Neutral Polymorphisms Research Articles

Genetic and Phenotypic Divergence in a Dung Beetle 50 Years After Its Introduction to Australia.

Species translocations are increasingly being used in conservation and for biological control. The success of a translocation can be strongly influenced by the evolutionary processes occurring during the early phase of the introduction and the subsequent spread to new regions. In this study, morphological variation and population genetic structure were assessed in the African dung beetle Digitonthophagus gazella, a species that was intentionally introduced to Australia for biological control in 1968 and subsequently spread widely across the northern part of the continent. A dataset based on 1594 neutral single nucleotide polymorphism (SNP) loci that were genotyped in 187 individuals from 12 sites revealed significant genetic divergences between sites (global F ST = 0.118) and provides evidence of restricted gene flow among established populations at small to moderate spatial scales (74-500 km). Geometric morphometric analyses revealed significant divergence among populations in the shape of the foretibia, a trait ecologically important for tunnelling in soil and dung. Moreover, phenotypic divergence in this trait for both sexes was significantly higher than genetic differentiation at selectively neutral loci (P ST > F ST), suggesting that directional selection is contributing to the phenotypic divergences among populations. Our study shows how population structure can establish quickly in an introduced species and highlights the importance of considering local adaptation when performing translocations on established populations.

A comprehensive guide to bioinformatics tools and databases

The interest in the functional aspects of the genome has increased eventually with the expansion of genomic databases. In this review, various genetic alterations within the genome, such as Single Nucleotide Polymorphisms (SNPs), disease-associated mutations, neutral polymorphisms, and small insertions or deletions (INDELs), have been identified and characterized. These polymorphisms, particularly SNPs, have become widely employed in genetic analyses, serving as valuable molecular markers. They are applied across diverse genetic studies, including the reconstruction of haplotypes. In addition to experimental methods for investigating specific genetic variants, there has been a significant surge in bioinformatics research over the past decade, aimed at the molecular consequences of these genetic alterations. Haplotypes, which represent various alleles of a gene, can be reconstructed not only for entire chromosomes but also for specific genes, utilizing the information derived from SNPs. The computational approach to SNP and haplotype discovery has gained prominence due to the continuous expansion of sequence data within public databases. This growth enables more precise identification of SNPs. This article aims to introduce easily accessible and practical online tools for researchers. In summary, SNP and haplotype identification tools are indispensable in bioinformatics for studying genetic variation, population genetics, disease associations, and personalized medicine. They provide valuable insights into the genetic underpinnings of various traits and diseases, helping advance our understanding of genetics and its applications in healthcare.

Allele-Selective Thiomorpholino Antisense Oligonucleotides as a Therapeutic Approach for Fused-in-Sarcoma Amyotrophic Lateral Sclerosis.

Pathogenic variations in the fused in sarcoma (FUS) gene are associated with rare and aggressive forms of amyotrophic lateral sclerosis (ALS). As FUS-ALS is a dominant disease, a targeted, allele-selective approach to FUS knockdown is most suitable. Antisense oligonucleotides (AOs) are a promising therapeutic platform for treating such diseases. In this study, we have explored the potential for allele-selective knockdown of FUS. Gapmer-type AOs targeted to two common neutral polymorphisms in FUS were designed and evaluated in human fibroblasts. AOs had either methoxyethyl (MOE) or thiomorpholino (TMO) modifications. We found that the TMO modification improved allele selectivity and efficacy for the lead sequences when compared to the MOE counterparts. After TMO-modified gapmer knockdown of the target allele, up to 93% of FUS transcripts detected were from the non-target allele. Compared to MOE-modified AOs, the TMO-modified AOs also demonstrated reduced formation of structured nuclear inclusions and SFPQ aggregation that can be triggered by phosphorothioate-containing AOs. How overall length and gap length of the TMO-modified AOs affected allele selectivity, efficiency and off-target gene knockdown was also evaluated. We have shown that allele-selective knockdown of FUS may be a viable therapeutic strategy for treating FUS-ALS and demonstrated the benefits of the TMO modification for allele-selective applications.

