A comparison of metrics for estimating phylogenetic signal under alternative evolutionary models

Diniz‐Filho, José Alexandre Felizola; Santos, Thiago; Rangel, Thiago F.; Bini, Luis Maurício

doi:10.1590/s1415-47572012005000053

Cited by 50 publications

(49 citation statements)

References 48 publications

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“…Most were not significantly greater than zero: of 72 tests done, only 11 were significantly greater than zero at the 5% level, and only one at the 1% level (Table ). Values for Argyranthemum and Descurainia are consistent with Brownian motion‐level niche conservatism for temperature, while values for the other clades across all climatic variables are more consistent with lower levels of climatic niche similarity than expected under Brownian motion evolution (Diniz‐Filho et al ., ).…”

Section: Resultsmentioning

confidence: 97%

Biogeographic ranges do not support niche theory in radiating Canary Island plant clades

Steinbauer

Field

Fernández‐Palacios

et al. 2016

Global Ecology and Biogeography

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A note on versions:The version presented here may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher's version. Please see the repository url above for details on accessing the published version and note that access may require a subscription. Sonchus, separately, we tested relationships between phylogenetic distance and climatic 36 niche differentiation (in temperature, precipitation and their combination), using a high-37 resolution dataset. We also tested for niche conservatism using Blomberg's K and Pagel's λ. 38We compared climatic niche differentiation between pairs of species existing in sympatry with 39 that for pairs of species in allopatry. For each comparison, we focused on the climatic niche 40 space available to both species. 41Results: The relationships between phylogenetic distance and climatic niche differentiation 42 were mostly non-significant; some weak but significant positive relationships were found, 43 mainly for Aeonium and Sonchus. Where differences between sympatry and allopatry were 44 found, niche differentiation tended to be greater in allopatry. 45Main conclusions: The expectations from niche conservatism were frequently not met; 46 instead our results suggest considerable climatic niche lability. All significant differences in 47 climatic niche differentiation were opposite to the predictions from competitive displacement. 48

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Section: Resultsmentioning

confidence: 97%

Biogeographic ranges do not support niche theory in radiating Canary Island plant clades

Steinbauer

Field

Fernández‐Palacios

et al. 2016

Global Ecology and Biogeography

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“…Although Moran’s I, Blomberg’s K , and the Mantel tests are closely related mathematically [41,42], their performance depends heavily on the choice of genetic distance model [42]. For this reason, we used three different models of genetic distance.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic signal in the acoustic parameters of the advertisement calls of four clades of anurans

et al. 2013

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BackgroundAnuran vocalizations, especially their advertisement calls, are largely species-specific and can be used to identify taxonomic affiliations. Because anurans are not vocal learners, their vocalizations are generally assumed to have a strong genetic component. This suggests that the degree of similarity between advertisement calls may be related to large-scale phylogenetic relationships. To test this hypothesis, advertisement calls from 90 species belonging to four large clades (Bufo, Hylinae, Leptodactylus, and Rana) were analyzed. Phylogenetic distances were estimated based on the DNA sequences of the 12S mitochondrial ribosomal RNA gene, and, for a subset of 49 species, on the rhodopsin gene. Mean values for five acoustic parameters (coefficient of variation of root-mean-square amplitude, dominant frequency, spectral flux, spectral irregularity, and spectral flatness) were computed for each species. We then tested for phylogenetic signal on the body-size-corrected residuals of these five parameters, using three statistical tests (Moran’s I, Mantel, and Blomberg’s K) and three models of genetic distance (pairwise distances, Abouheif’s proximities, and the variance-covariance matrix derived from the phylogenetic tree).ResultsA significant phylogenetic signal was detected for most acoustic parameters on the 12S dataset, across statistical tests and genetic distance models, both for the entire sample of 90 species and within clades in several cases. A further analysis on a subset of 49 species using genetic distances derived from rhodopsin and from 12S broadly confirmed the results obtained on the larger sample, indicating that the phylogenetic signals observed in these acoustic parameters can be detected using a variety of genetic distance models derived either from a variable mitochondrial sequence or from a conserved nuclear gene.ConclusionsWe found a robust relationship, in a large number of species, between anuran phylogenetic relatedness and acoustic similarity in the advertisement calls in a taxon with no evidence for vocal learning, even after correcting for the effect of body size. This finding, covering a broad sample of species whose vocalizations are fairly diverse, indicates that the intense selection on certain call characteristics observed in many anurans does not eliminate all acoustic indicators of relatedness. Our approach could potentially be applied to other vocal taxa.

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“…Both indices are usually correlated, however, they are calculated differently and are sensitive to different topologies of phylogenies (Diniz‐Filho et al . ).…”

Section: Methodsmentioning

confidence: 97%

The evolution of host specialisation in avian brood parasites

Medina

Langmore

2016

Ecology Letters

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Traditional ecological theory predicts that specialisation can promote speciation; hence, recently derived species are specialists. However, an alternative view is that new species have broad niches, which become narrower and specialised over time. Here, we test these hypotheses using avian brood parasites and three different measures of host specialisation. Brood parasites provide an ideal system in which to investigate the evolution of specialisation, because some exploit more than 40 host species and others specialise on only one. We find that young brood parasite species are smaller and specialise on a narrower range of host sizes, as expected, if specialisation is linked with the generation of new species. Moreover, we show that highly virulent parasites are more specialised, supporting findings in other host-parasite systems. Finally, we demonstrate that different measures of specialisation can lead to different conclusions, and specialisation indices should be designed taking into account the biology of each system.

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A comparison of metrics for estimating phylogenetic signal under alternative evolutionary models

Cited by 50 publications

References 48 publications

Biogeographic ranges do not support niche theory in radiating Canary Island plant clades

Biogeographic ranges do not support niche theory in radiating Canary Island plant clades

Phylogenetic signal in the acoustic parameters of the advertisement calls of four clades of anurans

The evolution of host specialisation in avian brood parasites

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