MOTMOT: Models of trait macroevolution on trees (an update)

Puttick, Mark N.; Ingram, Travis; Clarke, Magnus; Thomas, Gavin H.

doi:10.1111/2041-210x.13343

Cited by 23 publications

(14 citation statements)

References 28 publications

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“…Nevertheless, we added host sample size as an explanatory variable in the diversity models. Host ED was calculated using the 'fair proportion' metric (Isaac et al 2007, Redding et al 2008 as implemented in the 'fairProportions' function in the motmot.2.0 R-package (Puttick et al 2018); species with few close relatives have higher fair proportion scores and thus greater ED than species with many close relatives. We calculated ED as the mean of the fair proportion scores across 100 trees sampled randomly from the posterior distribution of the Jetz et al (2012) analysis and restricted to species sampled at least once at Krankesjön; thus it was a local measure of ED.…”

Section: Statistical Analysesmentioning

confidence: 99%

Explaining prevalence, diversity and host specificity in a community of avian haemosporidian parasites

Ellis

Huang

Westerdahl

et al. 2020

Oikos

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Many hypotheses attempt to explain parasite–host associations, but rarely are they examined together in a single community. For hosts, key traits are the proportion of infected individuals (prevalence) and the diversity of parasites infecting them. A key parasite trait is host specificity, ranging from specialists infecting one or a few closely related species to generalists infecting many species. We tested 10 hypotheses to explain host‐parasite associations; five ‘host‐centric’ (e.g. prevalence is related to host abundance) and five ‘parasite‐centric’ (e.g. parasite abundance is related to host specificity). We analyzed a community of 67 locally transmitted avian haemosporidian parasite lineages (genera Plasmodium, Haemoproteus or Leucocytozoon), sampled from 2726 birds (64 species) in southern Sweden. Among host‐centric hypotheses, Haemoproteus and Leucocytozoon prevalence and Haemoproteus diversity were related to host habitat preferences, whereas there were no relationships with host abundance or body mass. Haemoproteus and Leucocytozoon prevalences were more similar among closely related than among distantly related host species. Haemoproteus prevalence and diversity were lower in host species with few close relatives (‘evolutionarily distinct’ hosts). Among parasite‐centric hypotheses, most lineages, even relative generalists, infected closely related host species more often than expected by chance. However, the host species of Haemoproteus and Leucocytozoon lineages overlapped less among lineages than expected by chance. Specialists did not reach higher prevalences than generalists on single host species. However, the abundance of Haemoproteus lineages was related to host specificity with generalists more common than specialists; this was driven by three closely related generalists. Host specificity of parasites was unrelated to the abundance or evolutionarily distinctiveness of their hosts. Parasite communities are likely structured by many factors and cannot be explained by hypotheses focusing solely on hosts or parasites. However, we found consistent effects of host phylogenetic relationships, plausibly a result of evolutionarily conserved host immune systems limiting parasite distributions.

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Section: Statistical Analysesmentioning

confidence: 99%

Explaining prevalence, diversity and host specificity in a community of avian haemosporidian parasites

Ellis

Huang

Westerdahl

et al. 2020

Oikos

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“…We pruned the phylogeny and trait values to include only those lineages that existed at the boundary (Puttick et al 2017), such that we did not consider values from lineages that were lost before the extinction or arose after it. We estimated the phylogenetic signal in trait values using Pagel's lambda (Pagel 1997(Pagel , 1999 alongside the regression parameters in the R package motmot (Puttick et al 2020).…”

