Weekly Round Up - January 15, 2016

Every week, members of the Wilson Sayres’ lab scour journals for interesting and relevant (to lab research) articles. We're back after taking some time off from the blog for winter break. This week's list will therefore be fairly long as we catch up on the articles published during the last 3-4 weeks. We hope you still take the time to skim through the titles though, as there are quite a few really interesting papers. Here's the list in no particular order:

Sex Chromosomes/Sex Determination

The eutherian pseudoautosomal region. Raudsepp and Chowdhary (2016) in Cytogenetic and Genome Research

Dynamics of vertebrate sex chromosome evolution: from equal size to giants and dwarfs Schartl et al. (2015) in Chromosoma

The emerging phylogenetic pattern of parthenogenesis in snakes Booth and Schuett (2016) in Biological Journal of the Linnean Society

Evolutionary stability of sex chromosomes in snakes Rovatsos et al. (2015) in Proc. Roy. Soc. B

Evolution of vertebrate sex chromosomes and dosage compensation Graves (2015) in Nature Reviews Genetics

Developmental dynamics of X-chromosome dosage compensation by the DCC and H4K20me1 in C. elegans Kramer et al. (2015) in PLOS Genetics

Probing Xist RNA structure in cells using targeted structure-seq Fang et al. (2o15) in PLOS Genetics

Cell-specific mRNA profiling of the C. elegans somatic gonadal precursor cells identifies suites of sex-biased and gonad-enriched transcripts Kroetz and Zarkower (2015) in G3

Sxl-dependent, tra/tra2-independent alternative splicing of the D. melanogaster X-linked gene found in neurons Sun et al. (2015) in G3

The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome Hurst et al. (2015) in PLOS Biology

A second transmissible cancer in Tasmanian devils Pye et al. (2016) in PNAS "DFT2 causes facial tumors that are grossly indistinguishable but histologically distinct from those caused by DFT1. DFT2 bears no detectable cytogenetic similarity to DFT1 and carries a Y chromosome, which contrasts with the female origin of DFT1."

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae) Li et al. (2016) in Genome Research

The pig X and Y chromosomes: structure, sequence, and evolution Skinner et al. (2016) in Genome Research

Evolution of haploid selection in predominantly diploid organisms Otto et al. (2015) in PNAS

The sex determination gene transformer regulates male-female differences in Drosophila body size Rideout et al. (2015) in PLoS Genetics

Coalescent times and patterns of genetic diversity in species with facultative sex: effects of gene conversion, population structure, and heterogeneity Hartfield et al. (2016) in Genetics

Genomics

Bayesian molecular clock dating of species divergences in the genomics era dos Reis et al. (2015) in Nature Reviews Genetics

Genome-wide patterns of selection in 230 ancient Eurasians Mathieson et al. (2015) in Nature

Time-dependent estimates of molecular evolutionary rates: evidence and causes Ho et al. (2015) in Molecular Ecology

Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions Qiu et al. (2015) in Nature Communications

DNA methylation: insights into human evolution Hernando-Herraez et al. (2015) in PLOS Genetics

Genomic insights into the ancestry and demographic history of South America Homburder et al. (2015) in PLOS Genetics

Comparative genomic analyses of the human NPHP1 locus reveal complex genomic architecture and its regional evolution Yuan et al. (2015) in PLOS Genetics

The 5300-year-old Helicobacter pylori genome of the Iceman Maixner et al. (2016) in Science

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake Malinsky et al. (2015) in Science

Reassignment of Drosophila willistoni genome scaffolds to chromosome II arms Garcia et al. (2015) in G3

Identification of genes uniquely expressed in the germ-line tissues of the jewel wasp Nasonia vitripennis Ferree et al. (2015) in G3

The hologenome concept: helpful or hollow? Moran and Sloan (2015) in PLOS Biology

Abundant contribution of short tandem repeats to gene expression variation in humans Gymrek et al. (2016) in Nature Genetics

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming Durruthy-Durruthy et al. (2016) in Nature Genetics

