Local Population Structure Research Articles

Environmental DNA Haplotyping Reveals Dispersal Patterns of Invasive Bluegill Sunfish, Lepomis macrochirus, in Japan

ABSTRACTBiological invasions represent a significant threat to global biodiversity. Population genetics plays a crucial role in addressing the invasion history of invasive species, as information on the genetic structure of local populations of invasive species is useful in estimating their source and dispersal. This study aimed to demonstrate the potential of an environmental DNA (eDNA)‐based approach for estimating the dispersal patterns of invasive species, using bluegill sunfish (Lepomis macrochirus), a freshwater fish introduced to Japan in 1960. We developed an eDNA haplotyping assay based on high‐throughput sequencing and validated its ability to reproduce the haplotype distribution of bluegill sunfish in Japan, which had previously been determined through DNA analysis of individual fish. We also detected a negative relationship between the number of detected haplotypes and the geographic distance from Lake Biwa, one of the initial introduction sites, to each study site. This genetic pattern can occur in introduced species as a result of serial founder events during their range expansion. Our results suggested that Lake Biwa is the source of bluegill sunfish distribution in Japan, which is consistent with the invasion records of this species. We demonstrated the potential of the eDNA haplotyping assay for estimating the dispersal patterns of invasive species, which would aid the preparation of countermeasures against emerging biological invasions by simultaneously enabling the early detection and tracking of invasive species.

Dünn in der Fläche? Regionale Disparitäten in der Hospiz- und Palliativversorgung in Deutschland

IntroductionOutpatient and inpatient hospice and palliative care services have been significantly expanded in Germany in recent decades and are increasingly being supplemented by day care services. However, the availability of these services varies greatly from region to region. The extent to which the availability of these care structures is matched by a regional need based on local population structures is as yet unknown. MethodsIn four Poisson regression models, the relationship between population indicators from the areas of demographics, employment, income, education and health and the number of offers of outpatient and inpatient hospice work and palliative care is exploratively examined. The cumulated data at district level is drawn from the INKAR database of the Federal Institute for Research on Building, Urban Affairs and Spatial Development on living conditions in Germany and from the guide of the German Association for Palliative Medicine. By means of logistic regression, factors influencing the establishment of day care services will also be identified. ResultsThe analysis included 401 districts and cities in Germany. The number of inhabitants, settlement density, and the average age of inhabitants are the strongest predictors of the number of palliative care services. In metropolitan regions, both outpatient palliative care services and palliative care units tend to be more frequently available, while the number of outpatient hospice services and inpatient hospices increases in districts with a higher number of inhabitants regardless of settlement density. The regression model was unable to demonstrate a significant influence on the emergence of semi-inpatient care facilities, neither for the population indicators nor for the existing care structures. DiscussionRegional population structures can only partially explain the geographically uneven distribution of hospice and palliative care services in districts and cities in Germany. Despite an increase in hospice and palliative care services, fewer hospice and palliative care structures are available in low population density regions that tend to have a higher share of older inhabitants. ConclusionFuture health care planning should give more consideration to other population characteristics than to population size alone in order to improve care in regions with higher care needs that are, for example, due to a higher proportion of older residents. Subsequent studies should investigate which population characteristics can best describe the actual care needs.

Understanding species limits through the formation of phylogeographic lineages.

The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well-defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype-environment interactions, and genome scans for selected loci. Employing these tests in eight lineage-pairs of snakes in North America, we show that six pairs represent 12 "good" species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid-Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data.

