Genomic evidence of speciation by fusion linked to trophic niche expansion in a recent radiation of grasshoppers

Post-divergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). While neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between two sister taxa that exhibit contrasting host-plant specializations: C. binotatus (scrub legumes) and C. saulcyi (gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirmed that C. s. algoaldensis represents a uniquely evolving lineage and supported the ancient hybrid origin of this taxon (ca. 1.4 Ma), which provides a mechanistic explanation for its broader trophic niche and sheds light on its uncertain phylogenetic position. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate its long-term persistence through geographic isolation from parental forms in topographically complex landscapes.

Implications of Genetic Structure for Aquaculture and Cultivar Translocation of the Kelp Ecklonia radiata in Northern New Zealand

The fast expansion of the global seaweed aquaculture industry has created an interest in translocating seedlings cultivated from wild type brood stock. However, such translocations must be applied with caution as introduced cultivars can reduce genetic structure and diversity of wild populations. An understanding of the genetic structure and connectivity of target species is required to guide decision making around aquaculture translocation activities. In this study we used 14 microsatellite loci in a three-level hierarchical sampling design to analyze the genetic structure and connectivity of the native kelp Ecklonia radiata across 12 sites among four geographic regions (Northland, Bay of Plenty, Gisborne, and Wellington) in the North Island of New Zealand. Our aim was to provide guidance for translocation of cultivars to prevent the introduction of locally absent genotypes of E. radiata. Strong genetic structure and low geneflow were observed at all hierarchical levels, indicating the presence of multiple genetically distinct sub-populations. On a regional scale, high genetic differentiation was found between the Wellington region and the other three regions (FST = 0.407–0.545), and within regions most sites were significantly different (measured by pairwise FST) with high relatedness found between individuals within sites (mean 28.2% ± 0.7 SE). Bayesian modeling and redundancy analysis showed a high degree of genetic clustering and indicate that ocean currents and other factors that have resulted in biogeographical breaks along the coast are likely to be the main factors shaping genetic structure and connectivity of E. radiata on the North Island, rather than isolation by distance. Based on these findings, we recommend that that cultivars of E. radiata should not be translocated outside their area of origin to avoid introducing locally absent genotypes to local sub-populations.

Comparing the population structure of the specialist Butler’s gartersnake (Thamnophis butleri) and the generalist eastern gartersnake (Thamnophis sirtalis sirtalis) in Ontario and Michigan

Species differing in life history attributes vary in their responses to features within a shared landscape. We evaluated genetic structure of sympatric gartersnake species in Southwestern Ontario, Canada and south-east Michigan, U.S.A., where habitat fragmentation is high due to agriculture and urbanization. We surveyed genetic structure of the habitat specialist, Butler’s gartersnake (Thamnophis butleri; Cope, 1889) and habitat generalist, eastern gartersnake (Thamnophis sirtalis sirtalis; Linnaeus, 1758) using DNA microsatellites. Bayesian clustering, Discriminant Analysis of Principal Components, and pairwise population comparisons revealed genetic differentiation among three major regional clusters of Butler’s gartersnake with evidence of further division within one. Genetic clustering of Butler’s gartersnake suggest that inhospitable habitat limits dispersal. Eastern gartersnakes showed less structure, with assignment tests implying a single genetic cluster. We found positive significant Mantel’s r for both species in the smallest distance class (<15 kms), but significant isolation by distance for Thamnophis butleri only. These findings together imply that connectivity for eastern gartersnakes is less impacted by habitat loss and fragmentation or that we were less able to detect their effects. Our study shows the value of multispecies comparisons in studies seeking to understand the underlying causes of genetic structure in natural populations.

