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Genetic admixture is central to primate evolution. We combined 50 years of field observations of immigration and group demography with genomic data from ~9 generations of hybrid baboons to investigate the consequences of admixture in the wild. Despite no obvious fitness costs to hybrids, we found signatures of selection against admixture similar to those described for archaic hominins. These patterns were concentrated near genes where ancestry is strongly associated with gene expression. Our analyses also show that introgression is partially predictable across the genome. This study demonstrates the value of integrating genomic and field data for revealing how “genomic signatures of selection” (e.g., reduced introgression in low-recombination regions) manifest in nature; moreover, it underscores the importance of other primates as living models for human evolution.

Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California's biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire.

PurposeThe authors seek to understand the formation of control- and security-related identities among organizational employees through and interpretive narrative analysis. The authors also seek to identify how the identities form over time and across contexts. Several identities are identified as well as the changes that may occur in the identities.Design/methodology/approachFew interpretive or critical studies exist in behavioral information security research to represent employee perspectives of power and control. Using qualitative interviews and narrative analysis of the interview transcripts, this paper analyzes the security- and control-related identities and values that employees adopt in organizational settings.FindingsTwo major categories of behavioral security compliance identities were identified: compliant and noncompliant. Specific identities within the compliant category included: faithful follower vs the reasoned follower, and other-preserving versus the self-preserving identities. The noncompliant category included: anti-authority identity, utilitarian identity, trusting identity and unaware identity. Furthermore, three patterns of identity changes were observed.Research limitations/implicationsThe authors’ narrative stories suggest that employee identities are complex and multi-faceted, and that they may be fluid and adaptive to situational factors. Future research should avoid assumptions that all employees are the same or that employee beliefs remain constant over time or in different contexts. Identities are also strongly rooted in individuals' rearing and other life experiences. Thus, security control is far broader than is studied in behavioral studies. The authors find that history matters and should be examined carefully.Practical implicationsThe authors’ study provides insights that managers can use to enhance security initiatives. It is clear that different employees build different control-related identities. Managers must understand that their employees are unique and will not all respond to policies, punishments, and other forms of control in the same way. The narratives also suggest that many organizations lack appropriate programs to enhance employees' awareness of security issues.Originality/valueThe authors’ narrative analysis suggests that employee security identities are complex and multi-faceted, and that they are fluid and adaptive to situational factors. Research should avoid assumptions that all employees are the same or that their beliefs remain constant over time or in different contexts. Identities are also strongly rooted in individuals' rearing and other life experiences. Their history matters and should be examined carefully.

Employees are a major cause of information security vulnerabilities and breaches. Organizations implement controls, such as information security policies, fear appeals, and computer monitoring, to manage the security threats that employees pose. Behavioral information security research seeks to understand how these security controls influence employees’ behaviors. In practice, organizations adopt many coexisting security controls in security control portfolios (SCPs). Unfortunately, the complexities of SCPs are not well understood in the information security literature. To assist in studying SCPs, we present a typology and a theoretical model of security control grounded in an extension of control theory. We identify twelve types of security controls that can exist in practice based on three important control dimensions. We develop a number of propositions to explain how the complementarity of security controls in SCPs affect motivation to protect information. Our efforts produce a behaviorally grounded extension of control theory that is well suited for studying individual-level security behavior governed by complex SCPs.

