近三年论文 · 15 篇 （点击展开摘要，时间倒序）
Molecular clock dating using complex mixture models: applied to ancient symbionts
Molecular clocks are a fundamental technique in evolutionary biology for establishing the timing and tempo of organismal divergence. However, currently available molecular clock methods, which often rely on simple homogeneous substitution models, can produce inaccurate time estimates, particularly for deep-time or rapidly evolving lineages where substitution heterogeneity and saturation are common. Hereby, we introduce phyloHessian (https://github.com/evolbeginner/phyloHessianWrapper), a Julia-based software to enable the use of complex mixture substitution models in molecular dating. phyloHessian computes the phylogenetic Hessian matrix and integrates it into PAML-MCMCtree's approximate likelihood framework to conduct dating analyses. Simulations mimicking phylogenies at different timescales demonstrate that complex mixture substitution models significantly enhance the accuracy of divergence time and substitution rate estimates in deep-time phylogenies. This pattern remains consistent across a wide range of uncertainties associated with molecular clock analysis. Additionally, mixture models display greater robustness to model and calibration specifications compared to their homogeneous counterparts. Empirical analysis of ancient symbiont lineages Microsporidia and Rickettsiales with different substitution models shows that mixture models, compared to homogeneous models, yield accelerated substitution rates and in some cases significantly different divergence times, leading to a revised understanding of their host association origins. Our findings underscore the importance of incorporating complex mixture substitution models for constructing reliable evolutionary timelines and elucidating the evolutionary history of deep-time or fast-evolving lineages.
Quantitative-genetic analysis of directional adaptation suggests low maximum sustainable rates of change in agreement with data from field populations
What rates of directional change are species likely to be capable of sustaining indefinitely such as in response to a warming climate? We derive estimates of the maximum rates of phenotypic change that populations can sustain in response to a directionally changing environment, using a quantitative genetics simulation model whose parameters are calibrated with data from natural populations. Sustainable directional change is largely limited to ≤2-4% of a trait standard deviation per generation, in agreement with an estimate derived from quantitative-genetic theory and with published field studies. Data from thirty-seven longitudinal field-studies of species' phenological responses to a warming climate yield rates of change that fall in the 68th-86th percentiles of our predictions for what populations can sustain, and there are suggestions that the rate of climate change may already have diminished their capacities to maintain these rates. Given the pace of climate change, species with generation times greater than four years may be especially at risk.
Identifying fragmented fossils and recent remains belonging to underrepresented taxa using geometric morphometrics
Abstract Fossils and more recent remains of dead organisms serve as natural archives of Earth’s recent and ancient history. It is often the case that small or fragmented specimens, especially microvertebrate bones, go unstudied. Accurate identification of such remains to a specific taxonomic level can help address a wide range of questions spanning paleontology, paleoecology, zooarchaeology, ecology, conservation science, forensics, and biogeography. Geometric morphometrics demonstrates significant potential for identifying fragmented lizard fossils to at least the family level based on shape differentiation. Our proof-of-concept study using lizard maxillae of extant species within the Pacific Northwest, USA, accurately identified fragmented maxillae with as few as six comparative specimens per genus. These findings establish a framework for addressing taxonomic challenges in fragmented bone specimen identification for taxa whose curated comparative specimens are small in number and unequal in representation.
Phlorest phylogeny derived from Hruschka et al. 2015 'Detecting regular sound changes in linguistics as events of concerted evolution'
Cite the source of the dataset as: Hruschka, D. J., Branford, S., Smith, E. D., Wilkins, J., Meade, A., Pagel, M., & Bhattacharya, T. (2015). Detecting regular sound changes in linguistics as events of concerted evolution. Current Biology, 25(1), 1-9.
Phlorest phylogeny derived from Grollemund et al. 2015 'Bantu expansion shows habitat alters the route and pace of human dispersals'
Cite the source of the dataset as: Grollemund R, Branford S, Bostoen K, Meade A, Venditti C & Pagel M. 2015. Bantu expansion shows habitat alters the route and pace of human dispersals. Proceedings of the National Academy of Sciences of the USA, 112(43), 13296-13301.
The radiation and geographic expansion of primates through diverse climates
One of the most influential hypotheses about primate evolution postulates that their origin, radiation, and major dispersals were associated with exceptionally warm conditions in tropical forests at northern latitudes (henceforth the warm tropical forest hypothesis ). However, this notion has proven difficult to test given the overall uncertainty about both geographic locations and paleoclimates of ancestral species. By the resolution of both challenges, we reveal that early primates dispersed and radiated in higher latitudes, through diverse climates, including cold, arid, and temperate conditions. Contrary to expectations of the warm tropical forest hypothesis, warmer global temperatures had no effect on dispersal distances or the speciation rate. Rather, the amount of change in local temperature and precipitation substantially predicted geographic and species diversity. Our results suggest that nontropical, changeable environments exerted strong selective pressures on primates with higher dispersal ability – promoting the primate radiation and their subsequent colonization of tropical climates millions of years after their origin.
Molecular Clock Dating of Deep-Time Evolution Using Complex Mixture Models
Abstract Molecular clocks are a fundamental technique in evolutionary biology for establishing the timing and tempo of organismal divergence. However, currently available molecular clock methods, which often rely on simple homogeneous substitution models, can produce inaccurate time estimates, particularly for deep-time or rapidly evolving lineages where substitution heterogeneity and saturation are common. Hereby, we introduce phyloHessian ( https://github.com/evolbeginner/phyloHessianWrapper ), a Julia-based software to enable the use of complex mixture substitution models in molecular dating. phyloHessian computes the phylogenetic Hessian matrix and integrates it into PAML-MCMCtree’s approximate likelihood framework to conduct dating analyses. Simulations mimicking phylogenies at different timescales demonstrate that complex mixture substitution models significantly enhance the accuracy of divergence time and substitution rate estimates in deep-time phylogenies. This pattern remains consistent across a wide range of uncertainties associated with molecular clock analysis. Additionally, mixture models display greater robustness to model and calibration specifications compared to their homogeneous counterparts. Empirical analysis of ancient symbiont lineages Microsporidia and Rickettsiales with different substitution models shows that mixture models, compared to homogeneous models, yield accelerated substitution rates and in some cases significantly different divergence times, leading to a revised understanding of their host association origins. Our findings underscore the importance of incorporating complex mixture substitution models for constructing reliable evolutionary timelines and elucidating the evolutionary history of deep-time or fast-evolving lineages.
