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Results for “genetics”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2022

Long-term population decline of a genetically homogenous continental-wide top Arctic predator

Genetic analysis can provide valuable information for conservation programs by unraveling the demographic trajectory of populations, by estimating effective population size, or by inferring genetic differentiation between populations. Here, we investigated the genetic differentiation within the Snowy Owl (Bubo scandiacus), a species identified as vulnerable by the IUCN, to (i) quantify connectivity among wintering areas, (ii) to evaluate current genetic diversity and effective population size and (iii) to infer changes in the historical effective population size changes from the last millennia to the recent past. The Snowy Owl, a highly mobile top predator, breeds across the Arctic tundra which is a region especially sensitive to current climate change. Using SNP-based analyses on Snowy Owls sampled across the North American nonbreeding range, we found an absence of genetic differentiation among individuals located up to 4,650 km apart. Our results suggest high genetic intermixing and effective dispersal at the continental scale despite documented philopatry to nonbreeding sites in winter. Reconstructing the population demographic indicated that North American Snowy Owls have been steadily declining since the Last Glacial Maximum ca 20,000 years ago and concurrently with global increases in temperature. Conservation programs should now consider North American Snowy Owls as a single, genetically homogenous continental-wide population which is most likely sensitive to the long-term global warming occurring since the Last Glacial Maximum.

ecology↗

bioRxiv2022

Population genomics provide insights into the global genetic structure of Colletotrichum graminicola, the causal agent of maize anthracnose

BackgroundColletotrichum graminicola, the causal agent of maize anthracnose, is an important crop disease worldwide. Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. The genus Colletotrichum is largely recognized as asexual, but several species have been reported to have a sexual cycle. Here, we employed a population genomics approach to investigate the genetic diversity and reproductive biology of C. graminicola isolates infecting maize. We sequenced 108 isolates of C. graminicola collected in 14 countries using restriction site-associated DNA sequencing (RAD-Seq) and whole-genome sequencing (WGS). ResultsClustering analyses based on single-nucleotide polymorphisms showed populational differentiation at a global scale, with three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen, and geographic subdivision. Distinct levels of genetic diversity were observed between these clades, suggesting different evolutionary histories. Intra and inter-continental migration was predicted between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality and evidence of genetic recombination were detected from the analysis of linkage disequilibrium and the pairwise homoplasy index (PHI) test for clonality. We show evidence that even if rare (possibly due to losses of sex and meiosis-associated genes) C. graminicola can undergo sexual recombination based on lab assays and genomic analyses. ConclusionsOur results support hypotheses of intra and intercontinental pathogen migration and genetic recombination with great impact on C. graminicola population structure.

genomics↗

bioRxiv2022

Nucleotide resolution genetic mapping in pigs by publicly accessible whole genome imputation

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in the genetic improvement animals. Despite recent advances in high throughput genotyping technologies, resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2,259 whole genome sequenced animals representing 44 pig breeds. We optimized the imputation procedure to achieve an average concordance rate in excess of 97%, non-reference concordance rate 91%, and r2 0.89. We demonstrated that genotype imputation using this resource can dramatically improve resolution of genetic mapping. Finally, we developed a public web server (swimgeno.org) to allow the pig genetics community to fully utilize this resource. We expect the resource and server to significantly facilitate genetic mapping and accelerate genetic improvement in pigs.

genomics↗

bioRxiv2022

Genetic, vocal, and body size divergence across the Northern Peruvian Low supports two species within the Masked Flowerpiercer (Diglossa cyanea)

