Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis).

Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M. trossulus. Such thermal adaptations might help to explain, mechanistically, the success with which the invasive marine mussel M. galloprovincialis has displaced native species in contact zones in the eastern (California) and western (Japan) Pacific. We tested for stabilizing amino acid substitutions in warm tolerant M. galloprovincialis relative to cold tolerant M. trossulus with a generalized linear model that compares in silico estimates of recent changes in protein stability among closely related congeners. Fixed substitutions in M. galloprovincialis were 3,180.0 calories per mol per substitution more stabilizing at genes with both elevated dN/dS ratios and transcriptional responses to heat stress, and 705.8 calories per mol per substitution more stabilizing across all 2,770 loci investigated. Amino acid substitutions concentrated in a small number of genes were more stabilizing in M. galloprovincialis compared with cold tolerant M. trossulus. We also tested for, but did not find, enrichment of a priori GO terms in genes with elevated dN/dS ratios in M. galloprovincialis. This might indicate that selection for thermodynamic stability is generic across all lineages, and suggests that the high change in estimated protein stability that we observed in M. galloprovincialis is driven by selection for extra stabilizing substitutions, rather than by higher incidence of selection in a greater number of genes in this lineage. Nonetheless, our finding of more stabilizing amino acid changes in the warm adapted lineage is important because it suggests that adaption for thermal stability has contributed to M. galloprovincialis' superior tolerance to heat stress, and that pairing tests for positive selection and tests for transcriptional response to heat stress can identify candidates of protein stability adaptation

Spatio-temporal distribution of Spiroplasma infections in the tsetse fly (Glossina fuscipes fuscipes) in northern Uganda

Copyright: © 2019 Schneider et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Tsetse flies (Glossina spp.) are vectors of parasitic trypanosomes, which cause human (HAT) and animal African trypanosomiasis (AAT) in sub-Saharan Africa. In Uganda, Glossina fuscipes fuscipes (Gff) is the main vector of HAT, where it transmits Gambiense disease in the northwest and Rhodesiense disease in central, southeast and western regions. Endosymbionts can influence transmission efficiency of parasites through their insect vectors via conferring a protective effect against the parasite. It is known that the bacterium Spiroplasma is capable of protecting its Drosophila host from infection with a parasitic nematode. This endosymbiont can also impact its host\u27s population structure via altering host reproductive traits. Here, we used field collections across 26 different Gff sampling sites in northern and western Uganda to investigate the association of Spiroplasma with geographic origin, seasonal conditions, Gff genetic background and sex, and trypanosome infection status. We also investigated the influence of Spiroplasma on Gff vector competence to trypanosome infections under laboratory conditions. Generalized linear models (GLM) showed that Spiroplasma probability was correlated with the geographic origin of Gff host and with the season of collection, with higher prevalence found in flies within the Albert Nile (0.42 vs 0.16) and Achwa River (0.36 vs 0.08) watersheds and with higher prevalence detected in flies collected in the intermediate than wet season. In contrast, there was no significant correlation of Spiroplasma prevalence with Gff host genetic background or sex once geographic origin was accounted for in generalized linear models. Additionally, we found a potential negative correlation of Spiroplasma with trypanosome infection, with only 2% of Spiroplasma infected flies harboring trypanosome co-infections. We also found that in a laboratory line of Gff, parasitic trypanosomes are less likely to colonize the midgut in individuals that harbor Spiroplasma infection. These results indicate that Spiroplasma infections in tsetse may be maintained by not only maternal but also via horizontal transmission routes, and Spiroplasma infections may also have important effects on trypanosome transmission efficiency of the host tsetse. Potential functional effects of Spiroplasma infection in Gff could have impacts on vector control approaches to reduce trypanosome infections

Multiple evolutionary origins of Trypanosoma evansi in Kenya

Trypanosoma evansi is the parasite causing surra, a form of trypanosomiasis in camels and other livestock, and a serious economic burden in Kenya and many other parts of the world. Trypanosoma evansi transmission can be sustained mechanically by tabanid and Stomoxys biting flies, whereas the closely related African trypanosomes T. brucei brucei and T. b. rhodesiense require cyclical development in tsetse flies (genus Glossina) for transmission. In this study, we investigated the evolutionary origins of T. evansi. We used 15 polymorphic microsatellites to quantify levels and patterns of genetic diversity among 41 T. evansi isolates and 66 isolates of T. b. brucei (n = 51) and T. b. rhodesiense (n = 15), including many from Kenya, a region where T. evansi may have evolved from T. brucei. We found that T. evansi strains belong to at least two distinct T. brucei genetic units and contain genetic diversity that is similar to that in T. brucei strains. Results indicated that the 41 T. evansi isolates originated from multiple T. brucei strains from different genetic backgrounds, implying independent origins of T. evansi from T. brucei strains. This surprising finding further suggested that the acquisition of the ability of T. evansi to be transmitted mechanically, and thus the ability to escape the obligate link with the African tsetse fly vector, has occurred repeatedly. These findings, if confirmed, have epidemiological implications, as T. brucei strains from different genetic backgrounds can become either causative agents of a dangerous, cosmopolitan livestock disease or of a lethal human disease, like for T. b. rhodesiense

Introgression, Natural Selection, And Thermal Tolerance In Blue Mussels (Genus Mytilus)

