4.7 Article

Speciation without gene-flow in hybridizing deer

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Evolutionary Biology

Population genomics of free-ranging Great Plains white-tailed and mule deer reflects a long history of interspecific hybridization

Fraser J. Combe et al.

Summary: Hybridization is a natural process that occurs at species boundaries, which can either promote speciation or break down species barriers, with minimal impact on management outcomes of distinct populations. White-tailed deer and mule deer in North America have overlapping distributions and capacity for interspecific hybridization. Recent environmental changes have led to mule deer contracting westward and white-tailed deer expanding westward, increasing gene flow and raising conservation implications.

EVOLUTIONARY APPLICATIONS (2022)

Article Zoology

Mitochondrial capture and subsequent genetic divergence generates a novel haplogroup: evidence from ancient and ongoing hybridization in mule and white-tailed deer

Emily A. Wright et al.

Summary: White-tailed deer and mule deer are sympatric in North America, and approximately 24% of individuals in some populations are hybrids. Phylogenetic analysis of mitochondrial DNA sequences revealed that white-tailed deer and mule deer diverged approximately 3.13 million years ago, followed by an ancient hybridization event around 1.32 million years ago. This hybridization event resulted in a unique and broadly distributed haplogroup found in western North America.

JOURNAL OF MAMMALOGY (2022)

Article Genetics & Heredity

Consequences of Hybridization in Mammals: A Systematic Review

Roya Adavoudi et al.

Summary: Hybridization, the breeding between two distinct taxonomic units, can introduce novel adaptive variation and increase fitness, but also threaten species genetic integrity and survival. Most studies focus on documenting hybridization events and analyzing their causes, while little is known about the consequences of hybridization and its impact on the parental species.
Editorial Material Evolutionary Biology

Global adaptation complicates the interpretation of genome scans for local adaptation

Tom R. Booker et al.

Summary: Spatially varying selection increases genetic differentiation between demes, leading to outliers in genome-wide distribution of summary statistics like F-ST, often misinterpreted as evidence of local adaptation. Global adaptation contributes significantly to molecular evolution, generating genetic differentiation patterns that may mistakenly be attributed to local adaptation in F-ST.

EVOLUTION LETTERS (2021)

Article Biochemistry & Molecular Biology

Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears

Axel Barlow et al.

Summary: Paleogenomics are valuable for studying evolutionary processes in real time, but challenges exist in recovering genetic data over extended timescales. Analysis of a 360,000 year old cave bear genome suggests widespread mito-nuclear discordance in the group, with mitochondrial transfer playing a key role in explaining the discordance. This study highlights the importance of petrous bones in extending the depth and time span of paleogenomic research.

CURRENT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Ancient and modern stickleback genomes reveal the demographic constraints on adaptation

Melanie Kirch et al.

Summary: The study used paleogenomics to compare ancient and modern stickleback populations, finding that modern lake populations have incomplete adaptation to freshwater, likely due to founder effects, drift, and selection reducing ancestral variation in the founder populations.

CURRENT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

African and Asian leopards are highly differentiated at the genomic level

Johanna L. A. Paijmans et al.

Summary: Leopards are the only big cats widely distributed in Africa and Asia, but their phylogeography and population history have not been studied with genomic tools. Research shows that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago, and they have higher population structuring and stronger isolation by distance compared to African leopards.

CURRENT BIOLOGY (2021)

Article Ecology

Defining the speciation continuum

Sean Stankowski et al.

Summary: The understanding of speciation is hindered by the long timescale it usually occurs over. The concept of a speciation continuum attempts to address this issue by reconstructing the process from multiple speciation events, but there is disagreement among researchers about its actual implications. The speciation continuum is defined as a continuum of reproductive isolation, providing a foundation for understanding the continuum of reproductive isolation in present-day populations.

EVOLUTION (2021)

Article Evolutionary Biology

Extent and direction of introgressive hybridization of mule and white-tailed deer in western Canada

Ty Russell et al.

Summary: Hybridization between mule deer and white-tailed deer is common in western North America. This study in western Canada found hybridization rates of around 1.0%, with white-tailed-like hybrids being more common. The research expanded on past studies by increasing hybrid detection power, demonstrating new molecular resources for future research, and observing asymmetrical directionality of introgression.

EVOLUTIONARY APPLICATIONS (2021)

Article Evolutionary Biology

Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer

Tyler K. Chafin et al.

Summary: Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer from eastern North America, leading to wildlife management becoming a national priority. A study in Arkansas utilizing molecular tools found genetic signatures from historic translocations are apparent and geographic barriers now influence the distribution of contemporary ancestry in deer populations.

EVOLUTIONARY APPLICATIONS (2021)

Article Ecology

Whole-genome resequencing reveals persistence of forest-associated mammals in Late Pleistocene refugia along North America's North Pacific Coast

Jocelyn P. Colella et al.

Summary: This study used genomic data to test the diversification processes of forest martens in North America, revealing the existence of forest-associated martens along the western edge of the Alexander Archipelago. This discovery enhances our understanding of refugial paleoenvironments and their impact on diversity in complex landscapes.

JOURNAL OF BIOGEOGRAPHY (2021)

Article Ecology

Phylogeographic history of Japanese macaques

Tsuyoshi Ito et al.

Summary: This study elucidates the phylogeographic variation of Japanese macaques, showing that it is mainly due to northeast-southwest divergence during the glacial period, followed by gene flow. Phylogenetic relationships and past distributions during the Last Glacial Maximum were inferred using genomic data and ecological niche modelling.

JOURNAL OF BIOGEOGRAPHY (2021)

Article Evolutionary Biology

Phylogeography of Cedros and Tiburon Island Mule Deer in North America's Desert Southwest

Ona S. Alminas et al.