Populations that become genetically isolated by geographical barriers may express phenotypic divergence more strongly in some traits than in others. Even when genetic differentiation among isolated populations accumulates at a rapid rate, this may not be reflected in phenotypic differentiation. This decoupling of trait divergence from genetic divergence has been found in multiple Andean bird lineages that occupy latitudinally long, linear ranges that are fragmented by ecological and topographic barriers. One of these montane birds is Diglossa cyanea (Thraupidae; Masked Flowerpiercer), a species with a distribution bisected by valleys and lowlands. Across these dispersal barriers one finds subspecies that differ only in subtle but diagnostic phenotypic differences. We evaluated genetic and phenotypic divergence throughout its distribution and found support for two distinct lineages sharply separated by the Maranon River valley at the Northern Peruvian Low (NPL). Specifically, we found that the two populations from the opposite sides of the NPL show deep divergence in mitochondrial DNA (mtDNA; [~]6.7% uncorrected p distance, n = 122), in song structure (exclusive final notes in southern populations, n = 88), and in wing length (longer wings in the southern population, n = 364). No genetic variation or song structure was observed within the large range of the southern group (from the NPL to central Bolivia) or within all northern populations (from the NPL to Venezuela). Moreover, these two lineages are possibly paraphyletic with respect to D. caerulescens (Bluish Flowerpiercer). Our results suggest that the southern taxon, D. c. melanopis, should be recognized as a species-level taxon, distinct from a redefined D. cyanea. We highlight the need to continue amassing complementary suites of datasets from field observations and experiments, laboratory analyses, and collection-based assessments, to better characterize the evolutionary history and taxonomic diversity of Neotropical montane birds. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/492535v2_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@199ddfborg.highwire.dtl.DTLVardef@bc8fb0org.highwire.dtl.DTLVardef@17d7da1org.highwire.dtl.DTLVardef@1c2d9e5_HPS_FORMAT_FIGEXP M_FIG C_FIG LAY SUMMARY We analyzed variation in genetics, songs, and body size among populations of a bird species of the Andean mountains (Masked Flowerpiercer) that shows relatively little plumage variation across its 3800-km long distribution from northern Venezuela to central Bolivia. We found that the Masked Flowerpiercer consists of two divergent populations separated by a deep geographic depression known as the Northern Peruvian Low (NPL) The degree of genetic divergence between them (in terms of mtDNA) is as great as between either of them and another species, the Bluish Flowerpiercer. The two populations also have distinct songs, with the song of the southern group ending with clear whistles that are completely absent in the northern group. The southern group also tend to have longer wings than do populations north of the NPL. The southern population should be treated as a separate species, Diglossa melanopis.

evolutionary biology↗

bioRxiv2022

Genome-wide identification of microsatellite markers and their application in genetic studies of wolfberry (Lycium barbarum)

The wolfberry (Lycium barbarum) has been an important traditional Chinese food and medicine for hundreds of years. However, few microsatellite markers have been developed for assessing the genetic diversity and genetic linkage maps among Lycium species in genetic research. In the present study, a total of 397,558 microsatellite loci were identified from whole wolfberry genome sequences with an overall density of 212.1 Mb/SSRs. Dinucleotide microsatellites were the most abundant type, representing 58.26% of the total microsatellite loci, followed by tri-, penta-, hexa-, and tetranucleotide. The AT motifs were the most abundant of all nucleotide repeat motifs, accounting for 44.52%. A set of 600 primer pairs were synthesized and preliminarily screened among four wolfberry accessions. Of these, 277 primer pairs were selected as polymorphic markers. In total, 22 highly polymorphic SSR markers were selected for the characterization of genetic diversity among 37 wolfberry accessions. A total of 323 alleles were detected with an average of 14.7 alleles per marker. The polymorphic information content (PIC) values ranged from 0.612 to 0.911. The dendrogram revealed that the phylogenetic relationships among these wolfberry accessions were consistent with their genetic background. Thus, the large number of genome-wide microsatellite markers developed from the wolfberry genome provides a valuable resource for genetic diversity, genetic map construction, quantitative trait locus (QTL) mapping, and marker-assisted selection breeding in Lycium species.

molecular biology↗

bioRxiv2022

Host genetic variants regulates CCR5 expression on immune cells: a study in people living with HIV and healthy controls

