4.5 Article

An elevational shift facilitated the Mesoamerican diversification of Azure-hooded Jays (Cyanolyca cucullata) during the Great American Biotic Interchange

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 Ecology

Disentangling the historical routes to community assembly in the global epicentre of biodiversity

Bouwe R. Reijenga et al.

Summary: The turnover of bird species across elevation can be explained by the displacement of elevation ranges upon contact, while the overlap of species along elevation gradients is primarily explained by conservatism of elevational ranges.

GLOBAL ECOLOGY AND BIOGEOGRAPHY (2023)

Article Evolutionary Biology

De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica

Devon A. DeRaad et al.

Summary: The study announces the successful assembly of a new reference genome for the California Scrub-Jay, providing high-quality genomic resources for future research on the evolutionary history of this species and related species.

JOURNAL OF HEREDITY (2023)

Article Ecology

Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley's classic species conundrum in Pipilo towhees

Devon A. DeRaad et al.

Summary: The study reassessed the gradient between Collared Towhee and Spotted Towhee in Central Mexico and found that the genetic and phenotypic traits of the cline centers have not shifted over 70 years, indicating the secondary contact between these species likely dates to the Pleistocene. The towhee system offers insights into the potential outcomes of hybridization across a dynamic landscape, including the formation of incipient hybrid lineages and novel genomic and phenotypic combinations.

EVOLUTION (2023)

Article Ecology

On the predictability of phenotypic divergence in geographic isolation

Benjamin G. Freeman et al.

Summary: In this study, we examined the evolution patterns of traits in 54 pairs of sister species of Andean forest birds living on either side of the Maranon Gap. We found that sexual traits showed predictable divergence correlated with genetic distance, while ecological traits showed unpredictable divergence. This indicates that sexual trait divergence occurs independently of adaptive ecological divergence in the Andean avifauna.

EVOLUTION (2023)

Article Evolutionary Biology

Geodispersal of the typical Neotropical cenocron from South America to the Mexican Transition Zone: a cladistic biogeographical test

Margarita M. Lopez-Garcia et al.

Summary: The analysis reveals that the Typical Neotropical taxa have dispersed from South America to the Mexican Transition Zone from the Pliocene to the present. Additionally, evidence of vicariant events related to the lifting of the Northern Andes and climatic changes during the Pleistocene were also found.

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2022)

Review Plant Sciences

The Andes through time: evolution and distribution of Andean floras

Oscar Alejandro Perez-Escobar et al.

Summary: This study provides a synthesis of the vascular plant diversity in the Andes and reveals that the Northern Andean mid-elevation cloud forests are the most species-rich ecosystems. The Andes play a crucial role as a source and sink of Neotropical plant diversity, and there have been significant biotic interchanges between the Andes, Amazonia, and other Neotropical biomes throughout history.

TRENDS IN PLANT SCIENCE (2022)

Article Biochemistry & Molecular Biology

snpfiltr: An R package for interactive and reproducible SNP filtering

Devon DeRaad

Summary: The SNPfiltR package in R provides functionalities for customizable and reproducible SNP filtering pipeline. It extends existing SNP filtering functionalities by automating the visualization of key parameters.

MOLECULAR ECOLOGY RESOURCES (2022)

Article Evolutionary Biology

Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays

Devon A. DeRaad et al.

Summary: Complex speciation can complicate phylogenetic relationships and species limits, but a comprehensive approach to genomic reconstruction can clarify evolutionary history. By studying Scrub-Jays, we found evidence supporting the distinctiveness of a southern Mexico lineage and the species status of a Texas endemic lineage. Despite clear overall isolation and species status, complex gene flow between California Scrub-Jays and Woodhouse's Scrub-Jays resulted in discordant gene trees.

SYSTEMATIC BIOLOGY (2022)

Article Ecology

Phylogenomics of arboreal alligator lizards shed light on the geographical diversification of cloud forest-adapted biotas

Jorge Gutierrez-Rodriguez et al.

Summary: This study provides insights into the geographical diversification of a complex of arboreal alligator lizards in neotropical montane cloud forests. The genomic data reveals a marked genetic structure within the complex, and the demographic reconstructions support the impact of Pleistocene geologic and climatic changes on the distribution of their habitats. The results suggest a model of divergence with introgression, indicating multiple opportunities for both allopatric isolation and secondary contact during Quaternary climatic oscillations.

