Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Bos grunniens)

The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole-genome re-sequencing

Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low-oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole-genome resequencing technology, along with 192 published sets of whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross-population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.

Study on the origin of the Baise horse based on whole-genome resequencing

The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse.

Development and application of microsatellite markers in Hippophae rhamnoides subsp. sinensis Rousi (Hippophae rhamnoides L.) based on transcriptome sequencing

Hippophae rhamnoides subsp. sinensis Rousi is a cold- and drought-tolerant pioneer species with significant economic and ecological value. Evaluating its genetic diversity and population structure is of great importance for guiding the development and utilization of resources. In this study, a total of 41,804 SSRs were generated by transcriptome sequencing of Hippophae rhamnoides subsp. sinensis Rousi. Among the different SSR motif types, mononucleotide repeats (26,972) were the most abundant, followed by trinucleotides, tetranucleotides, and pentanucleotides. 200 pairs of SSR primers were selected to detect polymorphisms, of which 15 pairs primers were selected as validated polymorphic SSRs used for genetic diversity and population structure analysis. A total of 63 alleles were identified with 15 pairs primers, with Nei's genetic diversity index ranged from 0.27 to 0.83 (average: 0.54), and the expected heterozygosity ranged from 0.16 to 0.73 (average: 0.46). The polymorphism information content ranged from 0.23 to 0.81 (average: 0.48). Genetic structure analyses showed that the 10 populations could be broadly categorized into two groups. AMOVA denoted that genetic variations primarily originated from within the populations, with minimal differences observed between the groups, accounting for only 7% of the total genetic variation. This implies that mutation in H. rhamnoides subsp. sinensis Rousi mainly occurred within the populations. The results showed that the 10 populations of H. rhamnoides subsp. sinensis Rousi are rich in genetic diversity, with low levels of population differentiation and a high degree of gene exchange, which should be taken into consideration for the future work of germplasm resource preservation and seedling breeding.

Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm

Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.

Measuring local genetic variation in permethrin-resistant head lice (Phthiraptera: Pediculidae) from Buenos Aires, Argentina

The cosmopolitan ectoparasite human head louse, Pediculus humanus capitis (De Geer)(Phthiraptera:Pediculidae), affects mostly school-aged children, with infestations reported every year mainly due to louse resistance to pyrethroids. One of the main resistance mechanisms of pyrethroids is the target site insensitivity (kdr), which is caused by single-nucleotide point mutations (SNPs) located in the voltage-sensitive sodium channel gene. In this study, we analyzed individual head lice toxicologically via the description of their susceptibility profile to permethrin and genetically through the genotypification of their kdr alleles as well as nuclear microsatellite loci. Lice were collected from 4 schools in the city of Buenos Aires, Argentina. The resistance ratios varied from 33.3% to 71.4%, with a frequency of the T917I kdr mutation of 87.31% and with 83.6% of the head lice being homozygous resistant to pyrethroids. Microsatellite data indicated that all the louse school populations had genotype proportions that deviated from Hardy-Weinberg expectations, with FIS > 0 reflecting a deficit of heterozygotes. Bottleneck analysis suggested that all louse school populations underwent a recent reduction in population sizes, while 3 of the 4 schools had gene flow values around 1, indicating ongoing gene flow among those schools. Our study suggests that school louse populations in the city of Buenos Aires may form a metapopulation, where each school represents a small population that undergoes extinction and recolonization processes under strong permethrin selection. This is the first multilevel analysis integrating toxicological, kdr-genotyping, and microsatellite data in human louse populations.

Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas

Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.