C-C chemokine receptor 5 (CCR5) is the main HIV co-receptor affecting susceptibility and disease course. Quantitative trait loci (QTL) mapping analysis was performed to assess genetic variants associated with CCR5 expression on circulating immune cells in 209 PLHIV using ART and 304 healthy controls, all of Western European ancestry. The proportions of CCR5 positive cells and CCR5 mean fluorescence intensity (MFI) were assessed by flow cytometry in monocytes and CD4+ and CD8+ T cell subsets using flow cytometry. We identified the rs60939770, which is an intergenic variant in cis-region to CCR5 gene not in linkage disequilibrium with CCR5d32, related to the proportion of CCR5+ memory T regulatory cells, both in PLHIV and healthy controls. Two genome-wide significant loci, in linkage equilibrium with CCR5d32, were found to be associated with CCR5 MFI of multiple subsets of mostly differentiated memory T cells in both groups. The expression of nearby chemokines receptors (CCR1, CCR2, CCR3, CCRL2), existing in the same the same topologically associating domain, were also influenced by these genetic variants. Furthermore, we show the genetic variants which modulate CCR5 surface expression affect the production of other inflammatory mediators, including monocyte- and lymphocyte-derived cytokines as well as CCL4 and IL-8. Our data indicate that the genetic regulation of CCR5 expression is cell-specific and affects the production of various inflammatory mediators. Author SummaryCCR5 plays a important role in the acquisition of HIV and it is associated to immune activation in people living with HIV (PLHIV). Using samples of cohorts composed of healthy individuals and PLHIV, we sought to map genomic regions that influence CCR5 expression on monocytes and subsets of CD4+ and CD8+ cells. We identified distinct genetic variants that are associated with CCR5 cell proportions or mean fluorescence intensity in subpopulations of T cells with memory functions in both healthy and PLHIV. The genetic variants also influenced the expression of other nearby chemokine receptors and the production of inflammatory mediators. Thus, we demonstrated that the genetic regulation of CCR5 expression is cell-type specific and may impact HIV susceptibility and disease progression.

systems biology↗

bioRxiv2022

Network analysis reveals the molecular bases of statin pleiotropy that vary with genetic background

Many approved drugs are pleiotropic, for example statins, whose main cholesterol lowering activity is complemented by anticancer and pro-diabetogenic mechanisms involving poorly characterized genetic interaction networks. We investigated these using the Saccharomyces cerevisiae genetic model where most genetic interactions known are limited to the statin-sensitive S288C genetic background. We therefore broadened our approach by investigating gene interactions to include two statin-resistant UWOPS87-2421 and Y55 genetic backgrounds. Networks were functionally focused by selection of HMG1 and BTS1 mevalonate pathway genes for detecting genetic interactions. Networks, multi-layered by genetic background, were analysed for modifying key genes using network centrality (degree, betweenness, closeness), pathway enrichment, functional community modules and gene ontology. Statin treatment induces the unfolded protein response and we found modifying genes related to dysregulated endocytosis and autophagic cell death. To translate results to human cells, human orthologues were searched for other drugs targets, thus identifying candidates for synergistic anticancer bioactivity.

systems biology↗

bioRxiv2022

The genetics of cortical organisation and development: a study of 2,347 neuroimaging phenotypes

Our understanding of the genetic architecture of the human cerebral cortex is limited both in terms of the diversity of brain structural phenotypes and the anatomical granularity of their associations with genetic variants. Here, we conducted genome-wide association meta-analysis of 13 structural and diffusion magnetic resonance imaging derived cortical phenotypes, measured globally and at 180 bilaterally averaged regions in 36,843 individuals from the UK Biobank and the ABCD cohorts. These phenotypes include cortical thickness, surface area, grey matter volume, and measures of folding, neurite density, and water diffusion. We identified 4,349 experiment-wide significant loci associated with global and regional phenotypes. Multiple lines of analyses identified four genetic latent structures and causal relationships between surface area and some measures of cortical folding. These latent structures partly relate to different underlying gene expression trajectories during development and are enriched for different cell types. We also identified differential enrichment for neurodevelopmental and constrained genes and demonstrate that common genetic variants associated with surface area and volume specifically are associated with cephalic disorders. Finally, we identified complex inter-phenotype and inter-regional genetic relationships among the 13 phenotypes which reflect developmental differences among them. These analyses help refine the role of common genetic variants in human cortical development and organisation. One sentence summaryGWAS of 2,347 neuroimaging phenotypes shed light on the global and regional genetic organisation of the cortex, underlying cellular and developmental processes, and links to neurodevelopmental and cephalic disorders.

neuroscience↗

bioRxiv2022

Subtle cultural boundaries reinforce genetic structure in England

Genes and languages both contain signatures of human history. Genetics and culture have each been shown to track population movements and demographic history. Complicating this picture, cultural traits may themselves influence the ways in which people interact with one another. For example, cultural differences can produce barriers to gene flow if they cause groups of people to differentiate themselves from one another. However, the degree of cultural difference necessary and the magnitude of these effects on gene flow remain unknown. In particular, language differences may limit population mixing, and we focus on whether subtle, dialect-level linguistic differences have influenced genetic population structure, likely by affecting mating preferences. Here, we analyze spatially dense linguistic and genetic data to examine whether the intensity of differences between and within dialects in England are associated with high genetic rates of change. We find that genetic variation and dialect markers have similar spatial distributions on a country-wide scale, and become less distinct as the scale of smaller administrative units such as counties. This covariation, combined with the absence of geographic barriers that could coordinate cultural and genetic differentiation, suggests that some dialect-level linguistic boundaries have influenced the genetic population structure in England.

