Population Genetic Research Articles

Autosomal and Y-STR genetic database from a population of the Spanish Civil War (1936-1939) and the postwar period.

Under the initiative of the "Direcció General de Memòria democràtica-Departament de Justícia" (Generalitat of Catalonia, Spain), a multi-disciplinar project was funded to identify the remains of people disappeared in Catalonia during and after the Spanish Civil War (1936-1939). Samples were officially sent by Autonomous Government of Catalonia to the Laboratory of Forensic and Population Genetics at Complutense University, Madrid, Spain, to be genotyped. Our study presents a database of 343 victims genotyped for STRs comprised in GlobalFiler™ PCR Amplification Kit (Thermofisher Scientific) and a subset of 292 typed with Y-STRs from Yfiler™ Plus PCR Amplification Kit (Thermofisher Scientific). Complete profiles amounted to 116 (33.81%) and 89 (30.48%) for autosomal and Y-STRs respectively. Allelic/haplotype frequencies, forensic parameters and HW equilibrium were calculated with STRAF software. Drop-out frequencies were also calculated for each locus. All the markers were in HW equilibrium (p > 0.05). Allelic drop-out frequencies were larger in the case of CSF1PO (1.5340E-01) and TPOX (1.2640E-01), probably due to extremely low DNA preservation combined with a less efficient PCR for these loci, among other causes. The comparison of our autosomal database with a set of modern European populations from STRidER database (ENFSI) reveals that the present study sample clusters with other West European samples. This is also the case for Y-STR when our study is compared with European and North African samples. Our results seem to suggest that modern Spanish forensic databases can be used to identify deceased persons during the Spanish Civil War and later, from their living descendants.

Hydatigera parva population genetics in Iberian rodents provides insights into its introduction from Africa.

Hydatigera parva population genetics in Iberian rodents provides insights into its introduction from Africa.

Swatting Flies: Biting Insects as Non-Invasive Samplers for Mammalian Population Genomics.

Advances in next-generation sequencing have allowed the use of DNA obtained from unusual sources for wildlife studies. However, these samples have been used predominantly to sequence mitochondrial DNA for species identification while population genetics analyses have been rare. Since next-generation sequencing allows indiscriminate detection of all DNA fragments in a sample, technically it should be possible to sequence whole genomes of animals from environmental samples. Here we used a blood-feeding insect, tsetse fly, to target whole genome sequences of wild animals. Using pools of flies, we compared the ability to recover genomic data from hosts using the short-read sequencing (Illumina) and adaptive sampling of long-read data generated using Oxford nanopore technology (ONT). We found that most of the short-read data (85%-99%) was dominated by tsetse fly DNA and that adaptive sampling on the ONT platform did not substantially reduce this proportion. However, once tsetse reads were removed, the remaining data for both platforms tended to belong to the dominant host expected in the tsetse fly blood meal. Reads mapping to elephants, warthogs and giraffes were recovered more reliably than for buffalo, and there was high variance in the contribution of DNA by individual flies to the pools, suggesting that there are host specific biases. For elephants, using short-read sequencing we were able to identify over 300,000 unfiltered SNPs, which we used to estimate the allele frequencies and expected heterozygosity for the population. Overall, our results show that at least for certain wild mammals, it is possible to recover genome-wide host data from blood-feeding insects.

Diversity and consequences of structural variation in the human genome.

The biomedical community is increasingly invested in capturing all genetic variants across human genomes, interpreting their functional consequences and translating these findings to the clinic. A crucial component of this endeavour is the discovery and characterization of structural variants (SVs), which are ubiquitous in the human population, heterogeneous in their mutational processes, key substrates for evolution and adaptation, and profound drivers of human disease. The recentemergence of new technologies and the remarkable scale ofsequence-based population studies have begun to crystalize our understanding of SVs as a mutational class and their widespread influence across phenotypes. In this Review, we summarize recent discoveries and new insights into SVs in the human genome in terms of their mutational patterns, population genetics, functional consequences, and impact on human traits and disease. We conclude by outlining three frontiers to be explored by the field over the next decade.

Fingerprint resemblance amongst siblings and non-siblings - Forensic and anthropological implications.

