The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified over 100 selective sweeps specific to domestic rabbits, but only a relatively small number of fixed (or nearly fixed) SNPs for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved non-coding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that due to a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few ‘domestication loci’.

An F(2) resource population, derived from a broiler x layer cross, was used to map quantitative trait loci (QTL) for body weights at days 1, 35 and 41, weight gain, feed intake, feed efficiency from 35 to 41 days and intestinal length. Up to 577 F(2) chickens were genotyped with 103 genetic markers covering 21 linkage groups. A preliminary QTL mapping report using this same population focused exclusively on GGA1. Regression methods were applied to line-cross and half-sib models for QTL interval mapping. Under the line-cross model, eight QTL were detected for body weight at 35 days (GGA2, 3 and 4), body weight at 41 days (GGA2, 3, 4 and 10) and intestine length (GGA4). Under the half-sib model, using sire as common parent, five QTL were detected for body weight at day 1 (GGA3 and 18), body weight at 35 days (GGA2 and 3) and body weight at 41 days (GGA3). When dam was used as common parent, seven QTL were mapped for body weight at day 1 (GGA2), body weight at day 35 (GGA2, 3 and 4) and body weight at day 41 (GGA2, 3 and 4). Growth differences in chicken lines appear to be controlled by a chronological change in a limited number of chromosomal regions.

The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In this study, we used next-generation sequencing to study genome-wide patterns of genetic differentiation between two hybridizing subspecies of rabbits (Oryctolagus cuniculus algirus and O. c. cuniculus) that are known to undergo high rates of gene exchange. Our primary objective was to identify specific genes or genomic regions that have resisted introgression and are likely to confer reproductive barriers in natural conditions. On the basis of 326,000 polymorphisms, we found low to moderate overall levels of differentiation between subspecies, and fewer than 200 genomic regions dispersed throughout the genome showing high differentiation consistent with a signature of reduced gene flow. Most differentiated regions were smaller than 200 Kb and contained very few genes. Remarkably, 30 regions were each found to contain a single gene, facilitating the identification of candidate genes underlying reproductive isolation. This gene-level resolution yielded several insights into the genetic basis and architecture of reproductive isolation in rabbits. Regions of high differentiation were enriched on the X-chromosome and near centromeres. Genes lying within differentiated regions were often associated with transcription and epigenetic activities, including chromatin organization, regulation of transcription, and DNA binding. Overall, our results from a naturally hybridizing system share important commonalities with hybrid incompatibility genes identified using laboratory crosses in mice and flies, highlighting general mechanisms underlying the maintenance of reproductive barriers.

An F(2) population established by crossing a broiler male line and a layer line was used to map quantitative trait loci (QTL) affecting abdominal fat weight, abdominal fat percentage and serum cholesterol and triglyceride concentrations. Two genetic models, the line-cross and the half-sib, were applied in the QTL analysis, both using the regression interval method. Three significant QTL and four suggestive QTL were mapped in the line-cross analysis and four significant and four suggestive QTL were mapped in the half-sib analysis. A total of five QTL were mapped for abdominal fat weight, six for abdominal fat percentage and four for triglyceride concentration in both analyses. New QTL associated with serum triglyceride concentration were mapped on GGA5, GGA23 and GG27. QTL mapped between markers LEI0029 and ADL0371 on GGA3 for abdominal fat percentage and abdominal fat weight and a suggestive QTL on GGA12 for abdominal fat percentage showed significant parent-of-origin effects. Some QTL mapped here match QTL regions mapped in previous studies using different populations, suggesting good candidate regions for fine-mapping and candidate gene searches.

<p style="text-align: justify;"><strong>Aim</strong>: To investigate the characteristics, relationships and trends in the phenology of four winegrape varieties and associated temperature relationships in the Lisbon wine region (LWR), between 1990 and 2011.</p><p style="text-align: justify;"><strong>Methods and results</strong>: Budburst, flowering and véraison dates of red (Castelão and Aragonez, syn. Tempranillo) and white (Chasselas and Fernão Pires) varieties were taken from an experimental vineyard in the LWR. Harvest dates were determined based on a similar maturity level for all varieties. From these data, varietal characteristics, temporal trends as well as relationships between phenology and temperature were assessed through stepwise multivariate linear regressions. Flowering was the most sensitive to temperature in the preceding months (March-April). Differences/similarities between the phenological timing of the different varieties are presented. With few exceptions, no trends were found in phenophases over the 1990-2011 period, whereas several significant negative slopes were displayed for phenological intervals, suggesting a role for accumulated thermal effects in phenological timing. Strong correlations were observed between phenophases, especially between flowering and véraison.</p><p style="text-align: justify;"><strong>Conclusion</strong>: The study highlights the key role played by temperature on phenology, particularly during springtime. Furthermore, an increase in temperature during that period will cause an advance in the timing of the following phenological events. Given the significant trends found, phenological shifts may occur in the long term, emphasizing the need to assess varietal characteristics and responses to regional climate.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: The present work is the first attempt to systematically examine temporal trends in phenology and corresponding relationships with temperature in a Portuguese viticultural area, providing valuable information on the development and suitability of grapevine varieties, which determine viticultural practices and winegrower’s income.</p>

