Patrick M. O'Grady

Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae).

The Hawaiian Archipelago is the most isolated island system on the planet and has been the subject of evolutionary research for over a century. The largest radiation of species in Hawaii is the Hawaiian Drosophilidae, a group of approximately 1000 species. Dispersal to isolated island systems like Hawaii is rare and the resultant flora and fauna shows high disharmony with mainland communities. The possibility that some lineages may have originated in Hawaii and subsequently ‘escaped’ to diversify on continental landmasses is expected to be rarer still. We present phylogenetic analysis of 134 partially sequenced mitochondrial genomes of Drosophilidae (approx. 1.3u200aMb of sequence total) to address major aspects of adaptive radiation and dispersal in Hawaii. We show that the genus Scaptomyza, a group that accounts for approximately one-third of the species-level diversity of Drosophilidae in the Hawaiian Islands, originated in Hawaii, diversified there, and subsequently colonized a number of island and continental landmasses elsewhere on the globe. We propose that a combination of small body size, rapid generation time and unique ecological and physiological adaptations have allowed this genus to effectively disperse and diversify.

Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis

The Hawaiian Drosophilidae are comprised of an estimated 1000 species, all arising from a single common ancestor in the last 25 million years. This group, because of its species diversity, marked sexual dimorphism and complex mating behavior, host plant specificity, and the well-known chronology of the Hawaiian Archipelago, is an excellent model system for evolutionary studies. Here we present a phylogeny of this group based on ~2.6 kb of mitochondrial DNA sequence. Our taxon sampling is the most extensive to date, with nearly 200 species representing all species groups and most subgroups from the larger clades. Our results suggest that the picture wing and modified mouthpart species, long believed to be derived within this radiation, may actually occupy a basal position in the phylogeny. The haleakale species group, in contrast, is strongly supported as sister to the AMC clade. We use the phylogenetic results to examine the evolution of two important ecological characters, the host family and type of substrate used for oviposition and larval development. Although both host and substrate transitions are common in the group, oviposition substrate is more conserved among species groups than host plant family. While the ancestral host plant family is equivocally reconstructed, our results suggest that the ancestor of this group may have used rotting bark as a primary oviposition substrate.

Diversification and dispersal of the Hawaiian Drosophilidae: The evolution of Scaptomyza

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.

Phylogenetic taxonomy in Drosophila: Problems and prospects

The genus Drosophila is one of the best-studied model systems in modern biology, with twelve fully sequenced genomes available. In spite of the large number of genetic and genomic resources, little is known concerning the phylogenetic relationships, ecology, and evolutionary history of all but a few species. Recent molecular systematic studies have shown that this genus is comprised of at least three independent lineages and that several other genera are actually embedded within Drosophila. This genus accounts for over 2000 described, and many more undescribed, species. While some Drosophila researchers are advocating dividing this genus into three or more separate genera, others favor maintaining Drosophila as a single large genus. With the recent sequencing of the genomes of multiple Drosophila species and their expanding use in comparative biology, it is critical that the Drosophila research community understands the taxonomic framework underlying the naming and relationships of these species. The subdivision of this genus has significant biological implications, ranging from the accurate annotation of single genes to understanding how ecological adaptations have occurred over the history of the group.

Mitochondrial phylogeny of the endemic Hawaiian craneflies (Diptera, Limoniidae, Dicranomyia): Implications for biogeography and species formation

Situated in the middle of the Pacific Ocean, over 3000 km from the nearest continental land mass, the Hawaiian Archipelago is the most remote island group on earth. The Hawaiian Islands are often referred to as a ‘‘conveyor belt” archipelago (Carson and Clague, 1995); as the Pacific plate moves to the northwest over a stationary hotspot, islands are formed, carried with the plate, and gradually subside at a more-or-less constant rate (Price and Clague, 2002; Ziegler, 2002). This hotspot has been active for over 40 million years (Carson and Clague, 1995) and has resulted in a chain of successively older islands, seamounts, and atolls stretching northwest across the Pacific. Currently, there are eight ‘‘high islands” in the southeast of the chain that, at over 1000 m in elevation, are able to support a diverse flora and fauna. The youngest island, dated at less than 600,000 years old, is the Big Island of Hawai‘i. Kaua‘i, at about 5 million years old, is the oldest high island (Price and Clague, 2002). Extreme isolation, coupled with the unique geology and environmental conditions of the islands, has made Hawai‘i a ‘‘natural laboratory” where the effects of evolution are readily observable (Kaneshiro, 1995). Over 850 endemic flowering plant (Wagner et al., 1990) and 4000 endemic insect species (Liebherr, 2001) are each thought to have been derived from about 200 colonization events. Colonist species can rapidly fill open ecological niches and diversify in situ, resulting in an amazing array of endemic fauna and flora. Newly emerging islands are then colonized from

Enhanced detection of groundwater contamination from a leaking waste disposal site by microbial community profiles

