Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?

Molina‐Venegas, Rafael; Rodrı́guez, Miguel Á.

doi:10.1186/s12862-017-0898-y

Cited by 134 publications

(118 citation statements)

References 49 publications

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“…However, estimated values based on synthesis‐based phylogenies were either highly correlated with (Blomberg's K) or close to (Pagel's λ) those estimated from the “true” phylogeny (tree_purpose) under the BM trait evolution model. A recent study that suggested Pagel's λ is more robust to polytomies and suboptimal branch‐length information in the phylogeny than Blomberg's K (Molina‐Venegas and Rodriguez ). Furthermore, another previous study found that Blomberg's K overestimated phylogenetic signal if a phylogeny has a large proportion of polytomies (Davies et al.…”

Section: Discussionmentioning

confidence: 99%

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Trotta

Marx

et al. 2019

Ecology

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Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose‐built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis‐based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose‐built phylogenies and their corresponding synthesis‐based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose‐built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel's λ and Blomberg's K). Synthesis‐based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose‐built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman's normalρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose‐built phylogenies. Trait phylogenetic signal estimated with synthesis‐based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg's K or close to Pagel's λ from purpose‐built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

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Section: Discussionmentioning

confidence: 99%

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Trotta

Marx

et al. 2019

Ecology

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“…This provides state‐of‐the‐art data on tree topology but not on branch lengths, which were set to a value of one. This is not much of a problem as branch lengths have only a minor effect on phylogenetic signal estimates (Molina‐Venegas & Rodríguez, ; Münkemüller et al., ). The grassland species’ phylogeny was estimated using MrBayes from rbcL and matK DNA fragments obtained from plant tissue (Ronquist et al., , see Appendix for lab techniques).…”

Section: Methodsmentioning

confidence: 99%

Related plant species respond similarly to chronic anthropogenic disturbance: Implications for conservation decision‐making

Martínez‐Blancas

Paz

Salazar

et al. 2018

Journal of Applied Ecology

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Many developing countries harbour large numbers of species that face little‐understood, gradual changes in their environment, including chronic anthropogenic disturbance (CAD), a high frequency but low intensity form of disturbance. These countries also lack the resources to study each species, so conservation practices have been generalized, assuming that complete taxonomic groups may be managed in the same ways. This approach could be justified if closely related species respond similarly to threats. We assessed if related species respond similarly to CAD, whether this affects phylogenetic diversity and if such patterns occur in different systems. Species’ identity and abundance was recorded in 59 sites differing in CAD intensity in a semi‐arid grassland and a tropical dry forest in Mexico. Disturbance response indices were calculated for each species. Nested analysis of variance coupled with null models were applied to determine if generalizations within taxa are justified and which taxonomic level explained the most variation in disturbance response among species. We obtained phylogenetic trees using molecular data for the grassland and published data for the tropical forest. Phylogenetic signal was measured with Pagel's λ. Community mean phylogenetic distance was regressed on CAD. Higher taxonomic levels explained more variation than expected by chance, indicating that related species respond similarly to CAD. However, only species in the same genus behaved similarly enough to make generalizations reliable. This is the result of an underlying, if modest, phylogenetic signal in CAD responses. Mean phylogenetic distance decreased with CAD in the grassland but not the tropical dry forest. This suggests that CAD was a stronger environmental filter in the grassland but weak in the tropical dry forest, where it was less intense. Policy implications. Species inform us how their relatives respond to chronic anthropogenic disturbance (CAD), supporting the idea that generalizations in management are possible. However, this procedure is seemingly reliable only within genera, which explain over 80% of the accumulated variance in species’ CAD responses, and not within orders or families. CAD may reduce phylogenetic diversity, perhaps leading to ecosystem function loss.

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“…Both analyses test for phylogenetic signal but under different frameworks (Blomberg et al, 2003;Pagel, 1999). For Blomberg's K, the variance is partitioned according to clades, where a K > 1 indicates significant variance between clades, and a K < 1 indicates variance within clades (Blomberg et al, 2003;Molina-Venegas & Rodríguez, 2017).…”

Section: Ta B L E 1 Boreoeutherian Species Sampled In This Studymentioning

confidence: 99%

Evidence of strong stabilizing effects on the evolution of boreoeutherian (Mammalia) dental proportions

Monson

Boisserie

Brasil

et al. 2019

Ecology and Evolution

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The dentition is an extremely important organ in mammals with variation in timing and sequence of eruption, crown morphology, and tooth size enabling a range of behavioral, dietary, and functional adaptations across the class. Within this suite of variable mammalian dental phenotypes, relative sizes of teeth reflect variation in the underlying genetic and developmental mechanisms. Two ratios of postcanine tooth lengths capture the relative size of premolars to molars (premolar–molar module, PMM), and among the three molars (molar module component, MMC), and are known to be heritable, independent of body size, and to vary significantly across primates. Here, we explore how these dental traits vary across mammals more broadly, focusing on terrestrial taxa in the clade of Boreoeutheria (Euarchontoglires and Laurasiatheria). We measured the postcanine teeth of N = 1,523 boreoeutherian mammals spanning six orders, 14 families, 36 genera, and 49 species to test hypotheses about associations between dental proportions and phylogenetic relatedness, diet, and life history in mammals. Boreoeutherian postcanine dental proportions sampled in this study carry conserved phylogenetic signal and are not associated with variation in diet. The incorporation of paleontological data provides further evidence that dental proportions may be slower to change than is dietary specialization. These results have implications for our understanding of dental variation and dietary adaptation in mammals.

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Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?

Cited by 134 publications

References 49 publications

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Related plant species respond similarly to chronic anthropogenic disturbance: Implications for conservation decision‐making

Evidence of strong stabilizing effects on the evolution of boreoeutherian (Mammalia) dental proportions

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