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Studies focusing on geographical genetic patterns of commensal species and on human history complement each other and provide proxies to trace common colonization events. On Madagascar, the unintentional introduction and spread of the commensal species Rattus rattus by people may have left a living clue of human colonization patterns and history. In this study, we addressed this question by characterizing the genetic structure of natural populations of R. rattus using both microsatellites and mitochondrial sequences, on an extensive sampling across the island. Such data sets were analysed by a combination of methods using population genetics, phylogeography and approximate Bayesian computation. Our results indicated two introduction events to Madagascar from the same ancestral source of R. rattus, one in the extreme north of the island and the other further south. The latter was the source of a large spatial expansion, which may have initially started from an original point located on the southern coast. The inferred timing of introduction events-several centuries ago-is temporally congruent with the Arabian trade network in the Indian Ocean, which was flourishing from the middle of the first millennium. [ABSTRACT FROM AUTHOR]

Progress in NGS technologies has opened up new opportunities for characterizing biodiversity, both for individual specimen identification and for environmental barcoding. Although the amount of data available to biologist is increasing, user-friendly tools to facilitate data analysis have yet to be developed. Our aim, with |SE|S|AM|E| B arcode, is to provide such support through a unified platform. The sequences are analysed through a pipeline that (i) processes NGS amplicon runs, filtering markers and samples, (ii) builds reference libraries and finally (iii) identifies (barcodes) the sequences in each amplicon from the reference library. We use a simulated data set for specimen identification and a recently published data set for environmental barcoding to validate the method. The results obtained are consistent with the expected characterizations ( in silico and previously published, respectively). |SE|S|AM|E| B arcode and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/. [ABSTRACT FROM AUTHOR]

The article presents a research study which focuses on the meiotic and geographic aspects of Gerbillus nigeriae that underwent Robertsonian (Rb) polymorphism found in West Africa. Study shows the existence of diploid variations on the said species despite the scarcity of its kind. It details Gerbillus' phylogeographic nature. The heterozygosity of the said species is also noted.

An understanding of the role of factors intrinsic to a species’ life history in structuring contemporary genetic variation is a fundamental, but understudied, aspect of evolutionary biology. Here, we assessed the influence of the propensity to outbreak in shaping worldwide genetic variation in Locusta migratoria, a cosmopolitan pest well known for its expression of density-dependent phase polyphenism. We scored 14 microsatellites in nine subspecies from 25 populations distributed over most of the species’ range in regions that vary in the historical frequency and extent of their outbreaks. We rejected the hypothesis that L. migratoria consists of two genetically distinct clusters adapted to habitats either rarely (nonoutbreaking) or cyclically (outbreaking) favourable to increases in population density. We also invalidated the current subspecific taxonomic classification based on morphometrics. Bayesian inferences indicated evidence of a homogenizing effect of outbreaks on L. migratoria population structure. Geographical and ecological barriers to gene flow in conjunction with historical events can also explain the observed patterns. By systematically assessing the effects of null alleles using computer simulations, we also provide a template for the analysis of microsatellite data sets characterized by a high prevalence of null alleles. [ABSTRACT FROM AUTHOR]

GENECLASS2 is a software that computes various genetic assignment criteria to assign or exclude reference populations as the origin of diploid or haploid individuals, as well as of groups of individuals, on the basis of multilocus genotype data. In addition to traditional assignment aims, the program allows the specific task of first-generation migrant detection. It includes several Monte Carlo resampling algorithms that compute for each individual its probability of belonging to each reference population or to be a resident. (i.e., not a first-generation migrant) in the population where it was sampled. A user-friendly interface facilitates the treatment of large datasets. [ABSTRACT FROM AUTHOR]

We propose a general formulation of the Bayesian method for assigning individuals to a population among a predetermined set of reference populations using molecular marker information. Compared to previously published methods, ours allows us to consider different types of prior information about allele frequencies by using a Dirichlet prior probability distribution. It also makes it possible to assign a set of individuals assumed to belong to the same population with increased accuracy using their pooled genotype data. The efficiency of the method is illustrated by application to a group of closely related coconut populations. An interesting feature of the Bayesian procedure is the way it handles imprecise information. With a poor or even incomplete dataset, assignment is still be possible and gives valid results: poor data quality is reflected in an ambiguous result rather than in a false conclusion. [ABSTRACT FROM AUTHOR]

Features information on BOTTLENECK, a population genetics computer program. Importance in conservation biology; Principle; Description of the input file.

Nine nonlinear models (degree-day with a 10 deg.C base, degree-day model, polynomial, normal distribution, Stinner model, Sharpe and DeMichele model, Logan model with or without a base, Hilbert and Logan model) were tested to describe the relationship between development rate and temperature for the European corn borer, Ostrinia nubilalis Hubner. These models were calibrated with laboratory experiments based on destructive sampling under sinusoidal temperatures from 9 to 42 deg.C. They were then evaluated and compared with field experiments, at temperatures from 4 to 37 deg.C, carried out as artificial infestations in various areas. Laboratory development models with the smallest time shifts between predicted and observed molts were the Sharpe and DeMichele model, polynomial model, normal distribution, and Stinner model. A classification with an adjusted coefficient of determination (taking into account the number of parameters in the model) slightly modified the results and the best models were the polynomial and the normal distribution, followed by the Stinner model and the degree-daymodel with a 10 deg.C base. The classification was almost reversed under field conditions. Large shifts occurred in all models in some experiments, thereby demonstrating that temperature was not the only factor involved. Models showing the smallest shifts under field conditions were the degree-day model and the Logan model. The experiments that showed the greater shifts corresponded to infestations on early oron late phenological stages of corn. Results confirmed that the experimental design and calibration method were adequate. The laboratory experiments provided a means of calibrating the models and of predicting results under field conditions from laboratory experiments. Future studies will focus on a precise quantitative analysis of factors affecting development other than temperature, notably infestation date,climatic factors, and phenological stage of corn. [ABSTRACT FROM AUTHOR]