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Smith College

Publication Date

Fall 2022

Program Name

Ecuador: Comparative Ecology and Conservation

Abstract

The Corredor Llanganates-Sangay is an extremely significant region for conservation, coined a “gift to the earth” by the World Wildlife Fund. Understanding amphibians species and populations is key due to their roles as hyper sensitive bioindicators. In recent years, portable sequencing equipment (Mini PCR thermocyclers, Oxford Nanopore Technology’s MinION sequencer, etc) make genetic data collection in remote areas possible, greatly increasing potential for conservation genetics and genomics. This study uses portable equipment to sequence two mitochondrial loci in 104 Anuran samples collected in four sites in the Corridor and presents phylogenies of each gene as well as a concatenated phylogeny. Data processing revealed limitations in existing bioinformatic tools, highlighting the need for simple in-house computational tools to quality check throughout the tree-building pipeline. These phylogenies reveal two potentially new clades of Pristimantis, which sit without any known species in clades with short branches. However, inconsistencies between this phylogeny and published phylogenies reveal that further steps are required to understand and curate data. Inconsistencies in tree topology are not unique to this study, due to evolutionary patterns that vary between genes of a single species. Thus, further understanding of amphibian gene evolution and genomics is necessary to develop methods to build reliable phylogenies as genetic data increases for this vulnerable clade of organisms.

Disciplines

Bioinformatics | Computational Biology | Genetics | Latin American Studies | Research Methods in Life Sciences | Zoology

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