My dissertation addressed questions of the origin and maintenance of biodiversity, and the genomic response to environmental change in blue mussels (genus Mytilus). In chapters One and Two I explored the nature of species barriers and the consequence of hybridization. The ecological and genetic factors determining the extent of introgression between species in secondary contact zones remain poorly understood. I investigated the relative importance of natural selection and the demographic expansion of invasive Mytilus galloprovincialis on the magnitude and the direction of introgression with the native M. trossulus in a hybrid zone in central California. I used double-digest restriction-site associated DNA sequencing (ddRADseq) to genotype 1,751 randomly-selected single nucleotide polymorphisms and accurately distinguish early and advanced generation hybrids for the first time in Mytilus. I found that ecologically based selection plays only a small direct role in maintaining reproductive isolation in the California hybrid zone, and that colonization history is an important control on the movement of genetic elements (i.e. introgression) during hybridization. Despite only low rates of hybridization between invasive Mediterranean blue mussel (M. galloprovincialis) and native blue mussel M. trossulus, introgression is occurring, and the geographic spread of M. galloprovincialis appears to drive the majority of introgression into the invasive species. My work reinforces the idea that demographic processes mediate the role played by natural selection in maintaining species barriers. Chapter Three focused on the genetic consequences of large-scale environmental change. I developed new techniques using mRNA sequencing and ancestral state reconstruction to estimate rates of structurally stabilizing substitutions in blue mussels. I found that warm-adapted Mytilus galloprovincialis have higher rates of stabilizing substitutions than cold-adapted M. trossulus, which suggests that natural selection can efficiently modify structural properties of proteins to fine-tune thermal tolerance based on small changes in temperature of just several ˚C. As a whole, my dissertation reiterates the importance of demographic processes in controlling the movement of genetic material during hybridization, indicates introgression may contribute to invasive success, and documents subtle natural selection for changes in protein properties of warm adapted M. galloprovincialis

INTROGRESS_v.1.22_input_file_(parent_2_data)

This is file 3 (parental 2 data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index

Data from: Introgression between invasive and native blue mussels (genus Mytilus) in the central California hybrid zone.

The ecological and genetic factors determining the extent of introgression between species in secondary contact zones remain poorly understood. Here, we investigate the relative importance of isolating barriers and the demographic expansion of invasive Mytilus galloprovincialis on the magnitude and the direction of introgression with the native Mytilus trossulus in a hybrid zone in central California. We use double-digest restriction-site-associated DNA sequencing (ddRADseq) to genotype 1337 randomly selected single nucleotide polymorphisms and accurately distinguish early and advanced generation hybrids for the first time in the central California Mytilus spp. hybrid zone. Weak levels of introgression were observed in both directions but were slightly more prevalent from the native M. trossulus into the invasive M. galloprovincialis. Few early and advanced backcrossed individuals were observed across the hybrid zone confirming the presence of strong barriers to interbreeding. Heterogeneous patterns of admixture across the zone of contact were consistent with the colonization history of M. galloprovincialis with more extensive introgression in northern localities furthest away from the putative site of introduction in southern California. These observations reinforce the importance of dynamic spatial and demographic expansions in determining patterns of introgression between close congeners, even in those with high dispersal potential and well-developed reproductive barriers. Our results suggest that the threat posed by invasive M. galloprovincialis is more ecological than genetic as it has displaced, and continues to displace the native M. trossulus from much of central and southern California

Genetic differentiation across eastern Pacific oceanographic barriers in the threatened seahorse Hippocampus ingens

Understanding the population structure and evolutionary history of the eastern Pacific seahorse Hippocampus ingens is critical for the effective management of this threatened species. Life history characteristics of H. ingens (site fidelity and brooding of young) may limit gene flow and lead to population differentiation. A recent study analyzing conserved fragments of the mitochondrial cyt b and control region found no population structure. We re-assess this conclusion with a phylogeographic analysis of relationships among 115 individuals of H. ingens over a broader geographic range (San Diego Bay in California, Gulf of California, Central America, Ecuador, and Peru) based on a more variable 428 base pair fragment of the control region. This expanded analysis affirms low overall nucleotide diversity relative to other seahorses (θπ = 0.004), and shows evidence of a recent bottleneck and population expansion since the middle Pleistocene. AMOVA analysis shows moderate overall population structure (ΦST = 0.10, P val = 0.00), and pairwise ΦST estimates indicate structure between the Gulf of California and all Pacific coast localities. Knowledge of population structure in H. ingens may improve conservation efforts by identifying evolutionarily important management units, and could determine source regions in the continuing trade of seahorses for traditional Chinese medicine. The level of genetic divergence observed between the Gulf of California and all other localities sampled may distinguish the Gulf as a separate management unit. Additional phylogeographic research with more quickly evolving genetic markers and targeted sampling at the mouth of the Gulf of California is warranted to inform strategies for conservation of this threatened seahorse

INTROGRESS_v.1.22_input_file_(admix_data)

This is file 4 (admix data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index

tags_from_STACKS_populations.pl_script

This was an output of the populations.pl script from the Stacks pipeline, used to filter SNPs scored in at least 75% of samples (parameter -r 0.75). This yielded a total of 1,337 SNPs. The original file name was "batch.8.catalog.tags.tsv". More information on the file format can be found at http://catchenlab.life.illinois.edu/stacks/comp/populations.php

STRUCTURE_v.2.3.4_input_file

This is the input file needed to run STRUCTURE v2.3.4 (Pritchard et al 2000; Falush et al 2003; Falush et al 2007), which we used to identify pure species and hybrids. STRUCTURE jointly assigns individuals probabilistically to the two parental classes without prior input. STRUCTURE analyses used all 1,337 SNPs that passed our primary filters. We used a burn in of 50,000 sweeps and then ran 100,000 sweeps in five separate runs checking for convergence of the estimated membership coefficient (Q) across runs