Biology subjects

Chaves, J. A.

Publications and source records attributed to Chaves, J. A..

3 recordsLinked to original sources

bioRxiv2020

Evolutionary history of the Galapagos Rail revealed by ancient mitogenomes and modern samples

The biotas of the Galapagos Islands are probably one of the best studied island systems and have provided a broad model of insular species origins and evolution. Nevertheless, some Galapagos species remain poorly characterized, such as the Galapagos Rail Laterallus spilonota. This bird species is one of the less explored groups of endemic vertebrates on these islands, due to its elusive behavior, cryptic plumage and restricted distribution. To date there is no genetic assessment of its origins and sister relationships to other taxa, and importantly, there is no data on its current genetic diversity. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here we examine the genetics of Galapagos Rails using a combination of mitogenome de novo assembly with multi-locus sequencing (mtDNA+nuDNA) from both modern and historical samples. We show that the Galapagos Rail is part of the American black rail clade, sister to Black Rail L. jamaicensis, with a colonization of Galapagos dated to 1.2 Mya. The separate analysis of cytb, ND2, and RAG-1 markers demonstrates shallow population structure across sampled islands, possibly due to elevated island connectivity. Additionally, birds sampled from Pinta possessed the lowest levels of genetic diversity, most likely reflecting the impact of past bottlenecks due to habitat loss caused by invasive goats grazing on sensitive habitat. The data presented here highlights the low genetic diversity in this endemic rail species and suggests the use of genetic data (both modern and historical) to guide conservation efforts.

evolutionary biology↗

bioRxiv2020

Urbanization alters ecological and evolutionary interaction between Darwin's Finches and Tribulus cistoides on the Galapagos Islands

Emerging evidence suggests that urbanization shapes the ecology and evolution of species interactions. Islands are particularly susceptible to urbanization due to the fragility of their ecosystems; however, few studies have examined the effects of urbanization on species interactions on islands. To address this gap, we studied the effects of urbanization on interactions between Darwins finches and its key food resource, Tribulus cistoides, in three towns on the Galapagos Islands. We assessed the effects of urbanization on seed and mericarp removal, mericarp morphology, and finch community composition using natural population surveys, experimental manipulations, and finch observations. We found that both seed and fruit removal rates were higher in urban compared to non-urban populations in the natural and experimental populations, and that urbanization modified selection on mericarp size and defense. Urban environments supported smaller and less diverse finch communities than non-urban environments. Together, our results suggest that urbanization can dramatically alter ecological interactions between Darwins finches and T. cistoides, leading to modified selection on T. cistoides populations. Our study demonstrates that urban development on islands can have profound effects on the ecology and evolution of trophic interactions.

evolutionary biology↗

bioRxiv2020

Sex identification in embryos and adults of Darwins finches

Darwins finches, endemic to the Galapagos and Cocos islands, are an iconic example of adaptive radiation and evolution under natural selection. Comparative genetic studies using embryos of Darwins finches have shed light on the possible evolutionary processes underlying the speciation of this clade. Molecular identification of the sex of embryonic samples is important for such studies, where this information often cannot be inferred otherwise. We tested a fast and simple chicken embryo protocol for extraction of genomic DNA on Darwins finch embryos. In addition, we suggest modifications to two of the previously reported PCR primer sets for CHD1, a gene used for sexing in adult passerine birds. The sex of all 29 tested embryos of six species of Darwins finches was determined successfully by PCR, using both primer sets. Hatchlings/nestlings and fledglings are also impossible to distinguish visually. This includes juveniles of sexually dimorphic species which are yet to moult in adult-like plumage and beak colouration. Furthermore, four species of Darwins finches are monomorphic, males and females looking alike. Therefore, sex assessment in the field can be a source of error, especially with respect to juveniles and mature monomorphic birds outside of the mating season. We caught 567 juveniles and adults belonging to six species of Darwins finches and only 44% had unambiguous sex-specific morphology. We sexed 363 birds by PCR, including individuals sexed based on marginal sex specific morphological traits (N=278) and birds which were impossible to classify in the field (N=39). For birds with marginal sex specific traits, PCR results revealed a 13% sexing error rate. This demonstrates that PCR based sexing can improve field studies on Darwins finches, especially when individuals with unclear sex-related morphology are involved. The protocols used here provide an easy and reliable way to sex Darwins finches throughout ontogeny, from embryos to adults.

molecular biology↗