Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Systematic Biology, Год журнала: 2024, Номер 73(1), С. 183 - 206

Опубликована: Янв. 1, 2024

Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies draw inferences about the phylodynamics and history viral transmission. However, these are often computationally expensive, which limits complexity realism phylodynamic makes them ill-suited for informing policy decisions real-time during rapidly developing outbreaks. Likelihood-free using deep learning pushing boundaries inference beyond constraints. In this paper, we extend, compare, contrast a recently developed method likelihood-free from trees. We trained multiple neural networks simulated outbreaks that spread among 5 locations found they achieve close same levels accuracy as Bayesian under true simulation model. compared robustness model misspecification network method. both had comparable performance, converging on similar biases. also implemented uncertainty quantification called conformalized quantile regression demonstrate patterns sensitivity highest posterior density (HPD) greatly overlap with HPDs, but have lower precision (more conservative). Finally, tested against phylogeographic data recent study SARS-Cov-2 pandemic Europe obtained estimates region-specific epidemiological parameters location common ancestor Europe. Along being accurate robust likelihood-based methods, our average over 3 orders magnitude faster after training. Our results support notion can be accurately mimic good bad statistical properties likelihood functions generative models.

Язык: Английский

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Lakes as model systems for understanding global change

Nature Climate Change, Год журнала: 2023, Номер 13(4), С. 304 - 306

Опубликована: Март 23, 2023

Язык: Английский

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A new small duckbilled dinosaur (Hadrosauridae: Lambeosaurinae) from Morocco and dinosaur diversity in the late Maastrichtian of North Africa

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Фев. 13, 2024

Abstract In the Late Cretaceous, northern and southern hemispheres evolved distinct dinosaurian faunas. Titanosaurians abelisaurids dominated Gondwanan continents; hadrosaurids, ceratopsians tyrannosaurs North America Asia. Recently, a lambeosaurine hadrosaurid, Ajnabia odysseus , was reported from late Maastrichtian phosphates of Oulad Abdoun Basin Morocco, suggesting dispersal between Laurasia Gondwana. Here we report new fossils Morocco showing lambeosaurines achieved high diversity in Africa. A skull represents dwarf lambeosaurine, Minqaria bata . resembles size, but differs ventrally positioned jugal facet sinusoidal toothrow. The animal is small, ~ 3.5 m long, fused braincase shows it mature. humerus femur belong to larger 6 implying at least three species coexisted. hadrosaurids Europe Africa suggests dispersal-driven radiation, with diversifying take advantage low ornithischian diversity. African are small compared American Asia however, perhaps due competition titanosaurians. Hadrosaurids unknown eastern Africa, Moroccan may be part insular fauna, represent an island radiation.

Язык: Английский

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Evolution of a Model System: New Insights from the Study of Anolis Lizards

Annual Review of Ecology Evolution and Systematics, Год журнала: 2023, Номер 54(1), С. 475 - 503

Опубликована: Авг. 22, 2023

Following decades of intensive study, Anolis lizards have emerged as a biological model system. We review how new research on anoles has advanced our understanding ecology and evolution, challenging long-standing paradigms opening areas inquiry. Recent anole reveals changes in behavior can restructure ecological communities both stimulate stymie sometimes simultaneously. Likewise, investigation spatial or phylogenetic evolutionary experiments documented repeatability across spatiotemporal scales, while also illuminating its limits. Current places promising for Anthropocene biology, with recent work illustrating species respond humans reconfigure natural habitats, alter the climate, create novel environments through urbanization introduction. Combined ongoing methodological developments genomics, phylogenetics, ecology, growing foundational knowledge positions them powerful system evolution years to come.

Язык: Английский

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Towards understanding insect species introduction and establishment: A community‐level barcoding approach using island beetles

Molecular Ecology, Год журнала: 2023, Номер 32(13), С. 3778 - 3792

Опубликована: Апрель 27, 2023

Abstract Since Darwin put forward his opposing hypotheses to explain the successful establishment of species in areas outside their native ranges, preadaptation and competition‐relatedness hypotheses, known as Darwin's naturalization conundrum, numerous studies have sought understand relative importance each. Here, we take advantage well‐characterized beetle communities across laurel forests Canary Islands for a first evaluation support two within arthropods. We generated mitogenome backbone tree comprising nearly half genera recorded phylogenetic placement introduced sampled forests, using cytochrome c oxidase I (COI) sequences. For comparative purposes, also assembled phylogenetically placed data set COI sequences that were not forests. Our results suggest stronger effect over resource competition, while revealing an underappreciated shortfall arthropod biodiversity data—knowledge being or introduced. name this Humboldtean similar arthropods should incorporate DNA barcode sequencing mitigate problem.

