Coalescent-based species tree inference has become widely used in the analysis of genome-scale multilocus and SNP datasets when the goal is inference of a species-level phylogeny. However, numerous evolutionary processes are known to violate the assumptions of a coalescence-only model and complicate inference of the species tree. One such process is hybrid speciation, in which a species shares its ancestry with two distinct species. Although many methods have been proposed to detect hybrid speciation, only a few have considered both hybridization and coalescence in a unified framework, and these are generally limited to the setting in which putative hybrid species must be identified in advance. Here we propose a method that can examine genome-scale data for a large number of taxa and detect those taxa that may have arisen via hybridization, as well as their potential “parental” taxa. The method is based on a model that considers both coalescence and hybridization together, and uses phylogenetic invariants to construct a test that scales well in terms of computational time for both the number of taxa and the amount of sequence data. We test the method using simulated data for up 20 taxa and 100,000bp, and find that the method accurately identifies both recent and ancient hybrid species in less than 30 seconds. We apply the method to two empirical datasets, one composed of Sistrurus rattlesnakes for which hybrid speciation is not supported by previous work, and one consisting of several species of Heliconius butterflies for which some evidence of hybrid speciation has been previously found.

Are organisms free to reach their adaptive optima or constrained by hard-wired developmental programs? Recent evidence suggests that the arrangement of stomata on abaxial (lower) and adaxial (upper) leaf surfaces may be an important adaptation in plants, but stomatal traits on each surface likely share developmental pathways that could hamper evolution. We reviewed the quantitative genetics of stomatal density to look for loci that (1) affected ab- or adaxial density independently or (2) pleiotropically affected stomatal density on both surfaces. We also used phylogenetic comparative methods to test for independent versus correlated evolution of stomatal traits (density, size, and pore index) on each surface from 14 amphistomatous wild tomato taxa (Solanum; Solanaceae). Naturally occurring and laboratory-induced genetic variation alters stomatal density on one surface without affecting the other, indicating that development does not strongly constrain the spectrum of available mutations. Among wild tomato taxa, traits most closely related to function (stomatal pore index and density) evolved independently on each surface, whereas stomatal size was constrained by correlated evolution. Genetics and phylogenetics demonstrate mostly independent evolution of stomatal function on each leaf surface, facilitating largely unfettered access to fitness optima.

Multigenerational pedigrees have been developed for free-ranging populations of many species, are frequently used to describe mating systems, and are used in studies of quantitative genetics. Here, we document the development of a 4449-individual pedigree for the Western Hudson Bay subpopulation of polar bears (Ursus maritimus), created from relationships inferred from field and genetic data collected over six generations of bears sampled between 1966 and 2011. Microsatellite genotypes for 22-25 loci were obtained for 2945 individuals, and parentage analysis was performed using the program FRANZ, including additional offspring-dam associations known only from capture data. Parentage assignments for a subset of 859 individuals were confirmed using an independent medium-density set of single nucleotide polymorphisms. To account for unsampled males in our population, we performed half-sib/full-sib analysis to reconstruct males using the program COLONY, resulting in a final pedigree containing 2957 assigned maternities and 1861 assigned paternities with only one observed case of inbreeding between close relatives. During genotyping, we identified two independently captured two-year-old males with identical genotypes at all 25 loci, showing–for the first time–a case of monozygotic twinning among polar bears. In addition, we documented six new cases of cub adoption, which we attribute to cub misidentification or misdirected maternal care by a female bereaved of her young. Importantly, none of these adoptions could be attributed to reduced female vigilance caused by immobilization to facilitate scientific handling, as has previously been suggested.

Herbivore induced defences are robust, evolve rapidly and activated in plants when specific elicitors, frequently found in the herbivores’ oral secretions (OS) are introduced into wounds during attack. How these complex induced defences evolve remains unclear. Here, we show that herbivore-induced transcriptomic responses in a wild tobacco, Nicotiana attenuata, display an evolutionary hourglass: the pattern that characterises the transcriptomic evolution of embryogenesis in animals, plants, and fungi. While relatively young and rapidly evolving genes involved in signal perception and processing to regulate defence metabolite biosynthesis are recruited both early (1 h) and late (9-21 h) in the defence elicitation process, a group of highly conserved and older genes involved in transcriptomic regulation are activated in the middle stage (5 h). The appearance of the evolutionary hourglass architecture in both developmental and defence elicitation processes may reflect the importance of robustness and evolvability in the signalling of these important biological processes.

