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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Article
  • Peer Reviewed
UC Santa Cruz Previously Published Works (2023)
Gametic isolation is thought to play an important role in the evolution of reproductive isolation in broadcast-spawning marine invertebrates. However, it is unclear whether gametic isolation commonly evolves early in the speciation process or only accumulates after other reproductive barriers are already in place. It is also unknown whether gametic isolation is an effective barrier to introgression following speciation. Here, we used whole-genome sequencing data and multiple complementary phylogenomic approaches to test whether the well-documented gametic incompatibilities among the strongylocentrotid sea urchins have limited introgression. We quantified phylogenetic discordance, inferred reticulate phylogenetic networks, and applied the Δ statistic using gene tree topologies reconstructed from multiple sequence alignments of protein-coding single-copy orthologs. In addition, we conducted ABBA-BABA tests on genome-wide single nucleotide variants and reconstructed a phylogeny of mitochondrial genomes. Our results revealed strong mito-nuclear discordance and considerable nonrandom gene tree discordance that cannot be explained by incomplete lineage sorting alone. Eight of the nine species examined demonstrated a history of introgression with at least one other species or ancestral lineage, indicating that introgression was common during the diversification of the strongylocentrotid urchins. There was strong support for introgression between four extant species pairs (Strongylocentrotus pallidus ⇔ S. droebachiensis, S. intermedius ⇔ S. pallidus, S. purpuratus ⇔ S. fragilis, and Mesocentrotus franciscanus ⇔ Pseudocentrotus depressus) and additional evidence for introgression on internal branches of the phylogeny. Our results suggest that the existing gametic incompatibilities among the strongylocentrotid urchin species have not been a complete barrier to hybridization and introgression following speciation. Their continued divergence in the face of widespread introgression indicates that other reproductive isolating barriers likely exist and may have been more critical in establishing reproductive isolation early in speciation.
    Cover page: Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics.
    • Thesis
    • Peer Reviewed
    UC Santa Cruz Electronic Theses and Dissertations (2018)

    Introgressive hybridization, the movement of genetic material between species, is increasingly being documented in many taxa. It has largely been studied at 100kb+ level. I pioneered a new technique that connects introgression to the biologically meaningful gene and intra-gene level. I studied the genomes of six Strongylocentrotid urchins and identified 171 candidate introgressed genes. I detected instances of repeated introgression that occurred between Strongylocentrotus purpuratus and Allocentrotus fragilis/S. droebachiensis as well as their common ancestor. I also detected an enrichment of membrane Gene Ontology (GO) terms and enrichment of positive selection in membrane genes, possibly because they are pathogen targets. This suggests for these genes that being positively selected did not restrict their introgression as predicted by theory. I also found that introgression did not correlate inversely with time since divergence which also contradicts theory. I found many introgression events between species that are currently allopatric suggesting that they were in contact in the past. I hypothesize that past climatic shifts could have driven species into sympatry for periods of time. My results show that introgression can be detected at the gene level allowing the investigation of biologically meaningful characteristics. I hope the field will move toward investigating introgression at the gene level, so a more complete biological profile of introgression can be built.

    • 3 supplemental PDFs
    Cover page: Quantifying Introgression at the Gene Level in Strongylocentrotid UrchinsCreative Commons 'BY-NC-ND' version 4.0 license
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2017)

    Background

    Comparative genomics studies investigating the signals of positive selection among groups of closely related species are still rare and limited in taxonomic breadth. Such studies show great promise in advancing our knowledge about the proportion and the identity of genes experiencing diversifying selection. However, methodological challenges have led to high levels of false positives in past studies. Here, we use the well-annotated genome of the purple sea urchin, Strongylocentrotus purpuratus, as a reference to investigate the signals of positive selection at 6520 single-copy orthologs from nine sea urchin species belonging to the family Strongylocentrotidae paying careful attention to minimizing false positives.