Population genetic structure of Hymenopellis radicata germplasm resources based on genome re-sequencing

Through whole-genome re-sequencing of 18 Hymenopellis radicata germplasm resources collected from diverse regions in China, we identified significant variations in the form of Single Nucleotide Polymorphisms (SNPs) and Insertions and Deletions (InDels). These variations were comprehensively annotated, shedding light on the mutation types present in the entire genome of the H. radicata germplasm. This analysis revealed the number and position information of each mutation and provided insights into the overall genomic landscape of H. radicata germplasm. Utilizing SNP data, we delved into the population structure of the 18 H. radicata germplasm resources. The results indicated the presence of 2,335,179 Indel sites and 12,050,448 SNP sites. The population structure analysis unveiled two distinct subgroups among the H. radicata germplasm resources. Phenotypic statistics, principal component analysis, and phylogenetic tree results echoed the findings of the population structure analysis. Different strains of H. radicata from various regions in China exhibited notable differences in genetic diversity, mycelial growth rate, yield, and fruiting body characteristics. Significant disparities were observed between the two subgroups, while strains within each subgroup shared common characteristics. This research establishes a solid foundation for integrating H. radicata into diverse breeding programs. The data underscore the potential of H. radicata for genetic improvement and exploitation in breeding initiatives, paving the way for future advancements in this field.

Point mutations including a novel Pro-197-Phe mutation confer cross-resistance to acetolactate synthase (ALS) inhibiting herbicides in Lactuca serriola in Australia

BACKGROUND

Control of prickly lettuce has become increasingly difficult for lentil growers in southern Australia because of widespread resistance to common herbicides, a lack of alternative herbicide options and the prolific production of highly mobile seed. This study aimed to quantify acetolactate synthase (ALS)-inhibiting herbicide resistance in the Mid North (MN) and Yorke Peninsula (YP) of South Australia, characterize the resistance mutations present and investigate population structure and gene flow in this species.

RESULTS

Resistance was identified in all populations tested, with average survival of 92% to chlorsulfuron and 95% to imazamox + imazapyr. Five different amino acid substitutions were identified at proline 197 of the ALS gene. There was no significant difference in the median lethal dose (LD50 ) between plants with these five different substitutions when treated with metsulfuron-methyl; however, the imidazolinone resistance level was higher in plants with a phenylalanine substitution and lower in plants with a serine. Population structure based on 701 single nucleotide polymorphisms and 271 individuals provided evidence for both independent evolution of the same mutation in different populations, as well as frequent short- to medium-distance dispersal accompanied by occasional long-distance dispersal events. The overall inbreeding coefficient (FIS ) was calculated at 0.5174, indicating an intermediate level of outcrossing despite the cross-pollination experiment showing only low outcrossing. In the structure analyses, most individuals from YP were assigned to a single cluster, whereas most individuals from MN were assigned 50% to each of two clusters, indicating some genetic differences between these two regions, but also evidence for dispersal between them.

CONCLUSIONS

Use of imidazolinone herbicides has selected for mutations conferring higher levels of resistance, such as the Pro-197-Phe mutation, and resulted in further spread of resistance in this species. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Analysis of the population genetic structure using microsatellite markers in goat populations in Taiwan

Due to the poor growth rate of the Taiwan black (TB) goat in Taiwan, many exotic breeds were brought into breeding schemes to improve TB goat. However, the excessive cross-breeding of alien species with TB goat has decreased its population numbers, genetic variation and biodiversity. Therefore, TB goat population considered an endemic species in Taiwan that needed to be conservation. The objective of the present study was to analyze the genetic structure and TB goat using genetic markers for genetic improvement and to sustain germplasm conservation and utilization. 15 microsatellite markers, divided into three sets, were used to analyze 690 goats sampled from 10 goat populations. The average number of alleles (Na) and effective alleles (Ne) was 11.87 ± 3.93 and 5.093 ± 1.768, respectively. The average expected heterozygosity (HE) and observed heterozygosity (HO) was 0.780 ± 0.084 and 0.602 ± 0.116, respectively. The average polymorphic information content (PIC) was 0.747 ± 0.103; FIS was 0.058 ± 0.075. All 15 microsatellite markers were highly polymorphic. The genetic distances between individuals were estimated to construct a phylogenetic tree. In present study, the 690 goat samples were divided into 8 clusters. The results indicated that these 15 microsatellite markers successfully clustered goat populations in Taiwan and could assist in the preservation of TB goats.