Anatolia: A Hotspot of Avian Genetic Diversity in the Western Palaearctic

Located at the crossroads of two continents and at the southeastern edge of the Mediterranean Basin, Anatolia was one of the most important Pleistocene glacial refugia in the Western Palaearctic. As part of the Irano-Anatolian, Caucasus and Mediterranean Basin biodiversity hotspots, this region is also home to a rich avian community including nearly 400 breeding species. Nevertheless, research addressing the genetic structure and diversity of local bird populations is limited, and information on glacial refugia in this region is still scant, especially when compared to other large Mediterranean peninsulas, namely the Balkan, Italian and Iberian ones. In this study, we contribute to filling this gap by addressing the biogeographic pattern of four common resident songbirds—the Eurasian blue tit (Cyanistes caeruleus), the great tit (Parus major), the Eurasian chaffinch (Fringilla coelebs) and the Eurasian blackbird (Turdus merula)—and one endemic species—the Krüper’s nuthatch (Sitta krueperi)—by amplifying two mitochondrial DNA genes in individuals from Anatolia (n = 329) and comparing their sequences to those of conspecifics from the rest of their distribution range across the western Palaearctic (n = 357) deposited in public databases. The overall genetic structure of these species is consistent with a scenario of isolation for multiple populations in different refugia across Anatolia and subsequent secondary contact in the wake of ice retreat, which makes this region a hotspot of genetic diversity for both widespread and endemic avian species.

Population Change and Residential Segregation in Italian Small Areas, 2011–2021: An Analysis With New Spatial Units

This article explores spatial patterns of demographic change and residential segregation in Italy over the past decade, a topic which has not been studied in detail in the literature. Population ageing and migration are unfolding rapidly in a number of European countries, generating tensions and challenges at local level. Aggregate regional or national statistics can conceal significant variations at local level, which are of considerable interest and relevance. This is particularly the case in Italy, where spatial heterogeneity and regional disparities are marked. The analysis presented in this paper uses a new source of data derived from large public archives, which permits comparisons to be made at local level with the 2011 census of population. In this way, it is possible to map out and to analyse demographic trends at a fine level of spatial definition. In order to exploit the potential of these data, the authors use a new set of spatial units which were derived by applying automatic rezoning procedures. These output areas are well suited to the study of the age structure of local populations, population change, and migration in a uniform way across the entire national territory, as the empirical results confirm.

Recruitment of Juvenile Snapper (Lutjanidae) in the Middle Florida Keys: Temporal Trends and Fine-Scale Habitat Associations

Juvenile recruitment is a major factor in the establishment and maintenance of local population structures of coral reef fishes. An understanding of the factors that affect juvenile recruitment and survival help explain spatial and temporal patterns in adult abundance, especially of commercially and recreationally fished species. Here, we examined the distribution and juvenile recruitment of 5 snapper species: Mutton Snapper (Lutjanus analis), Lane Snapper (L. synagris), Schoolmaster (L. apodus), Gray Snapper (L. griseus), and Yellowtail Snapper (Ocyurus chrysurus) collected in 1,314 seine samples conducted between 2007 and 2019 in the Middle Florida Keys. We use a generalized linear modeling routine to assess juvenile recruitment of each species as a function of temporal, environmental, and benthic habitat variables. Interannual variability in juvenile recruitment ranged between 2 and 15—fold differences in mean predicted abundance between the highest and lowest producing years by species. Predicted recruitment varied dramatically by species in 2010 following a historic cold spell in south Florida. Three of the 5 species (Lane Snapper, Yellowtail Snapper, and Schoolmaster) exhibited the lowest observed yearly recruitment in that year, while Gray Snapper recruitment peaked. For all species, recruitment indices exhibited strong seasonal trends with peak abundances observed in the fall. Aquatic vegetation type, aquatic vegetation cover, distance from shore, and water temperature were the most important predictors of abundance. Results of this study highlight species—specific preferences for settlement habitat, demonstrate the importance of local—scale recruitment processes, and provide updated, management—relevant juvenile abundance indices for shallow water snapper in the Middle Florida Keys.

Seascapes Shaped the Local Adaptation and Population Structure of South China Coast Yellowfin Seabream (Acanthopagrus latus).

Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.

Habitat specialisation and resource availability determine dispersal behaviour in four afro‐tropical butterflies

