BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

PLoS Computational Biology, Год журнала: 2019, Номер 15(4), С. e1006650 - e1006650

Опубликована: Апрель 8, 2019

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances nearly all aspects the joint modelling evolutionary data. It is increasingly appreciated that some questions can only be adequately answered by combining evidence from multiple independent sources data, including genome sequences, sampling dates, phenotypic radiocarbon fossil occurrences, and biogeographic range information among others. Including relevant data into a single model very challenging both conceptually computationally. Advanced computational software packages allow robust development compatible (sub-)models which composed full hierarchy have played key role these developments. Developing such frameworks scientific activity its own right, comes specific challenges, practical design, engineering challenges to statistical conceptual challenges. BEAST 2 one platform, was first announced over 4 ago. Here we describe series developments core platform occurred since release software, culminating 2.5 release.

Язык: Английский

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StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

Molecular Biology and Evolution, Год журнала: 2017, Номер 34(8), С. 2101 - 2114

Опубликована: Апрель 13, 2017

Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many with is intractably slow. An alternative to use heuristic which compromise accuracy or completeness in return speed. A common concatenation, assumes the evolutionary history each gene tree identical tree. This an inconsistent estimator topology, worse divergence times, and induces spurious substitution rate variation when incomplete lineage sorting present. Another class heuristics directly motivated by MSC avoids pitfalls concatenation cannot used times. To enable fuller available data more accurate inference topologies, rates, we have developed new version called StarBEAST2. improve convergence rates add analytical integration population sizes, novel MCMC operators other optimizations. Computational performance improved 13.5× 13.8× respectively analyzing two empirical sets, average 33.1× across 30 simulated sets. estimates per-species introduce relaxed clocks, show StarBEAST2 powerful robust than concatenation. through BEAUTi package manager BEAST 2.4 above.

Язык: Английский

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Bayesian Inference of Species Networks from Multilocus Sequence Data

Molecular Biology and Evolution, Год журнала: 2017, Номер 35(2), С. 504 - 517

Опубликована: Дек. 1, 2017

Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution modeled bifurcating trees embedded network. We present Bayesian approach to jointly infer networks from multilocus sequence data. A novel birth-hybridization process used prior for we assume multispecies network coalescent trees. verify ability our method correctly sample posterior distribution, thus through simulations. To quantify power method, reanalyze two large data sets genes spruces yeasts. For three closely related spruces, previously suggested homoploid event this clade; yeast data, find extensive events. Our available within BEAST 2 add-on SpeciesNetwork, provides an extensible framework inference reticulate evolution.

Язык: Английский

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Integrative approaches for species delimitation in Ascomycota

Fungal Diversity, Год журнала: 2021, Номер 109(1), С. 155 - 179

Опубликована: Июль 1, 2021

Язык: Английский

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Species delimitation 4.0: integrative taxonomy meets artificial intelligence

Trends in Ecology & Evolution, Год журнала: 2024, Номер 39(8), С. 771 - 784

Опубликована: Июнь 6, 2024

Although species are central units for biological research, recent findings in genomics raising awareness that what we call can be ill-founded entities due to solely morphology-based, regional descriptions. This particularly applies groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology ecology, etc.) become apparent: different favored concepts, lack universal characters/markers, missing appropriate analytical tools processes, and highly subjective ranking fusion datasets. Now, combined with artificial intelligence under a unified concept enable automated feature learning data integration, thus reduce subjectivity delimitation. approach will likely accelerate revising unraveling eukaryotic biodiversity.

Язык: Английский

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Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

PeerJ, Год журнала: 2019, Номер 7, С. e6399 - e6399

Опубликована: Фев. 14, 2019

Building the Tree of Life (ToL) is a major challenge modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing many heterogeneous genomic signals emerging from first decade large-scale phylogenetic analysis spawned high-throughput sequencing (HTS). Such include those most commonly encountered phylogenomic datasets, such as incomplete lineage sorting, but also reticulate processes with greater frequency, recombination introgression. Here focus specifically on how methods can accommodate heterogeneity incurred population genetic processes; do not discuss ignore processes, concatenation or supermatrix approaches supertrees. We suggest acquisition types markers used will remain restricted until posteriori marker choice are made possible routine whole-genome taxa interest. limitations potential extensions model supporting innovation today, multispecies coalescent (MSC). Macroevolutionary models use phylogenies, character mapping, often which building phylogenies increasingly rely assimilating an important goal moving forward. Finally, integrative cyberinfrastructure linking all steps process ToL, specimen field publication tracking data, well culture values contributors at each step, essential for progress.