Allelic Entropy and Times until Loss or Fixation of Neutral Polymorphisms.

In the diffusion approximation of the neutral Wright-Fisher model, the expected time until fixation or loss of a neutral allele is proportional to the initial entropy of the distribution of the allele in the population. No explanation is known for this coincidence. In this paper, we show that the rate of entropy dissipation is proportional to the number of segregating alleles. Since the final fixed state has zero entropy, the expected lifetime of segregating alleles is proportional to the initial entropy in the system. We show that classical formulae on the average time to loss of segregating alleles and the expected time to fixation of the last segregating allele stem from these properties of the diffusion process. We also extend our results to the case of population size changing in time. The dissipation of heterozygosity and entropy shows that superlinear population growth leads to infinite expected fixation times, i.e., neutral alleles in fast-growing populations could segregate forever without ever becoming fixed or disappearing by genetic drift.

Adaptive and Neutral Polymorphisms of the Onne-DAB Gene from the Major Histocompatibility Complex (MHC) in Sockeye Salmon Populations on the Asian Range

The variability of an MHC complex gene in sockeye salmon populations throughout the Asian range was studied to identify “footprints” indicative of pathogen-mediated selection and neutral demographic processes that have influenced these populations in both the recent and distant past. Genotype frequencies of a haplotype block consisting of two SNP loci (One_MHC2_109 and One_MHC2_190v2) in the Onne-DAB gene encoding the β-chain of the MHC class II molecule as well as allelic frequencies of 29 putative neutral SNPs have been traced in 27 sockeye salmon populations in the Asian Pacific coast. Differently directed clines of genetic diversity at the MHC2 loci were observed in sockeye salmon populations inhabiting the Sea of Okhotsk and Pacific coasts of the Kamchatka Peninsula. The formation of these clines can be attributed to a combination of historical processes associated with the colonization of the Asian range and the latitudinal gradient of abiotic and biotic factors influencing the variability of the Onne-DAB gene. In continental populations of sockeye salmon, balancing selection was not intense enough to conceal the impacts of demographic and historical processes associated with the fragmentation of the area in the late Pleistocene. In contrast, in island populations, balancing selection effectively maintained the diversity of the Onne-DAB gene despite a significant decrease in polymorphism observed in neutral regions of the genome.

Multiple Introductions and Distinct Genetic Groups of Canada Goldenrod (Solidago canadensis) in China Revealed by Genomic Single-Nucleotide Polymorphisms.

Despite numerous studies reported in the context of ecology, the introduction history of the infamous invasive plant Canada goldenrod (Solidago canadensis L.) remains elusive. In the present study, we explored the sources and the number of introduction events of this species from its native areas into China. Using the genotyping-by-sequencing approach, we identified 34,035 selectively neutral single-nucleotide polymorphism (SNP) markers to infer the evolutionary trajectories of 77 S. canadensis individuals. Both the principal component analysis and the ADMIXTURE analysis revealed two genetic groups that are sympatric to each other in China and suggested the absence of genetic admixtures. The phylogenetic analysis indicated three feasible introduction routes and multiple introduction events of Canada goldenrod into China. Specifically, the one from the USA directly into China, the other from the USA into China through Japan, and the third from the USA into China through Europe. Based on the site frequency spectrum of these identified SNPs, we inferred strong bottleneck events for both genetic groups, and that the multiple introductions did not rescue the decline of genetic diversity. To conclude, multiple introduction events, genetic bottlenecks, and potential human-mediated spread characterize the introduction history of Canada goldenrod in China. The present study harnesses the power of SNP data in deciphering the evolutionary trajectory of invasive plants and paves the way for future studies concerning the invasion mechanism of Canada goldenrod.