Abstract Ecological demands, such as sex and environmental conditions, determine species' behaviour, such as dispersal, and shape local population structures. However, only marginal knowledge of these factors exists for afro‐tropical insects so far. Therefore, we performed a mark–release–recapture study in the coastal region of Kenya over a period of 2 months, covering the dry and the rainy seasons. As study species, we used four co‐occurring but ecologically diverging butterfly species, the forest species Bicyclus safitza and Junonia natalica and the savannah species Junonia oenone and Byblia ilithyia. The study area represents an ecosystem mosaic consisting of anthropogenic habitats as well as natural forest and savannah, assessed by detailed landscape mapping. We obtained 1701 capture events, comprising 1224 individuals with an overall recapture rate of 24% (ranging from 15% to 48%). The analyses based on these results allowed an assessment of the population ecology, dispersal behaviour and habitat preferences of these species. Demographic models inferred different patterns of population dynamics among species. All species preferred the habitats they were known for. The observed dispersal distances were rather low ranging from a mean of 25 to 72 m, referring to taxa and sexes. The dispersal extrapolations were unreliably low for the negative exponential function, while the values for inverse power function were credible. The latter predicted a considerably higher long‐distance dispersal capacity in males than in females of the forest species B. safitza and J. natalica, while females dispersed more than males in the savannah species J. oenone and B. ilithyia. Our results obtained from these four ecologically diverging afro‐tropical butterfly species underline that species’ behaviour, such as dispersal, is strongly determined by habitat preferences, sex and the availability of resources.

Analysis of the genetic diversity and population structures of black locust (Robinia pseudoacacia L.) stands in Poland based on simple sequence repeat markers

Abstract Black locust (Robinia pseudoacacia L.) was introduced in Poland over 200 years ago, and its distribution area now covers the whole country, with the highest concentration of occurrence in the western part. Breeding of this species has been started in Poland for about 20 years, albeit on a limited scale, and two selected seed stands, 34 plus trees and two seed orchards have been registered. So far, selection efforts have not been coupled with the recognition of variation in the genetic structure of local populations. To fill the knowledge gap on genetic diversity, we selected the seven qualitatively best populations of R. pseudoacacia for our study. To clarify the origin of the Polish population of R. pseudoacacia, a sample from a seed stand in eastern Germany and from a seed orchard with Hungarian clones from the Oborniki Śląskie Forest District was added. In this study, three microsatellites were used to evaluate genotypes: Rops15, Rops16 and Rops18, with the Rops15 locus (motif AG) showing hypermutability. Moderate or high variability was observed in all microsatellite loci examined, with a total of 27 alleles identified. In all stands, the average observed number of alleles per locus was higher than the average effective number of alleles per locus. Three main clusters have been identified in the genetic structure of the population, one of which is represented by the population from the Regional Directorate of State Forests in Zielona Góra. The second group comprised the populations from Mieszkowice, the populations Pińczów and Wołów, and the population from Germany. The last one included population from Strzelce and Oborniki Śląskie, where the population from Hungary is represented. This may be of great importance for practice. Perhaps it is worth postulating the separation of two seed regions. Under most scenarios, climate change is projected to change the distribution of forest types and tree species in all biomes. It can be assumed that the importance of black locust in times of climate change is likely to increase.

Where do those data go? Reuse of screening results from clinical trials to estimate population prevalence of HBV infection in adults in Kilifi, Kenya

Chronic hepatitis B infection (CHB) is a significant problem worldwide with around 300 million people infected. Ambitious goals have been set towards its elimination as a public health threat by 2030. However, accurate seroprevalence estimates in many countries are lacking or fail to provide representative population estimates, particularly in the WHO African Region (AFRO). This means the full extent of HBV infection is not well described, leading to a lack of investment in diagnostics, treatment and disease prevention. Clinical trials in the WHO AFRO region have been increasing over time and many test for infectious diseases including hepatitis B virus (HBV) to determine baseline eligibility for participants, however these screening data are not reported. Here we review data from six clinical trials completed at the KEMRI-Wellcome Trust Research Programme between 2016 and 2023 that screened for HBV using hepatitis B surface antigen (HBsAg) as part of the trial exclusion criteria. 1727 people had HBsAg results available, of which 60 tested positive. We generated a crude period HBV prevalence estimate of 3.5% (95% CI 2.6–4.5%), and after standardisation for sex and age to account for the population structure of the Kilifi Health Demographics Surveillance System (KHDSS), the prevalence estimate increased to 5.0% (95% CI 3.4–6.6%). The underrepresentation of women in these trials was striking with 1263/1641 (77%) of participants being male. Alanine aminotransferase (ALT) was significantly higher in the HBsAg positive group but was not outside the normal range. We argue that routine collation and publishing of data from clinical trials could increase precision and geographical representation of global HBV prevalence estimates, enabling evidence-based provision of clinical care pathways and public health interventions to support progress towards global elimination targets. We do acknowledge when using clinical trials data for seroprevalence estimates, that local population structure data is necessary to allow standardisation of results, and the point of care tests used here are limited in sensitivity and specificity.

