Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains...

Sex determination is a critical developmental decision with major ecological and evolutionary consequences, yet a large variety of sex determination mechanisms exist and we have a poor understanding of how they evolve. Theoretical and empirical work suggest that compensatory adaptations to mutations in genes involved in sex determination may play a role in the evolution of these pathways. Here, we directly address this problem using experimental evolution in Caenorhabditis elegans lines fixed for a pair...

Theoretical treatments of egg size in fishes suggest that constraints on reproductive output should create trade-offs between the size and number of eggs produced per spawn. For marine reef fishes, the observation of distinct reproductive care strategies (demersal guarding, egg scattering, and pelagic spawning) has additionally prompted speculation that these strategies reflect alternative fitness optima with selection on egg size differing by reproductive mode and perhaps latitude. Here, we aggregate data from 278 reef fish...

Background: Although males and females need one another in order to reproduce, they often have different reproductive interests, which can lead to conflict between the sexes. The intensity and frequency of male-male competition for fertilization opportunities is thought to be an important contributor to this conflict. The nematode genus Caenorhabditis provides an opportunity to test this hypothesis because the frequency of males varies widely among species with different mating systems. Results: We find evidence that...

Immunogenetic data from wild primate populations have been difficult to obtain, due to logistic and methodological constraints. We applied a well-characterized deep sequencing method for MHC I typing, developed for macaques, to a population of wild red colobus to assess the feasibility of identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data from blood and tissue samples to assign haplotypes. Eighty-two sequences were classified as red colobus MHC I alleles distributed across six MHC I...

1. In northern Idaho (USA), more than 100 vascular plant species are disjunct <200 km from their main distribution along the Pacific Northwest coast. It remains unclear whether most species within this interior forest disjunction, including Tsuga mertensiana, survived the last glacial period in a north-Idaho refugium or whether these species colonized the region via long-distance dispersal during the Holocene. 2. Sediment cores were extracted from three mid- to high-elevation lakes within T. mertensiana dominated...

Larvae in the coastal ocean are transported toward shore by a variety of mechanisms. Crossing the surf zone is the last step in a shoreward migration and surf zones may act as semipermeable barriers altering delivery of larvae to the shore. We related variation in the structure of intertidal barnacle populations to surfzone width (surfzone hydrodynamics proxy), wave height, alongshore wind stress (upwelling proxy), solar radiation, and latitude at 40 rocky intertidal sites from San...

Managers are increasingly looking to apply concepts of resilience to better anticipate and understand conservation and restoration in a changing environment. In this study, we explore how information on demography (recruitment, growth and survival) and competitive effects in different environments and with different starting species abundances can be used to better understand resilience. We use observational and experimental data to better understand dynamics between native Stipa pulchra and exotic Avena barbata and fatua, grasses characteristic...

Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/sasin/calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence...

Outbreaks of marine infectious diseases have caused widespread mass mortalities, but the lack of baseline data has precluded evaluating whether disease is increasing or decreasing in the ocean. We use an established literature proxy method from Ward and Lafferty (2004) to analyze a 44-year global record of normalized disease reports from 1970 to 2013. Major marine hosts are combined into nine taxonomic groups, from seagrasses to marine mammals, to assess disease swings, defined as positive...

Most studies of visual processing are conducted under head- and gaze-restricted conditions. While this provides experimental control, it radically limits the natural exploration of the visual world which is typically achieved through directed eye, head, and body movements. As such, less is known about how animals naturally sample the external visual world to acquire relevant visual information in natural contexts. To determine how mice target their gaze and sample the visual world during natural behavior,...

Predicting species’ range shifts under future climate is a central goal of conservation ecology. Studying populations within and beyond multiple species’ current ranges can help identify whether demographic responses to climate change exhibit directionality, indicative of range shifts, and whether responses are uniform across a suite of species. We quantified the demographic responses of six native perennial prairie species planted within and, for two species, beyond their northern range limits to a three-year experimental manipulation...

Demographic studies measure drivers of plant fecundity such as seed production and survival, but few address environmental drivers of seed viability, such as germination and dormancy. Variation in climate and seed type may both directly and indirectly alter seed germination via altered fungal pathogen abundance. We examined seed germination and microbial communities of seeds of Danthonia californica, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and Festuca roemeri, which are solely chasmogamous. Seed...

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus....

Aim: How climate change will alter plant functional group composition is a critical question given the well-recognized effects of plant functional groups on ecosystem services. While climate can have direct effects on different functional groups, indirect effects mediated through changes in biotic interactions have the potential to amplify or counteract direct climatic effects. As a result, identifying the underlying causes for climate effects on plant communities is important to conservation and restoration initiatives. Location: Western...

For over 10,000 years, black abalone (Haliotis cracherodii) were an important resource in southern California, first for coastal Native Americans, then beginning in the nineteenth century, as one of the state's first commercial shellfisheries. By 1993, after years of heavy fishing, rising sea surface temperatures (SST), and the spread of withering syndrome (WS), black abalone populations declined dramatically, resulting in the closure of the Alta California fishery. After nearly 25 years of management and recovery...

Seadragons are widely recognized for their derived and novel traits. Research and conservation efforts involving these unique fish species and their relatives have been hindered by a lack of genomic resources. From this project we present full, annotated genomes of leafy and weedy seadragons, which help uncover surprising features of gene family and genome architecture evolution that likely relate to extreme phenotypic traits in seadragons, pipefishes, and seahorses. These genomes are important research resources for...

Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from...

The recent collapse of predatory sunflower sea stars (Pycnopodia helianthoides) due to sea star wasting disease (SSWD) is hypothesized to have contributed to proliferation of sea urchin barrens and losses of kelp forests on the North American West Coast. We used experiments and a model to test whether restored Pycnopodia populations may help recover kelp forests through their consumption of nutritionally poor purple sea urchins (Strongylocentrotus purpuratus) typical of barrens. Pycnopodia consumed 0.68 S. purpuratus...

Overview of RefSeq genomes used, including accession numbers.

Definitions (member lists) of species genome bins, separately for each environment.

The complete workflow (python, R and bash code) used for our analyses.

Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine ‘top-down’ and ‘bottom-up’ approaches with demographic modeling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to...

All landing pad sequences along with limited surrounding genomic region used in this study and described in the manuscript

How rapidly can animal populations in the wild evolve when faced with sudden environmental shifts? Uplift during the 1964 Great Alaska Earthquake abruptly created freshwater ponds on multiple islands in Prince William Sound and the Gulf of Alaska. In the short time since the earthquake, the phenotypes of resident freshwater threespine stickleback fish on at least three of these islands have changed dramatically from their oceanic ancestors. To test the hypothesis that these freshwater populations...