Incongruence in the phylogenomics era

Nature Reviews Genetics, Год журнала: 2023, Номер 24(12), С. 834 - 850

Опубликована: Июнь 27, 2023

Язык: Английский

---

Stepwise emergence of the neuronal gene expression program in early animal evolution

Cell, Год журнала: 2023, Номер 186(21), С. 4676 - 4693.e29

Опубликована: Сен. 19, 2023

The assembly of the neuronal and other major cell type programs occurred early in animal evolution. We can reconstruct this process by studying non-bilaterians like placozoans. These small disc-shaped animals not only have nine morphologically described types no neurons but also show coordinated behaviors triggered peptide-secreting cells. investigated possible affinities these peptidergic cells using phylogenetics, chromatin profiling, comparative single-cell genomics four found conserved expression across placozoans, including populations transdifferentiating cycling cells, suggestive active homeostasis. uncovered fourteen expressing neuronal-associated components pre-synaptic scaffold that derive from progenitor with neurogenesis signatures. In contrast, earlier-branching sponges ctenophores lacked expression. Our findings indicate key developmental effector gene modules evolved before advent cnidarian/bilaterian context paracrine signaling.

Язык: Английский

---

Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 21, 2025

Abstract Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), duplication loss (GDL), horizontal transfer (HGT) can complicate the estimation of species lengths. While several tools exist topology a addressing various causes discordance, much less attention has been paid length on multi-locus datasets. For single-copy trees, some methods available that summarize onto tree, including coalescent-based account ILS. no method exists multi-copy family trees have evolved with loss. To address this gap, we introduce CASTLES-Pro algorithm while accounting both GDL improves existing CASTLES by increasing its accuracy extends it handle ones. Our simulation studies show is generally more accurate than alternatives, eliminating systematic bias toward overestimating terminal often observed when using concatenation. Moreover, not theoretically designed HGT, maintains relatively high under rates random HGT. Code availability implemented inside software package ASTER, at https://github.com/chaoszhang/ASTER . Data The datasets scripts used in study https://github.com/ytabatabaee/CASTLES-Pro-paper

Язык: Английский

---

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

BMC Bioinformatics, Год журнала: 2023, Номер 24(1)

Опубликована: Окт. 14, 2023

Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) tree using supermatrix (SM) supertree (ST) approaches.EasyCGTree was implemented Perl programming languages built collection of published reputable programs. All programs were precompiled as standalone executable files contained EasyCGTree package. It can run after installing language environment. Several profile hidden Markov models (HMMs) prepared advance construct HMM database (PHD) that enclosed package available homolog searching. Customized also be build added PHD via EasyCGTree. Taking 43 genomes genus Paracoccus testing data set, consensus (a variant typical SM), SM, ST trees inferred successfully, SM compared those pipelines UBCG bcgTree, metrics cophenetic correlation coefficients (CCC) Robinson-Foulds distance (topological distance). The results suggested infer nearly identical topology (distance < 0.1) accuracy (CCC > 0.99) two pipelines.EasyCGTree an all-in-one automatic from input phylogenomic guaranteed accuracy, much easier install use than reference pipelines. In addition, conveniently explore prokaryotic evolutionary signals different perspective. version 4 freely Linux Windows users at Github ( https://github.com/zdf1987/EasyCGTree4 ).

Язык: Английский

---

A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification

Annals of Botany, Год журнала: 2025, Номер unknown

Опубликована: Янв. 19, 2025

Abstract Background and Aims Kalanchoe is a diverse genus in the Crassulaceae, with centres of diversity Madagascar sub-Saharan Africa. The known for its popularity horticulture, use as model system research on CAM photosynthesis vegetative reproduction, high invasive potential, traditional medicine. genus-rank circumscription infrageneric classification have been subject debate centuries, especially regarding status rank what now treated K. subg. Bryophyllum Kitchingia. We aim to generate densely sampled phylogeny s.l. evaluate current system. Methods inferred phylogenetic tree using ddRAD sequencing approach, covering 70% taxa four out five subgenera currently recognised genus. Key Results recovered well-supported clades, partially corresponding subgeneric classification. Calophygia resolves sister rest relationships among three remaining however, receive less support. predominantly mainland African forms strongly supported clade that Bryophyllum. These two clades are together containing mainly species from Kitchingia sect. Pubescentes. Conclusions backed up by our but requires further refinement. topology suggests Malagasy origin one dispersal event mainland, subsequent continental Africa Arabian Peninsula Southeast Asia. formation bulbils leaf margin restricted larger within thus only evolved once. Our provides framework taxonomic, evolutionary, physiological

