Population Genetic Patterns Research Articles

Oceanic islands act as drivers for the genetic diversity of marine species: Cardita calyculata (Linnaeus, 1758) in the NE Atlantic as a case-study

Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.

Population genetics of the freshwater red alga Batrachospermum gelatinosum (Rhodophyta) I: Frequent intragametophytic selfing in a monoicous, haploid-diploid species.

Life cycles with a prolonged haploid phase are thought to be correlated with greater rates of selfing and asexual reproduction. In red algae, recent population genetic studies have aimed to test this prediction but have mostly focused on marine species with separate sexes. We characterized the reproductive system of the obligately monoicous (i.e., hermaphroditic) freshwater red alga Batrachospermum gelatinosum and predicted that we would find genetic signatures of uniparental reproduction because of its haploid-diploid life cycle. We sampled 18 sites and genotyped 311 gametophytes with 10 polymorphic microsatellite loci to describe the reproductive system. Genotypic richness was low (<0.5) and pareto β values (describing clonal membership) were <0.7 for most sites. In taxa with separate sexes, these patterns are typically indicative of asexual reproduction. However, the genetic consequences of selfing in monoicous gametophytes are indistinguishable from those caused by asexual processes. Since we sampled gametophytes and have not yet genotyped the chantransia (i.e., the diploid phase), we interpretedlow diversity as a signature of intragametophytic selfing. Additionally, to understand the factors that drive selfing, we tested latitude and several other environmental variables, but none was significantly correlated with the genetic variation we observed. Nevertheless, future studies should genotype the chantransia to measure observed heterozygosity among other summary statistics to disentangle the effects of selfing versus asexual reproduction. Together, these data, coupled with further characterization of abiotic factors that influence population genetic patterns, will allow us to test potential drivers of reproductive system evolution.

Clonality contributes to the spread of Avrainvillea lacerata (Bryopsidales, Chlorophyta) in Hawai'i.

The relative rates of sexual versus asexual reproduction influence the partitioning of genetic diversity within and among populations. During range expansions, asexual reproduction often facilitates colonization and establishment. The arrival of the green alga Avrainvillea lacerata has caused shifts in habitat structure and community assemblages since its discovery in 1981 offshore of O'ahu, Hawai'i. Field observations suggest this species is spreading via vegetative reproduction. To characterize the reproductive system of A. lacerata in Hawai'i, we developed seven microsatellite loci and genotyped 321 blades collected between 2018 and 2023 from three intertidal sites at Maunalua Bay and 'Ewa Beach. We observed one to four alleles at multiple loci, suggesting A. lacerata is tetraploid. Each site was characterized by high genotypic richness (R > 0.8). However, clonal rates were also high, suggesting the vegetative spread of A. lacerata plays a significant role. The importance of clonal reproduction for the persistence of A. lacerata in Hawai'i is consistent with the ecological data collected for this species and observations of other abundant macroalgal invaders in Hawai'i and other regions of the world. These data demonstrate the necessity for implementing appropriate population genetic methods and provide insights into the biology of this alga that will contribute to future studies on effective management strategies incorporating its reproductive system. This study represents one of the few that investigate green algal population genetic patterns and contributes to our understanding of algal reproductive system evolution.

Comparative Genomics of Eight Complete Chloroplast Genomes of Phyllostachys Species