Fingerprints hold a crucial position in forensic science, primarily for identification purposes, with thumbprints emerging as the most frequently recovered evidence at crime scenes. The main purpose of the present study was to conduct a comparative analysis of thumbprints of siblings and non-sibling pairs to investigate resemblance and similarities in fingerprint patterns. Thumbprints of 144 individuals (72 siblings and 72 non-siblings) from 36 families were obtained. Jaccard Similarity Index was employed to analyse the similarity between the fingerprint patterns of siblings and non-siblings. The strength of association between the variables is evaluated by chi-square and Cramer's V tests. The results indicated a significant similarity (69.44%) in thumbprint patterns among sibling pairs, demonstrating congruence in their right thumbprints, while non-sibling pairs exhibited a mere 30.56% similarity in the right thumbprints. Statistical analyses revealed a significant association (p = 0.0002) between sibling pairs, indicating a strong correlation in right-hand thumbprint patterns. The study bears substantial implications across various fields, including anthropology, population genetics, medical genetics and forensic science. Moreover, it may facilitate the examination of population similarities and variations and may aid in enhancing forensic investigations by identifying familial resemblance and similarity.

Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm.

Human mitochondrial DNA (mtDNA) harbors essential mutations linked to aging, neurodegenerative diseases, and complex muscle disorders. Due to its uniparental and haploid inheritance, mtDNA captures matrilineal evolutionary trajectories, playing a crucial role in population and medical genetics. However, critical questions about the genomic diversity patterns, inheritance models, and evolutionary and medical functions of mtDNA remain unresolved or underexplored, particularly in the transition from traditional genotyping to large-scale genomic analyses. This review summarizes recent advancements in data-driven genomic research and technological innovations that address these questions and clarify the biological impact of nuclear-mitochondrial segments (NUMTs) and mtDNA variants on human health, disease, and evolution. We propose a streamlined pipeline to comprehensively identify mtDNA and NUMT genomic diversity using advanced sequencing and computational technologies. Haplotype-resolved mtDNA sequencing and assembly can distinguish authentic mtDNA variants from NUMTs, reduce diagnostic inaccuracies, and provide clearer insights into heteroplasmy patterns and the authenticity of paternal inheritance. This review emphasizes the need for integrative multi-omics approaches and emerging long-read sequencing technologies to gain new insights into mutation mechanisms, the influence of heteroplasmy and paternal inheritance on mtDNA diversity and disease susceptibility, and the detailed functions of NUMTs.

Molecular epidemiology and genetic diversity of disappearing Plasmodium vivax in southern Thailand

The evolution of genetic diversity and population structure of Plasmodium vivax as malaria elimination approaches remains unclear. This study analyzed the genetic variation and molecular epidemiology of P. vivax from Yala Province in southern Thailand, an area in the pre-elimination phase. Seventy P. vivax isolates, collected between 2017 and 2020, were genotyped for domain II of pvdbp and the 42-kDa region of pvmsp1 using amplicon deep sequencing. Data from Yala province were compared to published data from Tak province, where transmission was higher. Key analyses included nucleotide diversity (π), haplotype diversity (Hd), natural selection, recombination rates, and complexity of infection (COI). Genetic diversity in Yala was relatively low (π = 0.008dbp and 0.014msp1; Hd = 0.774dbp and 0.407msp1) compared to Tak (π = 0.012dbp and 0.027msp1; Hd = 0.849dbp and 0.962msp1). In Yala, polyclonal infections were found in 53.7% of pvdbpII and 47.8% of pvmsp142 isolates, with average COI of 1.6 and 1.7. Both genes were under balancing selection. Distinct genetic differences were found between Yala and Tak in pvmsp142, providing a local genotypic profile useful for tracing parasite origins.