    Results

    We identified 1008 (15.5%) candidate positive selection genes (PSGs). Tests for positive selection along the nine terminal branches of the phylogeny identified 824 genes that showed lineage-specific adaptive diversification (1.67% of branch-sites tests performed). Positively selected codons were not enriched at exon borders or near regions containing missing data, suggesting a limited contribution of false positives caused by alignment or annotation errors. Alignments were validated at 10 loci with re-sequencing using Sanger methods. No differences were observed in the rates of synonymous substitution (d S), GC content, and codon bias between the candidate PSGs and those not showing positive selection. However, the candidate PSGs had 68% higher rates of nonsynonymous substitution (d N) and 33% lower levels of heterozygosity, consistent with selective sweeps and opposite to that expected by a relaxation of selective constraint. Although positive selection was identified at reproductive proteins and innate immunity genes, the strongest signals of adaptive diversification were observed at extracellular matrix proteins, cell adhesion molecules, membrane receptors, and ion channels. Many candidate PSGs have been widely implicated as targets of pathogen binding, inactivation, mimicry, or exploitation in other groups (notably mammals).

    Conclusions

    Our study confirmed the widespread action of positive selection across sea urchin genomes and allowed us to reject the possibility that annotation and alignment errors (including paralogs) were responsible for creating false signals of adaptive molecular divergence. The candidate PSGs identified in our study represent promising targets for future research into the selective agents responsible for their adaptive diversification and their contribution to speciation.
      Cover page: Genome-wide signals of positive selection in strongylocentrotid sea urchins
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2013)
      Codon usage bias has been documented in a wide diversity of species, but the relative contributions of mutational bias and various forms of natural selection remain unclear. Here, we describe for the first time genome-wide patterns of codon bias at 4623 genes in the purple sea urchin, Strongylocentrotus purpuratus. Preferred codons were identified at 18 amino acids that exclusively used G or C at third positions, which contrasted with the strong AT bias of the genome (overall GC content is 36.9%). The GC content of third positions and coding regions exhibited significant correlations with the magnitude of codon bias. In contrast, the GC content of introns and flanking regions was indistinguishable from the genome-wide background, which suggested a limited contribution of mutational bias to synonymous codon usage. Five distinct clusters of genes were identified that had significantly different synonymous codon usage patterns. A significant correlation was observed between codon bias and mRNA expression supporting translational selection, but this relationship was driven by only one highly biased cluster that represented only 8.6% of all genes. In all five clusters preferred codons were evolutionarily conserved to a similar degree despite differences in their synonymous codon usage distributions and magnitude of codon bias. The third positions of preferred codons in two codon usage groups also paired significantly more often in stems than in loops of mRNA secondary structure predictions, which suggested that codon bias might also affect mRNA stability. Our results suggest that mutational bias has played a minor role in determining codon bias in S. purpuratus and that preferred codon usage may be heterogeneous across different genes and subject to different forms of natural selection.
        Cover page: Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus
        • Thesis
        • Peer Reviewed
        UC Santa Cruz Electronic Theses and Dissertations (2014)

        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.

        • 4 supplemental files
        Cover page: Introgression, Natural Selection, And Thermal Tolerance In Blue Mussels (Genus Mytilus)
        • Multimedia
        • Peer Reviewed
        UC Santa Cruz Electronic Theses and Dissertations (2024)

        Understanding the genomic architecture of speciation remains a challenge in evolutionary biology. Among broadcast-spawning marine invertebrates, reproductive isolation is thought to be established and maintained by the divergence of gamete recognition proteins located on the surfaces of sperm and egg cells. However, it remains unclear whether gametic isolation has been an effective barrier to gene flow during and/or following speciation. In this dissertation, I characterized the history of introgression among the North Pacific sea urchin species of the family Strongylocentrotidae to deepen our understanding of their diversification and evaluate the importance of gametic isolation in speciation. Using whole-genome sequencing data from each strongylocentrotid species and cutting-edge phylogenomic approaches, I documented widespread introgression in both extant taxa and ancestral lineages, demonstrating that gametic isolation did not effectively limit introgression. I implemented a phylogenetic hidden Markov model to locate the specific regions of the genome affected by introgression, finding evidence of strong selection against introgression across much of the genome. Although introgressed variation has predominantly persisted in slowly evolving, low-divergence genomic regions, numerous protein-coding genes showed both introgression and historical positive selection, suggesting an adaptive role for introgression. Finally, I showed that the two gamete recognition proteins responsible for species-selectivity in sea urchin fertilization, sperm protein bindin and its egg receptor, EBR1, have experienced historical adaptive introgression, a pattern inconsistent with expectations for barrier loci. My findings contribute to the body of literature evaluating the biological consequences of introgression and question the importance of gamete recognition proteins in the evolution of reproductive isolation among incipient strongylocentrotid sea urchin species.

