PHYLOGENETIC SYSTEMATICS: THEORY AND PRACTICE

 

I am broadly interested in practical and conceptual issues associated with phylogenetic inference of large and complex datasets, which often include the combination of genetic and phenotypic characters (Peloso et al. 2011, Amer. Mus. Novitat.; Orrico et al. 2020, Cladistics). For example, I use empirical analyses of data from non-model organisms to investigate how phylogenetic inference is influenced by the nuances of taxon and character sampling (e.g., Carvalho et al. 2016, Am. Mus. Novit; Peloso et al. 2016, Cladistics).

 

For my work on the systematics and evolution of the frog family Microhylidae, I used a NGS method (target enrichment) to obtain a large genetic dataset for a phylogenetic inference of the group. Microhylidae is globally distributed and one of the biggest and most diverse amphibian clades—although the monophyly of the family is broadly accepted, its internal relationships remain largely contentious. I have shown that even with a substantial genomic dataset, these problematic nodes remain volatile to variations in amount of data included, as well as to methods used for sequence alignment and phylogenetic inference (Peloso et al. 2016, Cladistics). I am currently working on a larger, combined genomic (including NGS data) and phenotypic (including CT data), dataset to infer how the use of anatomical and behavioral data will influence recovery and support for unstable nodes of the phylogeny.

Even with a considerable increase in genomic data some relationships remain uncertain, but preliminary data suggests that inclusion of a densely sampled phenotypic matrix is able to consistently solve some of these relationships with high statistical support. In another work, together with a M.Sc. student, we used a mix of DNA sequences and anatomical data (osteology characters obtained mostly from CT scans) to infer the impact of missing data and the role of implied character weighting in the phylogeny of a Neotropical lizard family (Alopoglossidae) (Morales et al. 2020, Cladistics). In both these studies, we documented empirically that analytical methods and source of evidence have a huge impact in the phylogeny, in its derived taxonomy, and in subsequent interpretation of biological phenomena, such as biogeography and trait evolution.

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More recently, in collaboration with amphibian specialists from all over the world, we assembled a comprehensive genomic dataset to infer the phylogeny and divergence time estimates for the whole Amphibia (Hime et al. 2020, Syst. Biol.). Our results clarify several contentious relationships and, surprisingly, report younger origin and diversifications then previously reported for many lineages. We also provide some insights into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.

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COMPARATIVE EVOLUTIONARY BIOLOGY

 

I am interested in using phylogenies to test hypotheses in evolution and biogeography. I am particularly interested in understanding how landscape evolution and the appearance of key morphological or behavioral traits have shaped diversification in amphibians.

 

Phenotypic Evolution

The question of how animals and plants have repeatedly “conquered” terrestrial environments has puzzled biologists for centuries. Amphibians are widely known for a stereotyped dependence on water for reproduction (aquatic eggs and tadpoles). However, many lineages evolved some independence from water bodies, culminating in total liberty from an aquatic environment for breeding and development (i.e., terrestrial eggs and no larval phase). Concomitant to the adaptations in reproductive biology are morphological adaptations to their lifestyle, such as loss of bones (due to miniaturization), multiple appearances of finger disks and bone elongation (for arboreality), and development of vertebral crests (possibly related to fossoriality). I have long been interested in investigating correlations between phylogeny, reproductive mode evolution and morphology in amphibians. I have studied this correlation in the microhylid genus Chiasmocleis (broadly distributed in South America), and recovered a strong association between miniaturization and terrestriality in this clade (Peloso et al. 2014, Bul. Amer. Mus. Nat. Hist.). We later showed that miniaturization is also correlated with a range of anatomical specializations in the group (De Sá et al. 2019, Mol. Phyl. Evol.).

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I continue to study phenotypic evolution in Microhylidae, in the last few years have compiled a large genomic dataset together with representative CT-scans of several species in the group to infer correlates between phylogenetic diversity and ecological and phenotypic disparity. A part of this dataset was recently analyzed with collaborator Dr. Antoine Fouquet, where we found phylogenetically correlated phenotypes that emerged concomitantly with dispersals during the Miocene, and possibly represent adaptations to different habitats, such as soils with different physical properties

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Biogeography and Phylogeography

In recent years, I have become more interested in investigating geological and ecological processes driving amphibian and reptile diversification in the Neotropics. To achieve this, I use a combination of biogeography and statistical phylogeography methods to address the timing and mode of diversification in these groups. Initial findings suggest that some common patterns of diversification found in other Neotropical vertebrate groups do not widely apply to the amphibian groups we investigated. For example, in two unrelated amphibian genera with disjunct populations in the Amazon and Atlantic rainforests, our time estimate suggests that past connections between the two biomes is considerably older (early Miocene) than ages estimated for connections in birds and mammals (usually late Miocene to Pleistocene) (Pirani, Peloso et al. 2019, Mol. Phyl. Evol.; De Sá et al. 2019, Mol. Phyl. Evol.). Another important result, obtained in a comparative analysis of effectiveness of major Amazonian rivers in creating barriers to geneflow in amphibians and reptiles, is that not all major rivers are definite vicariant barriers, and that the divergence process indeed varies across time, space and species (Pirani et al. 2019, J. Biog.).