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BMC Plant Biology Feb 2024Geological movements and climatic fluctuations stand as pivotal catalysts driving speciation and phylogenetic evolution. The genus Polyspora Sweet (Theaceae),...
BACKGROUND
Geological movements and climatic fluctuations stand as pivotal catalysts driving speciation and phylogenetic evolution. The genus Polyspora Sweet (Theaceae), prominently found across the Malay Archipelagos and Indochina Peninsula in tropical Asia, exhibits its northernmost distribution in China. In this study, we investigated the evolutionary and biogeographical history of the genus Polyspora in China, shedding light on the mechanisms by which these species respond to ancient geological and climatic fluctuations.
METHODS
Phylogenetic relationships of 32 representative species of Theaceae were reconstructed based on the chloroplast genome and ribosome 18-26 S rRNA datasets. Species divergence time was estimated using molecular clock and five fossil calibration. The phylogeography and population genetics in 379 individuals from 32 populations of eight species were analyzed using chloroplast gene sequences (trnH-psbA, rpoB-trnC and petN-psbM), revealing the glacial refugia of each species, and exploring the causes of the phylogeographic patterns.
RESULTS
We found that Chinese Polyspora species diverged in the middle Miocene, showing a tropical-subtropical divergence order. A total of 52 haplotypes were identified by the combined chloroplast sequences. Chinese Polyspora exhibited a distinct phylogeographical structure, which could be divided into two clades and eight genealogical subdivisions. The divergence between the two clades occurred approximately 20.67 Ma. Analysis of molecular variance revealed that the genetic variation mainly occurred between species (77.91%). At the species level, Polyspora axillaris consists of three lineages, while P. speciosa had two lineages. The major lineages of Chinese Polyspora diverged between 12 and 15 Ma during the middle to late Miocene. The peak period of haplotype differentiation in each species occurred around the transition from the last interglacial to the last glacial period, approximately 6 Ma ago.
CONCLUSION
The primary geographical distribution pattern of Chinese Polyspora was established prior to the last glacial maximum, and the population historical dynamics were relatively stable. The geological and climatic turbulence during the Quaternary glacial period had minimal impact on the distribution pattern of the genus. The genus coped with Quaternary climate turbulence by glacial in situ survival in multiple refuges. The Sino-Vietnam border and Nanling corridor might be the genetic mixing center of Polyspora.
Topics: Humans; Phylogeography; Phylogeny; Genetics, Population; China; Asia; Haplotypes; Genetic Variation; DNA, Chloroplast; Evolution, Molecular
PubMed: 38317071
DOI: 10.1186/s12870-024-04783-5 -
Genetics Jun 2024The rate at which recombination events occur in a population is an indicator of its effective population size and the organism's reproduction mode. It determines the...
The rate at which recombination events occur in a population is an indicator of its effective population size and the organism's reproduction mode. It determines the extent of linkage disequilibrium along the genome and, thereby, the efficacy of both purifying and positive selection. The population recombination rate can be inferred using models of genome evolution in populations. Classic methods based on the patterns of linkage disequilibrium provide the most accurate estimates, providing large sample sizes are used and the demography of the population is properly accounted for. Here, the capacity of approaches based on the sequentially Markov coalescent (SMC) to infer the genome-average recombination rate from as little as a single diploid genome is examined. SMC approaches provide highly accurate estimates even in the presence of changing population sizes, providing that (1) within genome heterogeneity is accounted for and (2) classic maximum-likelihood optimization algorithms are employed to fit the model. SMC-based estimates proved sensitive to gene conversion, leading to an overestimation of the recombination rate if conversion events are frequent. Conversely, methods based on the correlation of heterozygosity succeed in disentangling the rate of crossing over from that of gene conversion events, but only when the population size is constant and the recombination landscape homogeneous. These results call for a convergence of these two methods to obtain accurate and comparable estimates of recombination rates between populations.