evolutionary biology↗

bioRxiv2022

Interplay between demography and selection: a forward model illuminates the temporal genetic signatures of rapid adaptation in plant pathogens

Pathogen species are experiencing strong joint demographic and selective events, especially when they adapt to a new host, for example through overcoming plant resistance. Stochasticity in the founding event and the associated demographic variations hinder our understanding of the expected evolutionary trajectories and the genetic structure emerging at both neutral and selected loci. What would be the typical genetic signatures of such a rapid adaptation event is not elucidated. Here, we build a demogenetic model to monitor pathogen population dynamics and genetic evolution on two host compartments (susceptible and resistant). We design our model to fit two plant pathogen life cycles, with and without host alternation. Our aim is to draw a typology of eco-evolutionary dynamics. Using time-series clustering, we identify three main scenarios: 1) small variations in the pathogen population size and small changes in genetic structure, 2) a strong founder event on the resistant host that in turn leads to the emergence of genetic structure on the susceptible host, and 3) evolutionary rescue that results in a strong founder event on the resistant host, preceded by a bottleneck on the susceptible host. We pinpoint differences between life cycles with notably more evolutionary rescue with host alternation. Beyond the selective event itself, the demographic trajectory imposes specific changes in the genetic structure of the pathogen population. Most of these genetic changes are transient, with a signature of resistance overcoming that vanishes within a few years only. Considering time-series is therefore of utmost importance to accurately decipher pathogen evolution.

evolutionary biology↗

bioRxiv2022

On the genetic consequences of habitat contraction: edge effects and habitat loss

Natural climate change and recent anthropogenic activities have largely contributed to habitat loss and fragmentation across the world, leading to 70% of worldwide remaining forests to be within 1 km of forests edges (Haddad et al., 2015). Ecological studies have shown that edge-effect influences ecological communities, species richness and abundance across many taxa, contributing to worldwide decline in biodiversity. Since edge-effect reduces species abundance and connectivity, it is also expected to negatively influence species genetic variation. In fact, previous theoretical studies had showed that populations closer to the edges of a finite stepping-stone model tends to have shorter coalescence times, and therefore, lower genetic diversity, than central populations. However, predicting the impact of edge effect on local genetic diversity remains challenging in realistic and more complex habitat fragments, where the additive effect of multiple edges is expected to take place. In the present study we explore the genetic consequence of habitat loss at the scale of a habitat fragment (patch-scale), looking at the interplay between patch-size and edge-effect on spatial genetic diversity. We propose a statistical approach to estimate edge-impacted effective population size from habitat cover information and use this measure to predict spatial genetic diversity in both equilibrium and non-equilibrium populations. We address these questions using spatially-explicit simulations and propose a spatially-explicit analytical framework able to model spatio-temporal changes in genetic diversity due to edge-effect and habitat loss.

evolutionary biology↗

bioRxiv2022

inMTSCCA: An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omics Brain Imaging Genetics

Identifying genetic risk factors for Alzheimers disease (AD) is an important research topic. To date, different endophenotypes such as imaging-derived endophenotypes and proteomic expression-derived endophenotypes have shown the great value in uncovering risk genes compared to case-control studies. Biologically, a co-varying pattern of these different omics derived endophenotypes could result from the shared genetic basis. However, existing methods mainly focus on the effect of endophenotypes, and that of cross-endophenotype associations remains largely unexploited. In this paper, we used both endophenotypes and their cross-associations of multi-omics to identify genetic risk factors, and proposed two integrated multi-task sparse canonical correlation analysis (MTSCCA) methods, i.e., pairwise endophenotype correlation guided MTSCCA (pcMTSCCA) and high-order endophenotype correlation guided MTSCCA (hocMTSCCA). pcMTSCCA employed pairwise correlations between MRI-derived, plasma-derived, and cerebrospinal fluid (CSF) derived endophenotypes as an additional penalty. hocMTSCCA used high-order correlations among these multi-omics for regularization. To figure out genetic risk factors at individual and group levels, as well as altered endophenotypic markers, we introduced sparsity-inducing penalties in both models. We compared pcMTSCCA and hocMTSCCA with three related methods on both simulation data and real neuroimaging, proteomic analytes, and genetic data. The results showed that our methods obtained better or comparable canonical correlation coefficients (CCCs) and feature subsets than benchmarks. Most importantly, the identified genetic loci and heterogeneous endophenotypic markers showed high relevance. Therefore, jointly using multi-omics endophenotypes and their cross-endophenotype associations are promising to reveal genetic risk factors, and both methods are qualified for this complicated task. The source code and manual of inMTSCCA is available at: https://ngdc.cncb.ac.cn/biocode/tools/BT007330.

