Bayesian Prediction of Multivariate Ecology from Phenotypic Data Yields New Insights into the Diets of Extant and Extinct Taxa.

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations, such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Furthermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa but yields new insights into the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet but serves as a general framework for predicting multivariate ecology from phenotypic traits.

Molecular data from the holotype of the enigmatic Bornean Black Shrew, Suncusater Medway, 1965 (Soricidae, Crocidurinae), place it in the genus Palawanosorex.

Although Borneo has received more attention from biologists than most other islands in the Malay Archipelago, many questions regarding the systematic relationships of Bornean mammals remain. Using next-generation sequencing technology, we obtained mitochondrial DNA sequences from the holotype of Suncusater, the only known specimen of this shrew. Several shrews collected recently in Sarawak are closely aligned, both morphologically and mitochondrially, with the holotype of S.ater. Phylogenetic analyses of mitochondrial sequences indicate that the S.ater holotype and new Sarawak specimens do not belong to the genus Suncus, but instead are most closely related to Palawanosorexmuscorum. Until now Palawanosorex has been known only from the neighboring Philippine island of Palawan. Additional sequences from nuclear ultra-conserved elements from the new Sarawak specimens strongly support a sister relationship to P.muscorum. We therefore transfer ater to Palawanosorex. The new specimens demonstrate that P.ater is more widespread in northern Borneo than previously recorded. Continued sampling of Bornean mammal diversity and reexamination of type material are critical in understanding the evolutionary history of the biologically rich Malay Archipelago.

Rethinking Gloger's Rule: Climate, Light Environments, and Color in a Large Family of Tropical Birds (Furnariidae).

AbstractEcogeographic rules provide a framework within which to test evolutionary hypotheses of adaptation. Gloger's rule predicts that endothermic animals should have darker colors in warm/rainy climates. This rule also predicts that animals should be more rufous in warm/dry climates, the so-called complex Gloger's rule. Empirical studies frequently demonstrate that animals are darker in cool/wet climates rather than in warm/wet climates. Furthermore, sensory ecology predicts that, to enhance crypsis, animals should be darker in darker light environments. We aimed to disentangle the effects of climate and light environments on plumage color in the large Neotropical passerine family Furnariidae. We found that birds in cooler and rainier climates had darker plumage even after controlling for habitat type. Birds in darker habitats had darker plumage even after controlling for climate. The effects of temperature and precipitation interact so that the negative effect of precipitation on brightness is strongest in cool temperatures. Finally, birds tended to be more rufous in warm/dry habitats but also, surprisingly, in cool/wet locales. We suggest that Gloger's rule results from complementary selective pressures arising from myriad ecological factors, including crypsis, thermoregulation, parasite deterrence, and resistance to feather abrasion.

Locomotory mode transitions alter phenotypic evolution and lineage diversification in an ecologically rich clade of mammals.

The relationship between organismal function and form is a cornerstone of biology because functional diversity is key to generating and maintaining ecological diversity. Morphological changes often occur in unison with behavioral or ecological transitions, and this process may foster diversification, but alternately could trap a species on an adaptive peak. We estimated the most comprehensive phylogenetic hypothesis of Murinae, a young (∼15 million years) and diverse (∼700 species) clade of mammals. We then tested for correlated evolution among four morphological traits with potential links to locomotor modes (Arboreal, General, Terrestrial, and Amphibious), then investigated the effects of locomotion on morphological and lineage diversification. We found unique combinations of trait values for each locomotor mode, including strong covariance between the tail and hindfoot lengths of specialized Arboreal and ecologically flexible General species. Low diversification rates and long branch lengths suggest that specialized lineages represent stable evolutionary "cul-de-sacs." General species, characterized by the classic "rat-like" body plan and broad locomotor abilities, have narrow optimal trait values and slow phenotypic evolution, but high lineage diversification rates. Our findings suggest that versatile, generalist forms act as seeds of species diversity and morphological specialization, which together build ecologically diverse radiations.

Environment predicts repeated body size shifts in a recent radiation of Australian mammals.

Closely related species that occur across steep environmental gradients often display clear body size differences, and examining this pattern is crucial to understanding how environmental variation shapes diversity. Australian endemic rodents in the Pseudomys Division (Muridae: Murinae) have repeatedly colonized the arid, monsoon, and mesic biomes over the last 5 million years. Using occurrence records, body mass data, and Bayesian phylogenetic models, we test whether body mass of 31 species in the Pseudomys Division can be predicted by their biome association. We also model the effect of eight environmental variables on body mass. Despite high phylogenetic signal in body mass evolution across the phylogeny, we find that mass predictably increases in the mesic biome and decreases in arid and monsoon biomes. As per Bergmann's rule, temperature is strongly correlated with body mass, as well as several other variables. Our results highlight two important findings. First, body size in Australian rodents has tracked with climate through the Pleistocene, likely due to several environmental variables rather than a single factor. Second, support for both Brownian motion and predictable change at different taxonomic levels in the Pseudomys Division phylogeny demonstrates how the level at which we test hypotheses can alter interpretation of evolutionary processes.