Topics: Recombination, Genetic; Models, Genetic; Markov Chains; Linkage Disequilibrium; Genome; Algorithms; Genetics, Population; Gene Conversion; Animals; Humans; Population Density
PubMed: 38565705
DOI: 10.1093/genetics/iyae051 -
Annual Review of Biomedical Data Science Aug 2023Admixed populations constitute a large portion of global human genetic diversity, yet they are often left out of genomics analyses. This exclusion is problematic, as it... (Review)
Review
Admixed populations constitute a large portion of global human genetic diversity, yet they are often left out of genomics analyses. This exclusion is problematic, as it leads to disparities in the understanding of the genetic structure and history of diverse cohorts and the performance of genomic medicine across populations. Admixed populations have particular statistical challenges, as they inherit genomic segments from multiple source populations-the primary reason they have historically been excluded from genetic studies. In recent years, however, an increasing number of statistical methods and software tools have been developed to account for and leverage admixture in the context of genomics analyses. Here, we provide a survey of such computational strategies for the informed consideration of admixture to allow for the well-calibrated inclusion of mixed ancestry populations in large-scale genomics studies, and we detail persisting gaps in existing tools.
Topics: Humans; Genetics, Population; Genomics; Software; Genome, Human
PubMed: 37127050
DOI: 10.1146/annurev-biodatasci-020722-014310 -
Nature Ecology & Evolution Feb 2024
Topics: Genetics, Population; Phylogeny; Prokaryotic Cells
PubMed: 38177691
DOI: 10.1038/s41559-023-02276-6 -
American Journal of Biological... Aug 2023Genes and languages both contain signatures of human evolution, population movement, and demographic history. Cultural traits like language are transmitted by...
OBJECTIVES
Genes and languages both contain signatures of human evolution, population movement, and demographic history. Cultural traits like language are transmitted by interactions between people, and these traits influence how people interact. In particular, if groups of people differentiate each other based on some qualities of their cultures, and if these qualities are passed to the next generation, then this differentiation can result in barriers to gene flow. Previous work finds such barriers to gene flow between groups that speak different languages, and we explore this phenomenon further: can more subtle cultural differences also produce genetic structure in a population? We focus on whether subtle, dialect-level linguistic differences in England have influenced genetic population structure, likely by affecting mating preferences.
MATERIALS AND METHODS
We analyze spatially dense linguistic and genetic data-both of which independently contain spatially structured variation in England-to examine whether the cultural differences represented by variation in English phonology colocalize with higher genetic rates of change.
RESULTS
We find that genetic variation and dialect markers have similar spatial distributions on a country-wide scale, and that throughout England, linguistic boundaries colocalize with the boundaries of genetic clusters found using fineSTRUCTURE.
DISCUSSION
This gene-language covariation, in the absence of geographic barriers that could coordinate cultural and genetic differentiation, suggests that similar social forces influenced both dialect boundaries and the genetic population structure of England.
Topics: Humans; Language; Linguistics; Genetics, Population; Genetic Drift; England
PubMed: 37377289
DOI: 10.1002/ajpa.24789 -
Proceedings of the National Academy of... Apr 2024Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and...
Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype-by-sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone. The sandy inland mouse () experiences marked boom-bust population dynamics in response to the highly variable desert environment. We show that heterozygosity levels declined, and population differentiation () increased, during bust periods when populations became small and isolated, but that heterozygosity was rapidly restored during episodic population booms. In contrast, the lesser hairy-footed dunnart (), a desert marsupial that maintains relatively stable population sizes, showed no linear declines in heterozygosity. These results reveal two contrasting ways in which genetic diversity is maintained in highly variable environments. In one species, diversity is conserved through the maintenance of stable population sizes across time. In the other species, diversity is conserved through rapid genetic mixing during population booms that restores heterozygosity lost during population busts.
Topics: Animals; Mice; Australia; Population Dynamics; Genotype; Mammals; Heterozygote; Marsupialia; Genetic Variation; Genetics, Population
PubMed: 38621118
DOI: 10.1073/pnas.2320590121 -
Molecular Ecology Resources Oct 2023In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from...
In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the 'true' cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the 'true' costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the 'true' scenario (cost distance Mantel correlations), but this 'true' scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the 'true' scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data.
