Genome scans and elusive candidate genes: detecting the variation that matters for speciation

Next‐generation sequencing is providing us with vast amounts of genetic data, yet we are currently struggling in our attempts to make sense of them. In particular, it has proven difficult to link phenotypic divergence and speciation to genome level divergence. In the current issue of Molecular Ecology, Ruegg et al. ( 2014 ) present new empirical results from two closely related bird taxa. They use a promising approach combining genome scan and candidate gene analysis. Their results suggest that we may have been looking in vain for candidate speciation genes by focusing only on genes found within genomic islands of divergence. This is because genes important in divergence and speciation may not be detected by genome scans and because features of the genomic architecture per se may have a large effect on the pattern of genome divergence.     

Structural requirements of quassinoids for the inhibition of cell transformation

The effects of eleven quassinoids on Rous sarcoma virus induced cell transformation and on growth of normal cells were examined. At concentrations of 0.15-1 μg/ml they inhibited foci formation (76–99 %) without toxic effects on normal cells. The most active compounds also affected virus production by transformed cells. In intact normal and transformed cells, protein and DNA synthesis was equally affected after 3 hours of exposure to quassinoids of both cell types. RNA synthesis was not inhibited. This study has shown that the structural requirement of a C-15 ester in the quassinoids for antileukemic activity $\text{in vitro}$ and $\text{in vivo}$ is not essential for their antitransforming activity.     

Dark diversity in Amazonian stream fish communities: What factors determine species absence along environmental gradients?

1. Species distribution models often fail to predict observed patterns of species diversity, and this is because some species within a regional pool that are tolerant of conditions at a given location may nevertheless be absent from the local community. These missing species have been termed “dark diversity”. In the present study, we investigated which factors explain dark diversity among fish assemblages in Amazonian streams.
2. We sampled 71 streams in areas with different types of land use within two river basins and estimated dark diversity from patterns of species co-occurrence, using Beals’ index, along environmental gradients. From this procedure, taxa are designated as dark diversity components when they are absent from a given stream, but often co-occur with the local species at other streams, indicating similar ecological requirements. We used generalised linear models both to determine whether environmental or landscape variables, connectivity, instream environmental heterogeneity or some combination of these factors explained dark diversity of fishes, and to evaluate whether ecomorphology is associated with the extent to which a species contributes to dark diversity and which specific traits contribute the most to explaining variation in dark diversity.
3. Mean local diversity exceeded observed dark diversity. The magnitude of dark diversity was directly associated with the proportion of secondary forest in the immediate catchment and with the index of proximity to anthropogenic impact. Species that have high affinity for environments with higher current velocity, low swimming ability and that capture food mainly on the surface contributed more to dark diversity, which suggests that swimming ability, habitat preference and aspects related to diet are key predictors of the probability that a given species will be present at locations with suitable habitat.
4. Our findings reinforce the idea that dark diversity results from interactions between species traits and environmental factors, including anthropogenic impacts. Understanding the interplay among environmental factors and species traits that contribute to dark diversity provides targets for improved ecosystem restoration and sustainability of native species assemblages.

     

A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome

The house sparrow is an important model species for studying physiological, ecological and evolutionary processes in wild populations. Here, we present a medium density, genome wide linkage map for house sparrow (Passer domesticus) that has aided the assembly of the house sparrow reference genome, and that will provide an important resource for ongoing mapping of genes controlling important traits in the ecology and evolution of this species. Using a custom house sparrow 10 K iSelect Illumina SNP chip we have assigned 6,498 SNPs to 29 autosomal linkage groups, based on a mean of 430 informative meioses per SNP. The map was constructed by combining the information from linkage with that of the physical position of SNPs within scaffold sequences in an iterative process. Averaged between the sexes; the linkage map had a total length of 2,004 cM, with a longer map for females (2,240 cM) than males (1,801 cM). Additionally, recombination rates also varied along the chromosomes. Comparison of the linkage map to the reference genomes of zebra finch, collared flycatcher and chicken, showed a chromosome fusion of the two avian chromosomes 8 and 4A in house sparrow. Lastly, information from the linkage map was utilized to conduct analysis of linkage disequilibrium (LD) in eight populations with different effective population sizes (N_e) in order to quantify the background level LD. Together, these results aid the design of future association studies, facilitate the development of new genomic tools and support the body of research that describes the evolution of the avian genome.     

Reproductive biology of the white marlin (Kajikia albida) in the southwestern and equatorial Atlantic Ocean

The present work describes the reproductive biology of the white marlin (Kajikia albida) caught in the southwestern and equatorial Atlantic Ocean. The gonads of 924 fish were collected by observers on board Brazilian tuna longliners, between November 2004 and December 2006. The spawning season was assessed by the monthly frequency distribution of distinct stages of maturity and monthly mean female gonadosomatic index GSI. Sixty-one percent (n = 656) of the fish examined were female, with a Lower Jaw Fork Length (LJFL) between 83 and 236 cm (mean = 155.5 ± 16.63). The 268 males had a LJFL between 90 and 220 cm (mean = 152.3 ± 34.62). Although the northeastern region of Brazil does not appear to be a significant spawning area for the species, the results suggest a higher reproductive activity in the third quarter of the year. Using a Bayesian logistic model approach, length at 50% maturity was estimated at 145.04 cm (credibility interval of 95%, 143.94–146.09 cm), for females, and at 140.03 cm (credibility interval of 95%, 137.28–142.52 cm), for males.