Next-generation cophylogeny: unravelling eco-evolutionary processes

I Blasco-Costa, A Hayward, R Poulin… - Trends in Ecology & …, 2021 - cell.com
A fundamental question in evolutionary biology is how microevolutionary processes
translate into species diversification. Cophylogeny provides an appropriate framework to …

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high‐Andean diversification (Asteraceae: Astereae: Diplostephium)

OM Vargas, EM Ortiz, BB Simpson - New Phytologist, 2017 - Wiley Online Library
High‐throughput sequencing is hel** biologists to overcome the difficulties of inferring the
phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of …

PACo: a novel procrustes application to cophylogenetic analysis

JA Balbuena, R Míguez-Lozano, I Blasco-Costa - PloS one, 2013 - journals.plos.org
We present Procrustean Approach to Cophylogeny (PACo), a novel statistical tool to test for
congruence between phylogenetic trees, or between phylogenetic distance matrices of …

FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction

M Musil, RT Khan, A Beier, J Stourac… - Briefings in …, 2021 - academic.oup.com
There is a great interest in increasing proteins' stability to widen their usability in numerous
biomedical and biotechnological applications. However, native proteins cannot usually …

Unifying approaches from statistical genetics and phylogenetics for map** phenotypes in structured populations

JG Schraiber, MD Edge, M Pennell - PLoS biology, 2024 - journals.plos.org
In both statistical genetics and phylogenetics, a major goal is to identify correlations between
genetic loci or other aspects of the phenotype or environment and a focal trait. In these 2 …

Hundreds of nuclear and plastid loci yield novel insights into orchid relationships

OA Pérez‐Escobar, S Dodsworth… - American Journal of …, 2021 - Wiley Online Library
PREMISE The inference of evolutionary relationships in the species‐rich family Orchidaceae
has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous …

paco: implementing Procrustean Approach to Cophylogeny in R

MC Hutchinson, EF Cagua, JA Balbuena… - Methods in Ecology …, 2017 - Wiley Online Library
The concordance of evolutionary histories and extant species interactions provides a useful
metric for addressing questions of how the structure of ecological communities is influenced …

Phylogenetic convolutional neural networks in metagenomics

D Fioravanti, Y Giarratano, V Maggio, C Agostinelli… - BMC …, 2018 - Springer
Abstract Background Convolutional Neural Networks can be effectively used only when data
are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of …

The radiation of cynodonts and the ground plan of mammalian morphological diversity

M Ruta, J Botha-Brink, SA Mitchell… - Proceedings of the …, 2013 - royalsocietypublishing.org
Cynodont therapsids diversified extensively after the Permo-Triassic mass extinction event,
and gave rise to mammals in the Jurassic. We use an enlarged and revised dataset of …

Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China

H Kong, FL Condamine, AJ Harris, J Chen… - Molecular …, 2017 - Wiley Online Library
Karst ecosystems in southern China are species‐rich and have high levels of endemism, yet
little is known regarding the evolutionary processes responsible for the origin and …