Distribution of the four type VI secretion systems in Pseudomonas aeruginosa and classification of their core and accessory effectors

Bacterial type VI secretion systems (T6SSs) are puncturing molecular machines that transport effector proteins to kill microbes, manipulate eukaryotic cells, or facilitate nutrient uptake. How and why T6SS machines and effectors differ within a species is not fully understood. Here, we applied molecular population genetics to the T6SSs in a global population of the opportunistic pathogen Pseudomonas aeruginosa. We reveal varying occurrence of up to four distinct T6SS machines. Moreover, we define conserved core T6SS effectors, likely critical for the biology of P. aeruginosa, and accessory effectors that can exhibit mutual exclusivity between strains. By ancestral reconstruction, we observed dynamic changes in the gain and loss of effector genes in the species’ evolutionary history. Our work highlights the potential importance of T6SS intraspecific diversity in bacterial ecology and evolution.

Assessing genetic diversity and population structure of f4:f5 wheat genotypes using morphological and microsatellite markers under heat stress

Diversity in the plant gene pool provides breeders with the opportunity to improve targeted traits. Enhancing the genetic background through the introgression of desired gene(s) is an effective strategy to combat stresses like heat. Two field experiments were carried out in 2019–20 and 2020–21 at the research fields of Genetics and Plant Breeding at Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh, to identify heat-tolerant wheat advance lines. In F4 generation, 60 advanced lines were selected from a pool of 160 line and in the F5 generation, 16 lines were selected from the previous selection. Analysis of variance revealed significant variation in both the F4 and F5 generations, with the F5 populations outperforming the check varieties. Grain weight demonstrated the highest heritability and genetic advance, while the plant yield exhibited moderate to high performance. Plant height had the most significant direct effect at the genotypic level, while grain weight had the highest impact at the phenotypic level. A total of 77 alleles were identified with an average of 4.53 alleles per locus. The genetic similarity analysis showed that Shatabdi and BARI Gom 25 had the highest similarity at 94%, followed by P3-18-10 with P3-11-3 at 90%, and P3-24-10 with P3-21-10 at 85%. The PCA, structural, and dendrogram analyses all indicated the same grouping of the selected lines. Therefore, selecting of these lines for the F6 generation would enhance resilience against heat stress.

Demographic and historical processes influencing Cochliomyia hominivorax (Diptera: Calliphoridae) population structure across South America

BackgroundIn this study, we investigated the genetic variability and population structure of the New World screwworm fly Cochliomyia hominivorax. We tested the hypothesis that the species exhibits a center–periphery distribution of genetic variability, with higher genetic diversity in central populations (e.g., Brazil) and lower diversity in peripheral populations.MethodsUsing microsatellite markers, we analyzed larvae collected from infested livestock across South America. The larvae were collected directly from various wound sites to ensure a broad representation of genetic diversity.ResultsContrary to our initial hypothesis, the results revealed consistent genetic variability across the species’ distribution, low population differentiation, and no evidence of isolation-by-distance patterns among subpopulations. The genetic analysis indicated an excess of homozygotes, potentially due to the Wahlund effect, null alleles, or selection pressure.ConclusionsThese findings suggest a complex metapopulation structure for C. hominivorax, challenging classical population genetics models. This complexity likely arises from the species’ high dispersal capability and frequent local extinctions followed by recolonization. These results have important implications for the design and implementation of control programs, emphasizing the need for coordinated and large-scale actions rather than isolated initiatives.Graphical

Cowpea genetic diversity, population structure and genome-wide association studies in Malawi: insights for breeding programs

Cowpea genetic diversity, population structure and genome-wide association studies in Malawi: insights for breeding programs

The Genetic Diversity, Population Structure, and Historical Dynamics of Wild Pyrus Species on the Yunnan–Kweichow Plateau

The Genetic Diversity, Population Structure, and Historical Dynamics of Wild Pyrus Species on the Yunnan–Kweichow Plateau

Range-wide understanding of genetic diversity and population structure of endangered Kashmir musk deer in North-Western Himalaya.