Genital divergence contributes to reproductive barriers between species. Emergence of a novel accessory structure, the baculum, has independently evolved and been lost throughout mammalian evolution, purportedly driven by sexual selection. In primates, the longest recorded baculum belongs to Macaca arctoides, the bear macaque. This species has been proposed to be of homoploid hybrid origin via ancient hybridization between representatives from the fascicularis and sinica species groups. To investigate the evolutionary origins of the bear macaque and its unique morphology, we used whole genome sequences to quantify gene flow and phylogenetic relationships in 10 individuals from 5 species, including the bear macaque (n=3), and two species each from the sinica (n=3) and fascicularis (n=4) species groups. The results of these analyses were concordant, and identified 608 genes in the bear macaque that supported both clustering between M. arctoides and the sinica group (topo2) and had shared derived alleles between species from the two groups. Similarly, 361 genes supported both clustering between M. arctoides and the fascicularis group (topo3) and had shared derived alleles between both groups. Further, sliding window analysis of phylogenetic relationships revealed 53% of the genomic regions supported placement of M. arctoides in the sinica species group (topo2), 16% supported placement in the fascicularis species group (topo3), and 11% supported M. arctoides in a grouping distinct from the sinica and fascicularis groups (topo1). Genomic regions with topo1 were intersected with previously identified QTL for mouse baculum morphology, and 47 genes were found, including five of sixteen major candidate loci that govern mouse baculum variation (KIF14, KIAA0586, RHOJ, TGM2, and DACT1). Although baculum morphology in the bear macaque is diverged from its parent taxa, it most closely resembles that of the fascicularis group. Outliers of shared ancestry from the fascicularis species group located within these same QTL regions overlap with the gene BMP4, which is an important component of the hedgehog signaling pathway that controls gonadogenesis. Two additional outlier genes (one shared with each species group) outside of the baculum QTL are known to interact with BMP4, suggesting this pathway may be involved in baculum morphology in primates. These results highlight how the mosaic ancestry of the bear macaque could explain its unique baculum evolution and collectively contribute to reproductive isolation. Introductory ParagraphIn mammals, the baculum has extreme morphological variability, a dynamic evolutionary history characterized by repeated gain and loss, and is often used in species identification. The bear macaque has divergent genital morphology, including the longest baculum among all primates, and is proposed to have evolved via ancient hybrid speciation. Here, population genetic and phylogenomic approaches were used to examine how ancient hybridization in the bear macaque may have shaped this important component of genital morphology. Results demonstrate extensive mosaicism across the genome, which is consistent with ancient genetic contributions from both putative parental taxa. Genetic regions associated with baculum morphology also had mosaic ancestry for several genes, including KIF14 and KIAA0586, major candidate genes for baculum morphology in mice, and BMP4, a developmental gene involved in gonadogenesis. These results have important implications for how hybridization may have shaped the evolution of reproductive isolation in this unusual species with complex speciation.

Robinson and colleagues respond to the points raised about their paper by Bakker et al.

Genital divergence is thought to contribute to reproductive barriers by establishing a "lock-and-key" mechanism for reproductive compatibility. One such example

Survival at high altitude requires adapting to extreme conditions such as environmental hypoxia. To understand high-altitude adaptations in a primate, we assembled the genome of the gelada (Theropithecus gelada), an endemic Ethiopian monkey, and complemented it with population resequencing, hematological, and morphometric data. Unexpectedly, we identified a novel karyotype that may contribute to reproductive isolation between gelada populations. We also identified genomic elements including protein-coding sequences and gene families that exhibit accelerated changes in geladas and may contribute to high-altitude adaptation. Our findings lend insight into mechanisms of speciation and adaptation while providing promising avenues for functional hypoxia research.

Admixture has profoundly influenced evolution across the tree of life, including in humans and other primates1,2. However, we have limited insight into the genetic and phenotypic consequences of admixture in primates, especially during its key early stages. Here, we address this gap by combining 50 years of field observations with population and functional genomic data from yellow (Papio cynocephalus) and anubis (P. anubis) baboons in Kenya, in a longitudinally studied population that has experienced both historical and recent admixture3. We use whole-genome sequencing to characterize the extent of the hybrid zone, estimate local ancestry for 442 known individuals, and predict the landscape of introgression across the genome. Despite no major fitness costs to hybrids, we identify signatures of selection against introgression that are strikingly similar to those described for archaic hominins4–6. These signatures are strongest near loci with large ancestry effects on gene expression, supporting the importance of gene regulation in primate evolution and the idea that selection targeted large regulatory effects following archaic hominin admixture7,8. Our results show that genomic data and field observations of hybrids are important and mutually informative. They therefore demonstrate the value of other primates as living models for phenomena that we cannot observe in our own lineage.