bioinformatics↗

bioRxiv2022

Integrative single cell multiomics analysis of human retina indicates a role for hierarchical transcription factors collaboration in genetic effects on gene regulation

BackgroundSystematic characterization of how genetic variation modulates gene regulation in a cell type specific context is essential for understanding complex traits. To address this question, we profiled gene expression and chromatin state of cells from healthy retinae of 20 human donors with a single-cell multiomics approach, and performed genomic sequencing. ResultsWe mapped single-cell eQTL (sc-eQTLs), single-cell caQTL (sc-caQTL), single-cell allelic specific chromatin accessibility (sc-ASCA) and single-cell allelic specific expression (sc-ASE) in major retinal cell types. By integrating these results, we identified and characterized regulatory elements and genetic variants effective on gene regulation in individual cell types. Most of the sc-eQTLs and sc-caQTLs identified show cell type specific effects, while the cis-elements containing the genetic variants with cell type specific effects tend to be accessible in multiple cell types. Furthermore, the transcription factors with binding sites perturbed by genetic variants tend to have higher expression in the cell types, where the variants have effect, than the cell types where the variants do not have effect. Finally, we identified the enriched cell types, candidate causal variants and genes, and cell type specific regulatory mechanism underlying GWAS loci. ConclusionsOverall, genetic effects on gene regulation are highly context dependent. Our results suggest that among cell types sharing a similar lineage, cell type dependent genetic effect is primarily driven by trans-factors rather than cell type specific chromatin state of cis-elements. Our findings indicate a role for hierarchical transcription factors collaboration in cell type specific effects of genetic variants on gene regulation.

genomics↗

bioRxiv2022

Public perceptions, knowledge and factors associated with the acceptability of genetically modified foods in Kampala city, Uganda

Food is a basic human need important for the survival of all human beings. The rapidly growing world population puts pressure on food sources, inviting the need to devise mechanisms to sustain it. Biotechnology has developed important measures for improving plants and livestock as a remedy for food security with aim to achieve the Sustainable Development goal two (2). Globally, the adoption and use of genetically modified foods (GMFs) has been controversial as it is in Uganda today due to concerns related to the risk uncertainties. This study was therefore conducted to assess the public perceptions, knowledge and factors that influence the acceptability of genetically modified foods in Kampala City. This was a cross sectional quantitative study that involved one hundred and ninety-eight participants. The data were collected using a survey tool and summarized using descriptive and linear regression analysis. The findings of this study showed that almost two-thirds of participants (129/198, 65%) had some basic knowledge on genetically modified foods. About 45.3% (90/198) of the participants perceived genetically modified foods as being unsafe for human consumption. Eighty-eight participants (44.3%) perceived them as being associated with major human health and environmental safety concerns. The acceptability of these foods was significantly associated with gender, education level, nutritional value and health effects. Female participants were more likely to accept genetically modified foods (OR.4.84 95% CI: 1.37 - 7.68). Those who perceived genetically modified foods as being of high nutrition value were more likely to accept them (OR. 3.07, 95% CI: 1.27 - 7.37). The public is predominantly aware of genetical modified foods since a big proportion had basic knowledge about them although with a lot of misinformation. People with a higher education level had positive perceptions on the use of these foods hence a need to educate the public to dispel misinformation that influences their acceptability

