Population Genetic Data Research Articles

Genomics reveals a genetically isolated population of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) distributed in the Sea of Japan.

The processes by which animals become genetically isolated in an open environment such as the ocean have not yet been fully elucidated. Morphologically different populations of Pacific white-sided dolphin Lagenorhynchus obliquidens are observed sympatrically in the Sea of Japan. However, genetic studies that exclusively used limited mitochondrial loci or microsatellite DNA have failed to demonstrate the existence of genetically distinct populations. Here, to reveal the population structure, we analysed genome-wide population genetic data using single nucleotide polymorphisms (SNPs) gathered in 2018-2021 from all domestic captive individuals in aquaria, the majority of which originated from the wild, as well as from some stranded individuals, together covering a wide area of coastal water around Japan (n=123). Multiplexed intersimple sequence repeat genotyping-by-sequencing analysis was performed to obtain the SNP data. Principal coordinate analysis and the clustering method structure indicated that two genetically-distinct populations exist, with little interpopulation gene flow revealed. In addition, the genotypic segregation was reflected in differences in external morphotype. Furthermore, a population demographic analysis based on the whole-genome sequences of an individual from each population indicated that sea-level changes during the Last Glacial Period probably led to allopatric divergence of this species in a limited area of the Sea of Japan, with that group subsequently sharing a distribution area with the other population. These findings yield insights into the formation of genetically isolated sympatric populations in the ocean.

Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes

Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.

A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making.

A recently published macrogenetic dataset of California's flora and fauna, CaliPopGen, comprehensively summarizes population genetic research published between 1985 and 2020. Integrating these genetic data into the requisite "best available science" upon which conservation professionals rely should facilitate the prioritization of populations based on genetic health. We evaluate the extent to which the CaliPopGen Dataset provides genetic diversity estimates that are 1) unbiased, 2) sufficient in quantity, 3) cover entire species' ranges, and 4) include potentially adaptive loci. We identified genetic diversity estimates for 4,462 spatially referenced populations of 432 species, confirming California's rich published history of population genetics research. Most recent studies used microsatellites markers, which have uniquely high levels of variation, and estimates of all genetic metrics varied significantly across marker types. Most studies used less than 10 loci for inferences, rendering parameter estimates potentially unreliable, and covered small spatial extents that include only a fraction of the studied species' California distribution (median 16.3%). In contrast, the ongoing California Conservation Genomics Project (CCGP) aims to cover the full geographical and environmental breadth of each species' occupied habitats, and uses a consistent approach based on whole-genome data. However, the CCGP will sequence only 12% of the number of individuals, and covers only about half the evolutionary diversity, of the CaliPopGen Database. There is clearly a place in the evaluation of the genetic health of California for both approaches going forward, especially if differences among studies can be minimized, and overlap emphasized. A complementary use of both datasets is warranted to inform optimal conservation decision-making. Finally, a synopsis of the available population genetic data for California, all other US states and 241 other countries, allows us to identify states and countries for which meaningful data summaries, such as CaliPopGen, could be collated and others, which have limited published data available and are prime targets for future, empirical work.

Dnadna: a deep learning framework for population genetics inference.

We present dnadna, a flexible python-based software for deep learning inference in population genetics. It is task-agnostic and aims at facilitating the development, reproducibility, dissemination and re-usability of neural networks designed for population genetic data. dnadna defines multiple user-friendly workflows. First, users can implement new architectures and tasks, while benefiting from dnadna utility functions, training procedure and test environment, which saves time and decreases the likelihood of bugs. Second, the implemented networks can be re-optimized based on user-specified training sets and/or tasks. Newly implemented architectures and pre-trained networks are easily shareable with the community for further benchmarking or other applications. Finally, users can apply pre-trained networks in order to predict evolutionary history from alternative real or simulated genetic datasets, without requiring extensive knowledge in deep learning or coding in general. dnadna comes with a peer-reviewed, exchangeable neural network, allowing demographic inference from SNP data, that can be used directly or retrained to solve other tasks. Toy networks are also available to ease the exploration of the software, and we expect that the range of available architectures will keep expanding thanks to community contributions. dnadna is a Python (≥3.7) package, its repository is available at gitlab.com/mlgenetics/dnadna and its associated documentation at mlgenetics.gitlab.io/dnadna/.

