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Research
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PN Serra dos Orgãos, RJ, Brazil. June 2016 |
I am a museum-trained evolutionary ornithologist interested in phylogenomics, population genetics, and comparative genomics. My research program aims to uncover the functional and genomic mechanisms underlying trait evolution associated with varying environmental conditions and understand how the interaction between phenotypes and the environment affects diversification across space and time. To that end, I integrate fieldwork, museum specimens, high-throughput genomic technologies, and bioinformatic tools. I conduct this research in Colombia, Peru, Brazil, and the USA, where I have active collaborations and on-going projects.
Some of the projects and research activities that I am currently involved in are:
Some of the projects and research activities that I am currently involved in are:
1. Genomic basis of phenotypic divergence associated to environmental conditions in the
Thamnophilidae
Thamnophilidae
Assessing how phenotypic and genomic differences are associated with different environmental conditions offers the opportunity to study the genetics of the phenotypes underlying adaptation. My current research's fundamental goal is to unravel the genetic basis of adaptation to dry and warm habitats in antbirds. In the Thamnophilidae, close to 20 species colonized independently South American dry regions but their sisters occur solely in humid habitats (Fig. 1; Bird illustrations from HBW). Dry-habitat specialists exhibit convergent phenotypes. For instance, male plumages in arid habitats tend to be convergently dominated by brown, buff, and rufous colors, whereas in humid regions, they are predominantly black or various shades of gray (Fig 1).
To identify the genomic basis of adaptation to dry and warm environments, I use vouchered tissue samples from museum specimens to assemble de novo reference genomes for species in the genera Thamnophilus and Sakesphorus restricted to dry climates, as well as their sisters from humid forests. Then I created a whole-genome alignment containing 15 antbird genomes that I am analyzing using comparative genomic tools. Because structural (i.e., protein-coding) and regulatory changes (i.e., gene expression) can drive adaptation, I am performing analyses targeting both types of regions. This type of integrative research questions is of high relevance not only from an evolutionary perspective but also from a conservation point of view given the environmental changes that populations are experiencing due to climate change and other environmental stressors. This research is a collaboration with Scott Edwards.
To identify the genomic basis of adaptation to dry and warm environments, I use vouchered tissue samples from museum specimens to assemble de novo reference genomes for species in the genera Thamnophilus and Sakesphorus restricted to dry climates, as well as their sisters from humid forests. Then I created a whole-genome alignment containing 15 antbird genomes that I am analyzing using comparative genomic tools. Because structural (i.e., protein-coding) and regulatory changes (i.e., gene expression) can drive adaptation, I am performing analyses targeting both types of regions. This type of integrative research questions is of high relevance not only from an evolutionary perspective but also from a conservation point of view given the environmental changes that populations are experiencing due to climate change and other environmental stressors. This research is a collaboration with Scott Edwards.
2. Systematics of a pantropical diversification: the suboscine passerine birds
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For most of my professional career, I have focused my research on the evolution of suboscines, a diverse group of pantropical passerines representing almost 15% of the world's avifauna. Suboscines primarily occur in the Neotropics. They account for nearly 40% of the breeding species and are key members of avian communities in virtually all habitats. Many species are widely distributed and can inhabit various habitats, whereas others are geographically restricted and exhibit varying degrees of ecological specialization. In collaboration with various museums and universities in the US and Brazil, we are constructing a species-level phylogeny of the suboscines using Massively Parallel Sequencing of ultraconserved elements (UCEs). This is a large collaborative effort co-led with Mike Harvey, Robb Brumfield, and Liz Derryberry.
A first bacth of results of this project can be seen here. |
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Hymenops perspicillatus, RS, Brazil. Photo by Ciro Albano
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Formicivora littoralis, RJ, Brazil. Photo by Ciro Albano
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3. Phenotypic and niche evolution in the antbirds (Thamnophilidae)
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The family Thamnophilidae provides an ideal scenario to study the patterns and mechanisms behind phenotypic and niche evolution in Suboscines. The integration of quantitative phylogenetic, geographical, ecological, vocal, and morphometric data at different spatial and taxonomic scales allow testing predictions regarding phenotypic evolution and diversification patterns.
For instance, phylogenetic comparative methods using a UCE-based species-level phylogeny and a comprehensive phenotypic dataset show that species occurring in more sensitive habitats to direct sunlight and precipitation in dry-warm climates tend to be smaller. This pattern suggests that even distantly related species are responding similarly to selective pressures in these environments. |
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4. Phylogenetic inference and the multispecies coalescent
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All of the research described above relies heavily on phylogenetic reconstructions and downstream phylogenetic comparative analyses. Therefore, I am interested in addressing the importance of adequate analytical methods to construct the Tree of Life to study the genomic underpinnings of phenotypic evolution.
In collaboration with various colleagues, I have been involved in efforts to highlight the importance of the multispecies coalescent model for phylogenetic inference and promote best practices for its use. [Figure taken from Bravo et al. 2019] |
5. Phylogeography and demographic history of South American birds
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In collaboration with various colleagues in North and South America, we are conducting phylogeographic and demographic studies using genome-scale data to shed light on the biogeographic history of the main South American biomes, such as the Atlantic Forest, the Andes, and Amazonia.
[Thamnophilus palliatus and T. tenuepunctatus – Illustrations HBW] |
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6. Systematics and species limits of Neotropical birds
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Until recently, we used to define species and genera almost exclusively based upon differences in morphological traits. Nowadays, the use of phylogenetic, vocal, and geographic datasets offer the opportunity to reexamine taxonomic limits and classification of those traditionally complex groups.
[Herpsilochmus sellowi female and male –Illustrations Andreza Silva] |
7. Inventories of poorly-known areas in South America
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I often join expeditions in different regions of South America. We usually discover unknown facts about the natural history, ecology, and distribution of South American taxa on those trips. Hopefully, sometime soon, those discoveries see the light in peer-reviewed publications.
[Serra do Mar, SP, Brazil, June 2014] |
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8. The importance of scientific collections
I am convinced that scientific collections are the primary resource to store and document adequately biological diversity and the keystone that promotes the proper production of scientific knowledge in fields such as systematic and evolutionary biology. Therefore, I am involved in outreach activities and workshops regarding their importance and the relevance of maintaining and continuing scientific collections.