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide., Using whole-genome sequencing data from 1,739 individuals, the GenomeAsia 100K Project catalogues genetic variation, population structure and disease associations to facilitate genetic studies in Asian populations and increase representation in genetics studies worldwide.

Spotted owls (SOs, Strix occidentalis) are a flagship species inhabiting old-growth forests in western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (S. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here, we use an updated SO genome assembly along with 51 high-coverage whole-genome sequences to examine population structure, hybridization, and recent changes in population size in SO and BO. We found that potential hybrids identified from intermediate plumage morphology were a mixture of pure BO, F1 hybrids, and F1 × BO backcrosses. Also, although SO underwent a population bottleneck around the time of the Pleistocene–Holocene transition, their population sizes rebounded and show no evidence of any historical (i.e., 100–10,000 years ago) population decline. This suggests that the current decrease in SO abundance is due to events in the past century. Finally, we estimate that western and eastern BOs have been genetically separated for thousands of years, instead of the previously assumed recent (i.e.

Genetics and archeology are two fields that provide complementary sources of information on our history as a species. We review what has been learned about human population history from recent genetic studies, including studies of geographic structure, population bottlenecks, and recent population growth. We also describe recent studies that highlight the importance of admixture in human history, from the mixing of different continental populations in the Americas over the past several centuries to ancient admixture between humans and Neanderthals tens of thousands of years ago.

Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.1 During the latter half of the twentieth century, North America's largest soaring bird,2 the California condor (Gymnogyps californianus; Critically Endangered3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor's recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable3) and the turkey vulture (Cathartes aura; Least Concern3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.

Population-scale genetic studies can identify drug targets and allow disease risk to be predicted with resulting benefit for management of individual health risks and system-wide allocation of health care delivery resources. Although population-scale projects are underway in many parts of the world, genetic variation between population groups means that additional projects are warranted. South Asia has a population whose genetics is the least characterized of any of the world’s major populations. Here we describe GenomeAsia studies that characterize population structure in South Asia and that create tools for economical and accurate genotyping at population-scale. Prior work on population structure characterized isolated population groups, the relevance of which to large-scale studies of disease genetics is unclear. For our studies we used whole genome sequence information from 4,807 individuals recruited in the health care delivery systems of Pakistan, India and Bangladesh to ensure relevance to population-scale studies of disease genetics. We combined this with WGS data from 927 individuals from isolated South Asian population groups, and developed a custom SNP array (called SARGAM) that is optimized for future human genetic studies in South Asia. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of homozygosity that approach 100 times that seen in outbred populations. We describe founder effects that increase the power to associate functional variants with disease processes and that make South Asia a uniquely powerful place for population-scale genetic studies.

Personalized medical care focuses on prediction of disease risk and response to medications. To build the risk models, access to both large-scale genomic resources and human genetic studies is required. The Taiwan Biobank (TWB) has generated high-coverage, whole-genome sequencing data from 1492 individuals and genome-wide SNP data from 103,106 individuals of Han Chinese ancestry using custom SNP arrays. Principal components analysis of the genotyping data showed that the full range of Han Chinese genetic variation was found in the cohort. The arrays also include thousands of known functional variants, allowing for simultaneous ascertainment of Mendelian disease-causing mutations and variants that affect drug metabolism. We found that 21.2% of the population are mutation carriers of autosomal recessive diseases, 3.1% have mutations in cancer-predisposing genes, and 87.3% carry variants that affect drug response. We highlight how TWB data provide insight into both population history and disease burden, while showing how widespread genetic testing can be used to improve clinical care.

