Genome sequencing and population genomics in non-model organisms

H Ellegren - Trends in ecology & evolution, 2014 - cell.com
High-throughput sequencing technologies are revolutionizing the life sciences. The past 12
months have seen a burst of genome sequences from non-model organisms, in each case …

A field guide to whole‐genome sequencing, assembly and annotation

R Ekblom, JBW Wolf - Evolutionary applications, 2014 - Wiley Online Library
Genome sequencing projects were long confined to biomedical model organisms and
required the concerted effort of large consortia. Rapid progress in high‐throughput …

Whole-genome analyses resolve early branches in the tree of life of modern birds

ED Jarvis, S Mirarab, AJ Aberer, B Li, P Houde, C Li… - Science, 2014 - science.org
To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …

Comparative genomics reveals insights into avian genome evolution and adaptation

G Zhang, C Li, Q Li, B Li, DM Larkin, C Lee, JF Storz… - Science, 2014 - science.org
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance
across many research fields. We explored bird macroevolution using full genomes from 48 …

Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates

D Chalopin, M Naville, F Plard… - Genome biology and …, 2015 - academic.oup.com
Transposable elements (TEs) are major components of vertebrate genomes, with major
roles in genome architecture and evolution. In order to characterize both common patterns …

The Genome 10K Project: a way forward

KP Koepfli, B Paten… - Annu. Rev. Anim …, 2015 - annualreviews.org
The Genome 10K Project was established in 2009 by a consortium of biologists and
genome scientists determined to facilitate the sequencing and analysis of the complete …

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

O Mazet, W Rodríguez, S Grusea, S Boitard, L Chikhi - Heredity, 2016 - nature.com
Most species are structured and influenced by processes that either increased or reduced
gene flow between populations. However, most population genetic inference methods …

A fast, reproducible, high-throughput variant calling workflow for population genomics

CD Mirchandani, AJ Shultz… - Molecular Biology …, 2024 - academic.oup.com
The increasing availability of genomic resequencing data sets and high-quality reference
genomes across the tree of life present exciting opportunities for comparative population …

PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers

K Nadachowska‐Brzyska, R Burri, L Smeds… - Molecular …, 2016 - Wiley Online Library
Climatic fluctuations during the Quaternary period governed the demography of species and
contributed to population differentiation and ultimately speciation. Studies of these past …

Genomic flatlining in the endangered island fox

JA Robinson, D Ortega-Del Vecchyo, Z Fan, BY Kim… - Current Biology, 2016 - cell.com
Genetic studies of rare and endangered species often focus on defining and preserving
genetically distinct populations, especially those having unique adaptations [1, 2]. Much less …