Biology subjects

Linderoth, T. P.

Publications and source records attributed to Linderoth, T. P..

3 recordsLinked to original sources

bioRxiv2024

Evolution and Diversification of the Aposematic Poison Frog, Oophaga pumilio, in Bocas del Toro

The aposematic strawberry poison frog, Oophaga pumilio, is an iconic model system for studying the evolution and maintenance of color variation. Through most of its range, this frog is red with blue limbs. However, frogs from the Bocas del Toro Province, Panama, show striking variance in color and pattern, both sympatrically and allopatrically. This observation contradicts standard models of the evolution of aposematism and has led to substantial speculation about its evolutionary and molecular causes. Since the enigma of O. pumilio phenotypic variation is partly unresolved because of its large, [~] 6.7 Gb genome, we here sequence exomes from 347 individuals from ten populations and map a number of genetic factors responsible for the color and pattern variation. The kit gene is the primary candidate underlying the blue-red polymorphism in Dolphin Bay, where an increase in melanosomes is correlated with blue coloration. Additionally, the ttc39b gene, a known enhancer of yellow-to-red carotenoid conversion in birds, is the primary factor behind the yellow-red polymorphism in the Bastimentos West area. The causal genetic regions show evidence of selective sweeps acting locally to spread the rare phenotype. Our analyses suggest an evolutionary model in which selection is driving the formation of new morphs in a dynamic system resulting from a trade-off between predation avoidance, intraspecific competition, and mate choice.

evolutionary biology↗

bioRxiv2023

A deep learning phenotyping method for genetic analysis of 3D micro-CT data

The number of Genome-Wide Association Studies (GWAS) has been growing rapidly in recent years due to developments in genotyping and sequencing platforms. When applied to quantitative traits, these and other statistical genetics approaches require large amounts of consistently and accurately measured phenotypes. Here, we introduce a computational toolbox based on deep convolutional neural networks that we have developed to phenotype quantitative traits describing morphology from micro-CT-scan image datasets. We illustrate the use of this Deep Learning Phenotyper (DLP) on a sample set of craniofacial CT scans of 118 samples from two very closely related species of Lake Malawi cichlid fish, Maylandia zebra and Cynotilapia zebroides. We show that the pipeline constructed and implemented here is capable of measuring morphological skeletal phenotypes with high accuracy. We also demonstrate how this pipeline can be integrated with existing GWAS frameworks to identify candidate association loci. We believe the methods we present here will be valuable for groups studying quantitative morphological traits not only in fishes, but in other vertebrates using CT scan datasets.

genetics↗

bioRxiv2020

Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs

The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly been studied from phylogenetic perspectives to understand how common ancestry and divergent evolution drive their formation. Other processes, such as gene flow between populations, have not received as much attention. Here we investigate the roles of divergence and gene flow between populations in the origin and maintenance of a leapfrog distribution in Phyllobates poison frogs. We found evidence for high levels of gene flow between neighboring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between "leapfroging" taxa has not played a prominent role as a driver of phenotypic diversity in Phyllobates. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.

evolutionary biology↗