The genetic basis of adaptation and speciation
How predictable is evolution? What’s the genetic basis of speciation and adaptation? Why do some lineages diversify more than others and arrive at the same ecological solutions over and over again?
Using field and genomic experiments, we investigate these questions in natural settings using genomic and GWA methods integrated with ecological and behavioral ecology.
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We focus mainly on mapping ecologically relevant genes for model-traits such as hypertorphic lips (a feeding adaptation) and pre-zygotic barriers in cichlid fishes. The Juanitas (Cichlidae: Crenicichla) are an exceptional system to test theoretical predictions of the genetic bases of adaptive radiations and ecological speciation.
Genome Evolution and Sex Determination in fishes
Genomes are invaluable tools that allow for the use of forward genetics and population genetics. We are currently focused on developing highly efficient approaches for obtaining chromosome-level reference genomes, pan genomes and population-based resequencing with long reads.
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To achieve this, we combine various sequencing platforms, tissue preservation methods and DNA purification methods. These range from a) genomic DNA, typically used for PCR-based and GBS methods; b) high molecular weight DNA, typically used for PacBio HiFi sequencing and c) ultra-high molecular weight DNA, used in Nanopore Ultralong Sequencing.
The differentiation of sex chromosomes has a great impact on genome evolution and can reveal the causes and consequences of variation in recombination rate. We combine genetic mapping in both experimental and natural populations with long-read sequencing to identify the causal genetic basis of sex determination, assemble and compare male and female genomes to test the general theory of sex chromosome evolution.
Fisheries Genomics
Genomic and evolutionary genetic methods are also valuable tools for applied and translational research. We apply these methods to advance the field of fisheries genetics in collaboration with Prof. Solé-Cava’s research group at the Centro Nacional para a Identificação Nacional do Pescado (CENIMP). We have recently published a large set of complete mitochondrial genomes from economically important fisheries from Latin America and are actively developing genomic tools to detect fraud in fisheries.
