The genomics of the domestication syndrome in a songbird model species.

Many domesticated animals share a syndromic phenotype marked by a suite of traits that include more variable patterns of coloration, reduced stress, aggression, and altered risk-taking and exploratory behaviors relative to their wild counterparts. Roughly 150 years after Darwin's pioneering insight into this phenomenon, reasonable progress has been made in understanding the evolutionary and biological basis of the so-called domesticated phenotype in mammals. However, the extent to which these processes are paralleled in non-mammalian domesticates is scant.

To Tame a Songbird: The Genomics of the Domestication Syndrome in a Songbird Model Species.

Many domesticated animals share a syndromic phenotype marked by a suite of traits that include more variable patterns of coloration, reduced stress, aggression, and altered risk-taking and exploratory behaviors relative to their wild counterparts. Roughly 150 years after Darwin's pioneering insight into this phenomenon, reasonable progress has been made in understanding the evolutionary and biological basis of the so-called domesticated phenotype in mammals. However, the extent to which these processes are paralleled in non-mammalian domesticates is scant.

Leveraging shared ancestral variation to detect local introgression.

Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson's D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions.

Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications.

Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied.

The Gene: An Evolutionary History of Recurrent Introgression and Natural Selection.

We study the gene , for which some modern humans carry a haplotype. is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the haplotype at high frequencies in admixed Latin American individuals, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans.

Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia.

Societies in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression.

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge.

A need for standardized reporting of introgression: Insights from studies across eukaryotes.

With the rise of affordable next-generation sequencing technology, introgression-or the exchange of genetic materials between taxa-has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes.

Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations.

Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic variation is partitioned within its putative ancestral range in Southern Africa remains unresolved. Here, we study patterns of population genetic structure, admixture, and the spatial structuring of candidate incompatibility alleles across a global sample, including 223 new accessions, predominantly from remote regions in Southern Africa.

Widespread introgression across a phylogeny of 155 Drosophila genomes.

Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here, we leverage 155 genome assemblies from 149 species to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila.

P-elements strengthen reproductive isolation within the Drosophila simulans species complex.

Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood.

Highly contiguous assemblies of 101 drosophilid genomes.

Over 100 years of studies in and related species in the genus have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated.

Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup.

Introgression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminates how and when gene flow is expected to occur.

Digest: Differentiating Fisherian sexual selection dynamics between haploids and diploids.

Female mate preference for males displaying costly traits is a puzzling phenomenon found in nature. Fisher was the first to propose a formal model describing this paradoxical system of sexual selection. Despite the many models constructed from his theory, much remains unknown about its mechanics, especially in different genetic settings.

Paternally Inherited P-Element Copy Number Affects the Magnitude of Hybrid Dysgenesis in Drosophila simulans and D. melanogaster.

Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. P-elements (PEs) in Drosophila are a well-studied TE that has strong phenotypic effects.

Digest: Species delimitation in the face of demographic processes.

Existing approaches to species delimitation use the extent of divergence between taxa. However, processes, such as gene flow during divergence or secondary contact, as well as population expansion and migration, complicate this task. Smith and Carstens introduce the R package delimitR, which uses machine learning to integrate gene flow into species delimitation inference.

Rapid and Predictable Evolution of Admixed Populations Between Two Species Pairs.

The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of : and ; and and Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for over 20 generations.

Digest: Biotic interactions shape local adaptation in teosinte populations.

Little is known about how microbial communities shape the expression of plant phenotypes and phenotypic correlations. This is precisely the question that O'Brien et al. addressed using populations of highland teosinte, a wild relative of maize.