Handling missing values in trait data

Global Ecology and Biogeography, Journal Year: 2020, Volume and Issue: 30(1), P. 51 - 62

Published: Oct. 18, 2020

Abstract Aim Trait data are widely used in ecological and evolutionary phylogenetic comparative studies, but often values not available for all species of interest. Traditionally, researchers have excluded without from analyses, estimation missing using imputation has been proposed as a better approach. However, methods largely designed randomly data, whereas trait at random (e.g., more bigger species). Here, we evaluate the performance approaches handling when considering biased datasets. Location Any. Time period Major taxa studied Methods We simulated continuous traits separate response variables to test nine complete‐case analysis (excluding dataset) under scenarios. characterized by estimating error imputed (deviation true value) inferred trait–response relationships relationship between response). Results Generally, Rphylopars produced most accurate estimate best preserved response–trait slope. estimates were still inaccurate, even with only 5% missing. Under severe biases, errors high every Imputation was always option, frequently outperforming Mice and, lesser degree, BHPMF imputation. , popular approach, performed poorly variable model. Main conclusions can handle effectively some conditions is solution. None tested could deal which be common recommend rigorous checking biases before after propose that assist working incomplete datasets detect minimize errors.

Language: Английский

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Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models

Methods in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 14(5), P. 1259 - 1275

Published: March 26, 2023

Abstract Traits underlie organismal responses to their environment and are essential predict community environmental conditions under global change. Species differ in life‐history traits, morphometrics, diet type, reproductive characteristics habitat utilization. Trait associations widely analysed using phylogenetic comparative methods (PCM) account for correlations among related species. Similarly, traits measured some but not all species, missing continuous (e.g. growth rate) can be imputed ‘phylogenetic trait imputation’ (PTI), based on evolutionary relatedness covariance. However, PTI has been available categorical estimating covariance without ecological constraints risks inferring implausible mechanisms. Here, we extend previous PCM by (1) specifying as a structural equation model (SEM), (2) incorporating both traits. Fitting SEM replaces the with set of linear path coefficients potential Estimated parameters then represent regression slopes (i.e. average change Y given an exogenous X) that used calculate direct effects (X impacts Y) indirect Z Y). We demonstrate structural‐equation mixed‐trait imputation 33 variables representing life history, reproductive, morphological, behavioural >32,000 described fishes worldwide. suggest one degree Celsius increase is associated 3.5% natural mortality (including 1.4% impact acts via temperature coefficient), 3.0% decrease fecundity (via maximum age length). Cross‐validation indicates explains 54%–89% variance withheld measurements area receiver‐operator‐characteristics curve 0.86–0.99 use classify into types, confirm signal three dominant strategies fishes. SEMs ensures estimated interpretable slopes, such inferred relationships compared long‐term rearing experiments.

Language: Английский

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Co-evolutionary dynamics of mammalian brain and body size

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(8), P. 1534 - 1542

Published: July 8, 2024

Despite decades of comparative studies, puzzling aspects the relationship between mammalian brain and body mass continue to defy satisfactory explanation. Here we show that several such arise from routinely fitting log-linear models data: correlated evolution is in fact log-curvilinear. This simultaneously accounts for phenomena which diverse biological explanations have been proposed, notably variability scaling coefficients across clades, low encephalization larger species so-called taxon-level problem. Our model implies a need revisit previous findings about relative mass. Accounting true relationship, document dramatically varying rates phylogeny, resolve question whether there an overall trend increase through time. We find only three orders, by far strongest primates, setting stage uniquely rapid directional ultimately producing computational powers human brain.

Language: Английский

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Terrestrial reproduction and parental care drive rapid evolution in the trade-off between offspring size and number across amphibians

PLoS Biology, Journal Year: 2022, Volume and Issue: 20(1), P. e3001495 - e3001495

Published: Jan. 4, 2022

The trade-off between offspring size and number is central to life history strategies. Both the evolutionary gain of parental care or more favorable habitats for development are predicted result in fewer, larger offspring. However, despite much research, it remains unclear whether how different forms drive evolution trade-off. Using data over 800 amphibian species, we demonstrate that, after controlling allometry, amphibians with direct those that lay eggs terrestrial environments have smaller clutches, while behaviors adaptations vary their effects on Specifically, among 11 considered at egg, tadpole juvenile stage, egg brooding, male attendance, female attendance increase size; feeding decrease size, feeding, transport clutch size. Unlike shows exceptionally high rates phenotypic change just 19 branches phylogeny, has evolved 135 branches, indicating episodes strong selection; environment, development, explain 80% these events. By explicitly considering diversity habitat by stage this study demonstrates conditions promote broods reveals influences nuanced ways than previously appreciated.

