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  1. In species where offspring survival is highly variable relative to adult survival, such as bighorn sheep ( Ovis canadensis ), physiological indicators of maternal investment could clarify the functional mechanisms of life history trade-offs and serve as important predictors of population dynamics. From a management perspective, simple predictors of juvenile survival measured non-lethally from maternal samples could aid in identifying at-risk populations or individuals before significant mortality occurs. Blood biochemical parameters can offer low-cost insights into animal health and physiology, therefore we sought to develop a simple biochemical predictor of juvenile survival based on maternal blood samples. We measured biochemical indicators of energy balance in adult bighorn sheep at a single time point in January or February, and then monitored survival through August of the same year to assess how those measures related to survival of individual adults and their juvenile offspring. Juvenile survival was lower over the subsequent spring and summer when maternal adult serum beta-hydroxybutyric acid (β-HBA) concentration was high, indicating a negative energy balance in the mothers. However, serum β-HBA did not correlate with adult survival over the same period. Our findings suggest that even when maternal body condition is high, short-term caloric deficit may be sufficient trigger to decrease investment in offspring survival. This mechanism could protect adult females from investing heavily in juvenile survival when resources become too limited to support population growth. Our study suggests that β-HBA could be a powerful monitoring tool for bighorn sheep and other threatened ruminant populations under resource limitation. 
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  2. Radiocarbon dating of the earliest occupational phases at the Cooper’s Ferry site in western Idaho indicates that people repeatedly occupied the Columbia River basin, starting between 16,560 and 15,280 calibrated years before the present (cal yr B.P.). Artifacts from these early occupations indicate the use of unfluted stemmed projectile point technologies before the appearance of the Clovis Paleoindian tradition and support early cultural connections with northeastern Asian Upper Paleolithic archaeological traditions. The Cooper’s Ferry site was initially occupied during a time that predates the opening of an ice-free corridor (≤14,800 cal yr B.P.), which supports the hypothesis that initial human migration into the Americas occurred via a Pacific coastal route. 
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  3. Abstract

    Determining how species move across complex and fragmented landscapes and interact with human‐made barriers is a major research focus in conservation. Studies estimating functional connectivity from movement, dispersal or gene flow usually rely on a single study period and rarely consider variation over time. We contrasted genetic structure and gene flow across barriers for a metapopulation of desert bighorn sheep (Ovis canadensis nelsoni) using genotypes collected 2000–2003 and 2013–2015. Based on the recently observed but unexpected spread of a respiratory pathogen across an interstate highway previously identified as a barrier to gene flow, we hypothesized that bighorn sheep changed how they interacted with that barrier, and that shifts in metapopulation structure influenced gene flow, genetic diversity and connectivity. Population assignment tests, genetic structure and genetic recapture demonstrated that bighorn sheep crossed the interstate highway in at least one location in 2013–2015, sharply reducing genetic structure between two populations, but supported conclusions of an earlier study that such crossings were very infrequent or unknown in 2000–2003. A recently expanded population established new links and caused decreases in genetic structure among multiple populations. Genetic diversity showed only slight increases in populations linked by new connections. Genetic structure and assignments revealed other previously undetected changes in movements and distribution, but much was consistent. Thus, we observed changes in both structural and functional connectivity over just two generations, but only in specific locations. Movement patterns of species should be revisited periodically to enable informed management, particularly in dynamic and fragmented systems.

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  4. The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants. 
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  5. The mammalian sex chromosome system (XX female/XY male) is ancient and highly conserved. The sex chromosome karyotype of the creeping vole (Microtus oregoni) represents a long-standing anomaly, with an X chromosome that is unpaired in females (X0) and exclusively maternally transmitted. We produced a highly contiguous male genome assembly, together with short-read genomes and transcriptomes for both sexes. We show thatM. oregonihas lost an independently segregating Y chromosome and that the male-specific sex chromosome is a second X chromosome that is largely homologous to the maternally transmitted X. Both maternally inherited and male-specific sex chromosomes carry fragments of the ancestral Y chromosome. Consequences of this recently transformed sex chromosome system include Y-like degeneration and gene amplification on the male-specific X, expression of ancestral Y-linked genes in females, and X inactivation of the male-specific chromosome in male somatic cells. The genome ofM. oregonielucidates the processes that shape the gene content and dosage of mammalian sex chromosomes and exemplifies a rare case of plasticity in an ancient sex chromosome system.

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