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  1. Abstract The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.
    Free, publicly-accessible full text available December 1, 2023
  2. Abstract Protein–protein interaction (PPI) networks represent complex intra-cellular protein interactions, and the presence or absence of such interactions can lead to biological changes in an organism. Recent network-based approaches have shown that a phenotype’s PPI network’s resilience to environmental perturbations is related to its placement in the tree of life; though we still do not know how or why certain intra-cellular factors can bring about this resilience. Here, we explore the influence of gene expression and network properties on PPI networks’ resilience. We use publicly available data of PPIs for E. coli , S. cerevisiae , and H. sapiens , where we compute changes in network resilience as new nodes (proteins) are added to the networks under three node addition mechanisms—random, degree-based, and gene-expression-based attachments. By calculating the resilience of the resulting networks, we estimate the effectiveness of these node addition mechanisms. We demonstrate that adding nodes with gene-expression-based preferential attachment (as opposed to random or degree-based) preserves and can increase the original resilience of PPI network in all three species, regardless of gene expression distribution or network structure. These findings introduce a general notion of prospective resilience , which highlights the key role of network structures in understanding themore »evolvability of phenotypic traits.« less
    Free, publicly-accessible full text available December 1, 2022
  3. Abstract Background The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge. Results Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila ’s superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroboratedmore »by morphological traits, the ‘Modified Oviscapt Clade’ containing Tephritoidea, Nerioidea, and other families, and the ‘Cleft Pedicel Clade’ containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data. Conclusions Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.« less
    Free, publicly-accessible full text available December 1, 2022
  4. This paper proposes a novel foreground lineariza- tion scheme for a high-speed current-steering (CS) digital-to- analog converter (DAC). The technique leverages neural networks (NNs) to derive a lookup-table (LUT) that maps the inverse of the DAC transfer characteristic onto the input codes. The algorithm is shown to improve conventional methods by at least 6dB in terms of intermodulation (IM) performance for frequencies up to 9GHz on a state-of-the-art 10-bit CS-DAC operating at 40.96GS/s (gigasamples-per-second) in 14nm CMOS.
  5. Artificial neural networks (NNs) in deep learning systems are critical drivers of emerging technologies such as computer vision, text classification, and natural language processing. Fundamental to their success is the development of accurate and efficient NN models. In this article, we report our work on Deep-n-Cheap—an open-source automated machine learning (AutoML) search framework for deep learning models. The search includes both architecture and training hyperparameters and supports convolutional neural networks and multi-layer perceptrons, applicable to multiple domains. Our framework is targeted for deployment on both benchmark and custom datasets, and as a result, offers a greater degree of search space customizability as compared to a more limited search over only pre-existing models from literature. We also introduce the technique of ‘search transfer’, which demonstrates the generalization capabilities of the models found by our framework to multiple datasets. Deep-n-Cheap includes a user-customizable complexity penalty which trades off performance with training time or number of parameters. Specifically, our framework can find models with performance comparable to state-of-the- art while taking 1–2 orders of magnitude less time to train than models from other AutoML and model search frameworks. Additionally, we investigate and develop insight into the search process that should aid future developmentmore »of deep learning models.« less
  6. Context. The PSR J2222−0137 binary system has a set of features that make it a unique laboratory for tests of gravity theories. Aims. To fully exploit the system’s potential for these tests, we aim to improve the measurements of its physical parameters, spin and orbital orientation, and post-Keplerian parameters, which quantify the observed relativistic effects. Methods. We describe an improved analysis of archival very long baseline interferometry (VLBI) data, which uses a coordinate convention in full agreement with that used in timing. We have also obtained much improved polarimetry of the pulsar with the Five hundred meter Aperture Spherical Telescope (FAST). We provide an improved analysis of significantly extended timing datasets taken with the Effelsberg, Nançay, and Lovell radio telescopes; this also includes previous timing data from the Green Bank Telescope. Results. From the VLBI analysis, we have obtained a new estimate of the position angle of the ascending node, Ω = 189 −18 +19 deg (all uncertainties are 68% confidence limits), and a new reference position for the pulsar with an improved and more conservative uncertainty estimate. The FAST polarimetric results, and in particular the detection of an interpulse, yield much improved estimates for the spin geometry of themore »pulsar, in particular an inclination of the spin axis of the pulsar of ∼84 deg. From the timing, we obtain a new ∼1% test of general relativity (GR) from the agreement of the Shapiro delay parameters and the rate of advance of periastron. Assuming GR in a self-consistent analysis of all effects, we obtain much improved masses: 1.831(10)  M ⊙ for the pulsar and 1.319(4)  M ⊙ for the white dwarf companion; the total mass, 3.150(14)  M ⊙ , confirms this as the most massive double degenerate binary known in the Galaxy. This analysis also yields the orbital orientation; in particular, the orbital inclination is 85.27(4) deg – indicating a close alignment between the spin of the pulsar and the orbital angular momentum – and Ω = 187.7(5.7) deg, which matches our new VLBI estimate. Finally, the timing also yields a precise measurement of the variation in the orbital period, Ṗ b = 0.251(8) × 10 −12 ss −1 ; this is consistent with the expected variation in the Doppler factor plus the orbital decay caused by the emission of gravitational waves predicted by GR. This agreement introduces stringent constraints on the emission of dipolar gravitational waves.« less
  7. Abstract Data from rock shelters in southern Belize show evidence of tool making, hunting, and aquatic resource exploitation by 10,500 cal b.c. ; the shelters functioned as mortuary sites between 7600 and 2000 cal b.c. Early Holocene contexts contain stemmed and barbed bifaces as part of a tradition found broadly throughout the neotropics. After around 6000 cal b.c. , bifacial tools largely disappear from the record, likely reflecting a shift to increasing reliance on plant foods, around the same time that the earliest domesticates appear in the archaeological record in the neotropics. We suggest that people living in southern Belize maintained close ties with neighbors to the south during the Early Holocene, but lagged behind in innovating new crops and farming technologies during the Middle Holocene. Maize farming in Belize intensified between 2750–2050 cal b.c. as maize became a dietary staple, 1000–1300 years later than in South America. Overall, we argue from multiple lines of data that the Neotropics of Central and South America were an area of shared information and technologies that heavily influenced cultural developments in southeastern Mesoamerica during the Early and Middle Holocene.