Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

Diversity of the mammalian olfactory receptor (OR) repertoire has been globally reshaped by niche specialization. However, little is known about the variability of the OR repertoire at a shallower evolutionary timeframe. The vast bat radiation exhibits an extraordinary variety of trophic and sensory specializations. Unlike other mammals, bats possess a unique and diverse OR gene repertoire. We elucidated whether the evolution of the OR gene repertoire can be linked to ecological niche specializations, such as sensory modalities and diet. The OR gene repertoires of 27 bat species spanning the chiropteran radiation were amplified and sequenced. For each species, intact and nonfunctional genes were assessed, and the OR gene abundances in each gene family were analyzed and compared. We identified a unique OR pattern linked to the frugivorous diet of New World fruit-eating bats and a similar convergent pattern in the Old World fruit-eating bats. Our results show a strong association between niche specialization and OR repertoire diversity even at a shallow evolutionary timeframe.

Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological, and behavioral transition undertaken by juveniles in preparation for seaward migration. O. mykiss is experimentally tractable and displays intra- and inter-population variation in migration propensity. Migratory individuals can produce non-migratory progeny and vice versa, indicating a high degree of phenotypic plasticity. One potential way that phenotypic plasticity might be linked to variation in migration-related life history tactics is through epigenetic regulation of gene expression. To explore this, we quantitatively measured genome-scale DNA methylation in fin tissue using reduced representation bisulfite sequencing of F2 siblings produced from a cross between steelhead (migratory) and rainbow trout (non-migratory) lines. We identified 57 differentially methylated regions (DMRs) between smolt and resident O. mykiss juveniles. DMRs were high in magnitude, with up to 62% differential methylation between life history types, and over half of the gene-associated DMRs were in transcriptional regulatory regions. Many of the DMRs encode proteins with activity relevant to migration-related transitions (e.g. circadian rhythm pathway, nervous system development, protein kinase activity). This study provides the first evidence of a relationship between epigenetic variation and life history divergence associated with migration-related traits in any species.

Accurate species identification is essential for ecological research and environmental monitoring. Some species are easy to identify visually, while identification of others is more challenging due to cryptic speciation (Hubert et al., 2008) and phenotypic plasticity (Pinzón et al., 2013). In these cases, as well as for more refined taxonomic discrimination (e.g., populations), genetic methods are often considerably more accurate (Benjamin et al., 2018; Vrijenhoek, 2009). To date, genetic identification has required a trained geneticist to receive the sample, conduct molecular methods (usually in a laboratory), analyse results and report the findings back to their field collaborators. This process can require days, and possibly even months, thus delaying the progression of research, conservation, and management actions based on the findings. In addition, laboratory facilities may not be available for genetic species identification

Release of sturgeon with abnormal ploidy into the wild may result in reduced fitness due to lowered fertility in the F 2 and subsequent generations. Further, there is evidence that ploidy affects reproductive development and caviar yield. Therefore, the ability to accurately characterize the ploidy of white sturgeon (Acipenser transmontanus) is essential for both commercial and conservation aquaculture. This study compares nuclear volume and whole erythrocyte long-axis lengths obtained using Coulter counter and blood smears, respectively, from captive white sturgeon from populations originating in California and Idaho. We examine which method provides the most accurate, time efficient and cost-effective characterization of ploidy in this species. Results from Coulter counter and blood smears were compared to results from flow cytometry, the gold standard for genome size analysis. Previous work suggests that blood smears can distinguish between 8N (diploid) and 12N (triploid) sturgeon, but further analysis is required to see if this method can also be used to identify 10N fish and to provide robust evidence of its utility in 8N and 12N fish across populations. In this study, we demonstrated that the Coulter counter had 100% agreement with flow cytometry in ploidy assignment, while blood smears vary in their accuracy based on population. Blood smears showed a high degree of overlap in erythrocyte long-axis length between 8N and 10N individuals as well as some overlap between 10N and 12N individuals in the California fish, and a high degree of overlap between 8N and 12N individuals in the Idaho fish. Although blood smears are time-intensive and vary in their ploidy assignment accuracy, they are a low-cost technique and as such may have some utility for caviar farms attempting to identify 12N individuals in a small number of broodstock. By comparing the accuracy, efficiency and cost of these three methods, sturgeon farmers and conservation hatcheries will be able to choose the best method for their needs in determining the ploidy of their fish. We determined that Coulter counter is equally accurate to flow cytometry and is also the most time efficient method for ploidy determination in white sturgeon.