Skyline‐plot methods for estimating demographic history from nucleotide sequences

SYW Ho, B Shapiro - Molecular ecology resources, 2011 - Wiley Online Library
Estimation of demographic history from nucleotide sequences represents an important
component of many studies in molecular ecology. For example, knowledge of a population's …

Isotopic tracking of large carnivore palaeoecology in the mammoth steppe

H Bocherens - Quaternary Science Reviews, 2015 - Elsevier
Isotopic tracking of carnivore palaeoecology is a relatively new approach that yielded
important results for the study of the non-analogue mammoth steppe biome. After describing …

A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA

JD Kapp, RE Green, B Shapiro - Journal of Heredity, 2021 - academic.oup.com
We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing
platform that has been optimized for ancient and degraded DNA. Our approach, the Santa …

Species-specific responses of Late Quaternary megafauna to climate and humans

ED Lorenzen, D Nogués-Bravo, L Orlando, J Weinstock… - Nature, 2011 - nature.com
Despite decades of research, the roles of climate and humans in driving the dramatic
extinctions of large-bodied mammals during the Late Quaternary period remain contentious …

Improving ancient DNA read mapping against modern reference genomes

M Schubert, A Ginolhac, S Lindgreen, JF Thompson… - BMC genomics, 2012 - Springer
Abstract Background Next-Generation Sequencing has revolutionized our approach to
ancient DNA (aDNA) research, by providing complete genomic sequences of ancient …

Partial genomic survival of cave bears in living brown bears

A Barlow, JA Cahill, S Hartmann, C Theunert… - Nature ecology & …, 2018 - nature.com
Although many large mammal species went extinct at the end of the Pleistocene epoch, their
DNA may persist due to past episodes of interspecies admixture. However, direct empirical …

[图书][B] Harvesting the biosphere: what we have taken from nature

V Smil - 2012 - books.google.com
An interdisciplinary and quantitative account of human claims on the biosphere's stores of
living matter, from prehistoric hunting to modern energy production. The biosphere—the …

Inferences from tip‐calibrated phylogenies: a review and a practical guide

A Rieux, F Balloux - Molecular ecology, 2016 - Wiley Online Library
Molecular dating of phylogenetic trees is a growing discipline using sequence data to co‐
estimate the timing of evolutionary events and rates of molecular evolution. All molecular …

True single-molecule DNA sequencing of a pleistocene horse bone

L Orlando, A Ginolhac, M Raghavan, J Vilstrup… - Genome …, 2011 - genome.cshlp.org
Second-generation sequencing platforms have revolutionized the field of ancient DNA,
opening access to complete genomes of past individuals and extinct species. However …

tipdatingbeast: an r package to assist the implementation of phylogenetic tip‐dating tests using beast

A Rieux, CE Khatchikian - Molecular Ecology Resources, 2017 - Wiley Online Library
Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences
sampled at different points in time to coestimate the timing of evolutionary events with rates …