Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

Is homoploid hybrid speciation that rare? An empiricist’s view

(2017) G Nieto Feliner et al.   HEREDITY

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

(2017) Amanda R. De La Torre et al.   MOLECULAR BIOLOGY AND EVOLUTION

Introgression from Populus balsamifera underlies adaptively significant variation and range boundaries in P. trichocarpa

(2017) Adriana Suarez-Gonzalez et al.   NEW PHYTOLOGIST

Rapid hybrid speciation in Darwin’s finches

(2017) Sangeet Lamichhaney et al.   SCIENCE

Genomic evidence for polyphyletic origins and interlineage gene flow within complex taxa: a case study ofPicea brachytylain the Qinghai-Tibet Plateau

(2016) Dafu Ru et al.   MOLECULAR ECOLOGY

Genomic and functional approaches reveal a case of adaptive introgression fromPopulus balsamifera(balsam poplar) inP. trichocarpa(black cottonwood)

(2016) Adriana Suarez-Gonzalez et al.   MOLECULAR ECOLOGY

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

(2016) Andrew D. Foote et al.   Nature Communications

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Paleoaltimetry reconstructions of the Tibetan Plateau: progress and contradictions

(2015) Tao Deng et al.   National Science Review

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)

(2015) Nicolas Delhomme et al.   PLoS One

The role of homoploid hybridization in evolution: A century of studies synthesizing genetics and ecology

(2014) S. B. Yakimowski et al.   AMERICAN JOURNAL OF BOTANY

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

(2014) Molly Schumer et al.   EVOLUTION

Distributional dynamics and interspecific gene flow inPicea likiangensisandP. wilsoniitriggered by climate change on the Qinghai-Tibet Plateau

(2014) Yongshuai Sun et al.   JOURNAL OF BIOGEOGRAPHY

Pliocene intraspecific divergence and Plio-Pleistocene range expansions withinPicea likiangensis(Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau

(2014) Long Li et al.   MOLECULAR ECOLOGY

Origin and speciation of Picea schrenkiana and Picea smithiana in the Center Asian Highlands and Himalayas

(2014) Lili Li et al.   PLANT MOLECULAR BIOLOGY REPORTER

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication

(2014) Mingzhou Li et al.   Scientific Reports

Population genetic evidence for speciation pattern and gene flow between Picea wilsonii, P. morrisonicola and P. neoveitchii

(2013) Jiabin Zou et al.   ANNALS OF BOTANY

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genomic Divergence during Speciation Driven by Adaptation to Altitude

(2013) Mark A. Chapman et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion

(2013) Yongshuai Sun et al.   MOLECULAR ECOLOGY

A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences

(2013) Jared D. Lockwood et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

(2013) Mingzhou Li et al.   NATURE GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The genomics of selection in dogs and the parallel evolution between dogs and humans

(2013) Guo-dong Wang et al.   Nature Communications

Genomic islands of divergence are not affected by geography of speciation in sunflowers

(2013) S. Renaut et al.   Nature Communications

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

HYBRID SPECIATION AND INDEPENDENT EVOLUTION IN LINEAGES OF ALPINE BUTTERFLIES

(2012) Chris C. Nice et al.   EVOLUTION

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

Distinct Niche Divergence Characterizes the Homoploid Hybrid Speciation of Pinus densata on the Tibetan Plateau

(2011) Jian-Feng Mao et al.   AMERICAN NATURALIST

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau

(2011) Fang K. Du et al.   NEW PHYTOLOGIST

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Genetic Evidence for Hybrid Trait Speciation in Heliconius Butterflies

(2010) Camilo Salazar et al.   PLoS Genetics

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci

(2009) Yuan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing

(2008) Yaniv Erlich et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

THE RATE OF GENOME STABILIZATION IN HOMOPLOID HYBRID SPECIES

(2007) C. Alex Buerkle et al.   EVOLUTION