Biology subjects

Lauterbur, M. E.

Publications and source records attributed to Lauterbur, M. E..

3 recordsLinked to original sources

bioRxiv2019

orthoCapture: Facilitating Gene Capture Probe Design for Non-Model Species

In non-model species, targeted gene capture (selective enrichment of specific genomic regions of interest) applications in molecular ecology have been limited by the practicalities of capture design. Currently, the minimal requirement for designing capture probes is a transcriptome, or established reference genome for the species of interest. When an established, annotated reference genome is unavailable, one common approach is to design probes from annotated reference genomes (or transcriptomes) of related species. Unfortunately, as divergence between probes and the genome of interest increases, such as occurs during directional selection, capture performance decreases. Here I introduce orthoCapture, a tool to overcome such limitations by mining unannotated whole-genome sequence (WGS) data from non-model species and/or their close relatives to allow probe design using multiple genomic sources. orthoCapture finds orthologs in WGS data from multiple related species to create a set of exon sequences that encompasses the diversity of the exons of interest. These \"design sequences\" can then be used to design capture probes for the species of interest. orthoCapture thus eliminates the need for transcriptome or whole-genome sequencing for bait capture experiments, making this technique accessible for molecular ecology and conservation studies. Use of orthoCapture is via command-line interface on Unix systems, and requires the input of a gene sequence from an unrelated annotated genome and a fasta database from a target, unannotated genome (e.g., whole-genome shotgun contigs). The output, sequence templates from the nonannotated genomic data, allows probe creation by any commercial company providing gene capture services.

bioinformatics↗

bioRxiv2019

Coalescent models at small effective population sizes and population declines are positively misleading

Population genetics employs two major models for conceptualizing genetic relationships among individuals - outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

genetics↗

bioRxiv2019

A fruitful endeavor: scent cues and echolocation behavior used by Carollia castanea to find fruit

Frugivores have evolved sensory and behavioral adaptations that allow them to find ripe fruit effectively, but the relative importance of different senses in varying foraging scenarios is poorly known. Within Neotropical ecosystems, short-tailed fruit bats (Carollia: Phyllostomidae) are abundant nocturnal frugivores, relying primarily on plants of the genus Piper as a food resource. Previous research has demonstrated Carollia employ olfaction and echolocation to locate Piper fruit, but it is unknown how their sensory use and foraging decisions are influenced by the complex diversity of chemical cues that fruiting plants produce. Using wild C. castanea and their preferred food, Piper scintillans, we conducted behavioral experiments to test two main hypotheses: (1) foraging decisions in C. castanea are primarily driven by ripe fruit scent and secondarily by vegetation scent, and (2) C. castanea re-weight their sensory inputs to account for available environmental cues, such that bats rely more heavily on echolocation in the absence of adequate scent cues. Our results suggest that C. castanea requires olfactory information and relies almost exclusively on ripe fruit scent to make foraging attempts. Ripe fruit scent is chemically distinct from vegetation scent in P. scintillans, with a greater abundance of {beta}-caryophyllene, germacrene D and {beta}-elemene, and a few unique compounds. Although variation in echolocation call parameters was independent of scent cue presence, bats emitted longer and more frequent echolocation calls in trials where no fruit scent was present. Altogether, these results highlight the adaptations, plasticity, and potential constraints in the sensory system of neotropical fruit bats. SIGNIFICANCE STATEMENTLittle is known about the relative importance of different senses and which plant cues are most important for fruit location by frugivores. We conducted behavioral experiments on short-tailed fruit bats (Carollia castanea), which use a combination of olfaction and echolocation to find ripe fruit, and their preferred food source (Piper scintillans) to test (1) which plant scent cues drive food selection and (2) if bats alter their echolocation behaviors based on which scent cues are present. We find that C. castanea rely almost exclusively on ripe fruit scent to forage, and echolocate more frequently when fruit scent is absent. Ripe fruit scent is chemically different from vegetation scent in P. scintillans, potentially providing a clear signal of food availability to mutualistic bats. These results highlight the sensory adaptations and behavioral flexibility of fruit bats as they navigate the cues provided by fruiting plants.

ecology↗