Biology subjects

Shaw, K. L.

Publications and source records attributed to Shaw, K. L..

9 recordsLinked to original sources

bioRxiv2026

Revised genomic resources for the swordtail cricket, Laupala kohalensis Otte 1994

Advances in genetic tools such as next and third generation sequencing, paired with a focus on representative clades, provide insight into how processes including adaptation, admixture, and genome structure shape the evolution and maintenance of species. However, our understanding of the genomics of speciation is dominated by systems where ecological adaptations are thought to cause initial barriers to gene exchange. In contrast to other model systems, the 38 species of the genus Laupala constitute a very rapid radiation, where evolution of reproductive barriers and speciation is thought to be driven by sexual selection. Here, with novel PacBio HiFi reads and RNA- and Iso-Seq data, we provide a highly contiguous, chromosome-level genome and markedly improved annotation of the endemic Hawaiian cricket, Laupala kohalensis Otte, 1994. Our new resources advance previous efforts, placing 99% of 47 scaffolds on 7 autosomes and 1 sex chromosome in the 1.67 Gb assembly, with a 98.8% BUSCO score (insecta_db10), N50 of [~]268 Mb, and L50 of 3. Using a custom repeat library, we estimate the genome to have 46.09% repeat content, and the new annotation includes an increased estimate of 17,670 genes, which coincides with that known from other Orthopterans. Notably, we find a large nuclear DNA segment of mitochondrial origin on chromosome 7. This new resource provides a powerful tool to identify and compare genomic causes of phenotypic diversification in a system characterized by strong signatures of sexual differentiation, representing an underappreciated but potentially widespread cause of speciation.

genomics↗

bioRxiv2025

Genomic data confirms phenotypic predictions of hybridization between cryptic Hawaiian cricket species

Hybridization is increasingly recognized as an important driver of species radiations, yet its detection in morphologically cryptic taxa remains challenging. The Hawaiian crickets of the genus Laupala represent a rapid non-adaptive radiation in which species are morphologically indistinguishable but differ in acoustic mating signals. Here we report the first discovery of natural hybridization in the Laupala radiation. During field surveys on Maui, we observed crickets with intermediate pulse rates and unusually high acoustic variation at sites where the ranges of Laupala makaio (slow singer) and Laupala orientalis (fast singer) converge. We hypothesized these represented natural hybrids and tested this prediction using genomic data from genotyping-by-sequencing (GBS). Maximum likelihood phylogenetic analysis showed that fast-singing putative hybrids clustered with L. orientalis and the slow-singing ones with L. makaio, yet all putative hybrids formed a cohesive geographic group. Using 9,345 ancestry-informative markers, we calculated hybrid indices and heterozygosity values for triangle plot analysis. All hybrids showed excess L. makaio ancestry (predicted from analysis of pulse rate patterns) and were classified as later-generation hybrids or backcrosses to L. makaio, with no F1 hybrids detected. Critically, we found a strong positive correlation (R = +0.74, p = 4.1x10-) between pulse rate and hybrid index at the site with highest pulse rate variation, showing that genomic ancestry predicts pulse rate phenotype. Morphological comparisons confirmed that hybrids were cryptic, reinforcing the difficulty of detecting hybridization without genomic data. Together, our results provide the first demonstration of natural hybridization in Laupala, showing that phenotypic predictions based on acoustic intermediacy can be confirmed with genomic evidence. The discovery of natural hybridization in Laupala opens new avenues for investigating how hybridization contributes to rapid diversification in non-adaptive radiations, paralleling patterns observed in some adaptive radiations.

evolutionary biology↗

bioRxiv2025

Sexual isolation maintains species boundaries between Hawaiian crickets in sympatry despite weak habitat isolation

Understanding the relative importance of different reproductive isolating barriers in maintaining species boundaries is fundamental to understanding how closely related species coexist without hybridizing. Habitat isolation and sexual isolation are often the first barriers between closely related species, yet they are rarely studied together, making their relative contributions to reproductive isolation unclear. We conducted the first comprehensive study of both barriers in Hawaiian swordtail crickets (Laupala), focusing on the recently diverged, sympatric species pair Laupala kona and Laupala hualalai. Using genomic data, we confirmed that the two species are genetically distinct, which can only be achieved by strong reproductive isolation through a prolonged time period. Through field surveys, we quantified microhabitat use, spatial distribution, and diets, and found extensive ecological overlap. Both species occupied similar substrates, elevations, and microclimates, and occurred in mixed-species aggregations. They only differ in their diets (inferred from stable isotopes), which might have some implications in reducing encounter rates. Despite this weak habitat isolation, they have divergent sexual traits and exhibit strong sexual isolation in lab assays. The species differ significantly in male pulse rate and cuticular hydrocarbon profiles, and females consistently preferred conspecific song stimuli. Mating trials showed almost complete sexual incompatibility between heterospecific pairs, with very rare interspecies copulations. Together, these results demonstrate that sexual isolation, rather than habitat partitioning, maintains species boundaries between L. hualalai and L. kona in sympatry. Our findings highlight the sufficiency of sexual isolation to prevent hybridization even in the absence of strong ecological divergence, providing rare empirical evidence that sexual barriers alone can maintain reproductive isolation in natural populations.

evolutionary biology↗

bioRxiv2024

Scalable assessment of genome editing off-targets associated with genetic variants

