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  1. Free, publicly-accessible full text available December 1, 2024
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  4. Abstract Objectives

    Long‐tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long‐tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long‐tailed macaques using low‐coverage nuclear DNA (nDNA) data from museum specimens.

    Methods

    We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long‐tailed macaque museum specimens from localities throughout Southeast Asia.

    Results

    We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades withinM. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island‐living individuals, including those from southern Sumatra.

    Conclusions

    Overall, we demonstrate that low‐coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.

     
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  5. Abstract The EXO-200 experiment searched for neutrinoless double-beta decay of 136 Xe with a single-phase liquid xenon detector. It used an active mass of 110 kg of 80.6%-enriched liquid xenon in an ultra-low background time projection chamber with ionization and scintillation detection and readout. This paper describes the design and performance of the various support systems necessary for detector operation, including cryogenics, xenon handling, and controls. Novel features of the system were driven by the need to protect the thin-walled detector chamber containing the liquid xenon, to achieve high chemical purity of the Xe, and to maintain thermal uniformity across the detector. 
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