(1) Background: The genus Phyllostachys belongs to the subfamily Bambusoideae within the family Gramineae. Bamboos of this genus are distinguished by their remarkable genetic traits, including exceptional resistance to both cold and drought conditions. These species possess considerable economic, ecological, and aesthetic value, finding extensive use in forestry and landscape design across China. (2) Methods: This study employed Illumina’s second-generation sequencing technology to sequence the chloroplast genomes of eight Phyllostachys species, followed by their assembly and annotation. (3) Results: The chloroplast genomes of the genus exhibit a characteristic tetrad structure with an average sequence length of 139,699 bp and an average GC content of 38.9%. A total of 130 genes have been annotated across eight bamboo species, comprising 75 protein-coding genes, 28 tRNA genes, and four rRNA genes. Global alignment and nucleotide polymorphism analyses indicate that the chloroplast genome of Phyllostachys is highly conserved overall. The boundaries of the four chloroplast regions are relatively conserved and exhibit minimal differences. Among these regions, three coding region genes—atpH, trnQ-UUG, and petB—and five non-coding regions—rpl32-trnL-UAG, rpl14-rpl16, rpl22-rps19, rps12-clpP, and trnR-UCU-trnM-CAU—exhibit high polymorphism and can be used as potential hotspot areas for subsequent research. A total of 266 simple sequence repeat (SSR) loci were identified by SSR analysis in the chloroplast genomes of eight bamboo species; the largest number of mononucleotide repeats was 154, predominantly consisting of A/T. Codon bias in the chloroplast genomes of the eight bamboo species indicates a preference for codons ending with A and U. Additionally, the UUA codon, which encodes leucine (Leu), is positioned between codons encoding phenylalanine (Phe), lysine (Lys), leucine (Leu), serine (Ser), and tyrosine (Tyr), indicating certain differences among these species. (4) Conclusions: This study aims to offer novel insights into the population genetics, phylogenetic relationships, and evolutionary patterns of Phyllostachys.

Population genomics of seal lice provides insights into the postglacial history of northern European seals.

Genetic analyses of host-specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population-genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent-based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome-based reconstructions of long-term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts.

Population genetics and evolutionary history of the intertidal brittle star Ophiothrix (Ophiothrix) exigua in the northern China Sea.

Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species.

Distinct phylogeographic and population genetic patterns of decapod species across Mediterranean biogeographic barriers

Abstract The Mediterranean Sea is a semi-enclosed oceanic basin that communicates with the Atlantic Ocean and can be subdivided into seven geographical regions. It is considered a hotspot of biodiversity and is characterised by high rates of endemism. Over the past decades, many studies showed the presence of potential geographical breaks both across the Atlanto-Mediterranean transition and within the Mediterranean Sea. These investigations led to the identification of three distinct types of population genetic structures: (1) populations characterized by panmixia; (2) Atlanto-Mediterranean geographical partitioning; and (3) possible further subdivision between East and West Mediterranean basins. In this review, mainly focused on Christoph Schubart’s works and interests, we summarize the different patterns of gene flows across the Atlanto-Mediterranean transition and within the Mediterranean Sea, recorded for decapod species living in littoral zones. Although some species share similar biological traits, larval dispersal mechanisms and habitat preferences, differences in their phylogeographic and population genetic structures do emerge. These findings confirm the complex nature of gene flows across the Atlanto-Mediterranean transition and within the Mediterranean basin and how difficult it is to achieve a generalised picture of the phylogeographical patterns of Atlantic-Mediterranean species.

Species distribution models predict genetic isolation of Hetaerina vulnerata Hagen in Selys, 1853 (Odonata, Calopterygidae).

Understanding how past and current environmental conditions shape the demographic and genetic distributions of organisms facilitates our predictions of how future environmental patterns may affect populations. The Canyon Rubyspot damselfly (Odonata: Zygoptera: Hetaerina vulnerata) is an insect with a range distribution from Colombia to the arid southwestern United States, where it inhabits shaded mountain streams in the arid southwestern United States. Past spatial fragmentation of habitat and limited dispersal capacity of H. vulnerata may cause population isolation and genetic differentiation, and projected climate change may exacerbate isolation by further restricting the species' distribution. We constructed species distribution models (SDMs) based on occurrences of H. vulnerata and environmental variables characterizing the species' niche. We inferred seven current potential population clusters isolated by unsuitable habitat. Paleoclimate models indicated habitat contiguity in past conditions; projected models indicated some habitat fragmentation in future scenarios. Seventy-eight H. vulnerata individuals from six of the current clusters were sequenced via ddRADseq and processed with Stacks. Principal components and phylogeographic analyses resolved three subpopulations; Structure resolved four subpopulations. F ST values were low (<0.05) for nearby populations and >0.15 for populations separated by expanses of unsuitable habitat. Isolation by distance was an existing but weak factor in determining genomic structure; isolation by environment and the intervening landscape explained a significant proportion of genetic distance. Hetaerina vulnerata populations were shown to be isolated by a lack of tree canopy coverage, an important habitat predictor for oviposition and territoriality. Thus, H. vulnerata populations are likely separated and are genetically isolated. Integrating SDMs with landscape genetics allowed us to identify populations separated by distance and unsuitable habitat, explaining population genetic patterns and probable fates for populations under future climate scenarios.

Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana)

The nonrandom distribution of chromosomal characteristics and functional elements—genomic architecture—impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure—ordination, clustering, and phylogenetic methods—we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.

Genetic structure of ten Artemia populations from China: cumulative effects of ancient geological events, climatic changes, and human activities

This study investigated the population genetics and distribution patterns of Artemia populations from ten inland salt lakes in China. A total of 1,274,698 Artemia single nucleotide polymorphisms (SNPs) were identified. The results showed that these populations could be geographically and genetically divided into four distinct groups, and that the Tibetan populations were further divided into two subpopulations with a trend of decreasing genetic diversity from west to east. The Tibetan population had the highest genetic diversity, whereas the Shanxi population had the lowest. There was moderate genetic differentiation between the Tibetan populations and greater genetic differentiation between the Xinjiang and Shanxi populations. IBD (isolation by distance) suggested that geographical isolation contributes to genetic differentiation. In addition, there was some degree of gene flow among the ten populations, with A. sinica showing unidirectional gene flow in all populations in the eastern Nagri region. Species distribution modeling showed that mean annual temperature, temperature seasonality, and annual precipitation were the main environmental factors affecting the distribution of Artemia populations and suitable habitats for Tibetan populations will be further reduced in the future. It is necessary to strengthen the protection of germplasm resources and formulate scientific protocols for the sustainable development and utilization of Artemia resources.

Evolutionary relationships, hybridization and diversification under domestication of the locoto chile (Capsicum pubescens) and its wild relatives.

Patterns of genetic variation in crops are the result of multiple processes that have occurred during their domestication and improvement, and are influenced by their wild progenitors that often remain understudied. The locoto chile, Capsicum pubescens, is a crop grown mainly in mid-highlands of South-Central America. This species is not known from the wild and exists only as a cultigen. The evolutionary affinities and exact origin of C. pubescens have still not been elucidated, with hypotheses suggesting its genetic relatedness and origin to two wild putative ancestral Capsicum species from the Central Andes, C.eximium and C. cardenasii. In the current study, RAD-sequencing was applied to obtain genome-wide data for 48 individuals of C. pubescens and its wild allies representing different geographical areas. Bayesian, Maximum Likelihood and coalescent-based analytical approaches were used to reconstruct population genetic patterns and phylogenetic relationships of the studied species. The results revealed that C. pubescens forms a well-defined monotypic lineage closely related to wild C. cardenasii and C. eximium, and also to C. eshbaughii. The primary lineages associated with the diversification under domestication of C. pubescens were also identified. Although direct ancestor-descendant relationship could not be inferred within this group of taxa, hybridization events were detected between C. pubescens and both C.cardenasii and C. eximium. Therefore, although hybrid origin of C. pubescens could not be inferred, gene flow involving its wild siblings was shown to be an important factor contributing to its contemporary genetic diversity. The data allowed for the inference of the center of origin of C. pubescens in central-western Bolivia highlands and for better understanding of the dynamics of its gene pool. The results of this study are essential for germplasm conservation and breeding purposes, and provide excellent basis for further research of the locoto chile and its wild relatives.

Sampling through space and time: multi-year analysis reveals dynamic population genetic patterns for an amphibian metapopulation

