Biology subjects

Sethuraman, A.

Publications and source records attributed to Sethuraman, A..

22 records · Page 2Linked to original sources

bioRxiv2019

Model-based Assessments of Differential Introgression and Linked Natural Selection During Divergence and Speciation

Demographic changes such as fluctuating population size and differential introgression can mask the effects of natural selection, and affect rates of genome evolution, local adaptation, reproductive isolation, and eventual speciation. Besides identifying differentially introgressing genes (and genomic regions) that are \"labeled\" to be retroactively causal to adaptive evolution and speciation, there is significant impetus to understand, and perhaps estimate the underlying demography that affects current genomic diversity. Using model-based likelihood methods to directly estimate, and decouple the effects of differential intogression and demography across genomic loci offers an ideal solution to detect differential introgression, and population demography and build hypotheses around its underlying evolutionary processes. We describe a computationally efficient parallelized implementation of mixture-model based isolation with migration (IM) analyses to assign loci to classes based on their shared coalescent histories (population sizes, or migration rates). We apply this method to several genomic data sets (great apes - chimpanzees and bonobos, Anopheles mosquitoes, threespine sticklebacks, Mullerian mimics of Heliconius butterflies, mice, European rabbits, and fruitflies), that have been previously characterized (perhaps erroneously) using genome-wide scans of differentiation. We show that we cannot reject a model of differential introgression, or linked selection across a majority of species analyzed, with two species showing the combined effects of differential introgression and linked natural selection across multiple, non-independent genomic loci.

evolutionary biology↗

bioRxiv2019

Lack of phenotypic variation in larval utilization of pea aphids in populations of the ladybeetle Hippodamia convergens

The convergent lady beetle (Hippodamia convergens) is a generalist natural enemy that is utilized extensively in augmentative biological control across the United States. Recent studies have pointed to both genetic and phenotypic differences in Western (California) versus Eastern (Kansas) populations of the species. Here we investigate (1) genetic population structure, and (2) phenotypic differences in the utilization of pea aphids at temperatures that resemble the Western United States in (a) Eastern versus Western populations, (b) F1 Eastern X Western hybrids versus their progenitor populations, and investigate the effects of interaction between (c) Eastern and Western populations. We found no differences in final pupal weight, or the net weight gain ratio through larval development from the third instar to pupal stage, despite genetic population structure. Our study points towards plastic response and effectiveness in feeding phenotypes of Eastern and Western populations of H. convergens, and the absence of hybrid vigor and heterozygote advantages in hybrids.

ecology↗

bioRxiv2019

The Effects of Gene Flow from Unsampled \"Ghost\" Populations on the Estimation of Evolutionary History under the Isolation with Migration Model

Unsampled or extinct ghost populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ghost populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ghost populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ghost population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ghost population. Without accounting for an unsampled ghost, summary statistics like FST are under-estimated, and{pi} is over-estimated with increased gene flow from the ghost. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ghosts. Considering the large effects of gene flow from these ghosts, we propose a multi-pronged approach to account for the presence of unsampled ghost populations in population genomics studies to reduce erroneous inferences.

evolutionary biology↗

bioRxiv2018

Coccinellid host morphology dictates morphological diversity of the parasitoid wasp Dinocampus coccinellae

Pararsitoid-host interactions involving host species that are newly introduced into the range of a generalist parasitoid provide systems that can be examined for phenotypic plasticity and evolutionary changes in parasitoid-host dynamics. The solitary Braconid parasitoid wasp, Dinocampus coccinellae, has a cosmopolitan distribution and parasitizes approximately 50 species of predatory lady beetles (ladybirds) in the family Coccinellidae. In this study we quantified the effect of six (4 native North American and 2 non-native North American) host species on the morphometrics of D. coccinellae. Adult lady beetles were collected from 13 locations in the United States and reared in the laboratory until D.coccinellae exited from their adult beetle hosts. Eighty-nine individual D. coccinellae females and their associated host were weighed and morphometric measurements were taken. The smallest lady beetle host Hippodamia parenthesis produced the smallest adult wasps; the largest host species, Coccinella septempunctata, produced the largest female wasps. A directional cline in morphology of wasps and their coccinellid hosts was also observed in a dry-weight regression (R2 = 0.4066, p-value < 0.0001). Two underlying mechanisms may explain the results of our study: (1) morphometric variation in D. coccinellae is governed by phenotypic plasticity with the size of the emerging offspring contingent on the size of the coccinellid host, and/or (2) that morphometric variation in D. coccinellae is governed by genomic adaptation to coccinellid host populations.

evolutionary biology↗