Phylogenetic reconstruction methods: an overview

A De Bruyn, DP Martin, P Lefeuvre - Molecular Plant Taxonomy: Methods …, 2014 - Springer
Initially designed to infer evolutionary relationships based on morphological and
physiological characters, phylogenetic reconstruction methods have greatly benefited from …

The forest for the trees: evaluating molecular phylogenies with an emphasis on higher-level Decapoda

L Timm, HD Bracken-Grissom - Journal of Crustacean Biology, 2015 - academic.oup.com
Since the late 1800s, several infraordinal relationships have been proposed for Decapoda;
however, reaching a consensus among higher-level relationships is proving difficult …

Geological changes of the Americas and their influence on the diversification of the Neotropical kissing bugs (Hemiptera: Reduviidae: Triatominae)

SA Justi, C Galvao, CG Schrago - PLoS neglected tropical …, 2016 - journals.plos.org
Background The family Reduviidae (Hemiptera: Heteroptera), or assassin bugs, is among
the most diverse families of the true bugs, with more than 6,000 species. The subfamily …

Language phylogenies

M Dunn - The Routledge handbook of historical linguistics, 2015 - taylorfrancis.com
Historical linguistics is currently undergoing something of a renaissance. This chapter
examines the extent to which historical linguistics has a general theory of change, and …

Multiple Non-Species-Specific Pathogens Possibly Triggered the Mass Mortality in Pinna nobilis

F Scarpa, D Sanna, I Azzena, D Mugetti, F Cerruti… - Life, 2020 - mdpi.com
The fan mussel, Pinna nobilis, represents the largest bivalve endemic to the Mediterranean
Sea. Since 2016, dramatic mass mortality of this species has been observed in several …

CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models

M Gil, MS Zanetti, S Zoller… - Molecular biology and …, 2013 - academic.oup.com
Markov models of codon substitution naturally incorporate the structure of the genetic code
and the selection intensity at the protein level, providing a more realistic representation of …

A deeper insight into evolutionary patterns and phylogenetic history of ASFV epidemics in Sardinia (Italy) through extensive genomic sequencing

MS Fiori, D Sanna, F Scarpa, M Floris, A Di Nardo… - Viruses, 2021 - mdpi.com
African swine fever virus (ASFV) is the etiological agent of the devastating disease African
swine fever (ASF), for which there is currently no licensed vaccine or treatment available …

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

L Rabaoui, L Yacoubi, D Sanna, M Casu… - Journal of Fish …, 2019 - Wiley Online Library
We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and
cosmopolitan Indo–West Pacific fish species belonging to 54 families and 13 orders. Novel …

Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program

A Rokas - Current protocols in molecular biology, 2011 - Wiley Online Library
Phylogenetic analysis is the study of evolutionary relationships among molecules,
phenotypes, and organisms. In the context of protein sequence data, phylogenetic analysis …

Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries

A Mirand, I Schuffenecker… - Journal of General …, 2010 - microbiologyresearch.org
Human enterovirus 71 (EV-71) is a cause of seasonal epidemics of hand, foot and mouth
disease, and of less common but severe neurological manifestations. Uncertainty persists …