Genetic diversity and conservation units: dealing with the species-population continuum in the age of genomics

DJ Coates, M Byrne, C Moritz - Frontiers in Ecology and Evolution, 2018 - frontiersin.org
Current approaches to biodiversity conservation are largely based on geographic areas,
ecosystems, ecological communities, and species, with less attention on genetic diversity …

Practical considerations for plant phylogenomics

MR McKain, MG Johnson… - Applications in plant …, 2018 - Wiley Online Library
The past decade has seen a major breakthrough in our ability to easily and inexpensively
sequence genome‐scale data from diverse lineages. The development of high‐throughput …

False gene and chromosome losses in genome assemblies caused by GC content variation and repeats

J Kim, C Lee, BJ Ko, DA Yoo, S Won, AM Phillippy… - Genome biology, 2022 - Springer
Background Many short-read genome assemblies have been found to be incomplete and
contain mis-assemblies. The Vertebrate Genomes Project has been producing new …

Bayesian divergence-time estimation with genome-wide single-nucleotide polymorphism data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian …

M Stange, MR Sánchez-Villagra… - Systematic …, 2018 - academic.oup.com
The closure of the Isthmus of Panama has long been considered to be one of the best
defined biogeographic calibration points for molecular divergence-time estimation …

[HTML][HTML] The role of DNA mismatch repair in immunotherapy of human cancer

Y He, L Zhang, R Zhou, Y Wang… - International Journal of …, 2022 - ncbi.nlm.nih.gov
DNA mismatch repair (MMR) is an important pathway which helps to maintain genomic
stability. Mutations in DNA MMR genes are found to promote cancer initiation and foster …

Allele phasing greatly improves the phylogenetic utility of ultraconserved elements

T Andermann, AM Fernandes, U Olsson… - Systematic …, 2019 - academic.oup.com
Advances in high-throughput sequencing techniques now allow relatively easy and
affordable sequencing of large portions of the genome, even for nonmodel organisms. Many …

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

GA Bravo, A Antonelli, CD Bacon, K Bartoszek… - PeerJ, 2019 - peerj.com
ABSTRACT Building the Tree of Life (ToL) is a major challenge of modern biology, requiring
advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that …

Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

NA Mason, NK Fletcher, BA Gill, WC Funk… - Systematics and …, 2020 - Taylor & Francis
Species are a fundamental unit of biodiversity that are delimited via genetic data and
coalescent-based methods with increasing frequency. Despite the widespread use of …

Rapid Radiation and Rampant Reticulation: Phylogenomics of South American Liolaemus Lizards

D Esquerré, JS Keogh, D Demangel… - Systematic …, 2022 - academic.oup.com
Understanding the factors that cause heterogeneity among gene trees can increase the
accuracy of species trees. Discordant signals across the genome are commonly produced …

DNA-based approaches for dairy products authentication: A review and perspectives

M Baptista, JT Cunha, L Domingues - Trends in Food Science & …, 2021 - Elsevier
Background Food fraud has become an increasingly worldwide problem mainly driven by
rapid innovation in the food sector and constantly changing consumer's choices. This led to …