Metapopulations are dynamic, and population genetics can reveal both spatial and temporal metapopulation variation. Yet, population genetic studies often focus on samples collected within a single time period or combine samples taken across time periods due to limited resources and the assumption that these approaches capture patterns and processes occurring over decadal and longer temporal scales. However, this may leave important fine-scale temporal variation in genetic composition undetected, particularly for metapopulations in which dynamic populations are expected. We investigated temporal patterns of population genetic diversity, effective population size, and differentiation across three sample periods for a dryland amphibian metapopulation. We sampled nine distinct Arizona treefrog (Hyla (Dryophytes) wrightorum) breeding ponds in 2014, 2018/2019, and 2021 and genotyped 17 microsatellite loci to quantify spatial and temporal population genetic dynamics. Genetic diversity within and between populations varied significantly among years. Most notably, we identified a concerning decline in allelic richness across populations, with an average − 26.11% difference between a population’s first and last sample period. Effective population sizes were generally small (Ne < 100) and variable within and among populations over time, with many populations falling below common conservation thresholds by the final sample period. Trends in global genetic diversity, as measured by heterozygosity, and population differentiation were relatively consistent across all sampling periods. Overall, we found that “snapshot” or single-time sampling approaches may miss temporal variability in genetic composition that has important conservation implications, including early warning signs of decline in genetic diversity.

The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera.

Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification. Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios. The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered. Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability.

Development of polymorphic microsatellite markers for distylous-homostylous Primula secundiflora (Primulaceae) using HiSeq sequencing.

Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.

Population genetic structure of tropical bed bug (Hemiptera: Cimicidae) populations and their breeding pattern in Iraq.

A study was conducted to investigate the population genetic structure and breeding pattern of 140 tropical bed bugs, Cimex hemipterus (F.) (Hemiptera: Cimicidae), collected from 14 infested sites in major cities in Iraq. The samples were genotyped using a set of 7 polymorphic microsatellite markers. High genetic variety was seen among populations, with an average of 2-9 alleles per locus. The number of alleles across 7 microsatellite loci was between 6 and 18. There was a notable disparity in the alleles per loci when comparing the overall population to those within it. The overall population exhibited an average observed heterozygosity of 0.175 and an average expected heterozygosity of 0.730. Among the population, the average observed heterozygosity was 0.173, while the average expected heterozygosity was 0.673. Analysis of molecular variance (AMOVA) revealed that 93% of the genetic variability was within the populations, and 7% was among them. The genetic differentiation coefficient (FST = 0.045), indicates a low degree of genetic differentiation and a high degree of inbreeding (FIS = 0.761), as indicated by notably significant positive inbreeding coefficients. Admixed individuals were revealed using STRUCTURE and neighbor-joining phylogenetic trees, demonstrating moderate gene flow between populations and a lack of genetic structure in the regional groups. Thus, both active dispersion and human-mediated dispersion possess the potential to influence the low population genetic structure of tropical bed bug C. hemipterus populations in Iraq, which can have implications toward tropical bed bug and management strategies.

Population genetic patterns across the native and invasive range of a widely distributed seagrass: Phylogeographic structure, invasive history and conservation implications.

The seagrass Zostera japonica is a dramatically declined endemic species in the Northwestern Pacific from the (sub)tropical to temperate areas, however, it is also an introduced species along the Pacific coast of North America from British Columbia to northern California. Understanding the population's genetic patterns can inform the conservation and management of this species. North Pacific. We used sequences of the nuclear rDNA internal transcribed spacer (ITS) and chloroplast trnK intron maturase (matK), and 24 microsatellite loci to survey 34 native and nonnative populations (>1000 individuals) of Z. japonica throughout the entire biogeographic range. We analysed the phylogeographic relationship, population genetic structure and genetic diversity of all populations and inferred possible origins and invasion pathways of the nonnative ones. All markers revealed a surprising and significant deep divergence between northern and southern populations of Z. japonica in the native region separated by a well-established biogeographical boundary. A secondary contact zone was found along the coasts of South Korea and Japan. Nonnative populations were found to originate from the central Pacific coast of Japan with multiple introductions from at least two different source populations, and secondary spread was likely aided by waterfowl. The divergence of the two distinct clades was likely due to the combined effects of historical isolation, adaptation to distinct environments and a contemporary physical barrier created by the Yangtze River, and the warm northward Kuroshio Current led to secondary contact after glacial separation. Existing exchanges among the nonnative populations indicate the potential for persistence and further expansion. This study not only helps to understand the underlying evolutionary potential of a widespread seagrass species following global climate change but also provides valuable insights for conservation and restoration.

Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos.