Язык: Английский

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Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Systematic Biology, Год журнала: 2018, Номер unknown

Опубликована: Май 13, 2018

Advances in high-throughput sequencing techniques now allow relatively easy and affordable of large portions the genome, even for nonmodel organisms. Many phylogenetic studies reduce costs by focusing their efforts on a selected set targeted loci, commonly enriched using sequence capture. The advantage this approach is that it recovers consistent each with high depth, which leads to more confidence assembly target sequences. High depth can also be used identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled studies. Instead, many scientists perform analyses contig result from de novo reads into contigs containing only canonical nucleobases, may both statistical power accuracy. Here, we develop an easy-to-use pipeline recover capture data, use simulated empirical data demonstrate utility integrating these performed under multispecies coalescent model. Our ultraconserved element locus collected South American hummingbird genus Topaza phased carry sufficient information infer genetic structure, lineage divergence, biogeographic history diversified during last 3 myr. results support recognition two species suggest rate gene flow across distances rainforest habitats rare admixture Amazon River. simulations provide evidence analyzing accurate estimates tree topology divergence times than common

Язык: Английский

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Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent

Systematic Biology, Год журнала: 2017, Номер 67(2), С. 269 - 284

Опубликована: Сен. 2, 2017

The use of genetic data for identifying species-level lineages across the tree life has received increasing attention in field systematics over past decade. multispecies coalescent model provides a framework understanding process lineage divergence and become widely adopted delimiting species. However, because these studies lack an explicit assessment fit, many cases, accuracy inferred species boundaries are unknown. This is concerning given large amount empirical theory that highlight complexity speciation process. Here, we seek to fill this gap by using simulation characterize sensitivity inference under (MSC) several violations assumptions thought be common data. We also assess fit MSC context delimitation. Our results show substantial variation sets. Posterior predictive tests find poorest performance sets were hypothesized impacted violations. while inferences assuming robust minor violations, such can biased some biologically plausible scenarios. Taken together, suggest researchers identify individual which delimitation likely problematic, thereby highlighting cases where additional lines evidence particularly important collect. study supports growing body work importance checking phylogenetics, usefulness tailoring reliability particular inferences. [Populations structure, gene flow, demographic changes, posterior prediction, simulation, genetics.].

Язык: Английский

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A mega-cryptic species complex hidden among one of the most common annelids in the North East Atlantic

PLoS ONE, Год журнала: 2018, Номер 13(6), С. e0198356 - e0198356

Опубликована: Июнь 20, 2018

We investigate mitochondrial (COI, 16S rDNA) and nuclear (ITS2, 28S genetic structure of North East Atlantic lineages Terebellides, a genus sedentary annelids mainly inhabiting continental shelf slope sediments. demonstrate the presence more than 25 species which only seven are formally described. Species boundaries determined with molecular data using broad range analytical methods. Many new common wide spread, majority found in sympatry several other complex. Being one most regularly encountered annelid taxa Atlantic, it is likely to find an undescribed Terebellides described one.

Язык: Английский

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Phylogeny of xerophilic aspergilli (subgenus Aspergillus) and taxonomic revision of section Restricti

Studies in Mycology, Год журнала: 2017, Номер 88, С. 161 - 236

Опубликована: Сен. 1, 2017

Aspergillus section Restricti together with sister (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus applied a multidisciplinary approach for definition species boundaries sect. Restricti. The was tested set 102 isolates comprising all currently accepted strongly supported by Maximum likelihood (ML) Bayesian inferrence (BI) analysis based β-tubulin (benA), calmodulin (CaM) RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging from various isolation sources four continents were characterized DNA sequencing, 193 selected phylogenetic analyses phenotypic studies. Species delimitation methods multispecies coalescent model employed sequences loci, i.e., ID region rDNA (ITS + 28S), CaM, benA RPB2, recognition 21 including 14 new. All these also ML BI analyses. recognised can be reliably identified examined genetic Phenotype performed support new includes colony characteristics seven cultivation media incubated at several temperatures, growth an osmotic gradient (six NaCl concentration 0 25 %) morphology scanning electron microscopy. micromorphology conidial heads, vesicle dimensions, temperature profiles parameters useful criteria identification. vast majority produce asperglaucide, asperphenamate or contrast Aspergillus. Mycophenolic acid detected first time least six members section. ascomata A. halophilicus do not contain auroglaucin, epiheveadride flavoglaucin which common Aspergillus, but shares echinulins

Язык: Английский

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