Язык: Английский

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SSARP: An R Package for Easily Creating Species- and Speciation- Area Relationships Using Web Databases

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

Опубликована: Янв. 2, 2025

Abstract A universal method of quantifying patterns biodiversity on islands is the species-area relationship (SAR). SARs visualize between species richness (the number species) and area land mass which they live. An extension this visualization, speciation-area (SpAR), helps researchers determine trends in speciation rate over a set masses. Comparing these relationships across island systems globally an extremely difficult task because gathering processing large amount occurrence data often requires to conduct lengthy literature searches combine datasets from several different sources. Here we present SSARP (Species/Speciation-Area Relationship Projector), R package that provides simple workflow for creating SpARs. The allows users gather GBIF, use mapping tools whether GPS points refer valid masses, associate those masses with their areas using built-in dataset names areas, create linear segmented regression. also multiple functions estimating rates SpAR. Using dramatically increase scope research through creation SpARs globe.

Язык: Английский

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Comparative phylogeography of four lizard taxa within an oceanic island

Molecular Phylogenetics and Evolution, Год журнала: 2025, Номер unknown, С. 108295 - 108295

Опубликована: Фев. 1, 2025

Язык: Английский

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Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(19)

Опубликована: Май 5, 2025

Hawaiian lobeliads exhibit extensive adaptive radiations and are considered the largest plant clade (143 species) endemic to any oceanic archipelago. Rapid insular prone reticulate evolution, yet detecting hybridization is often limited by inadequate sampling of taxa or independent loci. We analyzed 633 nuclear loci (including tetraploid duplications) whole plastomes for 89% extant species derive phylogenies lobeliads. Nuclear data provide strong support nine major clades in both likelihood ASTRAL analyses. All genera/sections monophyletic except Clermontia Cyanea . plastome conflict on short, deep branches; tree resolves a fleshy-fruited Clermontia/Cyanea-Brighamia/Delissea , sister Polynesian Sclerotheca with capsular-fruited clade. Incomplete lineage sorting rapid radiation starting 8.5–11.3 Ma sufficient explain uncertainty cytonuclear discordance along backbone. Sequence reticulation within especially identify 42 interisland dispersal events: accord strict progression rule, involving movement next younger island hotspot chain, consistent theory. Plastid overestimate such events 17%. have undergone parallel elevational distribution flower length all islands, multiple founders some differences. lobeliad diversification was driven an early intergeneric divergence habitat, followed ecological speciation Clermontia/Cyanea combined widespread single-island endemism, frequent dispersal, occasional hybridization.

Язык: Английский

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The ‘island syndrome’ is an alternative state

Journal of Biogeography, Год журнала: 2022, Номер 50(3), С. 467 - 475

Опубликована: Дек. 9, 2022

Abstract Aim In the half‐century since publication of Theory Island Biology, ecologists have come to recognize importance predation as a decisive determinant alternate states in many ecosystems. species are notorious for their vulnerability introduced predators, yet strength island predator regimes has not been fully incorporated into our understanding forces that structure consumer communities. Location The Greater and Lesser Antilles. Taxon Birds Anolis lizards. Methods Field surveys sclerophyll rainforest sites on islands ranging size from 3.5 km 2 Terre‐de‐Haut 76,000 Hispaniola. Results Evidence gathered 1970s 1980s shows Antillean anoles live at higher densities fewer resources, grow more slowly, reproduce later longer than mainland counterparts conformity with ‘island syndrome’. Data this period show bird communities display density overcompensation, community saturation, size‐structured foraging guilds, low diversity packing, all traits consistent syndrome regime intense competition. Mainland none these features. Main conclusions I propose is an alternative state distinguishes low‐predation high‐predation counterparts. It follows strong tend prevent colonizing. Conversely, invasion‐resistant, communities, despite diversity, colonizing islands. These predictions experimentally testable lizards and, if confirmed, could set biogeography new course.

Язык: Английский

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Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks

Science Advances, Год журнала: 2024, Номер 10(30)

Опубликована: Июль 24, 2024

Species life-history traits, paleoenvironment, and biotic interactions likely influence speciation extinction rates, affecting species richness over time. Birth-death models inferring the impact of these factors typically assume monotonic relationships between single predictors limiting our ability to assess more complex effects their relative importance interaction. We introduce a Bayesian birth-death model using unsupervised neural networks explore multifactorial nonlinear on rates fossil data. It infers lineage- time-specific disentangles predictor through explainable artificial intelligence techniques. Analysis proboscidean record revealed shaped by dietary flexibility biogeographic events. The emergence modern humans escalated causing recent diversity decline, while regional climate had lesser impact. Our paves way for an improved understanding intricate dynamics shaping clade diversification.

Язык: Английский

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