[1]xa0Groundwater biogeochemistry is adversely impacted when municipal solid waste leachate, rich in nutrients and anthropogenic compounds, percolates into the subsurface from leaking landfills. Detecting leachate contamination using statistical techniques is challenging because well strategies or analytical techniques may be insufficient for detecting low levels of groundwater contamination. We sampled profiles of the microbial community from monitoring wells surrounding a leaking landfill using terminal restriction fragment length polymorphism (T-RFLP) targeting the 16S rRNA gene. Results show in situ monitoring of bacteria, archaea, and the family Geobacteraceae improves characterization of groundwater quality. Bacterial T-RFLP profiles showed shifts correlated to known gradients of leachate and effectively detected changes along plume fringes that were not detected using hydrochemical data. Experimental sediment microcosms exposed to leachate-contaminated groundwater revealed a shift from a β-Proteobacteria and Actinobacteria dominated community to one dominated by Firmicutes and δ-Proteobacteria. This shift is consistent with the transition from oxic conditions to an anoxic, iron-reducing environment as a result of landfill leachate-derived contaminants and associated redox conditions. We suggest microbial communities are more sensitive than hydrochemistry data for characterizing low levels of groundwater contamination and thus provide a novel source of information for optimizing detection and long-term monitoring strategies at landfill sites.

Using whole genome presence/absence data to untangle function in 12 Drosophila genomes

The Drosophila 12 genome data set was used to construct whole genome, gene family presence/absence matrices using a broad range of E value cutoffs as criteria for gene family inclusion. The various matrices generated behave differently in phylogenetic analyses as a function of the e-value employed. Based on an optimality criterion that maximizes internal corroboration of information, we show that values of e-105 to e-125 extract the most internally consistent phylogenetic signal. Functional class of most genes and gene families can be accurately determined based on the D. melanogaster genome annotation. We used the gene ontology (GO) system to create partitions based on gene function. Several measures of phylogenetic congruence (diagnosis, consistency, partitioned support , hidden support) for different higher and lower level GO categories, were used to mine the data set for genes and gene families that show strong agreement or disagreement with the overall combined phylogenetic hypothesis. We propose that measures of phylogenetic congruence can be used as criteria to identify loci with related GO terms that have a significant impact on cladogenesis.

Microbial interactions and the ecology and evolution of Hawaiian Drosophilidae

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.

Morphological variation in the forelegs of the Hawaiian Drosophilidae. I. The AMC clade.

The Hawaiian Drosophilidae possess spectacular diversity in male foreleg modifications, many of which are unknown in other Diptera. The greatest diversity in foreleg morphology is in the antopocerus, modified tarsus, and ciliated tarsus clade (AMC Clade), a group of 95 species. The modified tarsus flies are divided into the bristle, ciliated, split, and spoon tarsus subgroups. The bristle tarsus species feature one or two rows of thickened setae on the basitarsus. The split tarsus species are characterized by only having four tarsal segments, in contrast to five tarsomeres in the remainder of Diptera. Based on comparisons of the apparent ground state of ventral setal rows across the Hawaiian Drosophila, we suggest that it is the second tarsal segment which has been lost. The spoon tarsus species are characterized by having the second tarsomere modified into a setae‐filled, concave‐shaped spoon. The ciliated tarsus species, all of which possess one or more elongate setae on the tarsus of males, are probably not monophyletic with respect to the bristle tarsus subgroup. The antopocerus flies are characterized by a long basitarsus, with extensive setation on the tibia and basitarsus of some species. The use of these foreleg modifications in courtship behavior has been previously described and it is suggested that they represent the results of sexual selection. The current work expands on previous morphological analyses, presenting a level of detail not previously possible without SEM images. The new characters revealed will figure prominently in future cladistic studies. J. Morphol. 2010.

The relative importance of introduced fishes, habitat characteristics, and land use for endemic shrimp occurrence in brackish anchialine pool ecosystems.

AbstractnAnchialine ecosystems are groundwater-fed brackish coastal habitats that contain high percentages of endemic fauna and are at risk from anthropogenic stressors, introduced species, and sea level rise. Data on endemic species distribution, habitat condition, and species/habitat interactions in this ecosystem are scarce across large spatial scales. This study offers the most thorough regional perspective on anchialine pool habitat characteristics along the western and southern coastlines of the island of Hawaii since the 1970s. Daytime surveys of 398 anchialine pools documented the widespread distribution of two dominant endemic shrimp Halocaridina rubra and Metabetaeus lohena in a wide range of habitats. Introduced fishes (tilapia, poeciliids) were present in about 25% of pools. Generalized additive models were used to determine the relationship between shrimp occurrence and pool characteristics, invasive species, water properties, and land use. Introduced fishes had a strong negative effect on the occurrence of H. rubra and M. lohena. High benthic silt cover and adjacent development also had significant negative relationships with shrimp occurrence. Our results indicate that conservation efforts should include controlling introduced fishes, preventing new introductions, minimizing siltation, and protecting groundwater resources and low-lying coastal areas.