Repetitive sequences in phylogeographic inference: a reply to Saltonstall and Lambertini (2012)

In 2011, Vachon and Freeland presented the results of a study that illustrated the importance of considering mutation patterns, including the potential for homoplasy, when deciding whether to include or exclude repetitive sequences from phylogeographic inferences. Saltonstall and Lambertini (2012) criticized this study by suggesting that some of the analyses and interpretations were flawed. In this reply, we explain why we disagree with most of their criticisms and identify some inconsistencies in their analyses. Most importantly, we reiterate the need to examine underlying assumptions, particularly with respect to mutation patterns, when using molecular genetic data to untangle evolutionary relationships.     

Temporally stable genetic variability and dynamic kinship structure in a fluctuating population of the root vole Microtus oeconomus

Genetic variability, kin structure and demography of a population are mutually dependent. Population genetic theory predicts that under demographically stable conditions, neutral genetic variability reaches equilibrium between gene flow and drift. However, density fluctuations and non‐random mating, resulting e.g. from kin clustering, may lead to changes in genetic composition over time. Theoretical models also predict that changes in kin structure may affect aggression level and recruitment, leading to density fluctuations. These predictions have been rarely tested in natural populations. The aim of this study was to analyse changes in genetic variability and kin structure in a local population of the root vole (Microtus oeconomus) that underwent a fourfold change in mean density over a 6‐year period. Intensive live‐trapping resulted in sampling 88% of individuals present in the study area, as estimated from mark–recapture data. Based on 642 individual genotypes at 20 microsatellite loci, we compared genetic variability and kin structure of this population between consecutive years. We found that immigration was negatively correlated with density, while the number of kin groups was positively correlated with density. This is consistent with theoretical predictions that changes in kin structure play an important role in population fluctuations. Despite the changes in density and kin structure, there was no genetic differentiation between years. Population‐level genetic diversity measures did not significantly vary in time and remained relatively high (H_E range: 0.72–0.78). These results show that a population that undergoes significant demographic and social changes may maintain high genetic variability and stable genetic composition.     

Control of Seed Growth in Soya Beans [Glycine max (L.) Merrill]

The seed is the primary sink for photosynthate during reproductivegrowth and an understanding of the mechanisms controlling therate of seed growth is necessary to understand completely theyield production process. The growth rate of individual seedsof seven soya bean [Glycine max (L.) Merrill] cultivars withgenetic differences in seed size varied from 10.8 to 3.9 mgseed^–1 day^–1. The growth rates were highly correlatedwith final seed size. The growth rate of cotyledons culturedin a complete nutrient medium was highly correlated with thegrowth rate of seeds developing on the plant and with finalseed size. The number of cells per seed in the cotyledons variedfrom 10.2 to 5.7 x 10⁶ across the seven cultivars. The numberof cells per seed in the cotyledons was significantly correlatedwith final seed size and the seed growth rate both on the plantand in the culture medium. The data suggest that genetic differencesin seed growth rates are controlled by the cotyledons and thenumber of cells in the cotyledons may be the mechanism of control. Glycine max L., soya bean, seed size, growth rate, cell number, sink activity