Trait macroevolution in the presence of covariates
Statistical characterisations of traits evolving on phylogenies combine the contributions of unique and shared influences on those traits, potentially confusing the interpretation of historical events of macroevolution. The Fabric model, introduced in 2022, identifies historical events of directional shifts in traits (e.g. becoming larger/smaller, faster/slower over evolutionary time) and of changes in macroevolutionary 'evolvability' or the realised historical ability of a trait to explore its trait-space. Here we extend the model to accommodate situations in which the trait is correlated with one or more covarying traits. The Fabric-regression model identifies a unique component of variance in the trait that is free of influences from correlated traits, while simultaneously estimating directional and evolvability effects. We show in a dataset of 1504 Mammalian species that inferences about historical directional shifts in brain size and in its evolvability, having accounted for body size, differ qualitatively from inferences about brain size alone, including finding many new effects not visible in the whole trait. A class of fundamental macroevolutionary questions awaits testing on the variation uniquely attributable to traits, and the ability to accommodate statistically one or more covariates opens the possibility of bringing the formal methods of causal inference to phylogenetic-comparative studies.
Bacterial and Archaeal Phenotypic Database (BAPdb)
Supplementary data for "Phenotypic reconstruction of the last universal common ancestor reveals a complex cell" <br>doi: https://doi.org/10.1101/2020.08.20.260398<br><br>
The radiation and geographic expansion of euprimates through diverse climates
The most influential hypothesis about euprimate evolution postulates that their origin, radiation, and major dispersals, were associated with the exceptional warmer conditions of the planet in the tropical forests of higher latitudes. However, this notion has proven difficult to test given the overall uncertainty about the geographic locations and palaeoclimates of ancestral species. By the resolution of both challenges, we reveal that early euprimates dispersed and radiated in higher latitudes and through diverse climates defined by the Köppen-Geiger classification system, including cold, arid, and temperate. Contrary to expectations of the hypothesis, historical global temperature had no effect on dispersal distance or speciation rate. But how much the local temperature and precipitation changed substantially predicted geographic and species diversity. Our results set a new perspective on euprimate origins and evolution. They suggest that non-tropical and changeable environments exerted strong selective pressures on euprimates with higher dispersal ability which promoted this group’s radiation and subsequent colonisation of tropical climates millions of years after their origin.
Deep-sea origin and depth colonization associated with phenotypic innovations in scleractinian corals
The deep sea (>200 m) is home to a surprisingly rich biota, which in some cases compares to that found in shallow areas. Scleractinian corals are an example of this - they are key species in both shallow and deep ecosystems. However, what evolutionary processes resulted in current depth distribution of the marine fauna is a long-standing question. Various conflicting hypotheses have been proposed, but few formal tests have been conducted. Here, we use global spatial distribution data to test the bathymetric origin and colonization trends across the depth gradient in scleractinian corals. Using a phylogenetic approach, we infer the origin and historical trends in directionality and speed of colonization during the diversification in depth. We also examine how the emergence of photo-symbiosis and coloniality, scleractinian corals' most conspicuous phenotypic innovations, have influenced this process. Our results strongly support an offshore-onshore pattern of evolution and varying dispersion capacities along depth associated with trait-defined lineages. These results highlight the relevance of the evolutionary processes occurring at different depths to explain the origin of extant marine biodiversity and the consequences of altering these processes by human impact, highlighting the need to include this overlooked evolutionary history in conservation plans.
Phlorest phylogeny derived from Grollemund et al. 2015 'Bantu expansion shows habitat alters the route and pace of human dispersals'
Cite the source of the dataset as: Grollemund R, Branford S, Bostoen K, Meade A, Venditti C & Pagel M. 2015. Bantu expansion shows habitat alters the route and pace of human dispersals. Proceedings of the National Academy of Sciences of the USA, 112(43), 13296-13301.
Phlorest phylogeny derived from Hruschka et al. 2015 'Detecting regular sound changes in linguistics as events of concerted evolution'
Cite the source of the dataset as: Hruschka, D. J., Branford, S., Smith, E. D., Wilkins, J., Meade, A., Pagel, M., & Bhattacharya, T. (2015). Detecting regular sound changes in linguistics as events of concerted evolution. Current Biology, 25(1), 1-9.
Phlorest phylogeny derived from Grollemund et al. 2015 'Bantu expansion shows habitat alters the route and pace of human dispersals'
Cite the source of the dataset as: Grollemund R, Branford S, Bostoen K, Meade A, Venditti C & Pagel M. 2015. Bantu expansion shows habitat alters the route and pace of human dispersals. Proceedings of the National Academy of Sciences of the USA, 112(43), 13296-13301.
Phlorest phylogeny derived from Hruschka et al. 2015 'Detecting regular sound changes in linguistics as events of concerted evolution'
Cite the source of the dataset as: Hruschka, D. J., Branford, S., Smith, E. D., Wilkins, J., Meade, A., Pagel, M., & Bhattacharya, T. (2015). Detecting regular sound changes in linguistics as events of concerted evolution. Current Biology, 25(1), 1-9.