Inferring fine-scale mutation and recombination rate maps in aye-ayes ( ).

The rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species, but also across individual genomes. Despite previous studies having demonstrated that failing to account for rate heterogeneity across the genome can bias the inference of both selective and neutral population genetic processes, mutation and recombination rate maps have to date only been generated for a relatively small number of organisms.

Inferring the demographic history of aye-ayes () from high-quality, whole-genome, population-level data.

The nocturnal aye-aye, , is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of population size using traditional census methods. Therefore, alternative estimates provided by population genetic inference are essential for yielding much needed information for conservation measures and for enabling ecological and evolutionary studies of this species.

A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes () utilizing a well-fit evolutionary baseline model.

The aye-aye () is one of the 25 most endangered primate species in the world, maintaining amongst the lowest genetic diversity of any primate measured to date. Characterizing patterns of genetic variation within aye-aye populations, and the relative influences of neutral and selective processes in shaping that variation, is thus important for future conservation efforts. In this study, we performed the first whole-genome scans for recent positive and balancing selection in the species, utilizing high-coverage population genomic data from newly sequenced individuals.

A Simulation Framework for Modeling the Within-Patient Evolutionary Dynamics of SARS-CoV-2.

The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to considerable interest in detecting novel beneficial mutations and other genomic changes that may signal the development of variants of concern (VOCs). The ability to accurately detect these changes within individual patient samples is important in enabling early detection of VOCs. Such genomic scans for rarely acting positive selection are best performed via comparison of empirical data with simulated data wherein commonly acting evolutionary factors, including mutation and recombination, reproductive and infection dynamics, and purifying and background selection, can be carefully accounted for and parameterized.

A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2.

The global impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to considerable interest in detecting novel beneficial mutations and other genomic changes that may signal the development of variants of concern (VOCs). The ability to accurately detect these changes within individual patient samples is important in enabling early detection of VOCs. Such genomic scans for positive selection are best performed via comparison of empirical data to simulated data wherein evolutionary factors, including mutation and recombination rates, reproductive and infection dynamics, and purifying and background selection, can be carefully accounted for and parameterized.

Multiple mechanisms contribute to isolation by environment in the redheaded pine sawfly, Neodiprion lecontei.

Isolation by environment (IBE) is a population genomic pattern that arises when ecological barriers reduce gene flow between populations. Although current evidence suggests IBE is common in nature, few studies have evaluated the underlying mechanisms that generate IBE patterns. In this study, we evaluate five proposed mechanisms of IBE (natural selection against immigrants, sexual selection against immigrants, selection against hybrids, biased dispersal, and environment-based phenological differences) that may give rise to host-associated differentiation within a sympatric population of the redheaded pine sawfly, Neodiprion lecontei, a species for which IBE has previously been detected.

Developing an Appropriate Evolutionary Baseline Model for the Study of Human Cytomegalovirus.

Human cytomegalovirus (HCMV) represents a major threat to human health, contributing to both birth defects in neonates as well as organ transplant failure and opportunistic infections in immunocompromised individuals. HCMV exhibits considerable interhost and intrahost diversity, which likely influences the pathogenicity of the virus. Therefore, understanding the relative contributions of various evolutionary forces in shaping patterns of variation is of critical importance both mechanistically and clinically.

Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.

Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial.

Body size as a magic trait in two plant-feeding insect species.

When gene flow accompanies speciation, recombination can decouple divergently selected loci and loci conferring reproductive isolation. This barrier to sympatric divergence disappears when assortative mating and disruptive selection involve the same "magic" trait. Although magic traits could be widespread, the relative importance of different types of magic traits to speciation remains unclear.

Gregariousness does not vary with geography, developmental stage, or group relatedness in feeding redheaded pine sawfly larvae.

Aggregations are widespread across the animal kingdom, yet the underlying proximate and ultimate causes are still largely unknown. An ideal system to investigate this simple, social behavior is the pine sawfly genus , which is experimentally tractable and exhibits interspecific variation in larval gregariousness. To assess intraspecific variation in this trait, we characterized aggregative tendency within a single widespread species, the redheaded pine sawfly ().

Evaluation of Bacillus thuringiensis israelensis as a Control Agent for Adult Anopheles gambiae.

Unlike the application of Bacillus thuringiensis israelensis (Bti) for the control of larval mosquitoes, studies of its effects on adults, for its possible use in attractive toxic sugar baits, have resulted in conflicting results. Five species have shown a decrease in adult survival due to Bti ingestion, whereas adults of Anopheles arabiensis have not. We sought to determine if ingestion of Bti by adults of Anopheles gambiae, a sibling species of An.

Olfactory basis of floral preference of the malaria vector Anopheles gambiae (Diptera: Culicidae) among common African plants.

Mosquitoes of both sexes feed on plants to obtain sugar. Nocturnal species probably locate the plants primarily by their volatile semiochemicals that also form the basis for the mosquitoes' innate plant-species preferences. To evaluate these olfactory preferences quantitatively, we used a two-choice wind-tunnel olfactometer to measure the upwind orientation of Anopheles gambiae Giles, an important vector of malaria in equatorial Africa, toward odor plumes produced by nine plant species common where this mosquito occurs.