scientific communication and education↗

bioRxiv2022

Phase-based genetic logic circuits

Bio-computation is the implementation of computational operations using biological substrates, such as cells engineered with synthetic genetic circuits. These genetic circuits can be composed of DNA parts with specific functions, such as promoters that initiate transcription, ribosome binding sites that initiate translation, and coding sequences that are translated into proteins. Compositions of such parts can encode genetic circuits in which the proteins produced by genes regulate each other in different ways. The expression level of each gene may be considered as a signal which may be high or low, encoding binary logic, and the combinations of genes can then encode logic circuits. This is equivalent to the level-based logic used in modern electronic computers in which the voltage forms the logical high or low states. A different approach to binary logic is to encode the high and low states in the phase of an oscillating signal. In this approach a signal in phase with a reference represents high, and a signal antiphase with the reference represents the logical low state. We present here designs and models for phase-based genetic NOT, OR, AND, MAJORITY and complementary MAJORITY gates, which together form multiple complete logical sets. We derive analytical expressions for the optimal model parameters for circuit function. Our simulation results suggest that this approach to genetic logic is feasible and could be less sensitive to gate input-output mismatch than level-based genetic logic. To demonstrate the scaleability of phase-based genetic logic, we used our complementary MAJORITY and NOT gates to design and simulate a fully functional 4-bit ripple adder circuit, and showed that it was robust to molecular noise.

synthetic biology↗

bioRxiv2023

Exploring the genetic diversity of the Japanese Population: Insights from a Large-Scale Whole Genome Sequencing Analysis

The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. Through high-coverage whole-genome sequencing (WGS) analysis of 9,850 samples from the National Center Biobank Network, we analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). Low frequency detrimental or pathogenic variants were found in these populations. The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Genes related to alcohol and lipid metabolism were affected by positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to be affected by positive natural selection; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production. Author summaryThe human population in the Japanese archipelago exhibits significant genetic diversity, with the Ryukyu Islands and other parts of the archipelago (Hondo) having undergone distinct evolutionary paths that have contributed to the genetic divergence of the populations in each region. In this study, whole genome sequencing of healthy individuals from national research hospital biobanks was utilized to investigate the genetic diversity of the Japanese population. Haplotypes were inferred from the genomic data, and a thorough population genetic analysis was conducted. The results indicated not only genetic differentiation between Hondo and the Ryukyu Islands, but also marked differences in past population size. In addition, gene genealogies were inferred from the haplotypes, and the patterns were scrutinized for evidence of natural selection. This analysis revealed unique traces of natural selection in East Asian populations, many of which were believed to be linked to dietary changes brought about by agriculture and food production.

genomics↗

bioRxiv2023

Transcriptomic analysis of diverse organisms reveals the rareness of genetic assimilation in environmental adaptations

Genetic assimilation is the evolutionary process by which an environmentally induced phenotype becomes genetically encoded and constitutive. Genetic assimilation has been proposed as the concluding step in the plasticity-first model of environmental adaptation and has been observed in multiple species, but its prevalence has not been systematically investigated. By analyzing transcriptomic data collected upon reciprocal transplant, we address this question in the experimental evolution, domestication, or natural evolution of a bacterial, a fungal, a plant, and four animal species. We find that genetic assimilation of environment-induced gene expression is the exception rather than the rule and that substantially more genes retain than lose their expression plasticity upon organismal adaptations to new environments. The probability of genetic assimilation varies among genes and decreases with the number of transcription factors controlling the gene and the expression level of the gene, supporting the hypothesis that genetic assimilation results primarily from passive losses of gene regulations that are not mutationally robust. Therefore, at the level of gene expression, our findings argue against the purported importance of genetic assimilation to environmental adaptation.

evolutionary biology↗

bioRxiv2023

Conserving genetic diversity during climate change:Niche marginality and discrepant monitoring capacity in Europe

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. Genetic diversity has been largely neglected in biodiversity monitoring, and when addressed is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. Genetic monitoring supports the conservation and management of fisheries, game, and threatened populations. It also can contribute to the assessment of predicted and realized impacts of climate change, and their management. We report the first accounting of genetic monitoring efforts among countries in Europe (their genetic monitoring capacity, GMC) to determine where GMC suggests the combination of national infrastructure, political support and resources for continued and expanded monitoring. Overlaying GMC with areas where species ranges approach current and future climate niche limits (i.e., niche marginality) helps identify whether GMC coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area extent, financial resources, and conservation policy influence GMC, high values of which inconsistently match joint species patterns of climate niche marginality. Populations at niche margins likely hold genetic diversity that is important to adaptation to changing climate, and our results illuminate the need in Europe for expanded genetic monitoring across the climate gradients occupied by species, a need arguably greatest in southeastern European countries.

ecology↗