We present a methodological phylogenetic reconstruction approach combining Maximum Parsimony and Phylogenetic Networks methods for the study of human evolution applied to phenotypic craniodental characters of 22 hominin species. The approach consists in selecting and validating a tree-like most parsimonious scenario out of several parsimony runs based on various numerical constraints. An intermediate step from tree to network methods is implemented by running an analysis with a reduced apomorphous character dataset that generates multiple parsimonious trees. These most parsimonious trees are then used as input for a Phylogenetic Networks analysis that results in consensus and reticulate networks. We show here that the phylogenetic tree-like definition of the genus is a relative concept linked to craniodental characters that come in support of hypothetical Last Common Ancestors of the most parsimonious scenario and infer that the reticulate network concords with recent findings in paleogenomic research regarding its mode of evolution.
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http://dx.doi.org/10.1016/j.isci.2021.102359 | DOI Listing |
PLoS One
January 2025
College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China.
Shrews in the genus Episoriculus are among the least-known mammals in China, where representatives occur mainly in the Himalayan and Hengduan mountains. We sequence one mitochondrial and three nuclear genes from 77 individuals referable to this genus, collect morphometric data for five shape and 11 skull measurements from 56 specimens, and use museum collections and GenBank sequences to analyze phylogenetic relationships between this and related genera in an integrated molecular and morphometric approach. Whereas historically anywhere from two to eight species have been recognized in this genus, we conclude that six (Episoriculus baileyi, E.
View Article and Find Full Text PDFSci Adv
January 2025
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.
View Article and Find Full Text PDFMol Biol Evol
January 2025
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
Southwest China is characterized by high plateaus, large mountain systems, and deeply incised dry valleys formed by major rivers and their tributaries. Despite the considerable attention given to alpine plant radiations in this region, the timing and mode of diversification of the numerous dry valley plant lineages remain unknown. To address this knowledge gap, we investigated the macroevolution of Isodon (Lamiaceae), a lineage commonly distributed in the dry valleys in southwest China and wetter areas of Asia and Africa.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia 46022, Spain.
The SWItch/Sucrose Non-Fermenting (SWI/SNF) complexes are evolutionarily conserved, ATP-dependent chromatin remodelers crucial for multiple nuclear functions in eukaryotes. Recently, plant BCL-DOMAIN HOMOLOG (BDH) proteins were identified as shared subunits of all plant SWI/SNF complexes, significantly impacting chromatin accessibility and various developmental processes in Arabidopsis. In this study, we performed a comprehensive characterization of mutants, revealing the role of BDH in hypocotyl cell elongation.
View Article and Find Full Text PDFMycoKeys
January 2025
College of Forestry, Southwest Forestry University, Kunming 650224, China Southwest Forestry University Kunming China.
In the ecosystem, wood-inhabiting fungi play an indispensable role in wood degradation and the cycle of substances. They are regarded as the "key player" in the process of wood decomposition because of their ability to produce various enzymes that break down woody lignin, cellulose, and hemicellulose. In this study, four new wood-inhabiting fungal species, , , , and , were collected from southwestern China and were proposed based on the morphological and molecular evidence.
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