Genetic differentiation and local adaptation of the Japanese honeybee, Apis cerana japonica

We examine the population genetic structure and divergence among the regional populations of the Japanese honeybee, Apis cerana japonica, by re-sequencing the genomes of 105 individuals from the three main Japanese islands with diverse climates. The genetic structure results indicated that these individuals are distinct from the mainland Chinese A. cerana samples. Furthermore, population structure analyses have identified three genetically distinct geographic regions in Japan: Northern (Tohoku-Kanto-Chubu districts), Central (Chugoku district), and Southern (Kyushu district). In some districts, "possible non-native" individuals, likely introduced from other regions in recent years, were discovered. Then, genome-wide scans were conducted to detect candidate genes for adaptation by two different approaches. We performed a population branch statistics (PBS) analysis to identify candidate genes for population-specific divergence. A latent factor mixed model (LFMM) was used to identify genes associated with climatic variables along a geographic gradient. The PBSmax analysis identified 25 candidate genes for population-specific divergence whereas the LFMM analysis identified 73 candidate genes for adaptation to climatic variables along a geographic gradient. However, no common genes were identified by both methods.

[Exploration of transcriptome SSR markers and its application in genetic diversity assessment of Asarum sieboldii]

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.

Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500 km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from the early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.

Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella

Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources.

Global population genetic structure and lineage differentiation of the stable fly, Stomoxys calcitrans

The bloodsucking fly, Stomoxys calcitrans (Diptera: Muscidae), is a cosmopolitan pest that transmits potential pathogens mechanically. We conduct phylogeographic analyses of S. calcitrans to resolve its global population genetic structure for establishing baseline of molecular studies. Results from mitochondrial gene suggested that the major divergence of S. calcitrans predominantly occurred 0.32-0.47 million years ago (Mya) and the subsequent diversifications took place during 0.13-0.27 Mya. The Ethiopian region was deduced as the most likely origin of S. calcitrans and the Nearctic lineages were considered to have originated from Oriental or Palaearctic regions. Our results further revealed that each biogeographic region of S. calcitrans likely maintains its genetic specialty, and yet, those non-monophyletic relationships were possibly caused by ancestral retention, dispersal with mammals, long-distance migration, and the international livestock industries. Moreover, the three highly diverged Ethiopian lineages may be putative cryptic species that require clarification of their veterinary importance. Unravelling the genetic structure of stable fly and preventing gene flow among biogeographic regions through anthropogenic activities are thus pivotal in livestock industry administration, particularly genetic exchange among differentiated lineages that might lead to the consequence of ecological trait alterations.

A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi

Limiting harm to organisms caused by genetic sampling is an important consideration for rare species, and a number of non-destructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the unionid freshwater mussel, the Texas pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared with swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence), while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.

Spatial genetic patterns and distribution dynamics of Begonia grandis (Begoniaceae), a widespread herbaceous species in China

Introduction

Begonia L., one of the 10 largest plant genera, contains over 2,100 species, most of which have a very limited distribution range. Understanding the spatial genetic structure and distribution dynamics of a widespread species in this genus will contribute to clarifying the mechanism responsible for Begonia speciation.

Methods

In this study, we used three chloroplast DNA markers (ndhF-rpl32, atpI-atpH, and ndhA intron), coupled with species distribution modeling (SDM), to investigate the population genetic structure and distribution dynamics of Begonia grandis Dryand., the species of Begonia with the widest distribution in China.

Results

Thirty-five haplotypes from 44 populations clustered into two groups, and haplotype divergence began in the Pleistocene (1.75 Mya). High genetic diversity (H _d = 0.894, H _T = 0.910), strong genetic differentiation (F _ST = 0.835), and significant phylogeographical structure (G _ST/N _ST = 0.848/0.917, P < 0.05) were observed. The distribution range of B. grandis migrated northwards after the last glacial maximum, but its core distribution area remained stable.

Discussion

Combined, the observed spatial genetic patterns and SDM results identified the Yunnan-Guizhou Plateau, the Three Gorges region, and the Daba Mountains as potential refugia of B. grandis. BEAST-derived chronogram and haplotype network analysis do not support the Flora Reipublicae Popularis Sinicae and Flora of China for subspecies classification based on morphological characteristics. Our results support the hypothesis that population-level allopatric differentiation may be an important speciation process for the Begonia genus and a key contributor to its rich diversity.