        • 1 supplemental PDF
        • 2 supplemental ZIPs
        • Thesis
        • Peer Reviewed
        UC Santa Cruz Electronic Theses and Dissertations (2012)

        The availability of complete genomes allows for direct and powerful tests of the different processes underlying molecular evolution and quantification of their relative contributions. Here, I evaluate the relative contributions of natural selection and random genetic drift in shaping the evolution of the genome of Strongylocentrotid sea urchins using the assembled genome of the purple sea urchin, Strongylocentrotus purpuratus and by sequencing the entire genome of eight additional closely related species. I use a phylogenomic approach taking advantage of the data provided by 3,848 nuclear genes to obtain a robust and well-resolved phylogeny of the group. I observe that synonymous codon usage is biased in S. purpuratus and that there are five distinct clusters of codon usage. I find evidence that natural selection acts on slightly advantageous mutations through changes in synonymous codon usage bias, involving translational efficiency and/or accuracy as well as mRNA folding stability. Finally, using the comparative genomics of the group and the rates of synonymous and non-synonymous substitutions between species I detected strong evidence for broadly acting purifying selection and extensive signals of positive Darwinian selection (27.6% of genes). Sea urchins have long served as model organisms and have provided key insights into our basic understanding of biology and will continue to continue furthering our understanding of the role of natural selection on shaping the genome in the future.

        • 7 supplemental files
        Cover page: Genomic signals of selection within and phylogenetic relationships among Strongylocentrotid sea urchins
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2017)
        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.
          Cover page: Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis)
          • Article
          • Peer Reviewed
          UC Santa Cruz Previously Published Works (2019)
          A major challenge in HIV vaccine development is the identification of immunogens able to elicit broadly neutralizing antibodies (bNAbs). While remarkable progress has been made in the isolation and characterization of bNAbs, the epitopes they recognize appear to be poorly immunogenic. Thus, none of the candidate vaccines developed to date has induced satisfactory levels of neutralizing antibodies to the HIV envelope protein (Env). One approach to the problem of poor immunogenicity is to build vaccines based on envelope (env) genes retrieved from rare individuals termed elite neutralizers (ENs) who at one time possessed specific sequences that stimulated the formation of bNAbs. Env proteins selected from these individuals could possess uncommon, yet to be defined, structural features that enhance the immunogenicity of epitopes recognized by bNAbs. Here we describe the recovery of envs from an EN that developed unusually broad and potent bNAbs. As longitudinal specimens were not available, we combined plasma and provirus sequences acquired from a single time-point to infer a phylogenetic tree. Combining ancestral reconstruction data with virus neutralization data allowed us to sift through the myriad of virus quasi-species that evolved in this individual to identify envelope sequences from the nodes that appeared to define the transition from neutralization sensitive envs to the neutralization resistant envs that occur in EN plasma. Synthetic genes from these nodes were functional in infectivity assays and sensitive to neutralization by bNAbs, and may provide a novel source of immunogens for HIV vaccine development.
            Cover page: Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens.
            • Article
            • Peer Reviewed
            UC Santa Cruz Previously Published Works (2019)
            A major challenge in HIV vaccine development is the identification of immunogens able to elicit broadly neutralizing antibodies (bNAbs). While remarkable progress has been made in the isolation and characterization of bNAbs, the epitopes they recognize appear to be poorly immunogenic. Thus, none of the candidate vaccines developed to date has induced satisfactory levels of neutralizing antibodies to the HIV envelope protein (Env). One approach to the problem of poor immunogenicity is to build vaccines based on envelope (env) genes retrieved from rare individuals termed elite neutralizers (ENs) who at one time possessed specific sequences that stimulated the formation of bNAbs. Env proteins selected from these individuals could possess uncommon, yet to be defined, structural features that enhance the immunogenicity of epitopes recognized by bNAbs. Here we describe the recovery of envs from an EN that developed unusually broad and potent bNAbs. As longitudinal specimens were not available, we combined plasma and provirus sequences acquired from a single time-point to infer a phylogenetic tree. Combining ancestral reconstruction data with virus neutralization data allowed us to sift through the myriad of virus quasi-species that evolved in this individual to identify envelope sequences from the nodes that appeared to define the transition from neutralization sensitive envs to the neutralization resistant envs that occur in EN plasma. Synthetic genes from these nodes were functional in infectivity assays and sensitive to neutralization by bNAbs, and may provide a novel source of immunogens for HIV vaccine development.
              Cover page: Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens
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