In humans, most germline mutations are inherited from the father. This observation has been widely interpreted as reflecting the replication errors that accrue during spermatogenesis. If so, the male bias in mutation should be substantially lower in a closely related species with similar rates of spermatogonial stem cell divisions but a shorter mean age of reproduction. To test this hypothesis, we resequenced two 3–4 generation nuclear families (totaling 29 individuals) of olive baboons (Papio anubis), who reproduce at approximately 10 years of age on average, and analyzed the data in parallel with three 3-generation human pedigrees (26 individuals). We estimated a mutation rate per generation in baboons of 0.57×10−8 per base pair, approximately half that of humans. Strikingly, however, the degree of male bias in germline mutations is approximately 4:1, similar to that of humans—indeed, a similar male bias is seen across mammals that reproduce months, years, or decades after birth. These results mirror the finding in humans that the male mutation bias is stable with parental ages and cast further doubt on the assumption that germline mutations track cell divisions. Our mutation rate estimates for baboons raise a further puzzle, suggesting a divergence time between apes and Old World monkeys of 65 million years, too old to be consistent with the fossil record; reconciling them now requires not only a slowdown of the mutation rate per generation in humans but also in baboons., Comparison of sex-specific de novo mutation rates in baboons and humans suggests that germline mutations do not track the number of cell divisions, and reveals a simultaneous slowdown in yearly mutation rates in both the baboon and human lineages.

Spotted owls (SO,Strix occidentalis) are a keystone species inhabiting old-growth forests in Western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO,Strix varia). The northern spotted owl (subspeciesS. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here we present a comprehensive look at genetic variation to elucidate the population histories of SO and invading western BO. Specifically, we present an improved SO genome assembly, based on 10x and Bionano Genomics data, along with 51 high-coverage whole-genome sequences including 11 SO from two subspecies (caurinaandoccidentalis), 25 BO, 2 confirmed and 13 potential hybrids. We identified potential hybrids based on intermediate morphology and found them to be a mixture of pure BO, F1 hybrids, and F1 x BO backcrosses. Unlike previous studies reporting asymmetries in the species-specific genders of the parents of F1 hybrids, we did not observe any significant asymmetry. Within species, we found that Western BO genetic variation is not simply a subset of the genetic variation in Eastern BO, suggesting that the two groups have been genetically isolated for longer (thousands of years) than previously suspected (80-130 years). Similarly, we found evidence of substantial genetic differentiation between the two SO subspecies. Finally, our analyses suggest that Northern SO experienced a moderate population bottleneck around the end of the last glaciation, while BO population sizes have always been large.

Background Baboons are a widely used nonhuman primate model for biomedical, evolutionary, and basic genetics research. Despite this importance, the genomic resources for baboons are limited. In particular, the current baboon reference genome Panu_3.0 is a highly fragmented, reference-guided (i.e., not fully de novo) assembly, and its poor quality inhibits our ability to conduct downstream genomic analyses. Findings Here we present a de novo genome assembly of the olive baboon (Papio anubis) that uses data from several recently developed single-molecule technologies. Our assembly, Panubis1.0, has an N50 contig size of ∼1.46 Mb (as opposed to 139 kb for Panu_3.0) and has single scaffolds that span each of the 20 autosomes and the X chromosome. Conclusions We highlight multiple lines of evidence (including Bionano Genomics data, pedigree linkage information, and linkage disequilibrium data) suggesting that there are several large assembly errors in Panu_3.0, which have been corrected in Panubis1.0.