Population Genetic Diversity of Two Blue Oat Mite Species on Triticum Hosts in China

Blue oat mite species, including Penthaleus major and P. tectus, are pests widely distributed across China that cause damage to winter wheat. This study evaluated the genetic diversity of P. major and P. tectus on Triticum hosts collected from 23 geographic locations based on mitochondrial cytochrome c oxidase subunit I (COI) sequences. We identified nine haplotypes in 438 P. major individuals from 21 geographic locations and five haplotypes in 139 P. tectus individuals from 11 geographic locations. Meanwhile, P. major exhibits high values of haplotype diversity (Hd) and nucleotide diversity (Pi) (Hd = 0.534 > 0.5 and Pi = 0.012 > 0.005), representing a large stable population with a long evolutionary history. P. tectus shows low values of Hd and Pi (Hd = 0.112 < 0.5 and Pi = 0 < 0.005), which suggest recent founder events. Moreover, demographic analysis suggested that P. major and P. tectus have not undergone a recent population expansion. The lowest genetic variation was observed in Xiangzhou (XZ-HB), Zaoyang (ZY-HB), Siyang (SY-JS), and Rongxian (RX-SC), with only one species and one haplotype identified in over 30 individuals. Robust genetic differentiation was found in P. major compared to P. tectus, which provides a theoretical basis for the widespread distribution of P. major in China.

Population structure of ALS-inhibiting herbicide-resistant Sonchus oleraceus in South Australia

BACKGROUND

Annual sowthistle is a weed that is difficult to control in lentil crops in southern Australia due to a lack of herbicide options, widespread herbicide resistance and prolific production of highly mobile seed. This study investigates herbicide resistance in annual sowthistle in the Mid-North (MN) and Yorke Peninsula (YP) regions of South Australia, identifies and characterizes the mechanisms of acetolactate-synthase (ALS)-inhibitor resistance in this amphidiploid species, and combines this with analyses of population structure and gene flow.

RESULTS

ALS-inhibitor-resistant annual sowthistle is widespread across the YP and MN of South Australia and is associated with a variety of Proline-197 mutations of the ALS gene, including leucine, alanine, arginine, serine, threonine and histidine. These mutations were found in different combinations on either of the two copies of the ALS gene. An additional 200 tissue samples were collected from across a single field on the YP and the ALS gene was sequenced for all these individuals. Different ALS-inhibitor resistance profiles were evident between mutation combinations and within mutation combinations, possibly mediated by differing subgenome assortment of the mutations, or altered gene experession of the two ALS homeologs. Population genetics analysis showed evidence of long-distance dispersal, resulting in highly mobile resistance genes, and multiple instances of resistance mutation evolution.

CONCLUSIONS

Continuing selection of Sonchus oleraceus populations with ALS-inhibiting herbicides has resulted in the accumulation of additional mutations within the ALS gene. New practices to control herbicide-resistant S. oleraceus should be examined, and control should focus on reducing seed set and dispersal to prevent the spread of emerging cases of resistance. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Temporal and Spatial Variation in the Population Structure of Spanish Fusarium circinatum Infecting Pine Stands

Fusarium circinatum is an introduced fungal pathogen extended to the northern regions of Spain that causes Pine Pitch Canker (PPC) disease. In this work, we analyzed the pathogen's genetic diversity to study changes over time and space since the first outbreak occurred in Spain. Using six polymorphic SSR markers, 15 MLGs were identified in 66 isolates, and only three haplotypes were found with frequencies higher than one. In general, genotypic diversity was low and decreased shortly over time in the northwestern regions while maintained at País Vasco, where only one haplotype (MLG32) was detected 10 years. This population also included isolates of a single mating type (MAT-2) and VCGs identified in only two groups, while isolates from NW regions were of both mating types and VCGs represented in 11 groups. The existence of haplotype MLG32 maintained on time and widely distributed suggests its good adaptation to the environment and the host. Results showed that the pathogen in País Vasco remains clearly differentiated from other northwestern populations. This fact was supported with no evidence of migration among regions. Results are explained by the asexual reproduction, but also selfing at least to a lesser extent that leads to identification of two new haplotypes.