Early stage of invasion of the quagga mussel (Dreissena rostriformis bugensis) within the interconnected lakes Lough Ree and Lough Derg of the Shannon River system, Ireland

Quagga and zebra mussels of the genus Dreissena are two of the most impactful freshwater invasive alien species that have spread widely across the globe. These species attach to natural and artificial substrates, form dense populations and filter large volumes of water causing ecological and economic damage. Following the quagga mussel’s discovery in the Shannon River system in Ireland, this study assesses its local distribution, population density, relative abundance, and population structure in the interconnected lakes Lough Ree and Lough Derg in order to determine the likely year and location of its introduction. Polymodal length-frequency analysis was used to distinguish between year cohorts and estimate growth rates. The quagga mussel is established widely across both lakes and is settling on a range of artificial surfaces, natural substrates, dead shells, plant material, and other invasive bivalves. High densities of quagga mussels exceeding 20 000 individuals per m2 were present on artificial surfaces in Lough Ree with total dreissenid densities reaching 26 758 per m2. The relative abundance of quagga mussels to zebra mussels on natural substrates is high in Lough Ree (up to 94.7%) and low in Lough Derg (up to 16.8%). Two to four year cohorts were present at all sites, with quagga mussels attaining large shell sizes over 34 mm in length. Growth varied between sites with a maximum estimated yearly growth rate of 16.8 mm. The time and place of the quagga mussel’s initial introduction in Ireland is still uncertain, but its widespread distribution, population structure, and high population density and relative abundance suggest it was first introduced to Lough Ree in 2016 or 2017.

The genetic connectivity of the silky shark (Carcharhinus falciformis) across Indonesia

Silky shark (Carcharhinus falciformis) has been listed as CITES Appendix II and Vulnerable by IUCN red list. Reports from Indian, Pacific and Atlantic Ocean showed a sharply declining C. falciformis population every year, including in Indonesia. Despite this issue, information on local and regional genetic population structure of this species is still lacking. In this research, we aim to assess the population condition of C. falciformis across Indonesia Fisheries Management Area (FMAs), using mitochondrial genetic data. A total of 225 fins or tissue samples collected from various traditional fish market and shark-fin exporters across Indonesia, then sequenced using mtDNA control region, yielding 510 bp of sequence. The overall Haplotype diversity is high (h: 0.534 ± 0.035). Meanwhile, the nucleotide diversity (θπ) is low (range of 0.00067 – 0.00201) compared to the Atlantic and Red Sea. In addition, the genetic diversity of C. falciformis in Indonesia is lower than other pelagic shark species. Furthermore, AMOVA and Fst results showed a significant structure between Aceh and other locations in Indonesia. Samples from across Indonesia also showed a certain degree of haplotype sharing but with significant genetic structure with others, additionally, the combined dataset revealed a pattern that is similar to previous studies, which showed that the Atlantic population is different from the rest. The distinct genetic population of C. falciformis observed in Aceh may indicate that this population should be managed separately. Meanwhile, the shared genetic information within the Timor Sea indicates the necessity of establishing a co-management plan between Indonesia and neighbouring countries such as Timor-Leste and Australia to ensure the sustainable use of this marine resource.

Identification of local camel populations in Turkiye using morphological, genetic, and breeding info.

The aim of this study was to investigate the demographic, morphological, and genetic characteristics of local camel populations reared in the Turkiye provinces of Aydin, Denizli, and Antalya, which have a long history of camel breeding. Although Turkiye has an old history of camel breeding in its historical process, the number of scientific studies aimed at identifying camel populations in Turkiye is almost negligible. In this study, local camel populations in Aydin, Denizli, and Antalya cities of Turkiye were examined in three dimensions as demographic, morphological, and genetic. A face-to-face survey of 117 breeders was used to determine demographic definitions. While the region where local camels were detected the most was determined as Antalya Region with 78.6%, it was determined that 82.6% of the breeders participating in the survey preferred to breed camels due to their docile temperament. Body measurements were made on 45 camels for morphological identification. Moreover, DNA were sampled with oral swabs from 57 camels for phylogenetic analyses using 16 SSR microsatellite loci to identify the genetic structure of local camel populations. The genetic analyses using SSR markers revealed that the camel populations in the Antalya region had a considerably more isolated genetic structure than the Aydin and Denizli populations, and consequently, these populations may be regarded the native camel population.