Section: Phylogenetic Analysis Of Mass Extinctionsmentioning

confidence: 99%

The complex effects of mass extinctions on morphological disparity

2020

Self Cite

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Studies of biodiversity through deep time have been a staple for biologists and paleontologists for over 60 years. Investigations of species richness (diversity) revealed that at least five mass extinctions punctuated the last half billion years, each seeing the rapid demise of a large proportion of contemporary taxa. In contrast to diversity, the response of morphological diversity (disparity) to mass extinctions is unclear. Generally, diversity and disparity are decoupled, such that diversity may decline as morphological disparity increases, and vice versa. Here, we develop simulations to model disparity changes across mass extinctions using continuous traits and birth-death trees. We find no simple null for disparity change following a mass extinction but do observe general patterns. The range of trait values decreases following either random or trait-selective mass extinctions, whereas variance and the density of morphospace occupation only decline following trait-selective events. General trends may differentiate random and trait-selective mass extinctions, but methods struggle to identify trait selectivity. Long-term effects of mass extinction trait selectivity change support for phylogenetic comparative methods away from the simulated Brownian motion toward Ornstein-Uhlenbeck and Early Burst models. We find that morphological change over mass extinction is best studied by quantifying multiple aspects of morphospace occupation.

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“…Among phytoplankton, measures of thermal 68 sensitivity of r max (E and W op ) have previously been shown to exhibit intermediate 69 phylogenetic heritability [27]. This indicates that among phytoplankton, thermal 70 sensitivity is not constant but evolves along the phylogeny, albeit not as a purely random 71 walk in trait space. To understand how variation in thermal sensitivity accumulates 72 across diverse autotroph and heterotroph groups, in this study we conduct a thorough 73 investigation of the evolutionary patterns of thermal sensitivity, focusing particularly on 74 r max .…”

Section: Introductionmentioning

confidence: 98%

Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate

Kontopoulos

Smith

Barraclough

et al. 2019

Preprint

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Developing a thorough understanding of how ectotherm physiology adapts to different thermal environments is of crucial importance, especially in the face of climate change. In particular, the study of how the relationship between trait performance and temperature (the "thermal performance curve"; TPC) evolves has been receiving increasing attention over the past years. A key aspect of the TPC is the thermal sensitivity, i.e., the rate at which trait values increase with temperature within temperature ranges typically experienced by the organism. For a given trait, the distribution of thermal sensitivity values across species is typically right-skewed. The mechanisms that underlie the shape of this distribution are hotly debated, ranging from strongly thermodynamically constrained evolution to adaptive evolution that can partly overcome thermodynamic constraints. Here we take a phylogenetic comparative approach and examine the evolution of the thermal sensitivity of population growth rate across phytoplankton and prokaryotes. We find that thermal sensitivity is moderately phylogenetically heritable and that the shape of its distribution is the outcome of frequent evolutionary convergence. More precisely, bursts of rapid evolution in thermal sensitivity can be detected throughout the phylogeny, increasing the amount of overlap among the distributions of thermal sensitivity of different clades. We obtain qualitatively similar results from evolutionary analyses of the thermal sensitivities of two underlying physiological traits, net photosynthesis rate and respiration rate of plants. Finally, we show that part of the variation in thermal sensitivity is driven by latitude, potentially as an adaptation to the magnitude of temperature fluctuations. Overall, our results indicate that adaptation can lead to large shifts in thermal sensitivity, suggesting that attention needs to be paid towards elucidating the implications of these evolutionary patterns for ecosystem function. Author summaryChanges in environmental temperature influence the performance of biological traits (e.g., respiration rate) in ectotherms, with the relationship between trait performance and temperature (the "thermal performance curve") being single-peaked. Understanding how thermal performance curves adapt to different environments is important for predicting how organisms will be impacted by climate change. One key aspect of the July 23, 2019 1/23 shape of these curves is the thermal sensitivity near temperatures typically experienced by the species. Currently, it remains unclear if thermal sensitivity can change through environmental adaptation or if it is nearly constant across environments. To address this question, in this study we use four datasets of thermal performance curves to reconstruct the evolution of thermal sensitivity across prokaryotes, phytoplankton, and plants. We show that thermal sensitivity does not evolve in a gradual manner, but can differ considerably even between closely related species. This suggests that thermal sensitivi...

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MOTMOT: Models of trait macroevolution on trees (an update)

Cited by 23 publications

References 28 publications

Explaining prevalence, diversity and host specificity in a community of avian haemosporidian parasites

Explaining prevalence, diversity and host specificity in a community of avian haemosporidian parasites

The complex effects of mass extinctions on morphological disparity

Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate

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