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They are often reared as a pure breed or used in crossbreeding and are a common component in synthetic breed development. This study evaluated genetic diversity, population structure, and breed divergence in 279 animals of Merino and Merino-based sheep breeds in South Africa using the Illumina Ovine SNP 50K BeadChip. The sheep breeds analysed included the three Merino-derived breeds of Dohne Merino (n = 50); Meatmaster (n = 47); and Afrino (n = 52) and five presumed ancestral populations of Merinos (Merino (n = 46); South African Merino (n = 10); and South African Mutton Merino (n = 8)); and the non-Merino founding breeds of Damara (n = 20); Ronderib Afrikaner (n = 17); and Nguni (n = 29). Highest genetic diversity values were observed in the Dohne Merino (DM), with H _o = 0.39 ± 0.01, followed by the Meatmaster and South African Merino (SAM), with H _o = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (DM) to 0.27 ± 0.05 (Nguni). Analysis of molecular variance (AMOVA) showed high within-population variance (>80%) across all population categories. The first principal component (PC1) separated the Merino, South African Mutton Merino (SAMM), DM, and Afrino (AFR) from the Meatmaster, Damara, Nguni, and Ronderib Afrikaner (RDA). PC2 aligned each Merino-derived breed with its presumed ancestors and separated the SAMM from the Merino and SAM. The iHS analysis yielded selection sweeps across the AFR (12 sweeps), Meatmaster (four sweeps), and DM (29 sweeps). Hair/wool trait genes such as FGF12; metabolic genes of ICA1, NXPH1, and GPR171; and immune response genes of IL22, IL26, IFNAR1, and IL10RB were reported. Other genes include HMGA, which was observed as selection signatures in other populations; WNT5A, important in the development of the skeleton and mammary glands; ANTXR2, associated with adaptation to variation in climatic conditions; and BMP2, which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. The DM vs. SAMM shared all six sweep regions on chromosomes 1, 10, and 11 with AFR vs. SAMM. Genes such as FGF12 on OAR 1:191.3-194.7 Mb and MAP2K4 on OAR 11:28.6-31.3 Mb were observed. The selection sweep on chromosome 10 region 28.6-30.3 Mb harbouring the RXFP2 for polledness was shared between the DM vs. Merino, the Meatmaster vs. Merino, and the Meatmaster vs. Nguni. The DM vs. Merino and the Meatmaster vs. Merino also shared an Rsb-based selection sweep on chromosome 1 region 268.5-269.9 Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations and some divergence driven by breed-specific selection goals. Overall, information regarding the evolution of these composite breeds from their founding population will guide future breed improvement programs and management and conservation efforts.

Pollinator type strongly impacts gene flow within and among plant populations for six Neotropical species

Animal pollinators directly affect plant gene flow by transferring pollen grains between individuals. Pollinators with restricted mobility are predicted to limit gene flow within and among populations, whereas pollinators that fly longer distances are likely to promote genetic cohesion. These predictions, however, remain poorly tested. We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the F_ST statistic) and stronger FSGS (as quantified with the S_P statistic) than hummingbird-pollinated species. We confirmed putative pollinators through a literature review and fieldwork, and inferred population genetic parameters with a genome-wide genotyping approach. In two of the three species pairs, insect-pollinated species had much greater (>2-fold) population-level genetic differentiation and correspondingly steeper declines in fine-scale genetic relatedness. In the Gesneriaceae pair, however, F_ST and S_P values were similar between species and to those of the other hummingbird-pollinated plants. In this pair, the insect pollinators are euglossine bees (as opposed to small bees and flies in the other pairs), which are thought to forage over large areas, and therefore may provide similar levels of gene flow as hummingbirds. Overall, our results shed light on how different animal pollination modes influence the spatial scale of plant gene flow, suggesting that small insects strongly decrease genetic cohesion.