The endangered Kashmir musk deer (Moschus cupreus), native to high-altitude Himalayas, is an ecological significant and endangered ungulate, threatened by habitat loss and poaching for musk pod distributed in western Himalayan ranges of India, Nepal and Afghanistan. Despite its critical conservation status and ecological importance in regulating vegetation dynamics, knowledge gaps persist regarding its population structure and genetic diversity, hindering effective management strategies. We aimed to understand the population genetics of Kashmir musk deer in north-western Himalayas using two mitochondrial DNA (mtDNA) regions and 11 microsatellite loci. Total of 63 consensus sequences were analyzed, revealing 10 haplotypes with high haplotype diversity (Hd = 0.906 ± 0.031) and moderate nucleotide diversity (π = 0.00539 ± 0.004) at mitochondrial markers. Microsatellite analysis indicated moderate genetic variability, with observed heterozygosity (Ho = 0.445 ± 0.049) and expected heterozygosity (He = 0.764 ± 0.039), comparable to the forest musk deer but relatively lower than that observed in other ungulates. Population structure analysis identified three potential genetic clusters, with evidence of genetic admixture in the Lahaul Valley, possibly due to gene flow from neighboring areas. Historical demographic analyses using Bayesian skyline plots and mismatch distribution curves indicated stable population sizes in the past, followed by recent declines in maternal effective population size. Our findings highlight the necessity of preserving the genetic diversity of the Kashmir musk deer to ensure its long-term survival. We recommend expanding the geographic range of sampling to include regions such as Chamba and Kinnaur districts in Himachal Pradesh, potential areas in Jammu and Kashmir and Uttarakhand, for more comprehensive population-level analysis. Such efforts will be crucial for developing targeted conservation strategies and mitigating the impacts of human activities on this endangered species.

Genetic Diversity of Diaphorina citri and Its Endosymbiont Across Diffusion Frontier and Epidemic Areas of Citrus Huanglongbing in China

Citrus huanglongbing (HLB) is one of the most severe diseases affecting the citrus industry, with Diaphorina citri (Hemiptera: Liviidae) serving as its primary natural vector. To understand the genetic diversity and population structure of D. citri in the context of HLB diffusion, we analyzed 13 populations from the HLB diffusion frontier and 25 populations from epidemic areas in China. The HLB diffusion frontier areas refer to the peripheral regions of HLB distribution in China, including the western Zhejiang, southern Jiangsu, northern Jiangxi, northern Hunan, and eastern Sichuan provinces. In contrast, the HLB epidemic areas represent regions in China where HLB is actively widespread and causing significant impacts. We utilized mitochondrial genes (COI, ND5, and Cytb) of D. citri and housekeeping genes (dnaQ, rpoC, and argH) of its endosymbiont Candidatus Carsonella ruddii (Ca. C. ruddii) for this analysis. Our findings revealed that the D. citri and Ca. C. ruddii in different regions showed low haplotype diversity and nucleotide diversity. While the genetic variation in D. citri populations primarily occurred within populations, the endosymbiont showed contrasting patterns in the HLB epidemic areas. We identified three dispersal paths: (1) migration of the Yunnan population to Sichuan, Guizhou, and Guangxi; (2) movement of the Guangdong population to Fujian, Jiangxi, and Zhejiang; and (3) dispersal of the Guangdong population to Hunan and Guangxi. Our study suggests that D. citri populations at the HLB diffusion frontier are predominantly transmitted from neighboring epidemic areas.

Host Specificity and Geographic Dispersion Shape Virome Diversity in Rhinolophus Bats.

Rhinolophus bats have been identified as natural reservoirs for viruses with global health implications, including severe acute respiratory syndrome-related coronaviruses (SARSr-CoV) and swine acute diarrhoea syndrome-related coronavirus (SADSr-CoV). In this study, we characterised the individual viromes of 603 bats to systematically investigate the diversity, abundance and geographic distribution of viral communities within R. affinis, R. sinicus and 11 other bat species. The massive metatranscriptomic data revealed substantial viral genome resources of 133 vertebrate-infecting viral clusters, which contain occasional cross-species transmission across mammalian orders and especially across bat families. Notably, those viruses included nine clusters closely related to human and/or livestock pathogens, such as SARS-CoVs and SADS-CoVs. The investigation also highlighted distinct features of viral diversity between and within bat colonies, which appear to be influenced by the distinct host population genetics of R. affinis and R. sinicus species. The comparison of SARSr-CoVs further showed varied impact of host specificity along genome-wide diversification and modular viral evolution among Rhinolophus species. Overall, the findings point to a complex interaction between host genetic diversity, and the way viruses spread and structure within natural populations, calling for continued surveillance efforts to understand factors driving viral transmission and emergence in human populations. These results present the underestimated spillover risk of bat viruses, highlighting the importance of enhancing preparedness and surveillance for emerging zoonotic viruses.