Purpose Drawing on sensemaking and emotion regulation research, the purpose of this paper is to reconceptualize core contributor withdrawal (CCW) in the context of online peer-production communities (OPPCs). To explain the underlying mechanisms that make core contributors withdraw from these communities, the authors propose a process theory of contributor withdrawal called the core contributor withdrawal theory (CCWT). Design/methodology/approach To support CCWT, a typology of unmet expectations of online communities is presented, which uncovers the cognitive and emotional processing involved. To illustrate the efficacy of CCWT, a case study of the English version of Wikipedia is provided as a representative OPPC. Findings CCWT identifies sensemaking and emotion regulation concerning contributors’ unmet expectations as causes of CCW from OPPCs, which first lead to declined expectations, burnout and psychological withdrawal and thereby to behavioral withdrawal. Research limitations/implications CCWT clearly identifies how and why important participation transitions, such as from core contributor to less active contributor or non-contributor, take place. By adopting process theories, CCWT provides a nuanced explanation of the cognitive and affective events that take place before core contributors withdraw from OPPCs. Practical implications CCWT highlights the challenge of online communities shifting from recruiting new contributors to preventing loss of existing contributors in the maturity stage. Additionally, by identifying the underlying cognitive and affective processes that core contributors experience in response to unexpected events, communities can develop safeguards to prevent or correct cognitions and emotions that lead to withdrawal. Originality/value CCWT provides a theoretical framework that accounts for the negative cognitions and affects that lead to core contributors’ withdrawal from online communities. It furthers the understanding of what motivates contributing to and what leads to withdrawal from OPPC.

Behavioral information security research exhibits a preoccupation with security policy, bureaucratic control, and policy compliance and noncompliance. This preoccupation implicitly treats employees as the sociological archetype described by Whyte (1956), the Organization Man. In doing so, the literature has dedicated less time to the study of other archetypes. In this paper, we compare the Organization Man to the Innovator, an amalgam of the Bricoleur and Engineer archetypes identified by Levi-Strauss (1966). We posit that the Innovator archetype may be more prevalent during times of organizational strain and excess. We develop a theoretical framework to explain how situational factors, namely organizational strain and excess, affect individuals' risk perceptions and their willingness to adopt different archetypal personae (i.e., dispositional factors). The framework further suggests that each archetypal persona will behave differently to common security situations. Finally, the framework suggests that the organization's perceptions of employee behavior will provide a feedback loop that further affects the adoption of different archetypes.

Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the post-introgression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI), in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse dataset, we report novel cases of selection on introgressed variation in living humans and shortlisted among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three introgressed haplotypes that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.

Text mining is a powerful form of business intelligence that is used increasingly to inform organizational decisions. Current text mining algorithms rely heavily on the lexical, syntactic, structural, and semantic features of text to extract meaning and insight for decision making. Although semantic analysis is a useful approach to meaning extraction, pragmatics suggests that a more accurate meaning of text can be extracted by examining the context in which the text is recorded. Given that massive amounts of textual data can be drawn from multiple and diverse sources, accounting for context is increasingly important. A conceptual model is provided to explain how concepts from pragmatics can improve existing text mining algorithms to provide more accurate information for decision making. Reversing the pragmatic process of meaning expression could lead to improved text mining algorithms. The theoretical process model developed herein can provide insight into the development and refinement of text mining algorithms that draw from diverse sources.

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

Background Data from the 1000 Genomes project is quite often used as a reference for human genomic analysis. However, its accuracy needs to be assessed to understand the quality of predictions made using this reference. We present here an assessment of the genotyping, phasing, and imputation accuracy data in the 1000 Genomes project. We compare the phased haplotype calls from the 1000 Genomes project to experimentally phased haplotypes for 28 of the same individuals sequenced using the 10X Genomics platform. Results We observe that phasing and imputation for rare variants are unreliable, which likely reflects the limited sample size of the 1000 Genomes project data. Further, it appears that using a population specific reference panel does not improve the accuracy of imputation over using the entire 1000 Genomes data set as a reference panel. We also note that the error rates and trends depend on the choice of definition of error, and hence any error reporting needs to take these definitions into account. Conclusions The quality of the 1000 Genomes data needs to be considered while using this database for further studies. This work presents an analysis that can be used for these assessments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5957-x) contains supplementary material, which is available to authorized users.

