Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth–death skyline model

Geological Society London Special Publications, Journal Year: 2024, Volume and Issue: 549(1)

Published: April 17, 2024

The current status of the Sino-Himalayan region as a biodiversity hotspot, particularly for flora, has often been linked to uplift Sino-Tibetan Plateau and Himalayan Hengduan Mountains. However, relationship between topological development onset diversification is yet be confirmed. Here, we apply Bayesian phylodynamic methods large phylogeny angiosperm species from Sino-Himalayas infer changes in their rates evolution through time. We find strong evidence high Paleocene, late Miocene Pliocene, negative Quaternary driven by an increase extinction rates. Our analyses suggest that global palaeotemperatures are unlikely driving force these rate shifts. Instead, collision Indian continent with Eurasia coeval topographic change Sino-Himalayas, Grassland Expansion impact Pleistocene glaciations on this altitudinally variable may have also demonstrate influence choice times shape inferred piecewise-constant trajectories phylodynamics, advocate use prior information when making decision.

Language: Английский

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No phylogenetic evidence for angiosperm mass extinction at the Cretaceous–Palaeogene (K-Pg) boundary

Biology Letters, Journal Year: 2023, Volume and Issue: 19(9)

Published: Sept. 1, 2023

The Cretaceous-Palaeogene mass extinction event (K-Pg) witnessed upwards of 75% animal species going extinct, most notably among these are the non-avian dinosaurs. A major question in macroevolution is whether this influenced rise flowering plants (angiosperms). fossil record suggests that K-Pg had a strong regional impact on angiosperms with up to extinctions, but only minor rates lineages (families and orders). Phylogenetic evidence for angiosperm dynamics through time remains unexplored. By analysing two mega-phylogenies containing approximately 32 000-73 000 extant species, here we show relatively constant throughout geological no at boundary. Despite high species-level observed record, our results support macroevolutionary resilience via survival higher lineages.

Language: Английский

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Reading tree leaves: inferring speciation anfd extinction processes using phylogenies

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 13, 2025

The birth–death process (BDP) is widely used in evolutionary biology as a model for generating phylogenetic trees of species. generalized (GBDP) allows rate variation over time, with speciation and extinction rates to be arbitrary functions time. Here we review the probability theory underpinning GBDP cladogenesis recent findings concerning its identifiability. continuous has been shown non-identifiable from lineage-through-time data: even species phylogenies infinite size parameters cannot estimated. However, restricted class BDPs piecewise-constant identifiable. We illustrate these results using simple examples discuss their implications biologists interested inferring past tempo mode evolution reconstructed trees. This article part theme issue ‘“A mathematical evolution”: models dating back 100 years’.

Language: Английский

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Explanations for latitudinal diversity gradients must invoke rate variation

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(33)

Published: Aug. 3, 2023

The latitudinal diversity gradient (LDG) describes the pattern of increasing numbers species from poles to equator. Although recognized for over 200 years, mechanisms responsible largest-scale and longest-known in macroecology are still actively debated. I argue here that any explanation LDG must invoke differential rates speciation, extinction, extirpation, or dispersal. These processes themselves may be governed by numerous abiotic biotic factors. Hypotheses claim not rates, such as ‘age area’ ‘time diversification’, eschew focus rate variation is assumed these explanations. There significant uncertainty how dispersal have varied regionally Earth history. However, better understand development LDGs, we need constrain this variation. Only then will drivers – they nature become clearer.

Language: Английский

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Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(8)

Published: July 28, 2023

Speciation rates vary substantially across the tree of life. These should be linked to rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining link speciation degree formation in clades have been shown either correlated or uncorrelated depending on group, but no study has yet examined relationship young group that is constrained spatially single-island system. We examine this correlation 109 gemsnakes (Pseudoxyrhophiidae) endemic Madagascar originating early Miocene, helps control for extinction variation time space. find over space 33 species gemsnakes. Rates show low variation, varies widely species, indicating are disconnected. suspect largely due persistence some lineages not susceptible extinction. Importantly, we discuss how delimiting populations versus may contribute problems understanding shallow deep evolutionary processes.

Language: Английский

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The Fossilised Birth-Death Model is Identifiable

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 12, 2024

Abstract Time-dependent birth-death sampling models have been used in numerous studies for inferring past evolutionary dynamics different areas, e.g. speciation and extinction rates macroevolutionary studies, or effective reproductive number epidemiological studies. These are branching processes where lineages can bifurcate, die, be sampled with time-dependent birth, death, rates, generating phylogenetic trees. It has shown that some subclasses of such models, sets result the same distributions reconstructed trees, therefore become unidentifiable from trees regardless their size. Here we show widely fossilised (FBD) identifiable. This subclass makes more realistic assumptions about fossilisation process certain infectious disease transmission than models. Namely, FBD assume stay rather being immediately removed upon sampling. Identifiability model justifies using statistical methods implement this to infer underlying temporal diversification directly molecular other comparative data. We further fossilised-birth-death an extra parameter, removal after probability, is unidentifiable. implies scenarios do not know how affects unable parameter together solely

