Causality from palaeontological time series

Palaeontology, Journal Year: 2018, Volume and Issue: 61(4), P. 495 - 509

Published: June 3, 2018

Abstract As custodians of deep time, palaeontologists have an obligation to seek the causes and consequences long‐term evolutionary trajectories processes ecosystem assembly collapse. Building explicit process models on relevant scales can be fraught with difficulties, causal inference is typically limited patterns association. In this review, we discuss some ways in which connections extracted from palaeontological time series provide overview three recently developed analytical frameworks that been applied questions, namely linear stochastic differential equations, convergent cross mapping transfer entropy. We outline how these methods differ conceptually, practice, point available software worked examples. end by discussing why a paradigm dynamical causality needed decipher messages encrypted patterns.

Language: Английский

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Opportunity Begets Opportunity to Drive Macroevolutionary Dynamics of a Diverse Lizard Radiation

Published: Jan. 18, 2024

Evolution proceeds unevenly across the tree of life, with some lineages accumulating diversity more rapidly than others. Explaining this disparity is challenging as similar evolutionary triggers often do not result in analogous shifts tree, and may reflect different triggers. We used a combination approaches to directly consider such context-dependency untangle complex network processes that shape macroevolutionary dynamics, focusing on Pleurodonta, diverse radiation lizards. Our framework shows lineage-wide signatures are lost when conditioned sub-lineages: viviparity appears accelerate diversification but its effect size overestimated by association Andean mountains. Conversely, signals erode at broader phylogenetic scales emerge shallower ones. Mountains general affect speciation rates; rather, occurrence mountains specifically promotes diversification. Likewise, evolution larger sizes catalyzes rates, only within certain ecological geographical settings. caution conventional methods fitting models entire trees mistakenly assign heterogeneity specific factors despite evidence against their plausibility. study takes significant stride toward disentangling confounding identifying plausible sources opportunities large radiations.

Language: Английский

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Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

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

Published: July 23, 2024

Many remarkable innovations have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by same underlying gene families, while other times many different families involved. Conversely, a family may be recruited for single trait or traits. To understand general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic count in 14,710 from 993 species Saccharomycotina yeasts. Using recently developed phylogenetic approach that reduces spurious correlations, discovered expansion contraction was significantly linked to gain loss 45/56 (80%) While 601/746 (81%) significant were associated with only one trait, also identified several 'keystone' up 13/56 (23%) all These results indicate yeasts governed narrow set major genetic elements mechanisms.

Language: Английский

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Parallel likelihood calculation for phylogenetic comparative models: The SPLITT C++ library

Methods in Ecology and Evolution, Journal Year: 2018, Volume and Issue: 10(4), P. 493 - 506

Published: Dec. 14, 2018

Abstract Phylogenetic comparative models ( PCM s) have been used to study macroevolutionary patterns, characterize adaptive phenotypic landscapes, quantify rates of evolution, measure trait heritability, and test various evolutionary hypotheses. A major obstacle applying these has the complexity evaluating their likelihood function. Recent works shown that for many s, can be obtained in time proportional size tree based on post‐order traversal, also known as pruning . Despite this progress, inferring complex multi‐trait s large trees remains a time‐intensive task. Here, we parallelizing algorithm generic technique speeding‐up ‐inference. We implement several parallel traversal algorithms form C++ library Serial Parallel LI neage Traversal Trees SPLITT ). Based , provide examples evaluation popular ranging from single‐trait Brownian motion model Ornstein‐Uhlenbeck mixed Gaussian phylogenetic models. Using Ornstein–Uhlenbeck POUMM ) showcase, run benchmarks up 24 CPU cores, reporting an order magnitude speed‐up calculation simulated balanced unbalanced 100,000 tips with 16 traits. Noticing depends multiple factors, is capable automatically select fastest strategy given hardware, tree‐topology, data. Combining Metropolis sampling real data, show Bayesian inference 10,000 reduced days less than hour. conclude effectively accelerates and, thus, statistical For inferences, recommend combining sampling. Beyond models, applied numerous other including discrete birth–death population dynamics Currently, supports multi‐core shared memory architectures, but extended distributed architectures well graphical processing units.

Language: Английский

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Maternal investment evolves with larger body size and higher diversification rate in sharks and rays

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Jan. 6, 2022

Summary Across vertebrates, live-bearing has evolved at least 150 times from ancestral egg-laying into a diverse array of forms and degrees prepartum maternal investment. 1,2 A key question is how this reproductive diversity arose whether diversification underlies species diversification? 3–11 To test these questions, we evaluate the most basal jawed sharks, rays, chimaeras Class Chondrichthyans, which have one greatest ranges ecological among vertebrates. 2,12 We reconstructed sequence mode evolution across time-calibrated molecular phylogeny 610 chondrichthyans. 13 find ancestral, seven times. Matrotrophy (i.e. contributions beyond yolk) 15 times, with evidence reversal. In transitions to matrotrophy are more prevalent in larger-bodied tropics. Further, associated near-doubling rate, but, there only small increase appearance increased rates speciation colonization novel habitats, contrary what been demonstrated teleosts. 3,4 This highlights potential difference between chondrichthyans other fishes, specifically slower rate isolation following speciation, suggesting different rate-limiting mechanisms for clades. 14 The chondrichthyan radiation, particularly throughout shallow tropical shelf seas oceanic pelagic appears be proliferation wide range investment developing offspring.

