Low levels of genetic divergence across geographically and linguistically diverse populations from India.
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ABSTRACT:
SUBMITTER: Rosenberg NA
PROVIDER: S-EPMC1713257 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Few genetic differences between human populations conform to the classic model of positive selection, in which a newly arisen mutation rapidly approaches fixation in one lineage, suggesting that adaptation more commonly occurs via moderate changes in standing variation at many loci. Detecting and characterizing this type of complex selection requires integrating individually ambiguous signatures across genomically and geographically extensive data. Here, we develop a novel approach to test the hypothesis that selection has favored modest divergence at particular loci multiple times in independent human populations. We find an excess of SNPs showing non-neutral parallel divergence, enriched for genic and nonsynonymous polymorphisms in genes encompassing diverse and often disease related functions. Repeated parallel evolution in the same direction suggests common selective pressures in disparate habitats. We test our method with extensive coalescent simulations and show that it is robust to a wide range of demographic events. Our results demonstrate phylogenetically orthogonal patterns of local adaptation caused by subtle shifts at many widespread polymorphisms that likely underlie substantial phenotypic diversity.
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Project description:Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST) was lower in comparison to phenotypic variation (P ST), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.
| S-EPMC5762629 | biostudies-literature
Project description:BackgroundHealth care systems have become increasingly more reliant on patients' ability to navigate the digital world. However, little research has been conducted on why some communities are less able or less likely to successfully engage with digital health technologies (DHTs), particularly among culturally and linguistically diverse (CaLD) populations.ObjectiveThis systematic review aimed to determine the barriers to and facilitators of interacting with DHTs from the perspectives of CaLD population groups, including racial or ethnic minority groups, immigrants and refugees, and Indigenous or First Nations people.MethodsA systematic review and thematic synthesis of qualitative studies was conducted. Peer-reviewed literature published between January 2011 and June 2022 was searched across 3 electronic databases. Terms for digital health were combined with terms for cultural or linguistic diversity, ethnic minority groups, or Indigenous and First Nations people and terms related to barriers to accessing digital technologies. A qualitative thematic synthesis was conducted to identify descriptive and analytical themes of barriers to and facilitators of interacting with DHTs. Quality appraisal was performed using the Mixed Methods Appraisal Tool.ResultsOf the 1418 studies identified in the electronic search, a total of 34 (2.4%) were included in this review. Half of the included studies (17/34, 50%) were conducted in the United States. There was considerable variation in terms of the CaLD backgrounds of the participants. In total, 26% (9/34) of the studies focused on Indigenous or First Nations communities, 41% (14/34) were conducted among ethnic minority populations, 15% (5/34) of the studies were conducted among immigrants, and 18% (6/34) were conducted in refugee communities. Of the 34 studies, 21 (62%) described the development or evaluation of a digital health intervention, whereas 13 (38%) studies did not include an intervention but instead focused on elucidating participants' views and behaviors in relation to digital health. From the 34 studies analyzed, 18 descriptive themes were identified, each describing barriers to and facilitators of interacting with DHTs, which were grouped into 7 overarching analytical themes: using technology, design components, language, culture, health and medical, trustworthiness, and interaction with others.ConclusionsThis study identified several analytic and descriptive themes influencing access to and uptake of DHTs among CaLD populations, including Indigenous and First Nations groups. We found that cultural factors affected all identified themes to some degree and that cultural and linguistic perspectives should be considered in the design and delivery of DHTs, with this best served through the inclusion of the target communities at all stages of development. This may improve the potential of DHTs to be more acceptable, appropriate, and accessible to population groups currently at risk of not obtaining the full benefits of digital health.
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Project description:Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference).
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Project description:Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
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Project description:Research Findings:This study aimed to (a) provide an in-depth description of the frequency and type of language interactions that children who are low-income and/or dual language learners (DLL) experience in their classrooms and (b) examine whether differenceFor instance, in a randomized control trial with 461 first grade s exist in children's language experiences based on children's DLL status and level of English proficiency. Using the Language Interaction Snapshot, we observed four focal children in each of 72 early childhood classrooms: one monolingual English-speaking child (i.e., non-DLL), one Spanish-dominant DLL child, and two bilingual Spanish-English DLL children. Findings indicate that both lead and assistant teachers predominantly spoke in English and implemented few evidence-based language practices. Children spoke more often to peers than to teachers. Little variation was noted in the quality of the language environment for children based on their DLL status or language proficiency. Practice:Results suggest clear directions for professional development (PD). PD must include both lead and assistant teachers and should focus on evidence-based language strategies for facilitating children's language development, including how to effectively teach DLLs. Teachers may also benefit from PD that supports use of small group activity and peer strategies.