Genomic diversity of SARS-CoV-2 in Malaysia

Background More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine failure due to immune evasion. Massive viral genome sequencing has been recommended to track the genetic changes that could lead to adverse consequences. Methods We sequenced SARS-CoV-2 respiratory isolates from the National Public Health Laboratory, Malaysia and examined them together with viral genomes deposited in GISAID by other Malaysian researchers, to understand the evolutionary trend of the virus circulating in the country. We studied the distribution of virus lineages and site-wise mutations, analysed genetic clustering with the goeBURST full Minimum Spanning Tree algorithm, examined the trend of viral nucleotide diversity over time and performed nucleotide substitution association analyses. Results We identified 22 sub-lineages, 13 clonal complexes, 178 sequence types and seven sites of linkage disequilibrium in 277 SARS-CoV-2 genomes sequenced between January and December 2020. B.1.524 was the largest lineage group. The number of mutations per genome ranged from 0 to 19. The mean genomic diversity value over 12 months was 3.26 × 10−4. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. Conclusion The SARS-CoV-2 virus accumulated an abundance of mutations in the first year of the COVID-19 pandemic in Malaysia. Its overall genetic diversity, however, is relatively low compared to other Asian countries with larger populations. Continuous genomic and epidemiological surveillance will help to clarify the evolutionary processes determining viral diversity and impacting on human health.

TAMI-76. INTEGRATED MULTI-OMICS REVEAL INTRATUMOUR HETEROGENEITY AND NOVEL THERAPEUTIC TARGETS IN PAEDIATRIC EPENDYMOMA

Ependymoma (EPN) is the second most common malignant paediatric brain tumour with a five-year survival rate of only 25% following relapse. While molecular heterogeneity between EPN tumours is well understood, little is known concerning spatially-distinct intratumour heterogeneity within patients. In this context, we present a multi-omics integration of expression data at transcriptomic and metabolomic levels revealing intratumour heterogeneity and novel therapeutic targets. Surgically resected ependymoma tissue from two epigenetic subgroups, posterior fossa-A (PF-A) and supratentorial RELA, were first homogenised and polar metabolites, lipids and RNA simultaneously extracted from the same cellular population. Using liquid chromatography-mass spectrometry (LC-MS) and RNAseq 115 metabolites and 1580 upregulated genes were identified between the two subgroups, therefore validating previously reported genetic clustering of these two subtypes. Sampling of anatomically distinct regions was performed between eight PF-A EPN patients and multi-omic data was compared across 28 intratumour regions, with at least 3 different regions per patient. Integration of genes and metabolites revealed 124 dysregulated metabolic pathways, encompassing 156 genes and 49 metabolites. A large number of interactions occur in the gluconeogenesis and glycine pathways in 6 out of 8 patients, putatively representing therapeutically relevant ubiquitous metabolic pathways critical for EPN survival. Each anatomical region also presented at least one unique gene-metabolite interaction demonstrating heterogeneity within and across PF-A EPN tumours. A subset of the eight most prevalent genes across patients (GAD1, NT5C, FBP1, FMO3, HK3, TALDO1, NT5E, ALDH3A1) were selected for in vitro metabolic assays using 10 repurposed cytotoxic agents against PF-A EPN cell lines derived from intratumour regions of the same patient. 5/8 genes map within the gluconeogenesis metabolic pathway, further highlighting its significance within PF-A EPN. This is the first instance where multi-omic data integration and intratumour heterogeneity has been investigated for paediatric EPN revealing novel potential targets in the context of gene-metabolite correlations.

Strong horizontal and vertical connectivity in the coral Pocillopora verrucosa from Ludao, Taiwan, a small oceanic island

Mesophotic habitats could be sheltered from natural and anthropogenic disturbances and act as reproductive refuges, providing propagules to replenish shallower populations. Molecular markers can be used as proxies evaluating the connectivity and inferring population structure and larval dispersal. This study characterizes population structure as well as horizontal and vertical genetic connectivity of the broadcasting coral Pocillopora verrucosa from Ludao, a small oceanic island off the eastern coast of Taiwan. We genotyped 75 P. verrucosa specimens from three sites (Gongguan, Dabaisha, and Guiwan) at three depth ranges (Shallow: 7–15 m, Mid-depth: 23–30 m, and Deep: 38–45 m), spanning shallow to upper mesophotic coral reefs, with eight microsatellite markers. F-statistics showed a moderate differentiation (FST = 0.106, p<0.05) between two adjacent locations (Dabaisha 23–30 and Dabaisha 38–45 m), but no differentiation elsewhere, suggesting high levels of connectivity among sites and depths. STRUCTURE analysis showed no genetic clustering among sites or depths, indicating that all Pocillopora individuals could be drawn from a single panmictic population. Simulations of recent migration assigned 30 individuals (40%) to a different location from where they were collected. Among them, 1/3 were assigned to deeper locations, 1/3 to shallower populations and 1/3 were assigned to the right depth but a different site. These results suggest high levels of vertical and horizontal connectivity, which could enhance the recovery of P. verrucosa following disturbances around Ludao, a feature that agrees with demographic studies portraying this species as an opportunistic scleractinian.