Meiotic recombination is crucial for human genetic diversity and chromosome segregation accuracy. Understanding its variation across individuals and the processes by which it goes awry are long-standing goals in human genetics. Current approaches for inferring recombination landscapes rely either on population genetic patterns of linkage disequilibrium (LD)-capturing a time-averaged view-or on direct detection of crossovers in gametes or multigeneration pedigrees, which limits data set scale and availability. Here, we introduce an approach for inferring sex-specific recombination landscapes using data from preimplantation genetic testing for aneuploidy (PGT-A). This method relies on low-coverage (<0.05×) whole-genome sequencing of in vitro fertilized (IVF) embryo biopsies. To overcome the data sparsity, our method exploits its inherent relatedness structure, knowledge of haplotypes from external population reference panels, and the frequent occurrence of monosomies in embryos, whereby the remaining chromosome is phased by default. Extensive simulations show our method's high accuracy, even at coverages as low as 0.02×. Applying this method to PGT-A data from 18,967 embryos, we mapped 70,660 recombination events with ∼150 kbp resolution, replicating established sex-specific recombination patterns. We observed a reduced total length of the female genetic map in trisomies compared with disomies, as well as chromosome-specific alterations in crossover distributions. Based on haplotype configurations in pericentromeric regions, our data indicate chromosome-specific propensities for different mechanisms of meiotic error. Our results provide a comprehensive view of the role of aberrant meiotic recombination in the origins of human aneuploidies and offer a versatile tool for mapping crossovers in low-coverage sequencing data from multiple siblings.

Population genetics and ecological niche modelling provide insights into management strategies of the herbivorous pest Phytomyza horticola (Diptera: Agromyzidae)

AbstractAimResearch on population genetic patterns and potential distribution dynamics can provide insights into the development of pest management strategies. Herein, we integrated population genetic analyses with the climatic niche approach to investigate spatial population genetic variations and potential geographical distribution (PGD) of the herbivorous pest Phytomyza horticola. We also analysed its population response patterns to both late Pleistocene climatic events and future climate change.LocationChina.MethodsWe analysed the patterns of genetic diversity distribution in 29 populations from 19 regions across China using three mitochondrial (COI, COII and Cytb) genes as markers. We estimated demographic histories using neutrality tests, mismatch distributions and Bayesian skyline plots. Changes in PGD were assessed using an ecological niche model.ResultsHigh genetic diversity was found in most populations, and the northern population exhibited higher haplotype diversity. The population genetic structure included the Tibet lineage and a large lineage comprising the remaining populations. Demographic analyses indicated that rapid population expansion occurred during the cold Last Glacial Maximum. In addition, our projections suggested that P. horticola currently has a vast PGD in China, for which the human influence index was the strongest variable. Large areas of cold northern regions were highly suitable for its survival. Under future global warming, highly suitable habitats will shift towards the higher latitudes.Main conclusionsP. horticola is widely distributed across varied environments, which may be attributed to its high degree of genetic variation. Human activities likely facilitated the current PGD and the frequent gene flow that homogenized differentiation among most populations. In addition, P. horticola exhibits strong adaptability to cold climates and environments from the past to the future. Considering future climatic changes, prevention and control should focus on high‐latitude regions, and vigilance regarding human‐mediated pest dispersals and outbreaks should be maintained.

Evolution under a model of functionally buffered deleterious mutations can lead to positive selection in protein-coding genes.

Selective pressures on DNA sequences often result in departures from neutral evolution that can be captured by the McDonald-Kreitman (MK) test. However, the nature of such selective forces often remains unknown to experimentalists. Amino acid fixations driven by natural selection in protein-coding genes are commonly associated with a genetic arms race or changing biological purposes, leading to proteins with new functionality. Here, we evaluate the expectations of population genetic patterns under a buffering mechanism driving selective amino acids to fixation, which is motivated by an observed phenotypic rescue of otherwise deleterious nonsynonymous substitutions at bag of marbles (bam) and Sex lethal (Sxl) in Drosophila melanogaster. These two genes were shown to experience strong episodic bursts of natural selection potentially due to infections of the endosymbiotic bacteria Wolbachia observed among multiple Drosophila species. Using simulations to implement and evaluate the evolutionary dynamics of a Wolbachia buffering model, we demonstrate that selectively fixed amino acid replacements will occur, but that the proportion of adaptive amino acid fixations and the statistical power of the MK test to detect the departure from an equilibrium neutral model are both significantly lower than seen for an arms race/change-in-function model that favors proteins with diversified amino acids. We find that the observed selection pattern at bam in a natural population of D. melanogaster is more consistent with an arms race model than with the buffering model.

