thus, whatever the evolutionary force (neutral or selective) at the origin of GC-rich isochores, this force is no longer effective in mammals. We propose a model based on the biased gene conversion hypothesis that accounts for the origin of GC-rich isochores in the ancestral amniote genome and for their decline in present-day mammals.

Alleles↗