POGZ truncating alleles cause syndromic intellectual disability White et al. (2016) in Genome Medicine

Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network Brodrick et al. (2016) in Genome Medicine

Genome editing: the end of the beginning Doudna and Gersbach (2015) in Genome Biology

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction McClay et al. (2015) in Genome Biology

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal sources of human methylome variation Busche et al. (2015) in Genome Biology

Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging Wood et al. (2015) in Genome Biology

Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevances of glucocorticoid Zannas et al. (2015) in Genome Biology

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome Cassidy et al. (2016) in PNAS

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs Mardsen et al. (2016) in PNAS

Evolution of stickleback in 50 years on earthquake-uplifted islands Lescak et al. (2015) in PNAS

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade Boothby et al. (2015)

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax) Lamichhaney et al. (2016) in Nature Genetics

Nuclear and mitochondrial DNA sequences from two Denisovan individuals Sawyer et al. (2015) in PNAS

Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication Kistler et al. (2015) in PNAS

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments Librado et al. (2015) in PNAS

Genomic data do not support comb jellies as the sister group to all other animals Pisani et al. (2015) in PNAS

The convergent cancer evolution toward a single cellular destination Chen and He (2016) in Molecular Biology and Evolution

Adaptive evolution favoring KLK4 downregulation in East Asians Marques et al. (2016) Molecular Biology and Evolution

Recombination rate variation modulates gene sequence evolution mainly via GC-biased gene conversion, not Hill-Robertson interference, in an avian system Bolivar et al. (2016) in Molecular Biology and Evolution

DNA methylation: insights into human evolution Hernando-Herraez et al. (2015) in PLoS Genetics

Origins of de novo genes in human and chimpanzee Ruiz-Orera et al. (2015) in PLoS Genetics

Genomic insights into the ancestry and demographic history of South America Homburger et al. (2015) in PLoS Genetics

Comparative genomic analyses of the human NPHP1 locus reveal complex genomic architecture and its regional evolution in primates Yuan et al. (2015) in PLoS Genetics

Combined genetic and genealoic studies uncover a large BAP1 cancer syndrome kindred tracing back nine generations to a common ancestor from the 1700s Carbone et al. (2015) in PLoS Genetics

Maternal modifiers and parent-of-origin bias of the autism-associated 16p11.2 CNV Duyzend et al. (2016) in the American Journal of Human Genetics

Detecting and characterizing the highly divergent plastid geome of the nonphotosynthetic parasitic plant Hydnora visseri (Hydnoraceae) Naumann et al. (2016) in Genome Biology and Evolution

Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes Warren et al. (2016) in Genome Biology and Evolution

Methods

The January issue of Molecular Ecology was a special issue dedicated to "Detecting selection in natural populations" and contains a number of interesting methodological, theoretical, and emprical papers on the subject

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data Finak et al. (2015) in Genome Biology

Fast and accurate approximate inference of transcript expression from RNA-seq data Hensman et al. (2015) in Bioinformatics

Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations Pybus et al. (2015) in Bioinformatics

Approximately independent linkage disequilibrium blocks in human populations Berisa and Pickrell (2016) in Bioinformatics

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Okonechinikov et al. (2016) in Bioinformatics

Meta-analysis of RNA-seq expression data across species, tissues and studies Sudmant et al. (2015) in Genome Biology

A molecular evolutionary reference for the human variome Liu et al. (2016) in Molecular Biology and Evolution

INTEGRATE: gene fusion discovery using whole genome and trascriptome data Zhang et al. (2016) in Genome Research

A simple model-based approach to inferring and visualizing cancer mutational signatures Shiraishi et al. (2015) in PLoS Genetics

Integration analysis of three Omics data using penalized regression methods: an application to bladder cancer Pineda et al. (2015) in PLoS Genetics

Melanoma cell colony expansion parameters revealed by approximate Bayesian computation Vo et al. (2015) in PLoS Genetics

Inferring bottlenecks from genome-wide samples of short sequence blocks Bunnefeld et al. (2015) in Genetics