HAL (Le Centre pour la Communication Scientifique Directe), Journal Year: 2021, Volume and Issue: 47, P. 136 - 150
Published: Aug. 1, 2021
Fungi are rich in complexes of cryptic species that need a combination different approaches to be delimited, including genomic information.
Language: Английский
Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown
Published: Dec. 20, 2022
Abstract Motivation Compositional heterogeneity – when the proportions of nucleotides and amino acids are not broadly similar across dataset - is a cause great number phylogenetic artefacts. Whilst variety methods can identify it post-hoc, few metrics exist to quantify compositional prior computationally intensive task tree reconstruction. Here we assess efficacy one such existing, widely used, metric: Relative Composition Frequency Variability (RCFV), using both real simulated data. Results Our results show that RCFV be biased by sequence length, taxa, possible character states within dataset. However, also find missing data does appear have an appreciable value on RCFV. We discuss theory behind this, consequences this for future usage propose new metric, nRCFV, which accounts these biases. Alongside present software calculates called nRCFV_Reader. Availability Implementation nRCFV has been implemented in RCFV_Reader, available at: https://github.com/JFFleming/RCFV_Reader. Both our simulation at Datadryad.
Language: Английский
Citations
1
Biological Journal of the Linnean Society, Journal Year: 2023, Volume and Issue: 139(2), P. 173 - 191
Published: May 11, 2023
Abstract We describe the current state of speciation in species complex marine gastropod Patelloida saccharina, using mitochondrial COI, 16S RNA, nuclear histone 3 gene and single-nucleotide polymorphism (SNP) markers from 165 specimens collected 37 localities across Japanese archipelago. In total, 28 unique COI haplotypes, 16 11 haplotypes 148 734 SNPs were obtained. Genetic assignments phylogenetic trees recovered three genetically distinct lineages: P. saccharina lanx an unknown sp. Shionomisaki, Wakayama Prefecture. The divergence between was estimated to have occurred around 44 000 years ago—too recent accumulated morphological differences that confounded taxonomic identification. Continuous exchange after initial split is suggested based on demographic history analyses, which allowed for introgression genome proliferation intermediate individuals. Speciation, despite existence a contact zone Ryukyu Islands, possibly due eventual reproductive isolation followed with flow. strongly supported by our results as two separate species, revision descriptions their phylogeny, distribution proposed.
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: Oct. 5, 2023
SUMMARY The Galápagos Islands are a prime example of natural laboratory for the study evolutionary radiations. While much attention has been devoted to iconic species like Darwin’s finches 1–4 , islands offer an equally unique but often overlooked opportunity plant radiations 5 . Yet, compared their animal counterparts, our understanding patterns and processes underpinning remains relatively limited 6,7 We present evidence early stages radiation in prickly-pear cactus ( Opuntia Cactaceae), lineage widespread across archipelago. Phylogenomic population genomic analyses show that notwithstanding overall low genetic differentiation populations, there is marked geographic structure broadly consistent with current taxonomy dynamic paleogeography Galápagos. Because such stands stark contrast exceptional eco-phenotypic diversity displayed by cacti islands, it plausible phenotypic plasticity precedes divergence source adaptive evolution, or introgression between populations facilitates local adaptation. Models relationships including admixture indicate gene flow common certain likely facilitated dispersal via animals known feed on flowers, fruits, seeds Scans reveal candidate loci associated seed traits environmental stressors, suggesting combination biotic interactions abiotic pressures due harsh conditions characterizing island life volcanic, equatorial archipelago may underlie diversification cacti. Considered concert, these results relevant both mechanisms history conservation biota.
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown
Published: Dec. 2, 2022
Abstract The repeated evolution of phenotypes is ubiquitous in nature and offers some the clearest evidence role natural selection evolution. genomic basis phenotypic often complex can arise from a combination gene flow, shared ancestral polymorphism de novo mutation. Here, we investigate ecomorph adaptive radiation Hawaiian spiny-leg Tetragnatha . This comprises four ecomorphs that are microhabitat-specialists, differ body pigmentation size (Green, Large Brown, Maroon, Small Brown). Using 76 newly generated low-coverage, whole-genome resequencing samples, coupled with population phylogenomic tools, studied evolutionary history to understand lineage genetic underpinnings Congruent previous works, find each has evolved twice, exception Brown ecomorph, which three times. Maroon likely involved hybridization events, whereas Green because either standing variation or Pairwise comparisons based on fixation index (F ST ) show divergent regions include genes functions associated (melanization), learning, neuronal synapse activity, circadian rhythms. These results linked multiple suggests previously unknown learning rhythms ecomorph.
Language: Английский
Citations
0
HAL (Le Centre pour la Communication Scientifique Directe), Journal Year: 2021, Volume and Issue: 47, P. 136 - 150
Published: Aug. 1, 2021
Fungi are rich in complexes of cryptic species that need a combination different approaches to be delimited, including genomic information.
Language: Английский
Citations
0