New paper: Genomic signatures of sex-biased demography

Oh hey look! Our paper is out today! 

http://authors.elsevier.com/a/1Tg3A_,2BdT7EGQ

Current Opinion in Genetics & Development
Volume 41, December 2016, Pages 62–71

Genetics of human origin

Genomic signatures of sex-biased demography: progress and prospects

Sex-biased demographic events have played a crucial role in shaping human history. Many of these processes affect genetic variation and can therefore leave detectable signatures in the genome because autosomal, X-linked, Y-linked, and mitochondrial DNA inheritance differ between sexes. Here, we discuss how sex-biased processes shape patterns of genetic diversity across the genome, review recent genomic evidence for sex-biased demography in modern human populations, and suggest directions for future research.

 

 

 

 

 

 

2016 Undergraduate Research Symposium

Three Undergraduate students from the Wilson Sayres lab presented posters of their research at the 2016 School of Life Sciences Undergraduate Research Symposium on April 15, 2016. 

Sarah Brotman: Genetic diversity on the human X chromosome does not support a strict pseudoautosomal boundary

Sam Daly: Male mutation bias in Drosophila. 

Valeria Valverde-Vesling: Modeling effects of time since human bottleneck on genetic diversity

You can click through photos here: 

ASU Staff and Personnel Policy #815

I just received this announcement, and am so happy to be a member of the Arizona State University community that developed it. 

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ASU has a new policy, effective March 25, #815 in the Staff Personnel Manual, entitled Romantic or Sexual Relationships Between Employees/Volunteers and Students. The new policy is below and available at http://www.asu.edu/aad/manuals/spp/spp815.html.

 

Romantic or Sexual Relationships Between Employees/Volunteers and Students

Staff and volunteers (collectively "staff") are prohibited from engaging in a romantic or sexual relationship with a student over whom they exert control or influence, real or perceived. Such control or influence includes, but is not limited to, service as a formal or informal advisor to a student organization or club, university program or activity; exercising responsibility over a student's academic status, such as academic advising; financial aid or residency determinations; or exercising responsibility over a student's housing such as a community assistant or director would exercise.

A staff member who, prior to the effective date of this policy, exercises control or influence as described above over a student with whom the staff member has an existing romantic or sexual relationship shall disclose the existance of the relationship to the head of their department or college. The head of the department or college shall immediately take steps to ensure that moving forward the staff member has no control or influence over the student.

This policy is in addition to all other university policies addressing the relationship of employees, faculty, or volunteers with students. Employment relationships shall be governed by existing university policy. Violation of this policy may lead to counseling or disciplinary action up to and including termination of employment. 

Crowd-funding Gila monster DNA analysis!

The Gila monster is an amazing creature for so many reasons, and now our lab and collaborators are going to be generating the first stages needed to understand its genome. 

To do this we are crowd-funding the money needed for these first steps, which will involve analyzing DNA from six different individuals (three males and three females). 

experiment.com/gilamonster


We are competing in an Animal Super power competition. The project with the most backers (not amount) wins an extra $1500 from Experiment.com towards their goal! (Second and third place also are awarded extra $ towards their project.) That would be fantastic! If you cannot contribute, please share

Super-power: Gila monsters are the only venomous lizard in the United States (and only one of two venomous lizards anywhere!), and a peptide in their venom is being used in successful clinical treatments for Type-II diabetes. Unlike most reptiles, they store fat in their tails, and store water in their bladders! They're the most amazing kind of monster.

For updates about the project, check out our lab notes: 
* Gila monster sex chromosomes: https://experiment.com/u/Xg1LQ
* Why don't we already have a Gila monster genome? https://experiment.com/u/mbQwdA

Gila monster genome!

Gila monster genome!

How to extract DNA from bananas

You can extract DNA from your food at home! We made instructional handouts in English and Spanish

These photos are from an outreach event where we helped people extract DNA from Bananas using common household products:

Saturday February 27, 2016
Night of the Open Door
Banana DNA Extractions and Phylogenetics

Although they had us in a lab, you can find all of the materials at the grocery store and do this in your own home or classroom: 

Materials

  • Ripe banana
  • Half cup of water
  • Teaspoon of salt
  • Resealable zip-top bag
  • Dishwashing soap or detergent
  • Rubbing alcohol
  • Coffee filter
  • Narrow glass
  • Narrow wooden stirrer
Busy extracting DNA!

Busy extracting DNA!

The whole process takes about 20minutes from start to finish, but what a finish: 

Strands of DNA from bananas

Strands of DNA from bananas

And what a great group of people helping to raise awareness about how awesome DNA is and what it can be used for!

