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Open Access Publications from the University of California

Scholarly Works (9 results)

  • Article
  • Peer Reviewed
UC Berkeley Previously Published Works (2012)
Replicate adaptive radiations occur when lineages repeatedly radiate and fill new but similar niches and converge phenotypically. While this is commonly seen in traditional island systems, it may also be present in host-parasite relationships, where hosts serve as islands. In a recent article in BMC Biology, Johnson and colleagues have produced the most extensive phylogeny of the avian lice (Ischnocera) to date, and find evidence for this pattern. This study opens the door to exploring adaptive radiations from a novel host-parasite perspective.
    Cover page: How a bird is an island
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2011)

    The Hawaiian Islands have been recognized as an ideal place to study evolutionary processes due to their remote location, multitude of ecological niches and diverse biota. As the oldest and largest radiation in the Hawaiian Islands the Hawaiian Drosophilidae have been the focus of decades of evolutionary research and subsequently the basis for understanding how much of the diversity within these islands and other island systems have been generated. This dissertation revolves around the diversification of a large clade of Hawaiian Drosophila, and examines the molecular evolution of this group at several different temporal scales. The antopocerus, modified tarsus, ciliated tarsus (AMC) clade is a group of 90 described Drosophila species that utilize decaying leafs as a host substrate and are characterized by a set of diagnostic secondary sexual characters: modifications in either antennal or tarsal morphologies. This research uses both phylogenetic and population genetic methods to study how this clade has evolved at increasingly finer evolutionary scales, from lineage to population level.

    The first chapter resolves the relationships within the AMC lineage, delimiting species group and subgroup relationships for the first time. This work complements recent phylogenetic studies focused on other lineages of Hawaiian Drosophila, most notably of the picture wing clade. This dissertation presents the most comprehensively sampled data set for the AMC in terms of both species and phylogenetic characters. The AMC clade is strongly supported as monophyletic and relationships among of the five major lineages in this radiation are proposed. Molecular dating analyses indicate a rapid radiation occurred about four million years ago, giving rise to all the extent lineages of AMC species. Interestingly, the AMC does not strictly follow the progression rule common to many other Hawaiian taxa. By comparing this lineage to other Hawaiian Drosophila lineages it is hypothesized that an initial burst of speciation occurred following colonization of the main Hawaiian Islands ands its magnitude was correlated with sexual selection within each group.

    Focusing more specifically on the spoon tarsus subgroup within the AMC, I redescribe this subgroup in chapter two. The species boundaries in this group are discussed in light of diagnostic secondary sexual characters of males. Drosophila septuosa Hardy is regarded as a junior synonym of Drosophila percnosoma Hardy. A new species, Drosophila kikalaeleele, is described. Drosophila fastigata Hardy, a species endemic to O`ahu, is added to the species subgroup, bringing the total number of known species to 12. An updated key to species is provided to the spoon tarsus subgroup. I employ several methods to delimit relationships at the species/population interface to get a more refined view of the evolution of this subgroup in chapter three. Eight of the twelve species in this subgroup are found only on the Island of Hawaii, suggesting that they have diverged within the past 500,000 years. This rapid diversification has made determining the relationships within this group difficult. We find widespread agreement between phylogenetic estimates derived from different methods. Notably, our analyses suggest that the spoon tarsus subgroup, as currently defined, is not monophyletic.

    The last chapter in this dissertation explores how biogeography influences microevolution within the spoon tarsus species, Drosophila waddingtoni, to understand the forces that drive macroevolution within the AMC clade. Previous chapters show that D. waddingtoni originated on the youngest island, Hawaii, and subsequently colonized the older islands of the Maui Nui complex, the opposite direction predicted by the progression rule. The recent origin of Hawaii suggests that this species will provide unique insight into the dynamics of recent island colonization events. Three nuclear and three mitochondrial genes are used to study gene flow and divergence following founder events. Biogeographic patterns, coupled with divergence time estimates suggest that the back colonization to Maui Nui occurred within the past 250,000 years and has since not led to significant population differentiation. These data also demonstrate that while migration between islands is possible and present in this species, it is not frequent enough to homogenize populations. Biogeography is identified as being a major driver in the diversification of this species.