Species boundaries and conservation implications of Cinnamomum japonicum, an endangered plant in China

AbstractClear species boundaries are crucial for plans and actions on biodiversity conservation. However, morphological similarities among allied species can result in taxonomic difficulties, thus impeding conservation efforts. In China, Cinnamomum japonicum Siebold is a well‐known endangered plant, yet suffers from longstanding taxonomic issues. Here, we explicitly evaluate whether C. japonicum, C. chenii, and C. chekiangense are the same phylogenetic species on the basis of a multi‐individual sampling strategy. We identified three sets of low‐copy orthologous genes from 19 Lauraceae taxa for phylogenetic inferences. Both the concatenation and coalescent‐based phylogenies supported that C. chenii individuals were embedded in the C. japonicum clade, indicating these two taxa are conspecific. Meanwhile, C. chekiangense accessions formed a monophyly which was not sister to C. japonicum. This result, together with the morphological differences that the leaves of C. japonicum are glabrous with a faveolate pattern of venation while those of C. chekiangense have trichomes and inevident lateral veins, led us to consider both as two distinct species. Based on 17 728 neutral single nucleotide polymorphisms (SNPs), the ADMIXTURE analysis suggested that the Chinese C. japonicum populations in Zhoushan Archipelago (=C. chenii) were genetically differentiated from the Japanese and Korean ones. Furthermore, ecological niche modeling predicted that the present distribution area of Chinese C. japonicum is likely to be unsuitable under global warming scenarios. Together with its limited distribution and genetic uniqueness, we recommend that Chinese C. japonicum deserves conservation priorities.

Diversity and enrichment of breeding material for resilience in European forests

Delivering material selected for breeding purposes into the wild in the context of sustainable forest management might reduce the levels of genetic diversity of future forests in comparison to that of natural populations. Another consequence might be a reduction of their resilience under uncertain future climatic and socio-economic conditions if these new populations lack adaptability. Despite the long tradition of breeding activities in Europe, there is still a need to assess the impact of genetically enriched material on forests’ resilience. In this study, we address (1) the genetic diversity of selected material compared to its wild ancestors, and (2) how to enrich breeding material to support forests’ resilience under changing socio-environmental conditions. We analysed 16 study cases of selected material delivered from breeding activities in four European forest tree species (Pinus halepensis Mill., Pinus nigra J.F. Arnold, Pinus pinaster Ait. and Populus nigra L.) with different levels of breeding. To answer these two questions, we first assessed and compared the genetic diversity of selected material versus natural populations using both putatively neutral and adaptive (based on diverging selection) Single Nucleotide Polymorphisms (SNPs). We then suggest how to enrich these populations for resilience under future climatic conditions by defining a core collection for each species including material from populations that will likely disappear under future conditions. Thanks to the large SNP datasets available for our focal species, we were able to detect some trends in our data. Expected and observed heterozygosity values for selected populations were almost always identical. The selected material showed small but significant genetic differentiation from their original population and their inbreeding coefficient was generally lower. However, the level of genetic improvement (i.e. low vs high) was not correlated with the observed genetic differences between selected material and natural populations.The genetic characterization of natural populations distributed across the species range, and the future projection of their range stability, made it possible to identify core-collections that would significantly enrich breeding populations under uncertain future environmental conditions.

Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections.