Language: Английский

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Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies

Bioinformatics and Biology Insights, Journal Year: 2025, Volume and Issue: 19

Published: March 1, 2025

The importance of genomic surveillance strategies for pathogens has been particularly evident during the coronavirus disease 2019 (COVID-19) pandemic, as data from causative agent, severe acute respiratory syndrome type 2 (SARS-CoV-2), have guided public health decisions worldwide. Bayesian phylodynamic inference, integrating epidemiology and evolutionary biology, become an essential tool in epidemiological surveillance. It enables estimation parameters, such reproductive number, pathogen sequence alone. Despite approach being widely adopted, abundance models often makes it challenging to select appropriate model specific research questions. This article illustrates application birth-death-sampling using data, with a focus on SARS-CoV-2. Targeting researchers less familiar phylodynamics, introduces comprehensive workflow, including conceptualisation study detailed steps preprocessing postprocessing. In addition, we demonstrate versatility through three case studies Germany, utilising BEAST2 software its implementations. Each addresses distinct question relevant not only SARS-CoV-2 but also other pathogens: Case 1 finds traces superspreading event at start early outbreak, exemplifying how simple can provide information that would otherwise be accessible extensive contact tracing. compares transmission dynamics nosocomial outbreak community transmission, highlighting integrative analysis. 3 investigates whether local patterns align national trends, demonstrating disentangle complex population substructure little additional information. For each study, emphasise critical points where assumptions properties may misalign outline validation assessments. Overall, aim examples epidemiology, balancing theoretical practical aspects.

Language: Английский

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The effects of cryptic diversity on diversification dynamics analyses in Crocodylia

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2043)

Published: March 1, 2025

Incomplete taxon sampling due to underestimation of present-day biodiversity biases diversification analysis by favouring slowdowns in speciation rates towards the recent time. For instance, dynamics studies Crocodylia, long-term low net-diversification and have been suggested characterize crocodylian evolution. However, cryptic diversity has never considered. Here, we explore effects incorporating into a extant crocodylians. We inferred time-calibrated cryptic-species-level phylogeny using cytochrome b sequences 45 lineages compared with formally recognized 26 species. Diversification rate estimates show increasing present time, which contrasts previous findings. Cryptic should be considered future macroevolutionary analyses; however, representation extinct taxa represents major challenge. Additionally, further investigation under different underlying genomic data is encouraged upon advances population genetics. Our case study adds knowledge demonstrates that species robust taxonomic assessment are essential broad implications for evolutionary biology ecology.

Language: Английский

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Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies

Evolution Letters, Journal Year: 2023, Volume and Issue: 8(2), P. 189 - 199

Published: Oct. 31, 2023

Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these may coincide with key evolutionary events such as the development novel morphological characters, acquisition adaptive traits, polyploidization or other structural genomic changes, dispersal to new habitat and subsequent increase environmental niche space. However, while multiple methods now exist estimate identify using phylogenetic topologies, appropriate use accuracy are hotly debated. Here we test whether five Bayesian methods-Bayesian Analysis Macroevolutionary Mixtures (BAMM), two implementations Lineage-Specific Birth-Death-Shift model (LSBDS PESTO), approximate Multi-Type Birth-Death (MTBD; implemented BEAST2), Cladogenetic Diversification Rate Shift (ClaDS2)-produce comparable results. We apply each set 65 empirical time-calibrated phylogenies compare inferences speciation rate, extinction net rate. find that often infer different speciation, extinction, net-diversification rates. Consequently, estimates lead interpretations macroevolutionary dynamics. The can be attributed fundamental differences among compared models. Therefore, inference strongly method dependent. advise biologists robustness conclusions carefully select based on validity underlying assumptions their particular system.

Language: Английский

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Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models

PLoS Computational Biology, Journal Year: 2024, Volume and Issue: 20(3), P. e1011640 - e1011640

Published: March 29, 2024

Birth-death models play a key role in phylodynamic analysis for their interpretation terms of epidemiological parameters. In particular, with piecewise-constant rates varying at different epochs time, to which we refer as episodic birth-death-sampling (EBDS) models, are valuable reflection changing transmission dynamics over time. A challenge, however, that persists current time-varying model inference procedures is lack computational efficiency. This limitation hinders the full utilization these large-scale analyses, especially when dealing high-dimensional parameter vectors exhibit strong correlations. We present here linear-time algorithm compute gradient birth-death sampling density respect all parameters, and implement this within gradient-based Hamiltonian Monte Carlo (HMC) sampler alleviate burden conducting under wide variety structures of, well priors for, EBDS processes. assess approach using three real world data examples, including HIV epidemic Odesa, Ukraine, seasonal influenza A/H3N2 virus New York state, America, Ebola outbreak West Africa. HMC exhibits substantial efficiency boost, delivering 10- 200-fold increase minimum effective sample size per unit-time, comparison Metropolis-Hastings-based approach. Additionally, show robustness our implementation both allowing flexible prior choices modeling various pathogens by accurately capturing trend viral reproductive number.

Language: Английский

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