Genetic Diversity and Structure of Local Chicken Populations Raised in Five Agroecological Zones of Togo

Local chickens are the most commonly raised poultry breed in rural areas of Togo, where they help in alleviating poverty and food insecurity in households. The current study aimed to ensure the sustainable management of this genetic resource by evaluating the genetic diversity, phylogenetic relationships, and population structure of local chicken populations from five agroecological zones (Dry Savannah, Atakora, Forest, Wet Savannah, and Littoral) in Togo. Genotyping was carried out using 15 microsatellite markers on 30 unrelated individuals per agroecological zone. Genetic diversity was assessed by estimating the number of alleles per locus, observed heterozygosity, unbiased expected heterozygosity, and the polymorphic information content (PIC). The genetic structure of the populations was analyzed using a Bayesian-based approach. The results revealed a high genetic diversity but weak population structuring among local chickens. Moreover, 98 alleles were detected in all population groups, varying from 3 to 12 per locus, with an average of 6.53 ± 2.67 alleles per locus. The PIC values varied from 0.436 to 0.690, with an average of 0.550 ± 0.087. The mean number of alleles per population across all markers ranged from 4.4 ± 1.4 (Dry Savannah) to 5.4 ± 2.0 (Forest). The unbiased expected heterozygosity was high and varied from 0.58 ± 0.07 (Atakora) to 0.65 ± 0.11 (Forest), while that observed varied between 0.46 ± 0.09 (Dry Savannah) and 0.57 ± 0.14 (Forest). All populations deviated significantly from the Hardy-Weinberg equilibrium. Across populations, FIT, FIS, and FST fixation indices were 0.150, 0.132, and 0.021, respectively. The genetic distances were low and varied from 0.022 (between Atakora and Dry Savannah) to 0.045 (between Atakora and Forest). These results could be used in potential genetic improvement programs or the preservation of local chickens in Togo.

Evidence of differentiation and population structure in Charolais cattle of Mexico.

Charolais is one of the most important beef cattle breeds in the world. In Mexico, it was introduced almost a century ago, and it has been suggested that particular breeding management and genetic material origin have caused a process of divergence among the current population. By a high-density SNP array genome-wide analysis, this study aimed to assess the proposed differentiation and population structure of local populations by genetic distances and structure approaches, and a European Charolais sample was included as a reference population. The differentiation statistics indicated that local populations exhibit moderate divergence, confirming a significant differentiation process between northeastern and northwestern Charolais populations (Fst≥ 0.043, D≥ 0.031). These results were strongly supported by PCA and structure analysis. Genetic isolation and low genetic flow between populations and divergent origins of introduced genetic material (i.e., semen) are likely the main drivers of the outcomes. Some implications are discussed.

Genetic diversity and molecular evolution of Plasmodium vivax Duffy Binding Protein and Merozoite Surface Protein-1 in northwestern Thailand.

The local diversity and population structure of malaria parasites vary across different regions of the world, reflecting variations in transmission intensity, host immunity, and vector species. This study aimed to use amplicon sequencing to investigate the genotypic patterns and population structure of P. vivax isolates from a highly endemic province of Thailand in recent years. Amplicon deep sequencing was performed on 70 samples for the 42-kDa region of pvmsp1 and domain II of pvdbp. Unique haplotypes were identified and a network constructed to illustrate genetic relatedness in northwestern Thailand. Based on this dataset of 70 samples collected between 2015 and 2021, 16 and 40 unique haplotypes were identified in pvdbpII and pvmsp142kDa, respectively. Nucleotide diversity was higher in pvmsp142kDa than in pvdbpII (π=0.027 and 0.012), as was haplotype diversity (Hd=0.962 and 0.849). pvmsp142kDa also showed a higher recombination rate and higher levels of genetic differentiation (Fst) in northwestern Thailand versus other regions (0.2761-0.4881). These data together suggested that the genetic diversity of P. vivax in northwestern Thailand at these two studied loci evolved under a balancing selection, most likely host immunity. The lower genetic diversity of pvdbpII may reflect its stronger functional constrain. In addition, despite the balancing selection, a decrease in genetic diversity was observed. Hd of pvdbpII decreased from 0.874 in 2015-2016 to 0.778 in 2018-2021; π of pvmsp142kDa decreased from 0.030 to 0.022 over the same period. Thus, the control activities must have had a strong impact on the parasite population size. The findings from this study provide an understanding of P. vivax population structure and the evolutionary force on vaccine candidates. They also established a new baseline for tracking future changes in P. vivax diversity in the most malarious area of Thailand.

Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex.

Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. Four hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males. These four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis

BackgroundAccurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here a falciparum variant calling pipeline based on GATK version 4 (GATK4) was optimized and applied to 6626 public Illumina WGS samples.MethodsControl WGS and accurate PacBio assemblies of 10 laboratory strains were leveraged to optimize parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs. From these controls, a high-quality training dataset was generated to recalibrate the raw variant data.ResultsOn current high-quality samples (read length = 250 bp, insert size = 405–524 bp), the optimized pipeline shows improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). Its sensitivity on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. The resulting combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. Finally, increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection.ConclusionsOverall, this study provides an optimized falciparum GATK4 pipeline resource for variant calling which should help improve genomic studies of malaria.

Lake Sinai virus is a diverse, globally distributed but not emerging multi-strain honeybee virus.

Domesticated honeybees and wild bees are some of the most important beneficial insects for human and environmental health, but infectious diseases pose a serious risk to these pollinators, particularly following the emergence of the ectoparasitic mite Varroa destructor as a viral vector. The acquisition of this novel viral vector from the Asian honeybee Apis ceranae has fundamentally changed viral epidemiology in its new host, the western honeybee A. mellifera. While the recently discovered Lake Sinai Viruses (LSV) have been associated with weak honeybee colonies, they have not been associated with vector-borne transmission. By combining a large-scale multi-year survey of LSV in Chinese A. mellifera and A. cerana honeybee colonies with globally available LSV-sequence data, we investigate the global epidemiology of this virus. We find that globally distributed LSV is a highly diverse multi-strain virus, which is predominantly associated with the western honeybee A. mellifera. In contrast to the vector-borne deformed wing virus, LSV is not an emerging disease. Instead, demographic reconstruction and strong global and local population structure indicates that it is a highly variable multi-strain virus in a stable association with its main host, the western honeybee. Prevalence patterns in China suggest a potential role for migratory beekeeping in the spread of this pathogen, demonstrating the potential for disease transmission with the man-made transport of beneficial insects.

Structure of local populations and phytocoenotic confinement of Elwendia persica in Turkestan Ridge, Uzbekistan

Abstract. Abduraimov OS, Mamatkulova IE, Mahmudov AV. 2023. Structure of local populations and phytocoenotic confinement of Elwendia persica in Turkestan Ridge, Uzbekistan. Biodiversitas 24: 1621-1628. The study of ecological and biological features of cenotic and food plants is not only of important general biological significance, but also serves as a basis for the science-based study of resources and the preservation of species diversity. Elwendia persica (Apiaceae) grows in different regions of Central Asia and has been used regularly for several centuries, especially in traditional cuisines. In particular, local residents in mountainous areas collect this plant and benefit economically. This study aimed to assess the coenopopulation and phytocoenotic confinement of E. persica in Turkestan ridge, Djizakh region, Uzbekistan. The study was carried out between 2018 and 2022 and the ontogenetic structure of four coenopopulations of E. persica was studied. Evaluation of age (? - delta) and efficiency (? - omega) of coenopopulations revealed that the studied populations were classified as young (coenopopulations 1, 3, 4) and transient (coenopopulations 2). Analysis of demographic results shows that the density of individuals in the studied communities ranged 1.4-2.05 ind./m2, whereas the ecological density was 1.64-2.73 ind./m2. The coenopopulations had an index of recreation of 0.52-3.57 and ageing index 0 to 0.13. These indicators show that the coenopopulations are in a normal state. The state of coenopopulations was positively affected by a large amount of annual rainfall on the territory.