    The AMC clade is a useful tool in understanding diversification in the Hawaiian Islands and rapid radiations in general. By examining this lineage from several different evolutionary timescales this dissertation research elucidates the processes involved in generating and maintaining diversity at all taxonomic levels. This research is also useful in extrapolating how evolution drives diversity in other Hawaiian Drosophilidae clades and other native Hawaiian lineages as well.

      Cover page: Diversification in the Hawaiian Drosophila
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2015)
      Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life.
        Cover page: Herbivory increases diversification across insect clades
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2013)
        The genus Scaptomyza is emerging as a model lineage in which to study biogeography and ecological adaptation. To place future research on these species into an evolutionary framework we present the most comprehensive phylogeny of Scaptomyza to date, based on 5042 bp of DNA sequence data and representatives from 13 of 21 subgenera. We infer strong support for the monophyly of almost all subgenera with exceptions corroborating hypotheses of conflict inferred from previous taxonomic studies. We find evidence that the lineage originated in the Hawaiian Islands and subsequently dispersed to the mainland and other remote oceanic islands. We also identify that many of the unique ecological niches exploited by this lineage (e.g., herbivory, spider predation) arose singly and independently.
          Cover page: Diversification and dispersal of the Hawaiian Drosophilidae: The evolution of Scaptomyza
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2014)
          Adaptive radiations are characterized by an increased rate of speciation and expanded range of habitats and ecological niches exploited by those species. The Hawaiian Drosophilidae is a classic adaptive radiation; a single ancestral species colonized Hawaii approximately 25 million years ago and gave rise to two monophyletic lineages, the Hawaiian Drosophila and the genus Scaptomyza. The Hawaiian Drosophila are largely saprophagous and rely on approximately 40 endemic plant families and their associated microbes to complete development. Scaptomyza are even more diverse in host breadth. While many species of Scaptomyza utilize decomposing plant substrates, some species have evolved to become herbivores, parasites on spider egg masses, and exploit microbes on living plant tissue. Understanding the origin of the ecological diversity encompassed by these nearly 700 described species has been a challenge. The central role of microbes in drosophilid ecology suggests bacterial and fungal associates may have played a role in the diversification of the Hawaiian Drosophilidae. Here we synthesize recent ecological and microbial community data from the Hawaiian Drosophilidae to examine the forces that may have led to this adaptive radiation. We propose that the evolutionary success of the Hawaiian Drosophilidae is due to a combination of factors, including adaptation to novel ecological niches facilitated by microbes.
            Cover page: Microbial interactions and the ecology and evolution of Hawaiian Drosophilidae
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2014)
            The Hawaiian Drosophilidae radiation is an ecologically and morphologically diverse clade of almost 700 described species. A phylogenetic approach is key to understanding the evolutionary forces that have given rise to this diverse lineage. Here we infer the phylogeny for the antopocerus, modified tarsus and ciliated tarsus (AMC) clade, a lineage comprising 16% (91 of 687 species) of the described Hawaiian Drosophilidae. To improve on previous analyses we constructed the largest dataset to date for the AMC, including a matrix of 15 genes for 68 species. Results strongly support most of the morphologically defined species groups as monophyletic. We explore the correlation of increased diversity in biogeography, sexual selection and ecology on the present day diversity seen in this lineage using a combination of dating methods, rearing records, and distributional data. Molecular dating analyses indicate that AMC lineage started diversifying about 4.4 million years ago, culminating in the present day AMC diversity. We do not find evidence that ecological speciation or sexual selection played a part in generating this diversity, but given the limited number of described larval substrates and secondary sexual characters analyzed we can not rule these factors out entirely. An increased rate of diversification in the AMC is found to overlap with the emergence of multiple islands in the current chain of high islands, specifically Oahu and Kauai.