Язык: Английский

---

CASTER: Direct species tree inference from whole-genome alignments

Science, Год журнала: 2025, Номер unknown

Опубликована: Янв. 23, 2025

Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference tree life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, current practice leaves out large chunks genomes. As more high-quality genomes become available, we urgently need methods infer directly from a multiple genome alignment. Here, introduce CASTER, theoretically justified site-based method that eliminates predefine recombination-free loci. CASTER is scalable hundreds mammalian whole We demonstrate accuracy in simulations include recombination apply several biological datasets, showing its per-site scores can reveal both artefactual patterns discordance across genome.

Язык: Английский

---

Iguanas rafted more than 8,000 km from North America to Fiji

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(12)

Опубликована: Март 17, 2025

Founder-event speciation can occur when one or more organisms colonize a distant, unoccupied area via long-distance dispersal, leading to the evolution of new species lineage. Species radiations established by long-distance, and especially transoceanic, dispersal cause substantial shifts in regional biodiversity. Here, we investigate occurrence timing greatest known oceanic event history terrestrial vertebrates—the rafting iguanas from North America Fiji. Iguanas are large-bodied herbivores that well-known overwater dispersers, including colonized Caribbean Galápagos islands. However, origin Fijian had not been comprehensively tested. We estimated phylogenetic relationships evolutionary timescale iguanid lizard radiation using genome-wide exons ultraconserved elements (UCEs). Those data indicate closest living relative extant is American desert iguana two taxa likely diverged during late Paleogene near after onset volcanism produced archipelago. Biogeographic models estimate as most probable ancestral range iguanas. Our analyses support hypothesis reached Fiji an extraordinary western America, which spanned fifth earth’s circumference (>8,000 km). Overwater strengthens importance founder-event diversification iguanids elucidates scope across vertebrates.

Язык: Английский

---

The meaning and measure of concordance factors in phylogenomics

Опубликована: Янв. 3, 2024

As phylogenomic datasets have grown in size, researchers developed new ways to measure biological variation and assess statistical support. Larger many more sites loci, therefore less sampling variance. While this means that we can accurately the mean signal these datasets. lower variance is often reflected widely used measures of branch support— such as bootstrap posterior probability—being uniformly high, limiting their utility. also revealed a large amount topologies found across individual single species tree inferred by most phylogenetic methods represents limited summary data. In contrast support, degree underlying topological among or loci should be approximately constant regardless size dataset. “Concordance factors” similar statistics become increasingly important tools phylogenetics. review, explain why concordance factors thought descriptors variation, rather than argue they provide information not contained We review growing suite derived from various measuring concordance, comparing them common framework reveals interrelationships. discuss how might change future move beyond estimating “tree life” towards myriad evolutionary histories genomic variation.

Язык: Английский

---

Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae)

Annals of Botany, Год журнала: 2024, Номер 134(1), С. 85 - 100

Опубликована: Март 25, 2024

Abstract Background and Aims The geographical origin evolutionary mechanisms underpinning the rich distinctive New Caledonian flora remain poorly understood. This is attributable to complex geological past of island scarcity well-resolved species-level phylogenies. Here, we infer phylogenetic relationships divergence times palms, which comprise 40 species. We use this framework elucidate biogeography palm lineages explore how extant species might have formed. Methods A tree including 37 77 relatives from tribe Areceae was inferred 151 nuclear genes obtained by targeted sequencing. Fossil-calibrated were estimated ancestral ranges inferred. Ancestral ecological preferences in terms elevation, precipitation substrate compared between sister their possible roles as drivers speciation. Key Results palms form four well-supported clades, inside are well resolved. Our results support current classification but suggest that Veillonia Campecarpus should be resurrected fail clarify whether Rhopalostylidinae or nested Basseliniinae. derived Guinean Australian ancestors, reached through at least three independent dispersal events Eocene Miocene. Palms then dispersed out Caledonia five times, mainly towards Pacific islands. Geographical transitions associated with speciation differed across time genera. Substrate more frequently older than younger ones. Conclusions Neighbouring areas a mosaic local habitats shaped Caledonia, played significant role generating diversity region. new spatio-temporal will enable population-level genetic studies unpick endemism.

Язык: Английский

---

Machine learning approaches delimit cryptic taxa in a previously intractable species complex

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 195, С. 108061 - 108061

Опубликована: Март 12, 2024

Язык: Английский

---