| S-EPMC6484442 | biostudies-literature
Project description:Ectothermic species are particularly sensitive to changes in temperature and may adapt to changes in thermal environments through evolutionary shifts in thermal physiology or thermoregulatory behaviour. Nevertheless, the heritability of thermal traits, which sets a limit on evolutionary potential, remains largely unexplored. In this study, we captured brown anole lizards (Anolis sagrei) from two populations that occur in contrasting thermal environments. We raised offspring from these populations in a laboratory common garden and compared the shape of their thermal performance curves to test for genetic divergence in thermal physiology. Thermal performance curves differed between populations in a common garden in ways partially consistent with divergent patterns of natural selection experienced by the source populations, implying that they had evolved in response to selection. Next, we estimated the heritability of thermal performance curves and of several traits related to thermoregulatory behaviour. We did not detect significant heritability in most components of the thermal performance curve or in several aspects of thermoregulatory behaviour, suggesting that contemporary selection is unlikely to result in rapid evolution. Our results indicate that the response to selection may be slow in the brown anole and that evolutionary change is unlikely to keep pace with current rates of environmental change.
| S-EPMC5966615 | biostudies-literature
Project description:PURPOSE:To determine the prevalence of cataract and its association with sun exposure and other environmental risk factors in three different geographically diverse populations of India. DESIGN:Population based cross sectional study during 2010-2016. PARTICIPANTS:People aged ? 40 years residing in randomly sampled villages were enumerated (12021) and 9735 (81%) underwent ophthalmic evaluation from plains, hilly and coastal regions (3595, 3231, 2909 respectively). METHODS:A detailed questionnaire-based interview about outdoor activity in present, past and remote past, usage of sun protective measures, exposure to smoke, and detailed ophthalmic examination including assessment of uncorrected and best corrected visual acuity, measurement of intraocular pressure, slit lamp examination, lens opacities categorization using LOCS III and posterior segment evaluation was done. Lifetime effective sun exposure was calculated using Melbourne formula and expressed as quintiles. These were supplemented with physical environmental measurements. MAIN OUTCOME MEASURES:Lifetime sun exposure hours, smoking, indoor kitchen smoke exposure and their association with cataract and subtypes. Prevalence of cataract calculated based on lens opacities or evidence of cataract surgery. RESULTS:Cataract was identified in 3231 (33.3%) participants. Prevalence of cataract in males (32.3%) and females (34.1%) was similar. Nuclear cataract was the commonest sub-type identified in 94.7% of affected eyes. Sun exposure had a significant association with cataract with odds ratio (OR) increasing from 1.6 (95% Confidence Intervals [CI]: 1.4, 1.9) in 3rd quintile, to 2.6 (CI: 2.2, 3.1) in 4th quintile and 9.4 (CI: 7.9, 11.2) in 5th quintile (p<0.0001). Cataract also showed a significant association with smoking (OR: 1.4, CI: 1.2, 1.6) and indoor kitchen smoke exposure (OR: 1.2, CI: 1.0-1.4). Nuclear cataract showed a positive association with increasing sun exposure in 3rd (? coefficient 0.5, CI:0.2-0.7), 4th (?: 0.9, CI: 0.7-1.1) and 5th (?: 2.1, CI:1.8-2.4) quintiles of sun exposure, smoking (?: 0.4, CI: 0.2-0.6) and indoor kitchen smoke exposure (?: 0.3, CI: 01-0.5) while cortical cataract showed a positive association with sun exposure only in 5th quintile (?: 2.6, CI:1.0-4.2). Posterior subcapsular cataract was not associated with any of the risk factors. CONCLUSION:Cataract is associated with increasing level of sun exposure, smoking and exposure to indoor kitchen smoke.
| S-EPMC6977762 | biostudies-literature
Project description:Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed. Population genetic analyses revealed limited genetic differentiation among the Tibetan pig populations. Evidence from deleterious variant analysis indicated that population-specific deleterious variants were the major component of all mutational loci. Contribution to the meta-population was largest in the TT (Qinghai-Tibet Plateau) population, based on gene diversity or allelic diversity. Selective sweep analysis revealed numerous genes, including RXFP1, FZD1, OR1F1, TBX19, MSTN, ESR1, MC1R, HIF3A, and EGLN2 which are involved in lung development, hard palate development, coat color, hormone metabolism, facial appearance, and perception of smell. These findings increase our understanding of the origins and domestication of the Tibetan pig, and help optimize the strategy for their conservation.
| S-EPMC7460208 | biostudies-literature
Project description:We genotyped 45 new samples from 4 populations of Northwest India and combined it with previously published data to characterize the population structure of modern Northwest Indian populations in the context of their geographic neighbors across South Asia and West Eurasia.
2018-12-05 | GSE119653 | GEO