Trait genetic architecture and population structure determine model selection for genomic prediction in natural Arabidopsis thaliana populations.

Genomic prediction applies to any agro- or ecologically relevant traits, with distinct ontologies and genetic architectures. Selecting the most appropriate model for the distribution of genetic effects and their associated allele frequencies in the training population is crucial. Linear regression models are often preferred for genomic prediction. However, linear models may not suit all genetic architectures and training populations. Machine Learning approaches have been proposed to improve genomic prediction owing to their capacity to capture complex biology including epistasis. However, the applicability of different genomic prediction models, including non-linear, non-parametric approaches, have not been rigorously assessed across a wide variety of plant traits in natural outbreeding populations. This study evaluates genomic prediction sensitivity to trait ontology and the impact of population structure on model selection and prediction accuracy. Examining 36 quantitative traits in 1000+ natural genotypes of the model plant Arabidopsis thaliana, we assessed the performance of penalised regression, random forest, and multilayer perceptron at producing genomic predictions. Regression models were generally the most accurate, except for biochemical traits where random forest performed best. We link this result to the genetic architecture of each trait - notably that biochemical traits have simpler genetic architecture than macroscopic traits. Moreover, complex macroscopic traits, particularly those related to flowering time and yield, were strongly correlated to population structure, while molecular traits were better predicted by fewer, independent markers. This study highlights the relevance of machine learning approaches for simple molecular traits and underscores the need to consider ancestral population history when designing training samples.

Phylogenomics and species delimitation in the Lepidophyma sylvaticum complex (Squamata: Xantusiidae) using ddRADseq and morphological data.

The Lepidophyma sylvaticum complex occurs from west-central Nuevo León to the Sierra de Chiconquiaco in central Veracruz, Mexico. Morphological studies have revealed population groups that are "moderately divergent from each other" within the complex. In addition, a molecular phylogenetic study found L. sylvaticum to be strongly structured and paraphyletic with respect to L. micropholis. We used ddRADseq and morphological data to evaluate the phylogenetic relationships and species boundaries within the complex. Phylogenetic analyses performed using both concatenation and coalescent methods estimated the same well-supported tree, composed of five allopatric, strongly supported lineages of L. sylvaticum (from Nuevo León [NL]; Sierra de Álvarez, San Luis Potosí [ASLP]; southeastern San Luis Potosí, Querétaro, Hidalgo, and northwestern Veracruz [HSQV]; Tamaulipas [T]; and Puebla and northern Veracruz [PV]) branching off (in that order) from the base of the tree, with L. micropholis as the sister taxon to the last of them. A population genetics analysis revealed one pattern of genetic structure in L. micropholis and three in L. sylvaticum: one in the L. sylvaticum NL and ASLP lineages, another in the L. sylvaticum HSQV and T lineages, and a third in the L. sylvaticum PV lineage. The six lineages identified were genetically distinctive across our phylogenetic and population genetics analyses, and congruent with geography. Species tree and phylogenetic network analyses, considering the six lineages as potentially independent, inferred trees identical to the concatenated tree. Additionally, the phylogenetic network analysis detected a recent introgression event from the L. sylvaticum T lineage into L. micropholis. A time-calibrated tree indicated that the diversification of the complex began in the late Miocene and continued into the Pleistocene. A species delimitation analysis, based on the genealogical divergence index, suggested that the L. sylvaticum NL, ASLP, and PV lineages are independent evolutionary lineages. A morphological analysis showed that L. micropholis and the L. sylvaticum NL and ASLP lineages were distinguishable from each other and from the remaining L. sylvaticum lineages. We conclude that the L. sylvaticum NL and ASLP lineages, the two oldest in the complex, represent independent evolutionary lineages, and propose recognizing the other four lineages as subspecies (historical sublineages) of L. sylvaticum sensu stricto.