At a time when effective tools for monitoring malaria control and eradication efforts are crucial, the increasing availability of molecular data motivates their application to epidemiology. The multiplicity of infection (MOI), defined as the number of genetically distinct parasite strains co-infecting a host, is one key epidemiological parameter for evaluating malaria interventions. Estimating MOI remains a challenge for high-transmission settings where individuals typically carry multiple co-occurring infections. Several quantitative approaches have been developed to estimate MOI, including two cost-effective ones relying on molecular data: i) THE REAL McCOIL method is based on putatively neutral single nucleotide polymorphism loci, and ii) the varcoding method is a fingerprinting approach that relies on the diversity and limited repertoire overlap of the var multigene family encoding the major Plasmodium falciparum blood-stage antigen PfEMP1 and is therefore under selection. In this study, we assess the robustness of the MOI estimates generated with these two approaches by simulating P. falciparum malaria dynamics under three transmission conditions using an extension of a previously developed stochastic agent-based model. We demonstrate that these approaches are complementary and best considered across distinct transmission intensities. While varcoding can underestimate MOI, it allows robust estimation, especially under high transmission where repertoire overlap is extremely limited from frequency-dependent selection. In contrast, THE REAL McCOIL often considerably overestimates MOI, but still provides reasonable estimates for low and moderate transmission. Regardless of transmission intensity, results for THE REAL McCOIL indicate that an inaccurate tail at high MOI values is generated, and that at high transmission, an apparently reasonable estimated MOI distribution can arise from some degree of compensation between overestimation and underestimation. As many countries pursue malaria elimination targets, defining the most suitable approach to estimate MOI based on sample size and local transmission intensity is highly recommended for monitoring the impact of intervention programs.

Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability.

Accurate predictions of the pathogenicity of mutations associated with genetic diseases are key to the success of precision medicine. Inherited missense mutations in the myocilin (MYOC) gene, within its olfactomedin (OLF) domain, constitute the strongest genetic link to primary open-angle glaucoma via a toxic gain of function, and thus MYOC is an attractive precision-medicine target. However, not all mutations in MYOC cause glaucoma, and common variants are expected to be neutral polymorphisms. The Genome Aggregation Database (gnomAD) lists ∼100 missense variants documented within OLF, all of which are relatively rare (allele frequency <0.001%) and nearly all are of unknown pathogenicity. To distinguish disease-causing OLF variants from benign OLF variants, we first characterized the most prevalent population-based variants using a suite of cellular and biophysical assays, and identified two variants with features of aggregation-prone familial disease variants. Next, we considered all available biochemical and clinical data to demonstrate that pathogenic and benign variants can be differentiated statistically based on a single metric: the thermal stability of OLF. Our results motivate genotyping MYOC in patients for clinical monitoring of this widespread, painless and irreversible ocular disease.

ГЕНОТИПІЧНА ТА ФЕНОТИПІЧНА ХАРАКТЕРИСТИКА СТІЙКОСТІ ДО АНТИМІКОБАКТЕРІАЛЬНИХ ПРЕПАРАТІВ 8 ШТАМІВ M. TUBERCULOSIS, ВИДІЛЕНИХ ВІД ХВОРИХ З ВПЕРШЕ ДІАГНОСТОВАНИМ ТУБЕРКУЛЬОЗОМ ЛЕГЕНЬ

