The Social System of Lariang Tarsiers <Emphasis Type="Italic">(Tarsius lariang)</Emphasis> as Revealed by Genetic Analyses

Previous sociobiological studies of tarsiers were invariably based on field observations. Sulawesi tarsiers are known for monogamous or facultative polygynous social mating systems, but, to date, no data exist to describe the genetic mating system. We here bring together behavioral studies and molecular tools for the first time to elucidate mating behavior and kinship within a tarsier population. We investigated the social system of the recently described Tarsius lariang, which researchers have never studied before. Between September and November 2005, we conducted field observations and sampling in central Sulawesi, Indonesia, where this species is endemic. Ten of 11 social groups of the focal population were composed of 1 adult male, 1 adult female, and putative offspring. To enlighten genetic relationships, we used 12 microsatellite loci and mitochondrial DNA sequences of 26 captured and sampled Lariang tarsiers for parentage and relatedness analyses. A significant number of young were the offspring of the sampled group adults, suggesting a predominantly monogamous social and genetic mating system. There is evidence for extrapair young in groups in which adult pairs exhibit close relationships, leading to the assumption that extrapair mating is solicited to avoid inbreeding. Ten of 11 social groups lived in monogamous social systems, indicating monogamy to be the rule in Tarsius lariang.     

Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework

Inferring the parentage of a sample of individuals is often a prerequisite for many types of analysis in molecular ecology, evolutionary biology and quantitative genetics. In all but a few cases, the method of parentage assignment is divorced from the methods used to estimate the parameters of primary interest, such as mate choice or heritability. Here we present a Bayesian approach that simultaneously estimates the parentage of a sample of individuals and a wide range of population-level parameters in which we are interested. We show that joint estimation of parentage and population-level parameters increases the power of parentage assignment, reduces bias in parameter estimation, and accurately evaluates uncertainty in both. We illustrate the method by analysing a number of simulated test data sets, and through a re-analysis of parentage in the Seychelles warbler, Acrocephalus sechellensis. A combination of behavioural, spatial and genetic data are used in the analyses and, importantly, the method does not require strong prior information about the relationship between nongenetic data and parentage.     

Crown defoliation decreases reproduction and wood growth in a marginal European beech population

Background and AimsAbiotic and biotic stresses related to climate change have been associated with increased crown defoliation, decreased growth and a higher risk of mortality in many forest tree species, but the impact of stresses on tree reproduction and forest regeneration remains understudied. At the dry, warm margin of species distributions, flowering, pollination and seed maturation are expected to be affected by drought, late frost and other stresses, eventually resulting in reproduction failure. Moreover, inter-individual variation in reproductive performance versus other performance traits (growth, survival) could have important consequences for population dynamics. This study investigated the relationships among individual crown defoliation, growth and reproduction in a drought-prone population of European beech, Fagus sylvatica.MethodsWe used a spatially explicit mating model and marker-based parentage analyses to estimate effective female and male fecundities of 432 reproductive trees, which were also monitored for basal area increment and crown defoliation over 9 years.Key ResultsFemale and male fecundities varied markedly between individuals, more than did growth. Both female fecundity and growth decreased with increasing crown defoliation and competition, and increased with size. Moreover, the negative effect of defoliation on female fecundity was size-dependent, with a slower decline in female fecundity with increasing defoliation for the large individuals. Finally, a trade-off between growth and female fecundity was observed in response to defoliation: some large trees maintained significant female fecundity at the expense of reduced growth in response to defoliation, while some other defoliated trees maintained high growth at the expense of reduced female fecundity.ConclusionsOur results suggest that, while decreasing their growth, some large defoliated trees still contribute to reproduction through seed production and pollination. This non-coordinated decline of growth and fecundity at individual level in response to stress may compromise the evolution of stress-resistance traits at population level, and increase forest tree vulnerability.     