              Cover page: Phylogenetics of the Antopocerus-Modified Tarsus Clade of Hawaiian Drosophila: Diversification across the Hawaiian Islands
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2015)
              Herbivory is a key innovation in insects, yet has only evolved in one-third of living orders. The evolution of herbivory likely involves major behavioral changes mediated by remodeling of canonical chemosensory modules. Herbivorous flies in the genus Scaptomyza (Drosophilidae) are compelling species in which to study the genomic architecture linked to the transition to herbivory because they recently evolved from microbe-feeding ancestors and are closely related to Drosophila melanogaster. We found that Scaptomyza flava, a leaf-mining specialist on plants in the family (Brassicaceae), was not attracted to yeast volatiles in a four-field olfactometer assay, whereas D. melanogaster was strongly attracted to these volatiles. Yeast-associated volatiles, especially short-chain aliphatic esters, elicited strong antennal responses in D. melanogaster, but weak antennal responses in electroantennographic recordings from S. flava. We sequenced the genome of S. flava and characterized this species' odorant receptor repertoire. Orthologs of odorant receptors, which detect yeast volatiles in D. melanogaster and mediate critical host-choice behavior, were deleted or pseudogenized in the genome of S. flava. These genes were lost step-wise during the evolution of Scaptomyza. Additionally, Scaptomyza has experienced gene duplication and likely positive selection in paralogs of Or67b in D. melanogaster. Olfactory sensory neurons expressing Or67b are sensitive to green-leaf volatiles. Major trophic shifts in insects are associated with chemoreceptor gene loss as recently evolved ecologies shape sensory repertoires.
                Cover page: Evolution of herbivory in Drosophilidae linked to loss of behaviors, antennal responses, odorant receptors, and ancestral diet
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2012)
                Herbivorous insects are among the most successful radiations of life. However, we know little about the processes underpinning the evolution of herbivory. We examined the evolution of herbivory in the fly, Scaptomyza flava, whose larvae are leaf miners on species of Brassicaceae, including the widely studied reference plant, Arabidopsis thaliana (Arabidopsis). Scaptomyza flava is phylogenetically nested within the paraphyletic genus Drosophila, and the whole genome sequences available for 12 species of Drosophila facilitated phylogenetic analysis and assembly of a transcriptome for S. flava. A time-calibrated phylogeny indicated that leaf mining in Scaptomyza evolved between 6 and 16 million years ago. Feeding assays showed that biosynthesis of glucosinolates, the major class of antiherbivore chemical defense compounds in mustard leaves, was upregulated by S. flava larval feeding. The presence of glucosinolates in wild-type (WT) Arabidopsis plants reduced S. flava larval weight gain and increased egg-adult development time relative to flies reared in glucosinolate knockout (GKO) plants. An analysis of gene expression differences in 5-day-old larvae reared on WT versus GKO plants showed a total of 341 transcripts that were differentially regulated by glucosinolate uptake in larval S. flava. Of these, approximately a third corresponded to homologs of Drosophila melanogaster genes associated with starvation, dietary toxin-, heat-, oxidation-, and aging-related stress. The upregulated transcripts exhibited elevated rates of protein evolution compared with unregulated transcripts. The remaining differentially regulated transcripts also contained a higher proportion of novel genes than the unregulated transcripts. Thus, the transition to herbivory in Scaptomyza appears to be coupled with the evolution of novel genes and the co-option of conserved stress-related genes.
                  Cover page: Genes involved in the evolution of herbivory by a leaf-mining, Drosophilid fly.
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2023)
                  Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.
                    Cover page: Evolution of chemosensory and detoxification gene families across herbivorous DrosophilidaeCreative Commons 'BY' version 4.0 license
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