Evolutionary rate variation in Old World monkeys

We analysed over 8 million base pairs of bacterial artificial chromosome-based sequence alignments of four Old World monkeys and the human genome. Our findings are as follows. (i) Genomic divergences among several Old World monkeys mirror those between well-studied hominoids. (ii) The X-chromosome evolves slower than autosomes, in accord with ‘male-driven evolution’. However, the degree of male mutation bias is lower in Old World monkeys than in hominoids. (iii) Evolutionary rates vary significantly between lineages. The baboon branch shows a particularly slow molecular evolution. Thus, lineage-specific evolutionary rate variation is a common theme of primate genome evolution. (iv) In contrast to the overall pattern, mutations originating from DNA methylation exhibit little variation between lineages. Our study illustrates the potential of primates as a model system to investigate genome evolution, in particular to elucidate molecular mechanisms of substitution rate variation.     

High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna) that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR) primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS) to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees.     

Inferring colonization history from analyses of spatial genetic structure within populations of Pinus strobus and Quercus rubra

Many factors interact to determine genetic structure within populations including adult density, the mating system, colonization history, natural selection, and the mechanism and spatial patterns of gene dispersal. We examined spatial genetic structure within colonizing populations of Quercus rubra seedlings and Pinus strobus juveniles and adults in an aspen-white pine forest in northern Michigan, USA. A 20-year spatially explicit demographic study of the forest enables us to interpret the results in light of recent colonization of the site for both species. We assayed 217 Q. rubra seedlings and 171 P. strobus individuals at 11 polymorphic loci using nine allozyme systems. Plant genotypes and locations were used in an analysis of spatial genetic structure. Q. rubra and P. strobus showed similar observed levels of heterozygosity, but Q. rubra seedlings have less heterozygosity than expected. Q. rubra seedlings show spatial genetic clumping of individuals on a scale to 25 m and levels of genetic relatedness expected from the clumped dispersion of half-siblings. In contrast, P. strobus has low levels of genetic relatedness at the smallest distance class and positive spatial genetic structure at scales < 10 m within the plot. The low density of adult Q. rubra outside the study plot and limited, spatially clumped rodent dispersal of acorns is likely responsible for the observed pattern of spatial genetic structure and the observed heterozygote deficit (i.e. a Wahlund effect). We attribute weaker patterns observed in P. strobus to the longer dispersal distance of seeds and the historical overlap of seed shadows from adults outside of the plot coupled with the overlap of seed shadows from younger, more recently established reproductive adults. The study demonstrates the utility of long-term demographic data in interpreting mechanisms responsible for generating contemporary patterns of genetic structure within populations.     

Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species

Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites—a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4–6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone—a geographical landmark in the Andes with high endemism and isolated microhabitats—was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity.     

Metapopulation structure and fine-scaled genetic structuring in crop-wild hybrid weed beets

This study explores the microspatial and temporal genetic variation in crop-wild hybrid weed beets that emerged from the seed bank in a cultivated field surveyed over two successive years. We demonstrate the occurrence of demes highly genetically differentiated, kin-structured, characterized by moderate effective population sizes, differing in propensity for selfing, and arising from nonrandom genetic subsets of the seed bank. Only one deme identified in the first survey year significantly contributed to the weed beets that emerged in the second year. Spatial structuring appears to be primarily due to gravity seed dispersal and limited pollen flow among weed beet demes. Within each genetic cluster identified by Bayesian assignments and multivariate analyses, F(IS) estimates and level of biparental inbreeding--revealed by progeny analyses--dropped to non-significant values. This suggests that random mating occurs at the scale of genetically distinct demes over a very short scale. Our results highlight the need to carefully depict genetic discontinuities in weed species, when attempting to describe their local genetic neighborhoods within which genetic drift and selective processes occur.     

The use and function of snake skins in the nests of Great Reed Warblers Acrocephalus arundinaceus

We documented and experimentally tested the use of snake skins in construction of nests in a Great Reed Warbler Acrocephalus arundinaceus population in southwestern Slovakia. There was no difference in predation rates of artificial nests that did or did not contain sloughs. We suggest that snake skins in Great Reed Warbler nests may serve as a post‐pairing signal revealing female parental quality.     

Female choice for heterozygous mates changes along successive matings in a lizard

Female mate choice and female multiple mating are major focuses of studies on sexual selection. In a multiple mating context, the benefits of mate choice can change along successive matings, and female choice would be expected to change accordingly. We investigated sequential female mate choice in the moderately polyandrous common lizard (Zootoca vivipara, synonym Lacerta vivipara). Along successive mating opportunities, we found that females were relatively unselective for the first mate, but accepted males of higher heterozygosity for subsequent mating, consistent with the trade-up choice hypothesis. We discuss the evidence of trade-up mate choice in squamates and generally trade-up for mate heterozygosity in order to motivate new studies to fill gaps on these questions.