Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (Tamias canipes, Tamias cinereicollis, Tamias dorsalis, T. quadrivittatus, Tamias rufus, and Tamias umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population-genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group. [Cytonuclear discordance; hyridization; introgression, phylogenomics; SVDquartets; Tamias.]

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Protein expression level is one of the strongest predictors of protein sequence evolutionary rate, with high-expression protein sequences evolving at slower rates than low-expression protein sequences largely because of constraints on protein folding and function. Expression evolutionary rates also have been shown to be negatively correlated with expression level across human and mouse orthologs over relatively long divergence times (i.e., 100 million years). Long-term evolutionary patterns, however, often cannot be extrapolated to microevolutionary processes (and vice versa), and whether this relationship holds for traits evolving under directional selection within a single species over ecological timescales (i.e., ,5000 years) is unknown and not necessarily expected. Expression is a metabolically costly process, and the expression level of a particular protein is predicted to be a tradeoff between the benefit of its function and the costs of its expression. Selection should drive the expression level of all proteins close to values that maximize fitness, particularly for high-expression proteins because of the increased energetic cost of production. Therefore, stabilizing selection may reduce the amount of standing expression variation for high-expression proteins, and in combination with physiological constraints that may place an upper bound on the range of beneficial expression variation, these constraints could severely limit the availability of beneficial expression variants. To determine whether rapid-expression evolution was restricted to low-expression proteins owing to these constraints on highly expressed proteins over ecological timescales, we compared venom protein expression levels across mainland and island populations for three species of pit vipers. We detected significant differentiation in protein expression levels in two of the three species and found that rapid-expression differentiation was restricted to low-expression proteins. Our results suggest that various constraints on high-expression proteins reduce the availability of beneficial expression variants relative to lowexpression proteins, enabling low-expression proteins to evolve and potentially lead to more rapid adaptation.KEYWORDS protein expression; selective constraints; evolutionary rates; adaptation T HE expression level of a protein is one of the strongest predictors of protein sequence evolutionary rate; sequences of highly expressed proteins evolve more slowly than low-expression proteins (Duret and Mouchiroud 1999;Pal et al. 2001;Gout et al. 2010;Yang et al. 2012;Nabholz et al. 2013;Park et al. 2013). This relationship may be a function of specific selective constraints on sequences to avoid protein misfolding (Drummond et al. 2005;Geiler-Samerotte et al. 2011), protein misinteractions (Yang et al. 2012, a decrease in protein function (Cherry 2010;Gout et al. 2010), and/or messenger RNA (mRNA) misfolding (Park et al. 2013). Analyses of microarray data have shown that expression evolutionary rate is also negatively...

The feeding systems of durophagous vertebrates are well suited for studying how the performance of feeding structures is affected by growth. For these animals, feeding structures that deviate from isometric growth (i.e. allometry) may be biologically meaningful in terms of disproportionate increases in bite-force generation across ontogeny. We measured body size, cranial morphology and bite-force generation in an ontogenetic series of loggerhead musk turtles Sternotherus minor and compared the scaling coefficients with predictions based on isometry. We found that morphological growth in S. minor is characterized by positive allometry in the dimensions of the head and beak (rhamphotheca) relative to body and head size. Because negative allometry or isometry in head size relative to body size is a nearly universal trait among vertebrates, S. minor appears to be unique in this regard. In addition, we found that bite forces scaled with positive allometry relative to nearly all morphological measurements. These results suggest that modified lever mechanics, and/or increased physiological cross-sectional area through changes in muscle architecture (i.e. fiber lengths, degree of pennation) of the jaw adductor musculature may have more explanatory power for bite-force generation than external head measures in this taxon. Lastly, we found that bite force scaled with negative allometry relative to lower beak depth and symphyseal length, indicating that the development of high bite forces requires a disproportionately more robust mandible. These results indicate how deviations from isometric growth may make it possible for durophagous vertebrates to generate, transfer and dissipate mechanical forces during growth.

Discovery of cryptic species is essential to understand the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well‐known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence‐capture data for 21,551 autosomal and 493 X‐linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow‐pine chipmunk (Tamias amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population‐level sequence data revealed that the so‐called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow‐pine chipmunk but does show evidence for recurrent hybridization with this and other species.