Language: Английский

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Evolutionary trade-offs between testes size and parenting in Neotropical glassfrogs

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2016)

Published: Feb. 14, 2024

In males, large testes size signifies high sperm production and is commonly linked to heightened competition levels. It may also evolve as a response an elevated risk of depletion due multiple mating or clutch sizes. Conversely, weapons, mate guarding allow individuals monopolize events preclude competition, thereby reducing the selection testes. Herein, we examined how paternal care, sexual dimorphism (SSD), weaponry female fecundity are in glassfrogs. We found that care was associated with reduction relative size, suggesting evolutionary trade-off between parenting. Although females were slightly larger than males species tended have clutches, there no significant relationship SSD, size. These findings suggest evolution glassfrogs influenced by risk, rather risk. infer precludes fertilization other consequently diminishes selective pressure for Our study highlights prominent role external fertilization.

Language: Английский

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Tetrapod sperm length evolution in relation to body mass is shaped by multiple trade-offs

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 22, 2024

Abstract Sperm length is highly variable across species and many questions about its variation remain open. Although in body mass may affect sperm evolution through influence on multiple factors, the extent to which linked remains elusive. Here, we use Pareto multi-task framework investigate relationship between tetrapods. We find that tetrapods occupy a triangular front, indicating trade-offs shape of relation mass. By exploring factors predicted evolution, mainly driven by competition clutch size, rather than genome size. Moreover, front maintained within endotherms, internal fertilizers, mammals birds, suggesting similar evolutionary Finally, demonstrate robust phylogenetic dependencies finite sampling bias. Our findings provide insights into mechanisms driving interspecific highlight importance considering optimizing reproductive traits.

Language: Английский

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Avian testicular structure, function, and regulation

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 67 - 106

Published: Jan. 1, 2024

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Climate and ecology predict latitudinal trends in sexual selection inferred from avian mating systems

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(11), P. e3002856 - e3002856

Published: Nov. 4, 2024

Sexual selection, one of the central pillars evolutionary theory, has powerful effects on organismal morphology, behaviour, and population dynamics. However, current knowledge about geographical variation in this mechanism its underlying drivers remains highly incomplete, part because standardised data strength sexual selection is sparse even for well-studied organisms. Here, we use information mating systems—including incidence polygamy extra-pair paternity—to estimate intensity 10,671 (>99.9%) bird species distributed worldwide. We show that avian varies latitudinally, peaking at higher latitudes, although gradient reversed world’s most sexually selected birds—specialist frugivores—which are strongly associated with tropical forests. Phylogenetic models further reveal explained by temperature seasonality coupled a suite climate-associated factors, including migration, diet, territoriality. Overall, these analyses suggest climatic conditions leading to short, intense breeding seasons, or abundant patchy food resources, increase potential birds, driving latitudinal gradients selection. Our findings help resolve longstanding debates spatial mechanisms linked reproductive biology also provide comprehensive species-level set studies phenotypic evolution context global change.

Language: Английский

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Rare polyandry and common monogamy in the firefly squid, Watasenia scintillans

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: July 3, 2020

Abstract In cephalopods, all species are considered to be polyandrous because of their common life history and reproductive traits reflecting a mating system. Contrary this belief, here we show several lines evidence for monogamy in the firefly squid, Watasenia scintillans . species, females capable long-term storage spermatangia, egg spawning even after complete disappearance males following breeding season. The stored spermatangia distributed equally between bilateral pouches under female’s neck collar. Such nonrandom pattern sperm prompted us hypothesize that might engage lifetime monandry. Hence, genotyped female-stored offspring, found 95% (18/19), had been delivered from single male embryos clutch sired by spermatozoa spermatangia. males, throughout season, relative testis mass was much smaller W. than other cephalopods examined previously. mean number male-stored spermatophores ~ 30, equivalent only 2.5 matings. Our genetic, demographic morphometrical data agree with mathematical model predicting monogyny is favored when potential mates scarce. Together, these results suggest mutual

Language: Английский

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Ejaculate Allocation and Sperm Characteristics Differ among Alternative Male Types in a Species of Fish with Cooperation and Competition among Unrelated Males

Cells, Journal Year: 2021, Volume and Issue: 10(10), P. 2612 - 2612

Published: Oct. 1, 2021

Sexual selection arising from sperm competition has driven the evolution of immense variation in ejaculate allocation and characteristics not only among species, but also males within a species. One question that received little attention is how cooperation affects these patterns. Here we ask male alternative reproductive types differ testes size, production, morphology ocellated wrasse, marine fish which unrelated cooperate compete during reproduction. Nesting build nests, court females provide care. Sneaker “sneak” spawn, while satellite sneak, help by chasing away sneakers. We found have larger absolute than either sneakers or nesting males, despite their cooperative role. invested relatively less satellites. Though produced smaller ejaculates no difference cell concentration number, implying may produce seminal fluid. Sperm tail length did significantly types, sneaker cells had heads sperm, consistent with past research showing slower sperm. Our results highlight social interactions can influence production.

Language: Английский

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