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Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000-59,500) y ago, and selection started around 9,000 (2,500-42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

Background and Context: automated feedback for programming assignments has great potential in promoting just-in-time learning, but there has been little work investigating the design of feedback in this context. Objective: to investigate the impacts of different designs of automated feedback on student learning at a fine-grained level, and how students interacted with and perceived the feedback. Method: a controlled quasi-experiment of 76 CS students, where students of each group received a different combination of three types of automated feedback for their programming assignments. Findings: feedback addressing the gap between expected and actual outputs is critical to effective learning; feedback lacking enough details may lead to system gaming behaviors. Implications: the design of feedback has substantial impacts on the efficacy of automated feedback for programming assignments; more research is needed to extend what is known about effective feedback design in this context.

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 43,000 (15,700–60,000) years ago, and selection started 12,000 (1,925-50,000) years ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

Design is a distinct discipline with its own practices, tools, professions, and areas of scholarship. However, practitioners from other fields often leverage aspects of design in their own work, leading to subfields like engineering design and architecture design that are neither wholly design nor wholly the intersecting discipline. Similarly, design and computing are known to intersect in educational contexts. Unfortunately, we do not yet have a clear understanding of how to characterize the kinds of design that may accompany computing topics, resulting in challenges to teaching and learning. This gap is particularly prevalent in K-12 computing education, where design is often used to promote student engagement but rarely studied as its own disciplinary phenomenon. Toward the goal of better understanding the nature and role of design in computing education, this article motivates and describes two qualitative, exploratory analyses of how design skills manifest in popular K-12 computing education curricula and activities. We find evidence to suggest two types of design within existing computing education curricula and standards: nondisciplinary "problem-space design," which deals with defining software requirements, and disciplinary "program-space design," which deals with choosing how best to meet those requirements. We find that these two types of computing design may exist independently, but they often overlap, creating an intriguing intersection of discipline-specific computing design educational activity. Finally, we discuss the practical implications of proceeding with research and educational practice in light of these results, highlighting the need for further exploration into the unique overlap of design and computing education.

Pedigrees provide the genealogical relationships among individuals at a fine resolution and serve an important function in many areas of genetic studies. One such use of pedigree information is in the estimation of the short-term effective population size [Formula: see text], which is of great relevance in fields such as conservation genetics. Despite the usefulness of pedigrees, however, they are often an unknown parameter and must be inferred from genetic data. In this study, we present a Bayesian method to jointly estimate pedigrees and [Formula: see text] from genetic markers using Markov Chain Monte Carlo. Our method supports analysis of a large number of markers and individuals within a single generation with the use of a composite likelihood, which significantly increases computational efficiency. We show, on simulated data, that our method is able to jointly estimate relationships up to first cousins and [Formula: see text] with high accuracy. We also apply the method on a real dataset of house sparrows to reconstruct their previously unreported pedigree.

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

Pedigrees contain information about the genealogical relationships among individuals and are of fundamental importance in many areas of genetic studies. However, pedigrees are often unknown and must be inferred from genetic data. Despite the importance of pedigree inference, existing methods are limited to inferring only close relationships or analyzing a small number of individuals or loci. We present a simulated annealing method for estimating pedigrees in large samples of otherwise seemingly unrelated individuals using genome-wide SNP data. The method supports complex pedigree structures such as polygamous families, multi-generational families, and pedigrees in which many of the member individuals are missing. Computational speed is greatly enhanced by the use of a composite likelihood function which approximates the full likelihood. We validate our method on simulated data and show that it can infer distant relatives more accurately than existing methods. Furthermore, we illustrate the utility of the method on a sample of Greenlandic Inuit.

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.

The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.