More Like this

1. Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations

   https://doi.org/10.1371/journal.pgen.1009695  

   Liu, Chenxing ; Lee, Myoung Keun ; Naqvi, Sahin ; Hoskens, Hanne ; Liu, Dongjing ; White, Julie D. ; Indencleef, Karlijne ; Matthews, Harold ; Eller, Ryan J. ; Li, Jiarui ; et al ( August 2021 , PLOS Genetics)

   Tishkoff, Sarah A. (Ed.)

   Facial morphology is highly variable, both within and among human populations, and a sizable portion of this variation is attributable to genetics. Previous genome scans have revealed more than 100 genetic loci associated with different aspects of normal-range facial variation. Most of these loci have been detected in Europeans, with few studies focusing on other ancestral groups. Consequently, the degree to which facial traits share a common genetic basis across diverse sets of humans remains largely unknown. We therefore investigated the genetic basis of facial morphology in an East African cohort. We applied an open-ended data-driven phenotyping approach to amore »sample of 2,595 3D facial images collected on Tanzanian children. This approach segments the face into hierarchically arranged, multivariate features that capture the shape variation after adjusting for age, sex, height, weight, facial size and population stratification. Genome scans of these multivariate shape phenotypes revealed significant (p < 2.5 × 10 −8 ) signals at 20 loci, which were enriched for active chromatin elements in human cranial neural crest cells and embryonic craniofacial tissue, consistent with an early developmental origin of the facial variation. Two of these associations were in highly conserved regions showing craniofacial-specific enhancer activity during embryological development (5q31.1 and 12q21.31). Six of the 20 loci surpassed a stricter threshold accounting for multiple phenotypes with study-wide significance (p < 6.25 × 10 −10 ). Cross-population comparisons indicated 10 association signals were shared with Europeans (seven sharing the same associated SNP), and facilitated fine-mapping of causal variants at previously reported loci. Taken together, these results may point to both shared and population-specific components to the genetic architecture of facial variation.« less
2. Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches

   https://doi.org/10.1038/s41598-019-56469-w  

   Cruz, Mariana Vargas ; Mori, Gustavo Maruyama ; Signori-Müller, Caroline ; da Silva, Carla Cristina ; Oh, Dong-Ha ; Dassanayake, Maheshi ; Zucchi, Maria Imaculada ; Oliveira, Rafael Silva ; de Souza, Anete Pereira ( December 2019 , Scientific Reports)

   Abstract Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana . In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differencesmore »identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.« less
3. Population differentiation and structural variation in the Manduca sexta genome across the United States

   https://doi.org/10.1093/g3journal/jkac047  

   Mongue, Andrew J ; Kawahara, Akito Y ( February 2022 , G3 Genes|Genomes|Genetics)

   Whitehead, A (Ed.)

   Abstract Many species that are extensively studied in the laboratory are less well characterized in their natural habitat, and laboratory strains represent only a small fraction of the variation in a species’ genome. Here we investigate genomic variation in 3 natural North American populations of an agricultural pest and a model insect for many scientific disciplines, the tobacco hornworm (Manduca sexta). We show that hornworms from Arizona, Kansas, and North Carolina are genetically distinct, with Arizona being particularly differentiated from the other 2 populations using Illumina whole-genome resequencing. Peaks of differentiation exist across the genome, but here, we focus inmore »on the most striking regions. In particular, we identify 2 likely segregating inversions found in the Arizona population. One inversion on the Z chromosome may enhance adaptive evolution of the sex chromosome. The larger, 8 Mb inversion on chromosome 12 contains a pseudogene which may be involved in the exploitation of a novel hostplant in Arizona, but functional genetic assays will be required to support this hypothesis. Nevertheless, our results reveal undiscovered natural variation and provide useful genomic data for both pest management and evolutionary genetics of this insect species.« less
4. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field

   https://doi.org/10.1093/jhered/esab019  

   Schweizer, Rena M ; Saarman, Norah ; Ramstad, Kristina M ; Forester, Brenna R ; Kelley, Joanna L ; Hand, Brian K ; Malison, Rachel L ; Ackiss, Amanda S ; Watsa, Mrinalini ; Nelson, Thomas C ; et al ( April 2021 , Journal of Heredity)

   Koepfli, Klaus-Peter (Ed.)

   Abstract A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions.more »Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors—and beyond—to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.« less
5. Drift, selection, and adaptive variation in small populations of a threatened rattlesnake

   https://doi.org/10.1111/mec.15517  

   Ochoa, A. ( June 2020 , Molecular ecology)

   An important goal of conservation genetics is to determine if the viability of small populations has been compromised by genetic drift leading to loss of adaptive variation. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the Eastern Massasauga rattlesnake (Sistrurus catenatus), a threatened snake that exists in small populations. We estimated levels of individual polymorphism in 46 toxin loci and 1467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus andmore »its closest relative, the Western Massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long-term and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that predate the effects of recent drift, and that functional variation in these loci persists despite small short-term effective sizes. We suggest that much of the adaptive variation present in populations may represent an example of “drift debt,” a non-equilibrium state where present-day measures overestimate the amount of functional genetic diversity that will be present in these populations in the future.« less