Summary: Mule deer in Mexico are facing conservation concerns, particularly the subspecies on islands. Genetic studies reveal unique genetic features in Cedros and Tiburon Island deer, emphasizing the need for conservation efforts to ensure their persistence and survival.

JOURNAL OF HEREDITY (2021)

Article Biochemistry & Molecular Biology

Ancient and modem genomes unravel the evolutionary history of the rhinoceros family

Shanlin Liu et al.

Summary: The study revealed an early divergence between rhinoceros lineages, resolving phylogenetic debates; while most rhinoceros genomes exhibit low levels of diversity, modern species have reduced genetic diversity and increased inbreeding.
Article Biochemistry & Molecular Biology

Balancing selection maintains ancient polymorphisms at conserved enhancers for the olfactory receptor genes of a Chinese marine fish

Qiaohong Liu et al.

Summary: The study demonstrates the role of balancing selection on the conserved enhancers of olfactory receptor genes in the Chinese sleeper, highlighting a mechanism for maintaining genetic diversity and adaptation in gene pools. This provides insight into how regulatory elements can contribute to receptor diversity and environmental adaptation.

MOLECULAR ECOLOGY (2021)

Article Genetics & Heredity

Tracking human population structure through time from whole genome sequences

Ke Wang et al.

PLOS GENETICS (2020)

Article Genetics & Heredity

Powerful Inference with the D-Statistic on Low-Coverage Whole-Genome Data

Samuele Soraggi et al.

G3-GENES GENOMES GENETICS (2018)

Review Evolutionary Biology

What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species

C. Ryan Campbell et al.

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2018)

Article Biochemistry & Molecular Biology

Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection

Federica Pierini et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Ecology

Genetic Structure and Recovery of White-Tailed Deer in Missouri

Kris Budd et al.

JOURNAL OF WILDLIFE MANAGEMENT (2018)

Article Genetics & Heredity

Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

Jonas Meisner et al.

GENETICS (2018)

Article Archaeology

The magic of improbable appendages: Deer antler objects in the archaeological record of the American South

Tanya M. Peres et al.

JOURNAL OF ARCHAEOLOGICAL SCIENCE-REPORTS (2018)

Article Biochemical Research Methods

Mosdepth: quick coverage calculation for genomes and exomes

Brent S. Pedersen et al.

BIOINFORMATICS (2018)

Article Ecology

Factors influencing reproductive success in male white-tailed deer

Chad H. Newbolt et al.

JOURNAL OF WILDLIFE MANAGEMENT (2017)

Article Multidisciplinary Sciences

Extraordinarily rapid speciation in a marine fish

Paolo Momigliano et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Plant Sciences

Natural hybridization in mangroves - an overview

P. Ragavan et al.

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY (2017)

Article Psychology, Biological

Mother-young recognition in goitered gazelle during hiding period

D. A. Blank et al.

BEHAVIOURAL PROCESSES (2017)

Article Biochemical Research Methods

MultiQC: summarize analysis results for multiple tools and samples in a single report

Philip Ewels et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

Sambamba: fast processing of NGS alignment formats

Artem Tarasov et al.

BIOINFORMATICS (2015)

Article Genetics & Heredity

Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities

Molly Schumer et al.

PLOS GENETICS (2015)

Article Biochemistry & Molecular Biology

Evaluating the Use of ABBA-BABA Statistics to Locate Introgressed Loci

Simon H. Martin et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Anatomy & Morphology

Reconstruction and Morphometric Analysis of the Nasal Airway of the White-Tailed Deer (Odocoileus virginianus) and Implications Regarding Respiratory and Olfactory Airflow

Allison N. Ranslow et al.

ANATOMICAL RECORD-ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Review Biochemistry & Molecular Biology

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

Tami E. Cruickshank et al.

MOLECULAR ECOLOGY (2014)

Article Genetics & Heredity

Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels et al.

NATURE GENETICS (2014)

Article Multidisciplinary Sciences

What Cues Do Ungulates Use to Assess Predation Risk in Dense Temperate Forests?

Dries P. J. Kuijper et al.

PLOS ONE (2014)

Article Multidisciplinary Sciences

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

J. W. Poelstra et al.

SCIENCE (2014)

Review Biochemistry & Molecular Biology

Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory

Asher D. Cutter

MOLECULAR PHYLOGENETICS AND EVOLUTION (2013)

Article Multidisciplinary Sciences

Mechanistic basis of infertility of mouse intersubspecific hybrids

Tanmoy Bhattacharyya et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

A linear complexity phasing method for thousands of genomes

Olivier Delaneau et al.

NATURE METHODS (2012)

Article Biology

Sperm-related phenotypes implicated in both maintenance and breakdown of a natural species barrier in the house mouse

Jana Albrechtova et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012)

Review Genetics & Heredity

The genomics of speciation-with-gene-flow

Jeffrey L. Feder et al.

TRENDS IN GENETICS (2012)

Article Genetics & Heredity

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

Joseph K. Pickrell et al.

PLOS GENETICS (2012)

Article Biochemistry & Molecular Biology

Testing for Ancient Admixture between Closely Related Populations

Eric Y. Durand et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

A Draft Sequence of the Neandertal Genome

Richard E. Green et al.

SCIENCE (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): Systematics, morphology, and biogeography

Clement Gilbert et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2006)

Review Ecology

Hybridization as an invasion of the genome

J Mallet

TRENDS IN ECOLOGY & EVOLUTION (2005)

Article Biochemistry & Molecular Biology

Comparative recombination rates in the rat, mouse, and human genomes

MI Jensen-Seaman et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal

A Aguilar et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

Evolution and phylogeny of old world deer

C Pitra et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2004)

Review Multidisciplinary Sciences

The genetic legacy of the Quaternary ice ages

G Hewitt

NATURE (2000)