Major objectives of the poultry industry are to increase meat production and to reduce carcass fatness, mainly abdominal fat. Information on growth performance and carcass composition are important for the selection of leaner meat chickens. To enhance our understanding of the genetic architecture underlying the chemical composition of chicken carcasses, an F(2) population developed from a broiler × layer cross was used to map quantitative trait loci (QTL) affecting protein, fat, water and ash contents in chicken carcasses. Two genetic models were applied in the QTL analysis: the line-cross and the half-sib models, both using the regression interval mapping method. Six significant and five suggestive QTL were mapped in the line-cross analysis, and four significant and six suggestive QTL were mapped in the half-sib analysis. A total of eleven QTL were mapped for fat (ether extract), five for protein, four for ash and one for water contents in the carcass using both analyses. No study to date has reported QTL for carcass chemical composition in chickens. Some QTL mapped here for carcass fat content match, as expected, QTL regions previously associated with abdominal fat in the same or in different populations, and novel QTL for protein, ash and water contents in the carcass are presented here. The results described here also reinforce the need for fine mapping and to perform multi-trait analyses to better understand the genetic architecture of these traits.

Aim A striking case of mitochondrial DNA (mtDNA) introgression occurs in the Iberian Peninsula: the mtDNA of Lepus timidus, a species that inhabited this territory during the Last Glacial Maximum (LGM), is almost fixed in the Iberian range of Lepus europaeus, is very frequent in the northern half of Iberia within Lepus granatensis, and is fixed in Lepus castroviejoi. Here, we used a transdisciplinary approach to understand the ecological drivers of the distribution of this introgressed mtDNA in the Iberian hare species. Location Europe, with an emphasis on the Iberian Peninsula. Methods First, we modelled the climatic niche of L. timidus to predict the favourability for the species during the LGM. Second, we gathered data regarding L. timidus mtDNA introgression for 1137 individuals (139 populations) from the Iberian Peninsula. We tested whether the climatic favourability for L. timidus during the LGM reflects the frequency of the introgressed mtDNA in the carrier hare populations. Results The climatic favourability for the LGM is positively related to the presence of individuals with L. timidus mtDNA, and discriminates better than by chance between individuals with and without this lineage. At the population level, the favourability values relate to the observed frequencies of mtDNA introgression and discriminate between populations with and without L. timidus mtDNA. Main conclusions The results suggest that the geographical distribution of L. timidus mtDNA introgression is linked to L. timidus distribution in Iberia during the LGM. Our study helps to improve our understanding of the role of climate in the reticulated evolutionary history of hares, and is a first step towards understanding the ecological impact of mtDNA introgression on Iberian hares.

Background: Evolution is considered the unifying concept in biology and is also a key theory underlying many areas of human knowledge. Teaching evolution from as early as kindergarten allows children to better understand concepts related with the biological world and prevents the development of negative feelings and misconceptions about the theory of evolution. However, evolution is absent from most of the educational curricula in the early school grades, even though some of its central concepts are common contents in the curricula of these initial years. Methods: In the present paper we present a set of activities that can be performed with elementary school students to explore and understand evolution and its impact on biological diversity, while promoting critical thinking and scientific literacy. These activities explore concepts of intra-specific diversity, genealogy and inheritance, natural selection, genetic drift, and systematics, using contexts that are familiar to students, and were articulated with the Portuguese official curriculum. Similar contents are present in elementary school curricula of other countries, namely Brazil, United Kingdom, France, United States of America, Canada, or Mozambique, and therefore the same activities can potentially be used in many different countries. Results and conclusions: Regardless of the complexity of the theory behind these concepts, our experience revealed that using these activities children were able to understand basic evolutionary mechanisms and to apply this knowledge in real case scenarios.