JOURNAL OF BIOGEOGRAPHY (2022)

Article Biochemistry & Molecular Biology

More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens

Whitney L. E. Tsai et al.

MOLECULAR ECOLOGY RESOURCES (2020)

Article Ornithology

Extensive paraphyly in the typical owl family (Strigidae)

Jessie F. Salter et al.

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Article Evolutionary Biology

Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird

Madhvi X. Venkatraman et al.

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2019)

Article Biochemistry & Molecular Biology

Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands

Whitney L. E. Tsai et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)

Article Ecology

pavo 2: New tools for the spectral and spatial analysis of colour in r

Rafael Maia et al.

METHODS IN ECOLOGY AND EVOLUTION (2019)

Article Evolutionary Biology

Leapfrogging the Mexican highlands: influence of biogeographical and ecological factors on the diversification of highland species

Itzue W. Caviedes-Solis et al.

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2018)

Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

Article Multidisciplinary Sciences

Climate change causes upslope shifts and mountaintop extirpations in a tropical bird community

Benjamin G. Freeman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemistry & Molecular Biology

VCFR: a package to manipulate and visualize variant call format data in R

Brian J. Knaus et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Article Biochemistry & Molecular Biology

Hidden histories of gene flow in highland birds revealed with genomic markers

Eugenia Zarza et al.

MOLECULAR ECOLOGY (2016)

Review Multidisciplinary Sciences

Formation of the Isthmus of Panama

Aaron O'Dea et al.

SCIENCE ADVANCES (2016)

Article Multidisciplinary Sciences

Biological evidence supports an early and complex emergence of the Isthmus of Panama

Christine D. Bacon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Middle Miocene closure of the Central American Seaway

C. Montes et al.

SCIENCE (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Evolutionary Biology

Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard

Robert W. Bryson et al.

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Evolutionary Biology

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist et al.

SYSTEMATIC BIOLOGY (2012)

Article Evolutionary Biology

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

Brant C. Faircloth et al.

SYSTEMATIC BIOLOGY (2012)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Article Ecology

The Central American land bridge as an engine of diversification in New World doves

Kevin P. Johnson et al.

JOURNAL OF BIOGEOGRAPHY (2011)

Article Ecology

Neotropical biodiversity: timing and potential drivers

Valenti Rull

TRENDS IN ECOLOGY & EVOLUTION (2011)

Article Biochemical Research Methods

DensiTree: making sense of sets of phylogenetic trees

Remco R. Bouckaert

BIOINFORMATICS (2010)

Article Biodiversity Conservation

The Great American Biotic Interchange revisited

Sarah Cody et al.

ECOGRAPHY (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 Biology

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

B. R. Barber et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

Review Biochemistry & Molecular Biology

Historical biogeography and speciation in the Neotropical highlands: Molecular phylogenetics of the jay genus Cyanolyca

Elisa Bonaccorso

MOLECULAR PHYLOGENETICS AND EVOLUTION (2009)

Article Multidisciplinary Sciences

The Great American Biotic Interchange in birds

Jason T. Weir et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Calibrating the avian molecular clock

J. T. Weir et al.

MOLECULAR ECOLOGY (2008)

Article Evolutionary Biology

Species concepts and species delimitation

Kevin De Queiroz

SYSTEMATIC BIOLOGY (2007)

Article Biochemistry & Molecular Biology

A multilocus phylogeny of New World jay genera

Elisa Bonaccorso et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2007)

Article Evolutionary Biology

Avifaunal interchange across the Panamanian isthmus: insights from Campylorhynchus wrens

F. Keith Barker

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2007)

Review Biochemistry & Molecular Biology

Molecular systematics and biogeography of the Neotropical monkey genus, Alouatta

L Cortes-Ortiz et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)

Article Multidisciplinary Sciences

Biodiversity hotspots for conservation priorities

N Myers et al.

NATURE (2000)

Review Ecology

Cladistic biogeography of the Mexican transition zone

CJ Marshall et al.

JOURNAL OF BIOGEOGRAPHY (2000)