Wilson Sayres lab, DNA extraction team

Wilson Sayres lab, DNA extraction team

Summer REU Participants

Two students from the lab were selected to participate in summer REUs (Research Experience for Undergraduates):

Sarah Brotman: Life Sciences Summer Research Programs (LSSURP), Cancer Research, Education and Training Experience (CREATE) at the University of Minnesota.

Daniel Cotter: 2016 UCSF Summer Research Training Program (SRTP)

Congratulations Sarah and Danny!

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

Targeted chromosomal transocations and essential gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans Chen et al. (2015) in Genetics

Miscellaneous

Holocene shifts in the assembly of plant and animal communities implicate human impacts Lyons et al. (2016) in Nature

Influence of extreme weather disasters on global crop production Lesk et al. (2016) in Nature

Multidrug evolutionary strategies to reverse antibiotic resistance Baym et al. (2016) in Science

Five selfish reasons to work reproducibly Markowetz (2015) in Genome Biology

Free mate choice enhances conservation breeding in the endangered giant panda Martin-Wintle et al. (2015) in Nature Communications

Rarity in mass extinctions and the future of ecosystems Hull et al. (2015) in Science

The founder strains of the collaborative cross express a complex combination of advantageous and deleterious traits for male reproduction Odet et al. (2015) in G3

Controlled access under review: improving the governance of genomic data access Shabani et al. (2015) in PLOS Biology

 

Weekly Roundup - December 4, 2015

Every week, members of the Wilson Sayres’ lab scour journals for interesting and relevant (to lab research) articles. Here’s what we found the week of December 4, 2015:

Sex Chromosomes

QTL mapping of sex determination loci supports an ancient pathway in ants and honey bees Miyakawa and Mikheyev (2015) in PLoS Genetics

Intergenomic interacations between mitochondrial and Y-linked genes shape male mating patterns and fertility in Drosophila melanogaster Yee et al. (2015) in Evolution

Genetics/Genomics

Genomics of cancer and a new era for cancer research Brennan and Wild (2015) in PLoS Genetics

Cattle sex-specific recombination and genetic control from a large pedigree analysis Ma et al. (2015) in PLoS Genetics

Convergent evolution during local adaptation to patchy landscapes Ralph and Coop (2015) in PLoS Genetics

Enhancer runaway and the evolution of diploid gene expression Fyon et al. (2015) in PLoS Genetics

Adaptations to high ethanol reveals complex evolutionary pathways Voordeckers et al. (2015) in PLoS Genetics

The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefontal cortex and reveals an underlying role of early growth response 1 Duclot and Kabbaj (2015) in Genome Biology

Genome-wide analysis of evolutionary markers of human influenza A(H1N1)pdm09 and A(H3N2) may guide selection of vaccine strain candidates Belanov et al. (2015) in Genome Biology and Evolution

Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type Isrie et al. (2015) in American Journal of Human Genetics

Mutations preventing regulated exon skipping in MET cause osteofibrous dysplasia Gray et al. (2015) in American Journal of Human Genetics

The epigenomic landscape of African rainforest hunter-gatherers and farmers Fagny et al. (2015) in Nature Communications

Methods

Calibrating the human mutation rate via ancestral recombination density in diploid genomes Lipson et al. (2015) in PLoS Genetics

Computing workflows for biologists: a roadmap Shade and Teal (2015) in PLoS Biology

Miscellaneous

Ernst Rüdin's unpublished 1922-1925 study "Inheritance of manic-depressive insanity": genetic research findings subordinated to eugenic ideology Kösters et al. (2015) in PLoS Genetics

Sex differences in parental care: gametic investment, sexual selection, and social environment Liker et al. (2015) in Evolution

Democratizing education? Examining access and usage patterns in massive open online courses Hansen and Reich (2015) in Science

Protected areas and global conservation of migratory birds Runge et al. (2015) in Science

Weekly Roundup - Week of November 27, 2015

Every week, members of the Wilson Sayres’ lab scour journals for interesting and relevant (to lab research) articles. Here’s what we found the week of November 27, 2015:

Sex Chromosomes

Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans Rogers (2015) in Molecular Biology and Evolution

Differentiation of sex chromosomes and karyotype characterisation in the dragonsnake Xenodermus javanicus (Squamata: Xenodermatidae) Rovatsos et al. (2015) in Cytogenic and Genome Research

Genomics/Genetics

Allelic mutations of KITLG, encoding KIT ligand, cause asymmetric and unilateral hearing loss and Waardenburg Syndrome Type 2. Zazo Seco et al. (2015) in American Journal of Human Genetics

Family wide molecular adaptations to underground life in African mole-rats revealed by phylogenomic analysis Davies et al. (2015) in Molecular Biology and Evolution

Reintroduction of a homocysteine level-associated allele into East Asians by Neanderthal introgression Hu et al. (2015) in Molecular Biology and Evolution

A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures Olalde et al. (2015) in Molecular Biology and Evolution