The article presents the experience of whole-genome sequencing of M. tuberculosis (MBT) strains. Materials and methods. 8 MBT isolates were tested. The strains were obtained from patients with newly detected pulmonary tuberculosis (NDPTB). Critical concentrations of anti-mycobacterial drugs (AMBD): H; R; E; Z; Lfx; Mfx; Am; cm; Lzd; Bdq; Dlm and Cfz were determined using the BACTEC MGIT system. Sequencing of MBT strains was performed on Illumina MiSeq equipment at the laboratory of microbiology and biochemistry of the National Institute of phthisiology and pulmonology (NIPP). The obtained whole-genome sequences of MBT strains were deposited in fastq files and analyzed using the PhyResSE program (https://bioinf.fz-borstel.de/mchips/phyresse/) with the bioanalytical solution package. The panel of this package includes gene targets involved in the development of MBT to AMBP. Phylogenetic information and a certain spoligotype make it possible to obtain neutral single nucleotide polymorphisms. The genetic profile of the drug was performed according to the WHO mutation catalog (https://www.who.int/publications/i/item/9789240028173). The results. The dominant in Ukraine Beijing genotype was represented by 7 strains. The non-beijing group included 1 strain: Ural. 7 MBT strains belonged to the Beijing family, Lineage 2 phylogenetic line with the same spoligotype indices. The analysis of mutations according to the “Catalogue of mutations of the M. tuberculosis complex and their association with drug resistance”, WHO, 2021, allowed all detected mutations to be divided into categories - associated with resistance, associated with resistance - intermediate, not associated with resistance, with uncertain significance. Comparison of the resistance profile with the corresponding genotype showed that isolates, belonging to the Beijing genotype, usually carried MDR/pre-XDR mutations. Comparison of the resistance profile with the corresponding genotype showed that isolates belonging to the Beijing genotype usually carried MDR/pre-XDR mutations. All MBT strains with resistance to R had mutations found in the rpoB gene. The canonical amino acid substitution of rpoB S450L, associated with a high level of resistance to R with a non-significant decrease in the viability of the strains, was identified in 6 isolates. Another clinically significant mutation in rpoB (S435Y) was found in 2 cases and only in representatives of the Beijing family. Mutations of the categories: not associated with resistance (rpoC (E1092D)) and of uncertain significance: rpoC (I491V), rpoB (H674N), rpoB (V496A), were detected only in combination with “strictly associated” positions in phenotypic-resistant isolates of the genotype Beijing. The canonical single amino acid substitution katG S315T was detected in all isolates selected for sequencing. All 8 strains resistant to H showed mutations in genes associated with resistance to the drug. Mutations in the key Bdq resistance genes - atpE and mmpR - were not detected in any genome. In 1 strain of MBT, a C154R mutation associated with Lzd resistance was detected in the rplC gene. Similarly, in 1 strain of MBT, a mutation in ddn (D30S0) was detected with an as yet undetermined significance of association with resistance to Dlm. Conclusions. The study provided information on the genetic diversity of modern MBT isolates in TB patients. The predominance of the Beijing genotype testified to the stable population structure of the TB pathogen and the preservation of trends of high levels of the spread of TB forms of infection on the territory of the country. The combination of phenotype and molecular genetic data made it possible to give a more complete assessment of DR isolates. A large share of MDR was caused by mutations that did not have a negative effect on the viability and transmissibility of the pathogen, indicating a large epidemic reservoir of MBT strains with MDR/pre-XDR. The highly transmissible strains of Beijing carried mostly single uncombined R and H mutations, which were associated with a high level of resistance. Key words: genetic diagnostics, sequencing, pulmonary tuberculosis.

Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation.

Comparing divergence in quantitative traits and neutral molecular markers, such as QST-FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into 2 geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesized to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single-nucleotide polymorphisms (SNPs) across 15 populations and 3 clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades, and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.

Demographic, physiological and genetic factors linked to the poleward range expansion of the snail Nerita yoldii along the shoreline of China.

Species range shift is one of the most significant consequences of climate change in the Anthropocene. A comprehensive study, including demographic, physiological and genetic factors linked to poleward range expansion, is crucial for understanding how the expanding population occupies the new habitat. In the present study, we investigated the demographic, physiological and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km over the former biogeographical break of the Yangtze River Estuary in recent decades. Data from neutral single nucleotide polymorphisms (SNPs) showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modelling analysis revealed that the new marginal populations experienced a strong genetic bottleneck followed by recent demographic expansion. Successful expansion that overcame the founder effect might be attributed to its high capacity for rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Lower transcriptional plasticity was observed in the new marginal populations. These results suggest a new biogeographical pattern of N. yoldii has formed with the occurrence of demographic, physiological and genetic changes, and emphasize the roles of adaptation of marginal populations during range expansion.

K3326* mutation in breast cancer

After more than 25 years since its identification in 1995, the mutational faults in the BRCA2 gene is recognized and accepted as a high-penetrance predisposition gene for breast cancer. Besides a large number of pathogenic mutations, there are thousands of VUS (variants of uncertain significance) described, with many of them localized on C-terminus. K3326* is a rare truncating variant on the C-terminus of BRCA2, which is reported in the literature, including ClinVar and Varsome database, as a neutral polymorphism. However, there is some evidence that suggests an elevated risk of breast cancer associated with K3326* variant. We present the case of a K3326* mutation carrier, affected patient aged 42 diagnosed with co-existing breast and ovarian cancer, suggesting that the variant is not neutral for breast and ovarian cancer risk. K3326 may need to be included in SNP panels and further investigated for breast cancer risk estimation.

