Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses have the potential to mitigate these difficulties. Here, we attempt to resolve phylogenetic relationships among eight shrew species (genus Crocidura) from the Philippines, a phylogenetic problem that has proven intractable with small (< 10 loci) data sets. We sequenced hundreds of ultraconserved elements and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a maximally supported and fully resolved tree. In contrast, the coalescent-based approaches produced similar topologies, but each had several poorly supported nodes. Using simulations, we demonstrate that the concatenated tree could be positively misleading. Our simulations also show that the tree shape we tend to infer, which involves a series of short internal branches, is difficult to resolve, even if substitution models are known and multiple individuals per species are sampled. As such, the low support we obtained for backbone relationships in our coalescent-based inferences reflects a real and appropriate lack of certainty. Our results illuminate the challenges of estimating a bifurcating tree in a rapid and recent radiation, providing a rare empirical example of a nearly simultaneous series of speciation events in a terrestrial animal lineage as it spreads across an oceanic archipelago.

Premise of the study: Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera. Methods: Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships. Results: Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal. Discussion: Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought. View full text

The development of various target enrichment methods in combination with next generation sequencing techniques has greatly facilitated the use of partially degraded DNA samples in genetic studies. We employed the MYbaits target enrichment system in combination with Ion Torrent sequencing on a broad range of DNA quality, extracted from tissues obtained from both natural history archives and through various opportunistic sampling methods, to sequence the mitogenome of 11 mobulid rays and two closely related species. Mobulids are large, elusive pelagic filter feeders, for which conservation concerns have recently be raised in connection to their vulnerable life histories and increasing fishing pressure. We show that the MYbaits target enrichment method can be used to effectively sequence large parts of the mitogenome from heavily degraded DNA samples, and provide a time and cost effective alternative for genetic studies of rare and/or difficult to sample species.

The main objective of this project was to generate a large single nucleotide polymorphism (SNP) marker resource for later saturation of the genetic linkage map and fine mapping of quantitative trait loci (QTL). Another objective of this project was to learn more about basic crocodile biology, namely immune function and stress, and the underlying genetic function to evaluate their incorporation into CrocPLAN. This report describes the development of new phenotypic trait panels for farmed saltwater crocodiles. Among these is the major crocodilian stress hormone, corticosterone (CORT), which should be useful for the development of animal welfare standards and the eventual selection of individuals in the future. Immune assays, some of which have never been previously used in crocodilians, were employed in this project to assess immune function. These immune assays, which are relatively easy to perform and cheap, could be employed in any farming setting to assess immune function in the future. Levels of estradiol (ESTR) and testosterone (TEST) are also detailed in this report, for the first time in the saltwater crocodile. At the same time as trying to expedite industry adoption of genetic improvement programs, it was necessary to expand on the current selection criteria available to gain a deeper insight into the breeding objectives already defined from RIRDC Project US-109A. The traits added were corticosterone (the main crocodilian stress hormone), two immune parameters, two sex hormones (testosterone and estradiol), two behaviour characters and four skin quality traits. Simultaneously, some of these traits could be used to gauge current industry practices which are set out in the “Code of Practice on the humane treatment of wild and farmed Australian crocodiles”. I am pleased to report that the lowest levels of corticosterone ever reported in saltwater crocodiles were found certifying the recommendations set out in the “code of practice”.