Topics: Gene Flow; Reproducibility of Results; Genetic Drift; Animal Distribution; Genetics, Population; Ecosystem; Models, Genetic
PubMed: 37332161
DOI: 10.1111/1755-0998.13821 -
F1000Research 2022A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest. Sequencing and mapping errors coupled with low...
A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest. Sequencing and mapping errors coupled with low and variable coverage hamper the identification of genotypes and variants and the estimation of population genetic parameters. Methods and implementations to estimate population genetic parameters from sequencing data available nowadays either are suitable for the analysis of genomes from model organisms only, require moderate sequencing coverage, or are not easily adaptable to specific applications. To address these issues, we introduce ngsJulia, a collection of templates and functions in Julia language to process short-read sequencing data for population genetic analysis. We further describe two implementations, ngsPool and ngsPloidy, for the analysis of pooled sequencing data and polyploid genomes, respectively. Through simulations, we illustrate the performance of estimating various population genetic parameters using these implementations, using both established and novel statistical methods. These results inform on optimal experimental design and demonstrate the applicability of methods in ngsJulia to estimate parameters of interest even from low coverage sequencing data. ngsJulia provide users with a flexible and efficient framework for ad hoc analysis of sequencing data.ngsJulia is available from: https://github.com/mfumagalli/ngsJulia.
Topics: Genetics, Population; Genome; Genotype; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37745626
DOI: 10.12688/f1000research.104368.2 -
Genetics, Selection, Evolution : GSE May 2024Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and...
Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics-namely, heterozygosities, F coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy-Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the form with being vectors of allele frequencies at markers in populations and . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; F differentiation coefficients; segregation variance; and Nei's genetic distance) can be obtained from elements of matrix .
Topics: Animals; Gene Frequency; Models, Genetic; Genetics, Population; Heterozygote; Alleles; Genomics; Genotype; Genome
PubMed: 38698373
DOI: 10.1186/s12711-024-00891-w -
Infection, Genetics and Evolution :... Jan 2024Aedes albopictus is an important vector of arboviral diseases, transmitting yellow fever, dengue fever, chikungunya and Zika. Monitoring its population genetic diversity...
BACKGROUND
Aedes albopictus is an important vector of arboviral diseases, transmitting yellow fever, dengue fever, chikungunya and Zika. Monitoring its population genetic diversity and genetic differentiation has become essential for the control of infectious disease epidemics, especially in the functional areas of ports of entry. Population genetic monitoring of Ae. albopictus in the port area can help in the monitoring of port mosquito invasions and establishing port sanitary and quarantine measures to prevent the introduction and transmission of vector-borne diseases.
METHODS
Seventeen populations of Ae. albopictus were collected from five port cities on Hainan Island and the Leizhou Peninsula, 8 populations were collected from port areas, 4 from urban areas and 5 from rural areas. Nine microsatellite loci and the mitochondrial COI gene were used to study the population genetic diversity, population genetic structure and interpopulation gene flow of Ae. albopictus.
RESULTS
The nine microsatellite loci used were highly polymorphic, with an average PIC value of 0.768. The UPGMA genetic tree, STRUCTURE barplot and PCoA analyses showed that the 17 Ae. albopictus populations could be divided into three genetic groups. All 17 populations showed high haplotype diversity (Hd = 0.8069-0.9678) and formed 133 distinct haplotypes. These haplotypes can be divided into four genetic clades, but they are not associated with the geographical distribution of Ae. albopictus. Fst and Nm showed strong gene flow and little differentiation among populations.
CONCLUSION
Ae. albopictus in port areas are not significantly different from urban and rural populations due to strong gene flow, which prevents differentiation and increases the genetic diversity of the populations. High genetic diversity facilitates mosquito adaptation to complex environmental changes, which is a challenge for vector-borne disease control in port areas.
Topics: Humans; Animals; Genetic Variation; Cities; Genetics, Population; Aedes; China; Zika Virus Infection; Zika Virus; Mosquito Vectors
PubMed: 38104852
DOI: 10.1016/j.meegid.2023.105539