Genome editing with RNA-guided DNA binding factors carries risk of off-target editing at homologous sequences. Genetic variants may introduce sequence changes that increase homology to a genome editing target, thereby increasing risk of off-target editing. Conventional methods to verify candidate off-targets rely on access to cells with genomic DNA carrying these sequences. However, for candidate off-targets associated with genetic variants, appropriate cells for experimental verification may not be available. Here we develop a method, Assessment By Stand-in Off-target LentiViral Ensemble with sequencing (ABSOLVE-seq), to integrate a set of candidate off-target sequences along with unique molecular identifiers (UMIs) in genomes of primary cells followed by clinically relevant gene editor delivery. Gene editing of dozens of candidate off-target sequences may be evaluated in a single experiment with high sensitivity, precision, and power. We provide an open-source pipeline to analyze sequencing data. This approach enables experimental assessment of the influence of human genetic diversity on specificity evaluation during gene editing therapy development.

genomics↗

bioRxiv2019

Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets

When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favored over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket Laupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and the likelihood that sharing QTL is related to phenotypic effect sizes. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.

evolutionary biology↗

bioRxiv2019

Genetic coupling of signal and preference facilitates sexual isolation during rapid speciation

The divergence of sexual signals is ultimately a coevolutionary process: while signals and preferences diverge between lineages, they must remain coordinated within lineages for matings to occur. Divergence in sexual signals makes a major contribution to evolving species barriers. Therefore, the genetic architecture underlying signal-preference coevolution is essential to understanding speciation but remains largely unknown. In Laupala crickets where male song pulse rate and female pulse rate preference have coevolved repeatedly and rapidly, we tested two contrasting hypotheses for the genetic architecture underlying signal-preference coevolution: linkage disequilibrium between unlinked loci and genetic coupling (pleiotropy of a shared locus or tight physical linkage). Through selective introgression and quantitative trait locus (QTL) fine mapping, we estimated the location of QTL underlying interspecific variation in both female preference and male pulse rate from the same mapping populations. Remarkably, map estimates of the pulse rate and preference loci are 0.06-0.23 cM apart, the strongest evidence to date for genetic coupling between signal and preference loci. As the second pair of co-localizing signal and preference loci in the Laupala genome, our finding supports an intriguing pattern, pointing to a major role for genetic coupling in the quantitative evolution of a reproductive barrier and rapid speciation in Laupala. Due to its effect on suppressing recombination, a coupled, quantitative genetic architecture offers a powerful and parsimonious genetic mechanism for signal-preference coevolution and the establishment of positive genetic covariance on which the Fisherian runaway process of sexual selection relies.

evolutionary biology↗

bioRxiv2018

Crystal structure of a Thermus aquaticus diversity-generating retroelement variable protein

Diversity-generating retroelements (DGRs) are widely distributed in bacteria, archaea, and microbial viruses, and bring about unparalleled levels of sequence variation in target proteins. While DGR variable proteins share low sequence identity, the structures of several such proteins have revealed the C-type lectin (CLec)-fold as a conserved scaffold for accommodating massive sequence variation. This conservation has led to the suggestion that the CLec-fold may be useful in molecular surface display applications. Thermostability is an attractive feature in such applications, and thus we studied the variable protein of a DGR encoded by the thermophile Thermus aquaticus. We report here the 2.8 [A] resolution crystal structure of the variable protein from the T. aquaticus DGR, called TaqVP, and confirm that it has a CLec-fold. Remarkably, its variable region is nearly identical in structure to those of several other CLec-fold DGR variable proteins despite low sequence identity among these. TaqVP was found to be thermostable, which appears to be a property shared by several CLec-fold DGR variable proteins. These results provide impetus for the pursuit of the DGR variable protein CLec-fold in molecular display applications.

biochemistry↗

bioRxiv2018

The genetic basis of inter-island mating behavior divergence

Mating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variation in the crickets Laupala eukolea and L. cerasina, which occur on different islands (Maui and Hawaii). We then compare these results with a similar study of an independently evolving species pair that diverged within the same island. Finally, we annotate the L. cerasina transcriptome and test whether QTL fall in functionally enriched genomic regions. We document a polygenic architecture behind song rhythm divergence in the inter-island species pair that is remarkably similar to that previously found for an intra-island species pair in the same genus. Importantly, QTL regions were significantly enriched for potential homologs of genes involved in pathways that may be modulating cricket song rhythm. These clusters of loci could constrain the spatial genomic distribution of genetic variation underlying cricket song variation and harbor several candidate genes that merit further study.

evolutionary biology↗

bioRxiv2017

The genomic architecture of a rapid island radiation: mapping chromosomal rearrangements and recombination rate variation in Laupala

Phenotypic evolution and speciation depend on recombination in many ways. Within populations, recombination can promote adaptation by bringing together favorable mutations and decoupling beneficial and deleterious alleles. As populations diverge, cross-over can give rise to maladapted recombinants and impede or reverse diversification. Suppressed recombination due to genomic rearrangements, modifier alleles, and intrinsic chromosomal properties may offer a shield against maladaptive gene flow eroding co-adapted gene complexes. Both theoretical and empirical results support this relationship. However, little is known about this relationship in the context of behavioral isolation, where co-evolving signals and preferences are the major hybridization barrier. Here we examine the genomic architecture of recently diverged, sexually isolated Hawaiian swordtail crickets (Laupala). We assemble a de novo genome and generate three dense linkage maps from interspecies crosses. In line with expectations based on the species recent divergence and successful interbreeding in the lab, the linkage maps are highly collinear and show no evidence for large-scale chromosomal rearrangements. The maps were then used to anchor the assembly to pseudomolecules and estimate recombination rates across the genome. We tested the hypothesis that loci involved in behavioral isolation (song and preference divergence) are in regions of low interspecific recombination. Contrary to our expectations, a genomic region where a male song QTL co-localizes with a female preference QTL was not associated with particularly low recombination rates. This study provides important novel genomic resources for an emerging evolutionary genetics model system and suggests that trait-preference co-evolution is not necessarily facilitated by locally suppressed recombination.

evolutionary biology↗