EEB Faculty Publications
Recent Submissions
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Geographic and Ecological Dimensions of Host Plant-Associated Genetic Differentiation and Speciation in theﾠRhagoletis cingulataﾠ(Diptera: Tephritidae) Sibling Species Group
(2019)Ascertaining the causes of adaptive radiation is central to understanding how new species arise and come to vary with their resources. The ecological theory posits adaptive radiation via divergent natural selection associated with novel resource use; an alternative suggests character displacement following speciation in allopatry and then secondary ... -
Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis
(2016)BACKGROUND: There are five major extant groups of Echinodermata: Crinoidea (feather stars and sea lillies), Ophiuroidea (brittle stars and basket stars), Asteroidea (sea stars), Echinoidea (sea urchins, sea biscuits, and sand dollars), and Holothuroidea (sea cucumbers). These animals are known for their pentaradial symmetry as adults, unique water ... -
Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals
(2014)Background: The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous studies have observed that human disease genes are of particularly ancient origin. While this suggests that many animal species have ... -
Individual and combined effects of two types of phenological shifts on predator–prey interactions
(2016)Timing of phenological events varies among years with natural variation in environmental conditions and is also shifting in response to climate change. These phenological shifts likely have many effects on species interactions. Most research on the ecological consequences of phenological shifts has focused on variation in simple metrics such as ... -
Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida
(2015)Annelida represents a large and morphologically diverse group of bilaterian organisms. The recently published polychaete and leech genome sequences revealed an equally dynamic range of diversity at the genomic level. The availability of more annelid genomes will allow for the identification of evolutionary genomic events that helped shape the annelid ... -
Conspecific Plasticity and Invasion: Invasive Populations of Chinese Tallow (Triadica sebifera)ﾠHave Performance Advantage over Native Populations Only in Low Soil Salinity
(2013)Global climate change may increase biological invasions in part because invasive species may have greater phenotypic plasticity than native species. This may be especially important for abiotic stresses such as salt inundation related to increased hurricane activity or sea level rise. If invasive species indeed have greater plasticity, this may reflect ... -
Ontogenetic functional diversity: Size structure of a keystone predator drives functioning of a complex ecosystem
(2013)A central challenge in community ecology is to understand the connection between biodiversity and the functioning of ecosystems. While traditional approaches have largely focused on species-level diversity, increasing evidence indicates that there exists substantial ecological diversity among individuals within species. By far, the largest source of ... -
Daptomycin Resistance in Enterococci Is Associated with Distinct Alterations of Cell Membrane Phospholipid Content
(2012)Background: The lipopeptide antibiotic, daptomycin (DAP) interacts with the bacterial cell membrane (CM). Development of DAP resistance during therapy in a clinical strain of Enterococcus faecalis was associated with mutations in genes encoding enzymes involved in cell envelope homeostasis and phospholipid metabolism. Here we characterized changes ... -
Hemichordate genomes and deuterostome origins
(2015)Acorn worms, also known as enteropneust (literally, ‘gut-breathing’) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequen -
Phenological synchronization drives demographic rates of populations
(2015)Phenology is increasingly recognized as an important factor structuring communities because it determines when and at what life stage organisms interact. Previous work indicates that changes in first or mean timing of a phenological event can affect populations and communities, but little is known about the consequences of changes in the distribution ... -
The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution
(2013)An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the ... -
Intraspecific priority effects and disease interact to alter population growth
(2014)Intraspecific variation may shape colonization of new habitat patches through a variety of mechanisms. In particular, trait variation among colonizing individuals can produce intraspecific priority effects (IPEs), where early arrivers of a single species affect the establishment or growth of later conspecifics. While we have some evidence for the ... -
Balancing anti-herbivore benefits and anti-pollinator costs of defensive mutualists
(2014)Quantifying costs and benefits of ostensibly mutualistic interactions is an important step toward understanding their evolutionary trajectories. In food-for-protection interactions between ants and extrafloral nectar (EFN)-bearing plants, tending by aggressive ants may deter herbivores, but it may also deter pollinators. The fitness costs of pollinator ... -
Climate warming increases biological control agent impact on a non-target species
(2015)Climate change may shift interactions of invasive plants, herbivorous insects and native plants, potentially affecting biological control efficacy and non-target effects on native species. Here, we show how climate warming affects impacts of a multivoltine introduced biocontrol beetle on the non-target native plant Alternanthera sessilis in China. ... -
The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima
(2014)Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia ... -
Computational approaches to species phylogeny inference and gene tree reconciliation
(2013)An intricate relationship exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against ... -
Species-specific defence responses facilitate conspecifics and inhibit heterospecifics in above-belowground herbivore interactions
(2014)Conspecific and heterospecific aboveground and belowground herbivores often occur together in nature and their interactions may determine community structure. Here we show how aboveground adults and belowground larvae of the tallow tree specialist beetle Bikasha collaris and multiple heterospecific aboveground species interact to determine herbivore ... -
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication
(2014)Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient ... -
An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
(2014)One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression ... -
Adaptation of Enterococcus faecalis to Daptomycin Reveals an Ordered Progression to Resistance
(2013)With increasing numbers of hospital-acquired antibiotic resistant infections each year and staggering health care costs, there is a clear need for new antimicrobial agents, as well as novel strategies to extend their clinical efficacy. While genomic studies have provided a wealth of information about the alleles associated with adaptation to antibiotics, ...
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