O-103 A method for mapping sex-specific meiotic crossovers from PGT-A data elucidates the role of aberrant recombination in the origins of aneuploidy

Abstract Study question How do the number and location of meiotic crossovers contribute to the formation of aneuploidies observed in preimplantation human embryos? Summary answer Normalized across chromosomes, trisomies possess 35% fewer crossovers on average compared to disomies, while the genomic distribution of crossovers is also substantially altered. What is known already Meiotic recombination is a crucial source of genetic diversity and is also critical for ensuring the accuracy of chromosome segregation. Understanding the landscape of meiotic recombination, its variation across individuals, and the processes by which it goes awry are long-standing goals in human genetics. Current approaches for inferring the landscape of recombination either rely on population genetic patterns of linkage disequilibrium—capturing a time-averaged view—or direct detection of crossovers in gametes or multi-generation pedigrees, limiting the scale and availability of relevant datasets. Moreover, most of these methods are designed for discovering recombination using data from normal, disomic chromosomes. Study design, size, duration We present a method for mapping sex-specific recombination landscapes from low-coverage (&amp;lt;0.1×) data from preimplantation genetic testing for aneuploidy (PGT-A) of embryos with arbitrary ploidy configurations. To overcome the sparsity of these data, our method exploits its inherent relatedness structure, knowledge of haplotypes from external population reference panels, as well as the frequent occurrence of chromosome loss in embryos, whereby the remaining chromosome is phased by default. Participants/materials, setting, methods We benchmarked our method by simulating crossovers between known haplotypes. Encouraged by the performance on simulated data we extended our study to retrospective analysis utilizing de-identified PGT-A data obtained between April 2021 and August 2022 at the CReATe Fertility Centre (Toronto, Canada). The data include 20,160 embryos (2,559 IVF patients) with an average depth of coverage of ∼0.05×, facilitating the mapping of crossovers at an average resolution of ∼150 kbp. Main results and the role of chance Our benchmarking results demonstrate high sensitivity and specificity across all ancestries at a coverage of 0.05x per homolog (AUC = 0.989), with AUC declining by 0.014 and 0.053 for when coverage is reduced to 0.025x and 0.013x, respectively. Extending our analysis to real PGT-A data, we observed that our inferred sex-specific landscapes of meiotic crossovers on disomic chromosomes were strongly correlated with published genetic maps from studies based on high-coverage sequencing of parent-offspring trios (r = 0.86 for female map; r = 0.53 for male map), broadly supporting the accuracy of our method. Notably, the total length of the female genetic map was reduced by 35% for trisomies compared to disomies, consistent with the hypothesized role of reduced crossovers and exchangeless chromosomes in the origins of female meiotic aneuploidy. In addition, the genomic distribution of crossovers is also altered in a chromosome-specific manner. Examples include a reduction in crossovers near the centromere of trisomies versus disomies of chromosome 16, as well as an enrichment of crossovers on the q-arm of trisomies versus disomies of chromosome 22. Together, our results provide a detailed corroboration of the hypothesis that aberrant meiotic recombination contributes to the origins of aneuploidies. Limitations, reasons for caution The accuracy of our method is influenced by genomic heterogeneity in depth of coverage, rates of heterozygosity, and mismatches between the ancestry of the reference panel and the tested sequence. Moreover, technical errors such as spurious alignment and genotyping could hinder analysis in repetitive genomic regions. Wider implications of the findings Together, our study helps clarify the dual function of meiotic recombination in generating genetic diversity while ensuring meiotic fidelity. Our method for patient-specific mapping of meiotic recombination phenotypes may offer clues about how dysregulation of this process contributes to infertility. Trial registration number NIH r R35GM13374