Association of the tomato co-chaperone gene Sldnaj harboring a promoter deletion with susceptibility to Tomato spotted wilt virus (TSWV)

Abstract Tomato spotted wilt virus (TSWV) poses a significant threat as a devastating pathogen to the global production and quality of tomato (Solanum lycopersicum). Mining novel resistance genes within the tomato germplasm is an effective and environmentally friendly approach to combat TSWV. In this study, we investigated the mechanisms underlying high TSWV resistance in a specific tomato line after experimental inoculation, despite not possessing any known TSWV resistance genes. The candidate causal genes of disease resistance traits were finely mapped by constructing different genetic populations and performing bulk segregant analysis sequencing. This approach identified SlDnaJ (Solyc10g081220) as a key locus potentially regulating TSWV resistance. We determined a structural variant of SlDnaJ (designated Sldnaj) containing a 61-bp promoter sequence deletion that was specifically present in the germplasm of the susceptible M82 tomato plant lines. Sldnaj-knockout transgenic plants were significantly more resistant to TSWV than wild-type plants. Up-regulated expression of Sldnaj affected the salicylic acid/jasmonic acid signaling pathway, which induced and promoted the systemic infection of TSWV in M82 susceptible plants. In summary, this study identified a new candidate TSWV susceptibility gene with a natural deletion variation in tomato. These findings provide insights into the molecular mechanism underlying pathogen resistance while offering a target for breeding strategies of tomato with TSWV resistance.

Trophy fish heads are a source of body size information for historical and contemporary ecology

Abstract This study investigated whether trophy taxidermy specimens of Australia’s largest freshwater fish, Murray cod (Maccullochella peelii), can provide accurate records of historical body size. Taxidermy mounts came mostly from informal collections in hotels from across the Murray–Darling Basin, south-eastern Australia, comprising 20% whole-body and 80% head forms. We compared the morphology of mounts to live Murray cod, collected from the mid–Murray River in 2018, and identified the head morphometrics that most accurately described length and weight of whole mounts and live fish. Eight morphological characters were analysed for 60 whole mounts, 172 head mounts and 51 live fish. We found that inter-orbital distance, inter-nare width and upper jaw length were relatively robust to taxidermy processes and were reliable features for predicting fish total length and total weight. Shrinkage in head morphometrics due to taxidermy was evident, however, and we recommend that this be considered when reconstructing length and weight measures. We discuss how estimated body length and weight from head morphometrics of trophy fish, coupled with analysis of the accompanying remaining tissue and hard parts, opens up opportunities to explore patterns in genetics, life history, movement and trophic ecology of historical fish populations and of past environments.

The Tasmanian Estuary Perch Population—A Threatened Species?

Estuary perch (Percalates colonorum) are a long-lived and slow-growing species which are distributed throughout southeastern Australian estuaries. In Tasmania, only one known population remains which is located in the Arthur River, on the remote northwest coast. Tasmania is the only Australian state to list estuary perch as a wholly protected species (recreational and commercial), while other populations across their mainland distribution appear to be robust. A survey undertaken on estuary perch in the Arthur River in 2014–2015 indicated that the population was small (825–2375 fish) and dominated by three age classes between 12 and 14 years old. This population also has extremely low genetic diversity and is genetically distinct to mainland populations due to its geographic isolation. During a re-survey in December 2023, 378 estuary perch were captured, with 191 tagged and released, and 31 fish retained for age and gonad analysis. Although three strong age classes were detected (five, eight and twenty-three years), numerous weak and missing cohorts were apparent. This study also confirms this population has a delayed spawning season in comparison to mainland populations, with growth models and tag recaptures (32 fish) demonstrating a very slow but sexually dimorphic growth rate. By combining the datasets of the 2014/15 and 2023 survey, we present an updated understanding of the biology and population dynamics of this unique Tasmanian population, which has previously never been published. The results confirm the population is still reproductively active and stable; however, due to their restricted distribution, variable recruitment, slow growth, and small population, further conservation efforts are still required. Further legislative listings at both the state and federal levels are planned, which if successful will provide additional protection and assist in applications for external funding and resources. This will support the development of a recovery plan which will consider re-stocking efforts and re-establishment of previously inhabited waters and investigate potential actions to improve the genetics of the Tasmanian population. Additionally, educational campaigns to inform the public and recreational fishers on the status of estuary perch in Tasmania will be undertaken.