Language: Английский

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Plant Functional Traits and the Multidimensional Phenotype

Oxford University Press eBooks, Journal Year: 2023, Volume and Issue: unknown, P. 159 - 212

Published: July 27, 2023

Abstract Modules are the basic architectural building blocks of a plant. Roots anchor plants in place, provide support for growing stems, acquire water and mineral nutrients from soil, transport minerals to aboveground tissues. Clonality bud banks neglected aspect plant form function. Stems canopies leaves branches, store water, minerals, carbohydrates. Leaves face fundamental constraint: they must lose gain carbon. The leaf economics spectrum describes trade-off between rate carbon fixation cost tissue construction. Defining globally comparable phenological traits is an important unsolved problem. innovation seeds revolutionized reproduction because fertilization was no longer limited wet environments, it enabled young travel dormant state find more favorable opportunities colonization. Our understanding dimensionality functional rapidly growing, but at least five dimensions important: spectrum, height, rooting depth, belowground collaboration with fungi, seed-or-resprout spectrum. Evolution branching process species that close together on evolutionary tree likely share similar phenotypic closely related, especially when strongly conserved. However, phylogenetic conservatism not only explanation trait similarity among related natural selection can also explain it.

Language: Английский

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Language follows a distinct mode of extra-genomic evolution

Published: Nov. 4, 2023

As one of the most specific, yet diverse human behaviors, language is shaped by both genomic and extra-genomic evolution. Sharing methods models between these modes evolution has significantly advanced our understanding inspired generalized theories its Progress hampered, however, fact that languages, i.e. linguistic evolution, maps only partially to other forms Contrasting it with biological eukaryotes cultural technology as best understood models, we show special yielding a stationary dynamic rather than stable solutions, this allows use change for social differentiation while maintaining global adaptiveness. Linguistic furthermore differs from technological requiring vertical transmission, allowing reconstruction phylogenies; eukaryotic foregoing genotype vs phenotype distinction, deliberate biased change. Recognising differences will improve empirical tools open new avenues analyzing how linguistic, cultural, interacted each when emerged in hominin lineage. Importantly, framework help cope unprecedented scientific ethical challenges presently arise rapid impacts language, urgently interventional clinical disorders, potential epigenetic effects on artificial intelligence communicators, losses diversity identity. Beyond distinctions made here allow identifying variation developing perspectives research.

Language: Английский

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Jointly Modeling the Evolution of Discrete and Continuous Traits

Published: July 13, 2022

Whether modeling the evolution of a discrete or continuous character, focal trait interest does not evolve in isolation and require comparative methods that model multivariate evolution. Progress along these lines has involved same class character there are fewer options when jointly traits one is other continuous. Here we develop such framework to explicitly estimate joint likelihood for characters. Specifically, our combines probability observing under generalized OU process with hidden Markov model, linked by shared underlying regime. We use simulation studies demonstrate this approach, hOUwie, can accurately evaluate parameter values across broad set models. then apply test whether fleshy dry fruits Ericaceae lineages correlated their climatic niche as represented aridity index. Consistent expectations, find have higher rates evolution, more conserved, humid optimum.

Language: Английский

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Perspectives on Plant Strategies

Oxford University Press eBooks, Journal Year: 2023, Volume and Issue: unknown, P. 3 - 20

Published: July 27, 2023

Abstract Widespread observations of convergent evolution—the selection for similar traits in environments among unrelated taxa—continue to motivate interest plant strategies. Some ecologists prefer simple models with as few strategies possible, whereas others propose dozens explain the diversity form and function. describe distinct categories but continuous variation suggests that align along dimensions. Psychological human behavior provide an analogous framework understanding Psychologists have also debated over merits versus complex categorical personalities. The five-factor model proposes humans exhibit five traits. Plant may be best described by independent are phenotypes resulting from natural enable a population persist given environment. To make progress, strategy theory must (1) unpack multiple dimensions productivity disturbance gradients into their component parts; (2) articulate causal relationships between functional life history traits; (3) able distinguish fundamental realized niches phenotype; (4) differentiate trait adaptations large-scale spatial climate soil temporal small-scale heterogeneity within local habitats.

Language: Английский

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Applying Plant Strategies in Conservation and Restoration

Oxford University Press eBooks, Journal Year: 2023, Volume and Issue: unknown, P. 307 - 326

Published: July 27, 2023

Abstract Conservation biology and ecological restoration are creative defiant sciences that express optimism in our ability to right the wrongs humans have inflicted on biodiversity. Plant strategies integral successful conservation restoration. is science of rarity applied prevent species functions from going extinct. Demographic analyses needed identify demographic rates most vulnerable extinction threats. The concept has been generalized new functional rarity. Traits can be used generalize across taxa assess responses grazing management as well vulnerability global change drivers inform actions. Restoration community reassembly because it manipulates abiotic conditions, pool, density non-native competitors. predictions trajectory dynamics ecosystem functioning over time. influence establishment success response different environmental conditions treatments, they might useful selection optimize outcomes. strategy theory directly relevant invasion ecology assisted migration. Experimental tests migration common garden settings compare gradients could represent some strongest plant theory.

Language: Английский

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