GENETIC STRUCTURE AND DIVERSITY OF DATE PALM (PHOENIX DACTYLIFERA L.) CULTIVARS IN IRAN REVEALED BY REMAP GENOTYPING

The date palm (Phoenix dactylifera L.) is the most important fruit-bearing crop in arid regions of the Middle East and North Africa. About 3,000 date varieties or cultivars are known worldwide that differ in flowering time, several agronomic traits, and fruit-related traits including moisture and sugar content. Phoenix dactylifera is the second most important horticultural crop of Iran that is cultivated mainly in the southern part of the country. It has about 400 known cultivars in Iran and therefore comprises an important part of the whole world date palm genetic resources. We have no detailed information on its population genetic structure. The present study was an attempt to provide the population genetic data on 14 date palm cultivars for the first time. The present study tried to identify genetic diversity of a few cultivars and provide data on their genetic structure with REMAP molecular marker. The results revealed a moderate level of genetic diversity both among and within the studied cultivars. We obtained mean genetic polymorphism of 20.8%.

Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize.

Maize is a staple food of smallholder farmers living in highland regions up to 4,000 m above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggest the maize's adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.

The population genetics characteristics of Ion AmpliSeq™ MH-74 plex microhaplotype research panel

A large number of microhaplotype markers have been investigated for various forensic purposes in recent years. In the present study, we have analysed population genetic data and sequencing performance of the Ion AmpliSeq™ MH-74 plex microhaplotype research panel. A total of 178 samples from 3 major biogeographic regions including 54 Africans, 61 Iraqis from the Middle East and 63 Germans were genotyped using this panel on the Ion S5™ MPS platform (Thermo Fisher Scientific). Then we obtained the allele frequencies, the effective number of alleles (Ae), and the forensic efficiency parameters of the 74 MHs. Finally, STRUCTURE analysis was used to evaluate and compare the biostatistical efficiency of the 74 MHs in the 3 major biogeographic regions. All results demonstrated that the Ion AmpliSeq™ MH-74 plex microhaplotype research panel is characterized by a reliable sequencing performance.

Identifying rare variants inconsistent with identity‐by‐descent in population‐scale whole‐genome sequencing data

Abstract Analyses of genetic variation typically assume that rare variants within a population are inherited from a single common ancestral event identity‐by‐descent (IBD). However, there are genetic and technical processes through which rare variants in population genetic data may deviate from this simple evolutionary model, including recurrent mutations, gene conversions and genotyping error. All these processes can decrease the expected length of shared background haplotype surrounding a rare variant if that variant was inherited from a single event descending from a common ancestor. No method exists to computationally infer rare variants inconsistent with this simple model—denoted here as ‘IBD‐inconsistent’—using unphased population sequencing data. We hypothesized that the difference in shared haplotype background length can distinguish variants consistent and inconsistent with this simple IBD transmission population sequencing data without pedigree information. We implemented a Bayesian hierarchical model and used Gibbs sampling to estimate the posterior probability of IBD state for rare variants, using simulated recurrent mutations to demonstrate that our approach accurately distinguishes rare variants consistent and inconsistent with a simple IBD inheritance model. Applying our method to whole‐genome sequencing data from 3,621 human individuals in the UK10K consortium, we found that IBD‐inconsistent variants correlated with higher local mutation rates and genomic features like replication timing. Using a heuristic to categorize IBD‐inconsistent variants as gene conversions, we found that potential gene conversions had expected properties such as enriched local GC content. By identifying IBD‐inconsistent variants, we can better understand the spectrum of recent mutations in human populations, a source of genetic variation driving evolution and a key factor in understanding recent demographic history.

Sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with S.

S* is a widely used statistic for detecting archaic admixture from population genetic data. Previous studies used freezing-archer to apply S*, which is only directly applicable to the specific case of Neanderthal and Denisovan introgression in Papuans. Here, we implemented sstar for a more general purpose. Compared with several tools, including SPrime, SkovHMM, and ArchaicSeeker2.0, for detecting introgressed fragments with simulations, our results suggest that sstar is robust to differences in demographic models, including ghost introgression and two-source introgression. We believe sstar will be a useful tool for detecting introgressed fragments in various scenarios and in non-human species.

Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population.

(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included in the Investigator DIPplex kit (Qiagen) were obtained in a sample of 631 unrelated Polish individuals. Allelic frequency data were compared with those reported for selected populations (3) Results: All the loci conformed with Hardy-Weinberg equilibrium after applying a Bonferroni correction and no pair-wise significant linkage disequilibrium was detected. (4) Conclusions: DIPplex Kit differences were high among populations worldwide. The InDel markers are highly discriminating for human identification purposes in the Polish population.

Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates

Biological invasions drive environmental change, potentially threatening native biodiversity, human health, and global economies. Population genomics is an increasingly popular tool in invasion biology, improving accuracy and providing new insights into the genetic factors that underpin invasion success compared to research based on a small number of genetic loci. We examine the extent to which population genomic resources, including reference genomes, have been used or are available for invasive species research. We find that 82% of species on the International Union for Conservation of Nature “100 Worst Invasive Alien Species” list have been studied using some form of population genetic data, but just 32% of these species have been studied using population genomic data. Further, 55% of the list’s species lack a reference genome. With incursion rates escalating globally, understanding how genome-driven processes facilitate invasion is critical, but despite a promising trend of increasing uptake, “invasion genomics” is still in its infancy. We discuss how population genomic data can enhance our understanding of biological invasion and inform proactive detection and management of invasive species, and we call for more research that specifically targets this area.

Uniting genetic and geographic databases to understand the relationship between latitude and population demography

It was not known that phylogenetic analysis of population genetic data would show geographic structure when Avise et al.(1979) introduced the unnamed field of phylogeography. Since then, the field has grown from using single gene fragments to whole genomes resulting in more than 22,000 publications. This seemingly simple relationship between geography and genetic variation has provided the foundation for studying speciation, species delimitation, hybrid zone dynamics, adaptation, conservation genetics, community assembly, and historical demography to name a few (see Burbrink & Ruane,2021; Edwards et al.,2016). As with many burgeoning fields, there is often little consideration of how to make data sets accessible for future researchers addressing more comprehensive questions under a common framework. For example, it is important in biogeography to examine how shared environments or barriers affect population structure across communities of species, or test if range size or latitude are correlated with genetic diversity across taxa (Myers et al.,2019; Smith et al.,2017). However, addressing these types of questions using existing data requires researchers to assemble large databases manually. Genetic and geographic databases used to store this information like NCBI Genbank (National Center for Biotechnology Information) and GBIF (Global Biodiversity Information Facility) are disconnected, and often of limited general use for conducting multitaxon studies. In this issue of Molecular Ecology Resources, Pelletier et al.(2022) have automated the process of connecting geography to DNA sequences via the phylogatR (phylogeographic data aggregation and repurposing) database.

Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations.

The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (<5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.

CaliPopGen: A genetic and life history database for the fauna and flora of California

CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985–2020) for 5,453 unique populations with genetic data from more than 187,394 individuals and 448 species (513 species plus subspecies) across molecular markers including allozymes, RFLPs, mtDNA, microsatellites, nDNA, and SNPs. Terrestrial habitats accounted for the majority (46.4%) of the genetic data. Taxonomic groups with the greatest representation were Magnoliophyta (20.31%), Insecta (13.4%), and Actinopterygii (12.85%). CaliPopGen also reports life-history data for most included species to enable analyses of the drivers of genetic diversity across the state. The large number of populations and wide taxonomic breadth will facilitate explorations of ecological patterns and processes across the varied geography of California. CaliPopGen covers all terrestrial and marine ecoregions of California and has a greater density of species and georeferenced populations than any previously published population genetic database. It is thus uniquely suited to inform conservation management at the regional and state levels across taxonomic groups.