Challenges in assessing pathogenicity based on frequency of variants in mismatch repair genes: an extreme case of a MSH2 variant and a meta-analysis

The clinical interpretation of variants in mismatch repair (MMR) genes associated with Lynch syndrome can be confusing when the functional nature of the variant is not clearly defined. We report an extreme case where a polymorphism in the MSH2 gene which had a low minor allele frequency, was misclassified as a mutation based on low evidential methods in the database and previous publications. We expanded this experience to perform a systematic meta-analysis in order to investigate other variants that have potentially been misclassified. Our results suggested that the interpretation of pathogenicity should be more cautious and emphasized the need for solid validation through multiple analyses including functional analysis for variants in MMR genes.     

Isolation and characterization of microsatellite markers in red‐flanked bushrobin,Tarsiger cyanurus (Aves: Turdidae)

Microsatellite markers were isolated from red‐flanked bushrobin, Tarsiger cyanurus, for parentage analysis. From an enriched genomic library using the fast isolation by AFLP of sequences containing repeats (FIASCO) method, six polymorphic loci were obtained. Seven to 21 alleles were identified in an analysis of 19 red‐flanked bushrobin, with observed heterozygosity ranging from 0.842 to 1.00. All loci showed Hardy–Weinberg equilibrium and linkage equilibrium. Total exclusion probability using six loci was 0.998 for neither parent known, and 0.999 for one parent known. We also tested the utility of these loci on four species of Turdidae. Although one of the loci failed to amplify in any species, the other primers successfully amplified in at least two of the species we tested.     

Renal bioaccumulation of trace elements in urban and rural Sri Lankan populations: A preliminary study based on post mortem tissue analysis

IntroductionEnvironmental pollution, especially by toxic trace elements, is a global health concern. Heavy metals such as Cadmium (Cd), Arsenic (As) and Lead (Pb) are associated with numerous disorders and are considered by some as an aetiological factor for the Chronic Kidney Disease (CKDu¹) epidemic in Sri Lanka. This study explores patterns of bioaccumulation of six trace elements in kidneys obtained during forensic autopsies from urban and rural regions in Sri Lanka.MethodsKidney samples obtained from one urban district (n = 13) and three rural districts (n = 18) were lyophilized, microwave digested and profiled by ICP-MS techniques.Results and DiscussionThe mean age of the sampled population was 47.9 ± 11.3 yrs. Median (IQR) for Cd, As, Pb, Cr, Zn and Se were, 14.67(8.04–22.47) μg/g, 0.44(0.29–0.56) μg/g, 0.11(0.07–0.30) μg/g, 0.15(0.1096–0.3274), 25.55(17.24–39.35) μg/g and 0.52(0.37−0.84) μg/g, respectively. Cd, Zn and Se levels were significantly higher (p < 0.05) among the urban samples compared to that of the rural group. Zn and Se levels were higher among younger age groups. As, Pb and Cr did not show any significant differences between the two cohorts nor any correlations with age.ConclusionThis population-specific baseline study provides an insight into the differences in exposure to toxic trace elements and essential elements between urban and rural populations. Residents in CKDu affected rural districts did not appear to be at risk of toxic heavy metal exposure, however their renal bioaccumulation of nephroprotective essential elements was lower than urban residents.     

Genetic evaluation with uncertain parentage: a comparison of methods

Summary The most common method for genetic evaluation when parents are unknown is best linear unbiased prediction with genetic groups (BLUP-G). With this method unknown parents are assumed to be unrelated to any other animals in the population. This assumption is unrealistic in most situations. If a finite number of potential parents can be identified and the probabilities of being the true parent can be assigned to these, genetic evaluation can be obtained given the uncertainty of parentage without introducing genetic groups into the model. The correct numerator relationship matrix with uncertain parentage () is derived. Rules are given to efficiently compute and ^-1. Computer simulation was used to compare BLUP-G with BLUP using . The simulated population consisted of ten sires and 200 dams per breeding season. The dams were always known; the sires were unknown for 10% or 30% of the males and 30% of the females. The number of potential sires was three (BLUP-₁ or ten (BLUP-₂), including the true sire in both cases. Equal probabilities were assigned to each potential sire. The increase in response with BLUP-₁ and BLUP-₂ relative to BLUP-G ranged from 4% to 8% in the fifth breeding season. Selection with BLUP-₁ or BLUP-₂ resulted in higher inbreeding, 17% and 12%, respectively, than with BLUP-G. Estimates of response to selection were unbiased with BLUP-₁ and BLUP-₂, but not unbiased with BLUP-G. Mean square error of estimated genetic means and mean prediction error variance were higher with BLUP-G than with blup-₁ or BLUP-₂.     

