phylogenetics / evolution

Phylogenomic analyses of the Austral podocarps (Podocarpus: Podocarpaceae) reveals unlikely hybrid ancestry of a New Zealand species

The paper identifies a hybrid lineage in the Austral podocarps using phylogenomic analyses, revealing that Podocarpus nivalis is a hybrid between P. laetus and P. lawrencei.

Fully Phased Telomere-to-Telomere Assemblies for Thoroughbred Horse and Donkey Haplotypes derived from a Mule Illuminate the Peculiar Evolution of Equid Centromeres

The paper presents telomere-to-telomere genome assemblies of a Thoroughbred horse and donkey derived from a mule, revealing insights into equid centromere evolution and plasticity.

Early Cretaceous Origin and Evolutionary History of Palms (Arecaceae) inferred from 1,033 Nuclear Genes and a New Synthesis of Fossil Evidence

This study reconstructs the evolutionary history of palms using 1,033 nuclear genes and fossil evidence, finding the family originated in the Early Cretaceous and diversified rapidly.

Coding sequence clustering universally predicts fine- and coarse-scale chromatin compartment landscapes

The paper identifies coding DNA sequence density as a universal predictor of chromatin compartmentalization across species, revealing its conservation over evolutionary time.

Comparative analysis of the EF-1α Intergenic Region in Babesia divergens isolates: Insights into TA Repeat Variation and Potential Regulatory Implications

This study compares the EF-1α intergenic region across Babesia divergens isolates, identifying TA repeat variation and its potential regulatory impact on gene expression.

Unraveling the phylogenetic signal of gene expression from single-cell RNA-seq data

This study evaluates six methods for calling single-nucleotide variants from scRNA-seq data and finds that some methods provide phylogenetically informative genotype calls, with implications for understanding cancer progression.

Automatic Discovery of Optimal Discrete Character Models

This paper introduces a method for automatically selecting optimal discrete character models using regularization and simulated annealing, showing improved statistical performance and biological realism.

Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes

This paper introduces DICAROS, a method for ancestral shape reconstruction that outperforms existing methods by combining LDDMM and Felsensteins Independent Contrasts, and applies it to swallowtail butterflies.

Systematics, diversification, and biogeography of Macromiidae (Odonata: Anisoptera)

This study presents a densely sampled phylogenetic analysis of Macromiidae dragonflies, revealing three major lineages and biogeographic origins across multiple regions.

Genetic analysis of Mycobacterium abscessus reveals genomic diversity linked to global plasmid distribution

The paper analyzes plasmid distribution in Mycobacterium abscessus using whole genome sequencing to show how plasmid transfer increases genomic diversity and aids in estimating bacterial contact history.

Looks can be deceiving: discordances in phylogeny and morphology within loricate choanoflagellates

The paper examines two new loricate choanoflagellate strains that show morphological discrepancies with their genetic relatives, challenging current taxonomic classifications based on morphology.

All for one or one for all? Disentangling the Juncus bufonius complex through morphometrics, cytometry and genomics

The paper uses genomic, cytometric, and morphometric data to clarify taxonomic relationships in the Juncus bufonius complex, finding that polyploids and diploids are distinct taxa, and morphometric characters are not reliable for species delimitation.

Genetic Evidence Indicates the Evolutionary Importance of the SARS-CoV-2 ORF9b protein

The paper shows that mutations increasing ORF9b expression are common in SARS-CoV-2 variants and PCI sequences, suggesting ORF9b's role in viral evolution and immune evasion.

The roles of Transposable Elements and Gene Family Dynamics in Shaping Diversity and Evolution in Diatoms

This study investigates how transposable elements and gene family dynamics contribute to diatom diversification across different scales and evolutionary timescales.

A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement.

The paper introduces krepp, a k-mer-based method for phylogenetic placement of reads on large reference phylogenies, showing improved scalability and accuracy compared to alignment-based methods.

Efficient Identification of Phylogenetically Informative Alignment Sites via Sparse Learning

The paper introduces a sparse learning method to identify phylogenetically informative sites in alignments, showing it matches full alignment results and provides an objective metric for evaluating alignment filtering tools.

A covarion model for phylogenetic estimation using discrete morphological datasets

This paper introduces the covariomorph model, an extension of the covarion model for morphological phylogenetics, showing it improves accuracy by accounting for lineage- and character-specific rate variation in 50% of empirical datasets.

Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins

PEINT simulates realistic protein evolution by modeling sequence changes over time, generating functional proteins that retain enzymatic activity.

A Dimeric SINE Discovered in Shrew Mole is Structurally Similar to Primate Alu

The paper identifies a new 7SL RNA-derived SINE in shrew moles, Urop, which is structurally similar to primate Alu and shows evolutionary parallels.

Genomes of the Golden Horde Elites and their Implications for the Rulers of the Mongol Empire

The paper analyzes the genomes of Golden Horde elites to confirm Genghis Khan's Y-chromosome haplogroup and trace their genetic ancestry.

The emergence of bacterial blight pathogen followed the dispersal pattern of rice in Asia

This study traces the evolutionary history and dispersal of the rice bacterial blight pathogen Xoo, linking its emergence to rice domestication and trade routes.

Tracing SARS-CoV-2 Evolution in Algeria: Insights from 2020-2023

The paper analyzes 449 SARS-CoV-2 genomic sequences from Algeria to trace viral evolution, identifying mutations, recombination events, and superspreading dynamics.

TriMouNet: An Algorithm for Inferring Level-1 Phylogenetic Networks from Multi-Locus Gene Tree Distributions.

TriMouNet infers level-1 phylogenetic networks from multi-locus gene tree distributions, identifying reticulations with low false positive rates when gene trees are accurate.

Mitochondrial Genome of the lesser known - Madras Hedgehog (Paraechinus nudiventris): Genomic characterization and comparative analysis within Erinaceidae

The paper presents and analyzes the complete mitochondrial genome of the Madras hedgehog, providing insights into its evolutionary history and divergence within Erinaceidae.

Molecular Clock Dating of Deep-Time Evolution Using Complex Mixture Models

This paper introduces phyloHessian, a tool using complex mixture substitution models to improve molecular clock dating accuracy for deep-time and fast-evolving lineages.

Testing for trait lability at macroevolutionary scales: is life history evolution labile in grasses?

The paper evaluates methods for detecting trait lability in grasses, finding inconsistent results across approaches and suggesting life history is stable in some clades.

Functional response predicts invasiveness but not trophic impact

Across 269 functional responses from 45 freshwater fish species, invasive species exceed non-invasive species only when sampled in their native range; introduced populations match non-invasive species.

Phylogenomics of Rhinogobius gobies reveal northern-southern divergence and trait evolution in China

This study uses phylogenomic data to resolve the evolutionary history of Rhinogobius gobies, revealing a north-south divergence and key morphological traits in Chinese species.

Phylogenomics and the origins of sharks

This study uses genome data from 48 chondrichthyan species to test shark monophyly, finding conflicting results across genomic markers.

Linking Ancient Refugia to Modern Diversity: Evidence of Multi-origin Postglacial Expansion of Sockeye Salmon on the Asian Range

The paper examines mtDNA diversity in sockeye salmon populations to trace biogeographical history, finding evidence of multi-origin postglacial expansions and refugia in Asia.