A convoluted tale of hybridization between two Petunia species from a transitional zone in South America

Recently diverged species may hybridize in their contact zones if complete reproductive isolation has not yet emerged. Petunia inflata and P. interior are closely related species with a narrow geographic distribution in Argentina and southern Brazil. They share morphological features, genetic markers, pollinators, and occupy a transitional area between the Pampa grasslands and the Brazilian Atlantic Forest. Here, we used genomic data to verify species boundaries, identify putative hybrids, and shed light on their speciation process. We characterized 59 individuals from allopatric and contact zones using genotyping-by-sequencing technology, resulting in a final dataset with 21,759 neutral single nucleotide polymorphisms used to perform structure, demographic, and hybridization analyses. These species belong to distinct evolutionary lineages that hybridized after secondary contact. A combination of geographic distance, elevation, and climate explains the genetic divergence between species. Niche overlap analysis revealed that even though these species have overlapping distributions and similar habitat preferences, they are more distinct than expected by chance, rejecting the niche conservatism hypothesis. Demographic analysis suggested that the Pleistocene climatic changes led species to diverge but they came into secondary contact during the Holocene. The secondary contact led to limited gene flow between species and bidirectional introgression. The distribution expansion of these species’ ancestor to a transitional zone between biomes, associated with elevational ranges and habitat fragmentation promoted speciation and niche differentiation.

Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species.

Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation-by-distance (IBD), isolation-by-adaptation (IBA), and isolation-by-colonization (IBC) have been recognized as the main divergence patterns. Still, it is not easy to distinguish which one is the main pattern as each one may act at different points in time or even simultaneously. Using an extensive genome coverage from a Petunia species complex with coastal and inland distribution and multiple analytical approaches on population genomics and phylogeography, we showed a complex interplay between neutral and selective forces acting on the divergence process. We found 18,887 SNPs potentially neutral and 924 potentially under selection (outlier) loci. All analyses pointed that each subspecies displays its own genetic component and evolutionary history. We suggested plausible ecological drivers for such divergence in a southernmost South Atlantic coastal plain in Brazil and Uruguay and identified a connection between adaptation and environment heterogeneity.

Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum.

Recognition of the important role of transposable elements (TEs) in eukaryotic genomes quickly led to a burgeoning literature modeling and estimating the effects of selection on TEs. Much of the empirical work on selection has focused on analyzing the site frequency spectrum (SFS) of TEs. But TE evolution differs from standard models in a number of ways that can impact the power and interpretation of the SFS. For example, rather than mutating under a clock-like model, transposition often occurs in bursts which can inflate particular frequency categories compared with expectations under a standard neutral model. If a TE burst has been recent, the excess of low-frequency polymorphisms can mimic the effect of purifying selection. Here, we investigate how transposition bursts affect the frequency distribution of TEs and the correlation between age and allele frequency. Using information on the TE age distribution, we propose an age-adjusted SFS to compare TEs and neutral polymorphisms to more effectively evaluate whether TEs are under selective constraints. We show that our approach can minimize instances of false inference of selective constraint, remains robust to simple demographic changes, and allows for a correct identification of even weak selection affecting TEs which experienced a transposition burst. The results presented here will help researchers working on TEs to more reliably identify the effects of selection on TEs without having to rely on the assumption of a constant transposition rate.

Creation of Yeast Models for Evaluating the Pathogenicity of Mutations in the Human Mitochondrial Gene MT-ATP6 and Discovering Therapeutic Molecules.