Origin and diversity of North American hard spring wheats

Genetic diversity is an important safeguard against crop vulnerability to biotic and abiotic stresses. Coefficient-of-parentage (COP) values of 248 North American hard spring wheat (Triticum aestivum L. em. Thell) cultivars released from 1901 to 1991 were used to estimate the genetic similarity of cultivars. COP values were used: to (1) quantify germ plasm sources and their contributions to the North American hard spring wheat gene pool; (2) measure changes in genetic diversity through time; and (3) identify major groupings of related cultivars. Landraces and local cultivars that contributed to the formation of the gene pool were: spring wheat (64%), winter wheat (16%), T. turgidum var. durum L. (10%), and T. turgidum var. emmer L. (8%). Fife, Hard Red Calcutta, and Turkey Red accounted for 18%, 13%, and 8%, respectively, of the hard spring wheat origins. Era and Butte in the US, and Neepawa and HY 320 in Canada, were the most commonly used named parents of cultivars released from 1981 to 1991. Both Canada and US had the greatest level of similarity among new cultivar releases in the 1930s (Canada: r=0.39, US: r=0.34). Genetic similarity in the US declined to r=0.14 in the 1940s and remained relatively constant thereafter. Similarity among released Canadian cultivars remained relatively high until the 1970s when the introduction of new market classes resulted in a 50% reduction in genetic similarity to approximately the same level of similarity found in the US. Cluster analysis was used to group cultivars released after 1941 into 13 clusters of similar genotypes. The cultivar clusters may have value for the stratified sampling of spring wheat germ plasm or in identifying diverse germ plasm for intermating.Contribution of the Idaho Agric. Exp. Stn. publication no. 95731. Missouri Pub. No. 12338     

Genetic diversity in Eastern U.S. soft winter wheat (Triticum aestivum L. em. Thell.) based on RFLPs and coefficients of parentage

 Genetic diversity in a set of 11 red and 11 white wheat lines from the Eastern U.S. soft wheat germplasm pool was measured using restriction fragment length polymorphism (RFLP) assay and coefficients of parentage (COP) analysis. On average, 78% of all bands revealed by three enzymes with 48 RFLP clones were monomorphic. Average pairwise genetic similarity (GS) was 0.97 when data from all enzymes were pooled. Probe Polymorphic Information Content (PIC) indexes ranged from 0 to 0.73 with a mean of 0.2. Fewer than 55% of the probes revealed any polymorphism. The frequency of polymorphism in the Eastern U.S. soft white winter (SWW) wheat gene pool was much lower than that observed in the Eastern U.S. soft red winter (SRW) wheat gene pool. SWW lines formed a single group on a dendrogram based on cluster analysis of RFLP-derived GS estimates, while SRW lines did not form a single group. COP values for all pairs of the Eastern U.S. soft wheat lines ranged from 0.02 to 0.9 with a mean of 0.21. SWW wheat lines traced to 53 ancestral lines and had an average COP of 0.51. The SRW wheat gene pool had more complex parentages (mean COP=0.15 and a total of 65 ancestral lines). COPs were correlated with RFLP-based GS for all line pairs (r=0.73, P<0.01). However, correlations between the two similarity measures were substantially lower when the SRW and SWW wheat gene pools were considered individually (r values of 0.23 and 0.28, respectively). The actual GS among unrelated lines in the U.S. Eastern soft wheat gene pool appears to be higher than that observed for unrelated landraces from Southwest Asia (0.96 vs. 0.905), suggesting that the ancestral landrace parents of this gene pool were themselves drawn from a base population where inbreeding, i.e., F, was greater than zero. Received:18 April 1996 / Accepted: 6 September 1996