Adaptation to temporally fluctuating environments can be achieved through direct phenotypic evolution, by phenotypic plasticity (either developmental plasticity or trans-generational plasticity), or by randomizing offspring phenotypes (often called diversifying bet-hedging). Theory has long held that plasticity can evolve when information about the future environment is reliable while bet-hedging can evolve when mixtures of phenotypes have high average fitness (leading to low among generation variance in fitness). To date, no study has studied the evolutionary routes that lead to the evolution of randomized offspring phenotypes on the one hand or deterministic maternal effects on the other. We develop simple, yet general, models of the evolution of maternal effects and are able to directly compare selection for deterministic and randomizing maternal effects and can also incorporate the notion of differential maternal costs of producing offspring with alternative phenotypes. We find that only a small set of parameters allow bet hedging type strategies to outcompete deterministic maternal effects. Not only must there be little or no informative cues available, but also the frequency with which different environments are present must fall within a narrow range. By contrast, when we consider the joint evolution of the maternal strategy and the set of offspring phenotypes we find that deterministic maternal effects can always invade the ancestral state (lacking any form of maternal effect). The long-term ESS may, however, involve some form of offspring randomization, but only if the phenotypes evolve extreme differences in environment-specific fitness. Overall we conclude that deterministic maternal effects are much more likely to evolve than offspring randomization, and offspring randomization will only be maintained if it results in extreme differences in environment-specific fitness.

As sequencing cost continues to decrease with fast advancing Next Generation Sequencing (NGS) technologies, variant discovery is becoming a more affordable and popular analysis method among research laboratories. Following variant calling and annotation, accurate variant filtering is a crucial step to extract meaningful biological information from sequencing data and to investigate disease etiology. However, the standard variant call file format (VCF) used to store this valuable information is not easy to handle without bioinformatics skills, thus preventing investigators from directly analysing their data. Here, we present BrowseVCF, an easy-to-use stand-alone software that enables researchers to browse, query and filter millions of variants in a few seconds. Top features include the possibility to store intermediate search results, to query user-defined gene lists, to group samples for family or tumour/normal studies, to download a report of the filters applied, and to export the filtered variants in spreadsheet format. Additionally, BrowseVCF is suitable for any DNA variant analysis (exome, whole-genome and targeted sequencing), can be used also for non-diploid genomes, and is able to discriminate between Single Nucleotide Polymorphisms (SNPs), Insertions/Deletions (InDels), and Multiple Nucleotide Polymorphisms (MNPs). Thanks to its portable implementation, BrowseVCF can be used either on personal computers or as part of automated analysis pipelines. The software can be initialised with a few clicks on any operating system without any special administrative or installation permissions, and is freely available for download from https://github.com/BSGOxford/BrowseVCF.

Both the ecological adaptations of an organism and its evolutionary history are recorded in a genome. We used Agrobacterium biovar 1, a diverse group of plant-associated bacteria as a model to search for genomic signatures of ecological adaptation in relation to diversification. We designed a new phylogenetic approach accounting for horizontal transfer and duplication to reconstruct the evolutionary history of Agrobacterium genomes and infer ancestral gene contents. We find that allowing for genes to be co-transferred and co-duplicated significantly improves scenarios of genome evolution. Most genes acquired before the diversification of major clades within Agrobacterium are organized in blocks of co-evolving genes encoding coherent pathways. This pattern of gene co-evolution rejects a neutral model of transfer, in which neighbouring genes would be transferred independently of their function. In addition, the conservation of acquired genes is driven by purifying selection on collectively coded functions. Based on this criterion, we identify the genomic determinants of ecological niche diversification within this group. The strong selective role of host plant rhizospheres in the history of Agrobacterium is evident from the recurrent acquisition of functions involved in the production of secreted secondary metabolites or extracellular matrix, and in the metabolism of plant-derived compounds such as phenolics and amino-acids. Our reconstructed genome history – from single gene trees with transfer and duplication events to blocks of co-evolved genes and functional annotations, etc. – is compiled in an integrative database, Agrogenom, which can be visualized and queried through an interactive web interface accessible at http://phylariane.univ-lyon1.fr/db/agrogenom/3.