Genetic Divergence among Populations of Invasive Alien Species Lantana camara L. from Selected Areas of Bangladesh

Lantana camara L., a well-known invasive alien species causing invasion and posing threat to native plant species community in different regions of Bangladesh. The present study aimed to investigate the genetic diversity of L. camara populations in different regions of Bangladesh. Eight RAPD markers were used in order to probe into its genetic variability. Total number of bands (202), polymorphic loci (104), per-centage of polymorphism (97.20%), average Shanon’s information index (0.3051±0.115), Nei’s gene diversity (0.4733±0.144) was found and in different populations and multiple divergent genetic clustering along with presence of unique alleles (4) for RAPD revealed high genetic diversity among the populations of L. camara in different regions of Bangladesh.

Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Animal body size has important evolutionary implications. The wolf spider genus Schizocosa Chamberlin, 1904 has developed as a model for studies on courtship, with visual and vibratory signals receiving attention; however, body size has never been carefully evaluated. Although species of Schizocosa can be distinguished from their close relatives by differences in genitalic structures, male ornamentation, and behavior, some species are morphologically similar, making diagnosis, and identification difficult. Evaluation of species boundaries using genetic data across Schizocosa is limited. The similar species S. maxima Dondale & Redner, 1978 and S. mccooki (Montgomery, 1904) are separated predominantly on the basis of size differences, with S. maxima being larger. We evaluate the evolution of size in these two Schizocosa species distributed in western North America, where gigantism of S. maxima is hypothesized to occur, particularly in California. We sampled subgenomic data (RADseq) and inferred the phylogeny of S. mccooki, S. maxima, and relatives. We apply a variational autoencoder machine learning approach to visualize population structuring within widespread S. mccooki and evaluate size within the context of a comparative phylogenetic framework to test the hypotheses related to genetic clustering of populations and gigantism. Our data show S. mccooki populations are not genealogically exclusive with respect to S. maxima. Likewise, S. maxima individuals are not recovered as a lineage and do not form an isolated genetic cluster, suggesting that the observed differences in size cannot be used to accurately delimit species. The cause of gigantism in S. maxima remains unexplained, but provides a framework for future studies of size variation and speciation.

Spatial Genetic Structure of the Insect-Vectored Conifer Pathogen Leptographium wageneri Suggests Long Distance Gene Flow Among Douglas-fir Plantations in Western Oregon

Many fungi in the Ophiostomatales are vectored by bark beetles that introduce these fungi directly into their tree hosts. Most of these fungal associates have little effect on their hosts, but some can cause serious diseases. One such fungus, Leptographium wageneri, causes an economically and ecologically important tree disease known as black stain root disease (BSRD). For this study, 159 full genome sequences of L. wageneri were analyzed using a population genomics approach to investigate the epidemiology, dispersal capabilities, and reproductive biology of this fungus. Analyses were performed with SNP haplotypes from 155 isolates of L. wageneri var. pseudotsugae collected in 16 Douglas-fir stands in Oregon and 4 isolates of L. wageneri var. wageneri collected in pinyon pine stands in southern California. These two host-specific varieties appear to be evolutionarily divergent, likely due a combination of factors such as host differentiation and geographic isolation. We analyzed gene flow and population structure within and among Douglas-fir plantations in western Oregon to infer the relative importance of local vs. long distance dispersal in structuring populations of L. wageneri var. pseudotsugae. Long-distance gene flow has occurred between Douglas-fir plantations, contributing to diversity and population structure within stands, and likely reflecting the behavior of an important insect vector. Genetic clustering analyses revealed the presence of unique local clusters within stands and plantations in addition to those common among multiple stands or plantations. Although populations of L. wageneri var. pseudotsugae are primarily asexual, two mating types were present in many stands, suggesting that recombination is at least possible and may contribute to genetic diversity.