About
32
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Introduction
I am fascinated by biology’s big picture, the process and history of evolution. I use a variety of molecular and computational tools to study genome evolution, phylogenetic relationships, and the genetic basis of adaptive traits. Examples of my diverse research interests include the deep history of animal evolution and the genomic architecture of sociality in ants. Currently I am investigating how the adaptive radiation of hamlets, a group of Caribbean reef fishes, is reflected in their genomes.
Additional affiliations
November 2020 - present
September 2015 - August 2019
June 2013 - September 2013
Publications
Publications (32)
Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ~4,000 novel genes, but only 64 of these genes are...
Taro, Colocasia esculenta, is one of the world's oldest root crops and of particular economic and cultural significance in Hawai'i, where historically more than 150 different landraces were grown. We developed a genome-wide set of more than 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South Pac...
Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the ʻAlalā (Corvus hawaiiensis; Hawaiian crow...
The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds wi...
Significance
Adaptive radiation, the evolutionary process whereby a lineage diversifies over a short period of time, often occurs in geographically isolated or newly formed habitats where colonizing species encounter unoccupied niches and reduced selective pressures. Rapid radiations may also occur in diverse and complex environments, but these cas...
Interest in bioactive pigments stems from their ecological role in adaptation, as well as their applications in various consumer products. The production of these bioactive pigments can be from a variety of biological sources, including simple microorganisms that may or may not be associated with a host. This study is particularly interested in the...
Taro ( Colocasia esculenta ) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae . Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro...
Taro [Colocasia esculenta (L.) Schott] is an ancient, tropical root crop that is morphologically diverse with over 10,000 landraces. It is the fifth most produced root crop in the world and is mainly grown in tropical Africa, China, New Guinea, and many Pacific islands. Taro typically is grown for its starchy corm (i.e., underground stem), although...
Reef‐building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this stud...
Background
Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that ha...
We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain IPB1 that was isolated from the Hawaiian marine sponge Iotrochota protea Genome mining complemented with bioassay studies will elucidate secondary metabolite biosynthetic pathways and will help explain the ecological interaction between host sponge and microor...
A key requirement for social cooperation is the mitigation and/or social regulation of aggression towards other group members. Populations of the harvester ant Pogonomyrmex californicus show the alternate social phenotypes of queens founding nests alone (haplometrosis) or in groups of unrelated yet cooperative individuals (pleometrosis). Pleometrot...
A central goal of biology is to uncover the genetic basis for the origin of new phenotypes. A particularly effective approach is to examine the genomic architecture of species that have secondarily lost a phenotype with respect to their close relatives. In the eusocial Hymenoptera, queens and workers have divergent phenotypes that may be produced v...
Desaturase genes are essential for biological processes, including lipid metabolism, cell signaling, and membrane fluidity regulation. Insect desaturases are particularly interesting for their role in chemical communication, and potential contribution to speciation, symbioses, and sociality. Here, we describe the acyl-CoA desaturase gene families o...
A conspicuous new species of praying mantid, Mythomantis serrata sp. nov., from the Malaysian part of Borneo is described and illustrated. A key to the three known species of the genus Mythomantis and their known geographic distribution is provided. Several morphological characters, most notably those in the male genitals, suggest a close relations...
The lophophorates are mainly marine, sessile invertebrates that are characterized by a lophophore, a horseshoe-shaped tentacular filter apparatus surrounding the mouth opening. Lophophorata comprises three divergent lineages, Phoronida, Brachiopoda and Ectoprocta (Bryozoa). Their phylogenetic relationships to other metazoan phyla as well as to each...
Within the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity.
The phy...
Myxozoa are microscopic obligate endoparasites with complex live cycles. Representatives are Myxobolus cerebralis, the causative agent of whirling disease in salmonids, and the enigmatic "orphan worm" Buddenbrockia plumatellae parasitizing in Bryozoa. Originally, Myxozoa were classified as protists, but later several metazoan characteristics were r...
Orphan genes are defined as genes which lack detectable similarity to genes in other species and therefore no clear signals of common descant (i.e. homology) can be inferred. Orphans are an enigmatic portion of the genome since their origin and function are mostly unknown and they typically make up 10 to 30% of all genes in a genome. Several case s...
Ants (Hymenoptera, Formicidae) represent one of the most successful eusocial taxa in terms of both their geographic distribution and species number. The publication of seven ant genomes within the past year was a quantum leap for socio- and ant genomics. The diversity of social organization in ants makes them excellent model organisms to study the...
The phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most species-rich lophophorate lineage, the ectoprocts. Although it is known that there are large differences in the nucleotide composition of mitoc...
Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species,...
We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparabl...
Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the forma...
We produced two new EST datasets of so far uncovered clades of ectoprocts to investigate the phylogenetic relationships within the lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida. Maximum-likelihood analyses based on 78 ribosomal proteins of 62 metazoan taxa support the monophyly of Ectoprocta and a sister group relationship of Phylact...
Compositional heterogeneity of sequences between taxa may cause systematic error in phylogenetic inference. The potential influence of such bias might be mitigated by strategies to reduce compositional heterogeneity in the data set or by phylogeny reconstruction methods that account for compositional heterogeneity. We adopted several of these strat...
Relatedness and genetic variability in colonies of social insects are strongly influenced by the number of queens present and the number of matings per queen, but also by the genetic variability in the population. Thus, multiple paternity will enhance within-colony genetic variability more strongly when the males a queen mates with are unrelated. T...
Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related...
Maximum likelihood and Bayesian inference analyses of seven concatenated fragments of nuclear-encoded housekeeping genes indicate that Lophotrochozoa is monophyletic, i.e., the lophophorate groups Bryozoa, Brachiopoda and Phoronida are more closely related to molluscs and annelids than to Deuterostomia or Ecdysozoa. Lophophorates themselves, howeve...
Phylogenetic analyses based on 79 ribosomal proteins of 38 metazoans, partly derived from 6 new expressed sequence tag projects
for Ectoprocta, Entoprocta, Sipuncula, Annelida, and Acanthocephala, indicate the monophyly of Bryozoa comprising Ectoprocta
and Entoprocta, 2 taxa that have been separated for more than a century based on seemingly profou...
Light-trapping was conducted in February and March 2003 near Kinabalu Park and in the Danum Valley Conservation Area in Sabah, Malaysia. During 18 sample nights a total of 106 praying mantids, comprising 28 species, were collected in three different habitat types: a heavily disturbed farmland site, a selectively logged forest and an undisturbed can...