Movements of southern elephant seals (Mirounga leonina) from Davis Base, Antarctica: combining population genetics and tracking data

Marine animals such as the southern elephant seal (Mirounga leonina) rely on a productive marine environment and are vulnerable to oceanic changes that can affect their reproduction and survival rates. Davis Base, Antarctica, acts as a moulting site for southern elephant seals that forage in Prydz Bay, but the mitochondrial haplotype diversity and natal source populations of these seals have not been characterized. In this study, we combined genetic and animal tracking data on these moulting seals to identify levels of mitochondrial haplotype diversity, natal source population, and movement behaviours during foraging and haul-out periods. Using partial sequences of the mitochondrial control region, we identified two major breeding mitochondrial lineages of seals at Davis Base. We found that the majority of the seals originated from breeding stocks within the South Atlantic Ocean and South Indian Ocean. One seal was grouped with the Macquarie Island breeding stock (South Pacific Ocean). The Macquarie Island population, unlike the other two stocks, is decreasing in size. Tracking data revealed long-distance foraging activity of the Macquarie Island seal around Crozet Islands. We speculate that changes to the Antarctic marine environment can result in a shift in foraging and movement strategies, which subsequently affects seal population growth rates.

Genetic polymorphisms of 66 InDel loci in the Chinese Han population.

Insertion/deletion polymorphism (InDel) genetic markers refer to insertion or deletion of DNA fragments into genomic DNA, which have advantages in the identification of degraded samples. In this study, we independently screened 66 highly polymorphic InDel markers from the dbSNP database to establish a multiplex PCR system for forensic DNA identification using next-generation sequencing system (66-plex InDels). We assessed the population genetic data among 251 Chinese Han population using this system and evaluated their potential forensic application. The results showed that all 66 InDel loci conformed to the Hardy-Weinberg equilibrium (P>0.000 758), and all the pairwise InDel loci were in linkage equilibrium after Bonferroni correction. The mean observed heterozygosity (Ho) was 0.482, the mean expected heterozygosity (He) was 0.483,the mean discrimination power (DP) was 0.612, the mean polymorphism information content (PIC) was 0.365, the total discrimination power (TDP) reached 0.999 999 999 999 999 999 999 999 999 428 18. The cumulative power of exclusion for 66 InDel loci was 0.999 739 in duo cases (CPEduo) and was 0.999 999 999 417 in trios cases (CPEtrio). The results show that the 66 InDel loci have high genetic polymorphisms in the Chinese Han population and can be used independently for forensic DNA identification and paternity testing.

Prevalence and population genetic data of colour vision deficiency among students from selected tertiary institutions in Lagos State, Nigeria

BackgroundColour vision deficiency (CVD), also referred to as colour blindness, is the failure or decreased ability to distinguish between certain colours under normal lighting conditions. It is an X-linked genetic disorder with varying degrees of prevalence in different populations. There is presently no report on the prevalence of CVD among students of the selected tertiary institution. Hence, the present study was aimed at determining the occurrence and genetics of CVD among students from designated tertiary institutions in Lagos state. A cross-sectional survey was employed in recruiting 1191 study subjects from three tertiary institutions in Lagos, Nigeria.ResultsThe overall occurrence of CVD among the study participants was 2.85%. There were 24 (4.29%) males and 10 (1.58%) females affected. Among the colour vision deficient individuals, 18 (1.51%) and 16 (1.34%) were deuteranomalous and protanomalous, respectively. Also, the prevalence of CVD varies across ethnic groups of the studied subjects with the highest occurrences (3.57%) observed in the Yoruba ethnic subpopulation and the least (1.45%) among the Hausas.ConclusionsMore males than females were found to be colour vision deficient, and there were more deutans than protans. Early screening for CVD should be encouraged among school children to guide the choice of future profession and help mitigate work hazards resulting from being colour deficient.

Parapatric Genetic Lineages Persist in a Multiply Introduced Non-native Bush-Cricket

