Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies.

In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.

BackgroundContamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing.ResultsUsing cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts.ConclusionsWe report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima’s D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0366-6) contains supplementary material, which is available to authorized users.

Wildland fires in Southern California can be divided into two categories: fall fires, which are typically driven by strong offshore Santa Ana winds, and summer fires, which occur with comparatively weak onshore winds and hot and dry weather. Both types of fire contribute significantly to annual burned area and economic loss. An improved understanding of the relationship between Southern California's meteorology and fire is needed to improve predictions of how fire will change in the future and to anticipate management needs. We used output from a regional climate model constrained by reanalysis observations to identify Santa Ana events and partition fires into those occurring during periods with and without Santa Ana conditions during 1959-2009. We then developed separate empirical regression models for Santa Ana and non-Santa Ana fires to quantify the effects of meteorology on fire number and size. These models explained approximately 58% of the seasonal and interannual variation in the number of Santa Ana fires and 36% of the variation in non-Santa Ana fires. The number of Santa Ana fires increased during years when relative humidity during Santa Ana events and fall precipitation were below average, indicating that fuel moisture is a key controller of ignition. Relative humidity strongly affected Santa Ana fire size. Cumulative precipitation during the previous three winters was significantly correlated with the number of non-Santa Ana fires, presumably through increased fine fuel density and connectivity between infrastructure and nearby vegetation. Both relative humidity and the preceding wet season precipitation influenced non-Santa Ana fire size. Regression models driven by meteorology explained 57% of the temporal variation in Santa Ana burned area and 22% of the variation in non-Santa Ana burned area. The area burned by non-Santa Ana fires has increased steadily by 1.7% year À1 since 1959 (p < 0.006); the occurrence of extremely large Santa Ana fires has increased abruptly since 2003. Our results underscore the need to separately consider the fuel and meteorological controls on Santa Ana and non-Santa Ana fires when projecting climate change impacts on regional fire.

The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life-history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome-wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA-seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes -a marker of the effective population size -in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels.

The area burned by Southern California wildfires has increased in recent decades, with implications for human health, infrastructure, and ecosystem management. Meteorology and fuel structure are universally recognized controllers of wildfire, but their relative importance, and hence the efficacy of abatement and suppression efforts, remains controversial. Southern California's wildfires can be partitioned by meteorology: fires typically occur either during Santa Ana winds (SA fires) in October through April, or warm and dry periods in June through September (non-SA fires). Previous work has not quantitatively distinguished between these fire regimes when assessing economic impacts or climate change influence. Here we separate five decades of fire perimeters into those coinciding with and without SA winds. The two fire types contributed almost equally to burned area, yet SA fires were responsible for 80% of cumulative 1990-2009 economic losses ($3.1 Billion). The damage disparity was driven by fire characteristics: SA fires spread three times faster, occurred closer to urban areas, and burned into areas with greater housing values. Non-SA fires were comparatively more sensitive to agedependent fuels, often occurred in higher elevation forests, lasted for extended periods, and accounted for 70% of total suppression costs. An improved distinction of fire type has implications for future projections and management. The area burned in non-SA fires is projected to increase 77% (±43%) by the mid-21st century with warmer and drier summers, and the SA area burned is projected to increase 64% (±76%), underscoring the need to evaluate the allocation and effectiveness of suppression investments.

Termite gut flagellates are colonized by host-specific lineages of ectosymbiotic and endosymbiotic bacteria. Previous studies have shown that flagellates of the genus Trichonympha may harbour more than one type of symbiont. Using a comprehensive approach that combined cloning of SSU rRNA genes with fluorescence in situ hybridization and electron microscopy, we investigated the phylogeny and subcellular locations of the symbionts in a variety of Trichonympha species from different termites. The flagellates in Trichonympha Cluster I were the only species associated with 'Endomicrobia', which were located in the posterior part of the cell, confirming previous results. Trichonympha species of Cluster II from the termite genus Incisitermes (family Kalotermitidae) lacked 'Endomicrobia' and were associated with endosymbiotic Actinobacteria, which is highly unusual. The endosymbionts, for which we suggest the name 'Candidatus Ancillula trichonymphae', represent a novel, deep-branching lineage in the Micrococcineae that consists exclusively of clones from termite guts. They preferentially colonized the anterior part of the flagellate host and were highly abundant in all species of Trichonympha Cluster II except Trichonympha globulosa. Here, they were outnumbered by a Desulfovibrio species associated with the cytoplasmic lamellae at the anterior cell pole. Such symbionts are present in both Trichonympha clusters, but not in all species. Unlike the intracellular location reported for the Desulfovibrio symbionts of Trichonympha agilis (Cluster I), the Desulfovibrio symbionts of T. globulosa (Cluster II) were situated in deep invaginations of the plasma membrane that were clearly connected to the exterior of the host cell.

Abstract. Wildfire ignition requires a combination of an open spark, and suitable weather and fuel conditions. Models of fire occurrence and burned area provide a good understanding of the physical and climatic factors that constrain and promote fire spread and recurrence, but information on how humans influence ignition patterns is still lacking at a scale compatible with integrated fire management. We investigated the relative importance of the physical, climatic and human factors regulating ignition probability across Southern California's National Forests. A 30-year exploratory analysis of one-way relationships indicated that distance to a road, distance to housing and topographic slope were the major determinants of ignition frequency. We used logistic and Poisson regression analyses to model ignition occurrence and frequency as a function of the dominant covariates. The resulting models explained ,70% of the spatial variability in ignition likelihood and 45% of the variability in ignition frequency. In turn, predicted ignition probability contributed to some of the spatial variability in burned area, particularly for summer fires. These models may enable estimates of fire ignition risk for the broader domain of Southern California and how this risk may change with future population and housing development. Our spatially explicit predictions may also be useful for strategic fire management in the region.Additional keywords: biophysical drivers, fire frequency, fire ignition, human influence, Mediterranean ecosystems, spatial regression model, wildland fire risk.