Numerous diseases in humans have been associated with mutations of the mitochondrial genome (mtDNA). This genome encodes 13 protein subunits of complexes involved in oxidative phosphorylation (OXPHOS), a process that provides aerobic eukaryotes with the energy-rich adenosine triphosphate molecule (ATP). Mutations of the mtDNA may therefore have dramatic consequences especially in tissues and organs with high energy demand. Evaluating the pathogenicity of these mutations may be difficult because they often affect only a fraction of the numerous copies of the mitochondrial genome (up to several thousands in a single cell), which is referred to as heteroplasmy. Furthermore, due to its exposure to reactive oxygen species (ROS) produced in mitochondria, the mtDNA is prone to mutations, and some may be simply neutral polymorphisms with no detrimental consequences on human health. Another difficulty is the absence of methods for genetically transforming human mitochondria. Face to these complexities, the yeast Saccharomyces cerevisiae provides a convenient model for investigating the consequences of human mtDNA mutations in a defined genetic background. Owing to its good fermentation capacity, it can survive the loss of OXPHOS, its mitochondrial genome can be manipulated, and genetic heterogeneity in its mitochondria is unstable. Taking advantage of these unique attributes, we herein describe a method we have developed for creating yeast models of mitochondrial ATP6 gene mutations detected in patients, to determine how they impact OXPHOS. Additionally, we describe how these models can be used to discover molecules with therapeutic potential.

Gene flow influences the genomic architecture of local adaptation in six riverine fish species.

Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from recombination and thus be selected for, but few studies have tested it with empirical data. Here, we used restriction site-associated sequencing to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We used four differentiation-based outlier tests and three genotype-environment association analyses to define neutral single nucleotide polymorphisms (SNPs) and outlier SNPs that were putatively under selection. We then examined the distribution of outlier SNPs along the genome and investigated whether these SNPs were found in genomic islands of differentiation and inversions. We found that gene flow varied among species, and outlier SNPs were clustered more tightly in species with higher gene flow. The two species with the highest overall FST (0.0303-0.0720) and therefore lowest gene flow showed little evidence of clusters of outlier SNPs, with outlier SNPs in these species spreading uniformly across the genome. In contrast, nearly all outlier SNPs in the species with the lowest FST (0.0003) were found in a single large putative inversion. Two other species with intermediate gene flow (FST ~0.0025-0.0050) also showed clustered genomic architectures, with most islands of differentiation clustered on a few chromosomes. Our results provide important empirical evidence to support the hypothesis that increasingly clustered architecture of local adaptation is associated with high gene flow.

Population genomics indicates micro‐refuges and riverine barriers for a southern South American grassland nightshade

AbstractAimPleistocene climate oscillations influenced the species distribution and genetic diversity in grasslands, and such climatic changes promoted expansion and contraction cycles, leading to fragmentation and isolation of evolutionary lineages in refuges. This study aimed to infer the evolutionary processes that most influenced the genetic diversity of a South American nightshade Petunia inhabiting subtropical grasslands under the Pleistocene influence.LocationPampa and Chaco.TaxonThe widely distributed herb Petunia axillaris subsp. parodii (Solanaceae).MethodsWe obtained high‐density genome coverage throughout the geographical distribution of Petunia axillaris subsp. parodii. We estimated the genetic diversity and structure to evaluate population differentiation and applied a model‐based demographic analysis to investigate the scenarios that could have influenced the species' evolutionary history. We evaluated the association between neutral and outlier polymorphisms with environmental variables to distinguish the influence of the geographical distance and environmental differences between populations.ResultsThere are three evolutionary lineages in P. axillaris subsp. parodii. The origin and differentiation of these lineages were related to the Pleistocene refuges and rivers acting as barriers to gene flow. We also identified 496 outlier loci related to adaptation to environmental conditions.Main conclusionThe Pleistocene climate changes drove lineage diversification isolated in micro‐refugia. Rivers and changes in their courses may have also acted on the population divergence, serving as barriers to gene flow or even as corridors for species range expansion. These findings contribute to the knowledge of the evolutionary processes that influenced the lineage diversification of South American subtropical grassland species.