Besides macaques, baboons are the most commonly used nonhuman primate in biomedical research. Despite this importance, the genomic resources for baboons are quite limited. In particular, the current baboon reference genome Panu_3.0 is a highly fragmented, reference-guided (i.e., not fully de novo) assembly, and its poor quality inhibits our ability to conduct downstream genomic analyses. Here we present a truly de novo genome assembly of the olive baboon (Papio anubis) that uses data from several recently developed single-molecule technologies. Our assembly, Panubis1.0, has an N50 contig size of ~1.46 Mb (as opposed to 139 Kb for Panu_3.0), and has single scaffolds that span each of the 20 autosomes and the X chromosome. We highlight multiple lines of evidence (including Bionano Genomics data, pedigree linkage information, and linkage disequilibrium data) suggesting that there are several large assembly errors in Panu_3.0, which have been corrected in Panubis1.0.

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.

Despite tremendous progress in genome sequencing, the basic goal of producing a phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is still unrealized. In this study, we describe an approach to performing de novo genome assembly and experimental phasing by integrating the data from Illumina short-read sequencing, 10X Genomics linked-read sequencing, and BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.

Bats are the only mammals capable of powered flight, but little is known about the genetic determinants that shape their wings. Here we generated a genome for Miniopterus natalensis and performed RNA-seq and ChIP-seq (H3K27ac and H3K27me3) analyses on its developing forelimb and hindlimb autopods at sequential embryonic stages to decipher the molecular events that underlie bat wing development. Over 7,000 genes and several long noncoding RNAs, including Tbx5-as1 and Hottip, were differentially expressed between forelimb and hindlimb, and across different stages. ChIP-seq analysis identified thousands of regions that are differentially modified in forelimb and hindlimb. Comparative genomics found 2,796 bat-accelerated regions within H3K27ac peaks, several of which cluster near limb-associated genes. Pathway analyses highlighted multiple ribosomal proteins and known limb patterning signaling pathways as differentially regulated and implicated increased forelimb mesenchymal condensation in differential growth. In combination, our work outlines multiple genetic components that likely contribute to bat wing formation, providing insights into this morphological innovation.

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing model-based whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.

Baboons (genus Papio) are broadly studied in the wild and in captivity. They are widely used as a nonhuman primate model for biomedical studies, and the Southwest National Primate Research Center (SNPRC) at Texas Biomedical Research Institute has maintained a large captive baboon colony for more than 50 yr. Unlike other model organisms, however, the genomic resources for baboons are severely lacking. This has hindered the progress of studies using baboons as a model for basic biology or human disease. Here, we describe a data set of 100 high-coverage whole-genome sequences obtained from the mixed colony of olive (P. anubis) and yellow (P. cynocephalus) baboons housed at the SNPRC. These data provide a comprehensive catalog of common genetic variation in baboons, as well as a fine-scale genetic map. We show how the data can be used to learn about ancestry and admixture and to correct errors in the colony records. Finally, we investigated the consequences of inbreeding within the SNPRC colony and found clear evidence for increased rates of infant mortality and increased homozygosity of putatively deleterious alleles in inbred individuals.

Supplementary details of materials and methods for article entitled 'Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California'.

As the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix variaandS. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of westernS. variathat suggested admixture withS. occidentalisappear unrelated toS. occidentalisancestry and may instead reflect local selection.

We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale assessment of the genome-wide nucleotide diversity acrossS. occidentalispopulations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all CaliforniaS. occidentalispopulations. We found no evidence of genetic differentiation between northern spotted owl (S. o. caurina) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl (S. o. occidentalis) than between populations ofS. o. occidentalisandS. o. caurinain northern California. The San Diego CountyS. o. occidentalispopulation was substantially diverged from the other threeS. occidentalispopulations. These whole-genome data support a pattern of isolation-by-distance across spotted owl populations in California, rather than elevated differentiation between currently recognized subspecies.