To understand colonization success of an invasive species we need to know the origin of the founders, where and when they were introduced, and how they spread from the introduction site(s) through the landscape. Admixture of different genetic lineages from multiple introductions is generally hypothesized to be beneficial to invasive species thanks to adaptive variation and heterozygosity-fitness correlations. In this study, population genetic and landscape data was gathered for Roesel’s bush-cricket,Roeseliana roeseliia small bush-cricket common in central and eastern Europe that currently is expanding its range in northern Europe. We examined how colonization history and landscape structure affect the spread of the species and its population genetic structure, as a consequence of multiple introductions. Using comprehensive information of the species ecology and dispersal, together with genetic structure inferred from samples from 29 locations in central Sweden (we employed data published by Preuss et al., 2015), we found that two parapatric founding lineages have coexisted with very little gene flow during a long time span. An isolation-by-distance pattern and a decrease of genetic diversity toward marginal areas were more pronounced in the lineage situated in forest dominated landscapes. Our findings are in strong contrast to the hypothesis that different genetic lineages will admix when introduced to the same area. The presence of the separate lineages decades after introduction and without physical barriers for gene flow shows that some mechanism prevents them from admixture. One possibility is that the lineages with different genetic setups have adapted independently to local conditions and their admixture resulted in loss of locally adapted genotypes and hybrid offspring, less viable than the respective ancestral genotypes. However, an alternative post-mating reproductive barrier and hybrid breakdown phenomenon should also be considered. Our data indicate that besides landscape characteristics, human transportation of agricultural goods may play an important role for the overall spatial genetic pattern of the species in the study area by aiding the spread of the species.

Drivers of unique and asynchronous population dynamics in Malagasy herpetofauna

AbstractAimA long history of isolation coupled with complex landscapes makes Madagascar ideal for exploring the historical factors that have shaped patterns of population diversity and endemism. Many species‐level studies have suggested Late Quaternary climate change may have influenced population dynamics in the tropics, but unique biomes and individual species properties may have driven idiosyncratic responses to these shifts. Here, we use community‐scale population genetic data to investigate the impact of Quaternary climate cycles on shared demographic response and investigate the contributions of both biotic and abiotic factors which shape these demographic trajectories.LocationMadagascar.TaxonReptiles and Amphibians.MethodsUsing community‐scale population genetic data, we implement a hierarchical approximate Bayesian computation approach to evaluate the degree of synchronous population expansion during glacial cycles across herpetofaunal assemblages both within and across discrete biomes and taxonomic groups. We use Bayesian model averaging to identify intrinsic and extrinsic conditions predictive of individualistic demographic change.ResultsWe find that demographic responses are not uniform across groups, with more than 50% of all populations showing signal of recent expansion. Our explanatory models indicate species occupying narrow elevational ranges had a higher probability of expansion, while amphibian assemblages showed higher genetic diversity and greater departures from population neutrality. Expansion events were largely asynchronous, with coexpansion found in less than half of all populations. Exceptionally, 69%–74% of all humid‐restricted populations coexpanded during the start of the Last Glacial Period at around 100 kya, supporting the hypothesis of a more extensive humid forest cover for Madagascar during this time.Main conclusionsWe show that differences in life history and regional biogeography have contributed to patterns of richness and endemism found across Madagascar, and historical connectivity across humid forests has been an important factor in shaping present‐day diversity and endemism on Madagascar, particularly for amphibians.

Insight into the genetic and forensic attributes of Brahmin population of Himachal Pradesh, India

We evaluated the genetic polymorphism of Brahmin population of Himachal Pradesh using the PowerPlex® 21 System (Promega, USA). Altogether, we observed 200 alleles among 170 genetically unrelated individuals of the Brahmin population by using 20 STR loci with average 10 ± 0.75 alleles per locus. The unbiased expected heterozygosity (UHe) in the population ranged from 0.70 to 0.93 with an average 0.82 ± 0.01. No locus deviated from Hardy Weinberg equilibrium except D2S1338. Locus Penta E was found to be the most polymorphic with the highest power of discrimination. The combined power of discrimination and the combined power of exclusion was 1 and 0.999999996 for 20 STR loci exhibiting suitability of this select panel of loci in forensic casework and population genetic studies. Additionally, we analysed the phylogenetic relationship of Brahmins of Himachal Pradesh with the available data of Brahmin populations from the other States of India. The results showed relatively high genetic affinity between the Brahmins of Himachal Pradesh and Madhya Pradesh. The study provides novel population genetic data of the Brahmin population of Himachal Pradesh which is forensically important considering the ‘DNA Technology (Use and Application) Regulation Bill, 2019’ recently introduced in Lok Sabha, Government of India in respect of matters under the Indian Penal Code, 1860, and for civil matters such as paternity suits and establishment of individual identity.