Polymerase zeta activity is linked to replication timing in humans: evidence from mutational signatures Seplyarskiy et al. (2015) in Molecular Biology and Evolution

Exploring massive incomplete lineage sorting in Arctoids (Laurasiatheria, Carnivora) Doronina et al. (2015) in Molecular Biology and Evolution

Population level purifying selection and gene expression shape subgenome evolution in maize Pophaly and Tellier (2015) in Molecular Biology and Evolution

The mosaic ancestry of the Drosophila genetic reference panel and the D. melanogaster reference genome reveals a network of epistatic fitness interactions Pool (2015) in Molecular Biology and Evolution

Inferring selective constraint from population genomic data suggest recent regulatory turnover in the human brain Schrider and Kern (2015) in Molecular Biology and Evolution

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors Asgharian et al. (2015) in Proceedings of the Royal Society: B

Identification and characterization of essential genes in the human genome Wang et al. (2015) in Science

Hemichordate genomes and deuterostome origins Simakov et al. (2015) in Nature

Stable recombination hotspots in birds Singhal et al. (2015) in Science

Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration Liu et al. (2015) in Nature Communications

Methods/Data

A comparative study of RNA-seq analysis strategies Jänes et al. (2015) in Briefings in Bioinformatics

Assessing the consistency of public human tissue RNA-seq data sets Danielsson et al. (2015) in Briefings in Bioinformatics

Beyond fruit-flies: population genomic advances in non-Drosohpila arthropods Hasselmann et al. (2015) in Briefings in Functional Genomics

Miscellaneous

Hybridization and the origin of contagious asexuality in Daphnia pulex Xu et al. (2015) in Molecular Biology and Evolution

Genes, circuits, and precision therapies for autism and related neurodevelopmental disorders Sahin and Sur (2015) in Science

The effects of life history and sexual selection on male and female plumage colouration Dale et al. (2015) in Nature

 

Weekly Roundup - Week of November 13, 2015

Every week, members of the Wilson Sayres’ lab scour journals for interesting and relevant (to lab research) articles. Here’s what we found the week of November 13, 2015:

Sex Chromosomes

The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex systems Charlesworth (2015) in Evolutionary Applications

Genetics/Genomics

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens Galen et al. (2015) in PNAS

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia Tackney et al. (2015) in PNAS

Allelic variation of cytochrome P450s drives resistance to bednet insecticides in a major malaria vector Ibrahim et al. (2015) in PLoS Genetics

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence Sonay et al (2015) in Genome Research

GC skew defines distinct RNA polymerase pause sites in CpG island promoters Kellner et al. (2015) in Genome Research

Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background Elvers et al. (2015) in Genome Research

Genetic adaptation to climate in white spruce involves small to moderate allele frequency shifts in functionally diverse genes Hornoy et al. (2015) in Genome Biology and Evolution

Calibrating the human mutation rate via ancestral recombination density in diploid genomes Lipson et al. (2015) in PLoS Genetics

The genomics of ecological vicariance in threespine stickleback fish Roesti et al. (2015) in Nature Communications

Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent Gallego Llorente et al. (2015) in Nature

Inferring the genetic history of lactase persistence along the Italian peninsula from a large genomic interval surrounding the LCT gene De Fanti et al. (2015) in American Journal of Physical Anthropology

CRISPR

This week, Genome Biology published a series of articles on CRISPR-Cas9:

Research Highlights

The Cpf1 CRISPR-Cas protein expands genome-editing tools Fagerlund et al. (2015) in Genome Biology

Pop in, pop out: a novel gene-targeting strategy for use with CRISPR-Cas9 Kühn and Chu (2015) in Genome Biology

CRISPR sabotage van der Oost and Brouns (2015) in Genome Biology

Reviews and Research Articles

Diversity of CRISPR-Cas immune systems and molecular machines Barrangou (2015) in Genome Biology

A novel two-step genome editing strategy with CRISPR-Cas9 provides new insights into telomerase action and TERT gene expression Xi et al. (2015) in Genome Biology

CRISPR/Cas9-mediated viral interference in plants Ali et al. (2015) in Genome Biology

Methods

Dating tips for divergence-time estimation O'Reilly et al. (2015) in Trends in Genetics

A new Fst-based method to uncover local adaptation using environmental variables de Villemereuil and Gaggiotti (2015) in Methods in Ecology and Evolution

Miscellaneous

Why significant variables aren't automatically good predictors Lo et al. (2015) in PNAS

Evolution and dispersal of mammoths across the Northern Hemisphere Lister and Sher (2015) in Science

Public data archiving in ecology and evolution: how well are we doing? Roche et al. (2015) in PLoS Biology

Widespread exploitation of the honeybee by early Neolithic farmers Roffet-Salque et al. (2015) in Nature