Phylogeography of the endangered "eyed" turtles (genus Sacalia) and the discovery of a lineage derived from natural interspecific hybridization

The herpetofauna of the Indomalayan bioregion of Asia suffers from severe habitat loss, unsustainable harvesting, and lack of research and conservation. Here, we investigated the range-wide phylogeography of the endangered "eyed" turtles (genus Sacalia, including the Beale's Eyed Turtle S. bealei and the Four-eyed Turtle S. quadriocellata) and discovered a natural interspecific hybrid turtle population in China. Based on phylogeny of the mitochondrial Cytochrome b gene of 101 samples in this study and public data, three major clades and six subclades were identified: S. bealei (SBE) in eastern-southern China, east S. quadriocellata in South China (northern east [SQUen] and southern east [SQUes] subclades), and west S. quadriocellata mainly in Vietnam (northern west [SQUwn], central west [SQUwc], and southern west [SQUws] subclades). We sequenced 16 nuclear DNA loci of 87 samples from SBE, SQUen, SQUes, and SQUwn subclades. Population genetic clustering analysis suggested a structure similar to the mitochondrial phylogeny, where most samples were classified into four genetic clusters corresponding to the four mtDNA subclades. However, a proportion of samples carrying SQUen mtDNA haplotypes formed an additional distinct cluster SHY. Those samples are found in the contact zone of the two species bearing mosaic and intermediate morphological characteristics. We detected an admixed ancestry in SHY from SBE and SQUen that conformed to an intrapopulation breeding scenario for at least hundreds of generations after the initial hybrid event, leading to a conclusion that SHY is a distinct and near-panmictic population derived from natural interspecific hybridization. In addition, SQUes (Hainan Island endemic) is of special concern due to significant isolation and low genetic diversity. We suggest that seven evolutionarily significant units should be recognized to facilitate appropriate conservation actions. These findings also highlight the urgent need for further herpetological research and conservation in this region.

Genetic Structure of the Ca Rater Mallorquí Dog Breed Inferred by Microsatellite Markers

Ca Rater Mallorquí is a dog breed from the Island of Mallorca (Spain) traditionally used as a hunting and ratting dog to prevent disease spread and economic losses related to rodent activities on farms. However, the census data shows a population decline that should be addressed by implementing a conservation program. The first step to implementing a conservation plan is knowing the genetic situation of the Ca Rater Mallorquí population. Therefore, we aimed to genetically characterise the breed in our study. We analysed 33 microsatellites recommended by the International Society of Animal Genetics (ISAG) in 77 samples. Data were obtained from 13 samples of Balearic, Spanish, and international dog breeds to study the genetic diversity among breeds. The population did not significantly deviate from the Hardy-Weinberg equilibrium with heterozygosity (Ho) of 0.655 and expected heterozygosity (He) of 0.685. The Wright's fixation indices, the Factorial Correspondence Analysis (FCA), a dendrogram representing Reynolds genetic distance between populations, and the pairwise F_ST values establish the Ca Rater Mallorquí as an independent breed distinct from the Balearic, Spanish, and international breeds.

Pleistocene-Holocene vicariance, not Anthropocene landscape change, explains the genetic structure of American black bear (Ursus americanus) populations in the American Southwest and northern Mexico

The phylogeography of the American black bear (Ursus americanus) is characterized by isolation into glacial refugia, followed by population expansion and genetic admixture. Anthropogenic activities, including overharvest, habitat loss, and transportation infrastructure, have also influenced their landscape genetic structure. We describe the genetic structure of the American black bear in the American Southwest and northern Mexico and investigate how prehistoric and contemporary forces shaped genetic structure and influenced gene flow. Using a suite of microsatellites and a sample of 550 bears, we identified 14 subpopulations organized hierarchically following the distribution of ecoregions and mountain ranges containing black bear habitat. The pattern of subdivision we observed is more likely a product of postglacial habitat fragmentation during the Pleistocene and Holocene, rather than a consequence of contemporary anthropogenic barriers to movement during the Anthropocene. We used linear mixed‐effects models to quantify the relationship between landscape resistance and genetic distance among individuals, which indicated that both isolation by resistance and geographic distance govern gene flow. Gene flow was highest among subpopulations occupying large tracts of contiguous habitat, was reduced among subpopulations in the Madrean Sky Island Archipelago, where montane habitat exists within a lowland matrix of arid lands, and was essentially nonexistent between two isolated subpopulations. We found significant asymmetric gene flow supporting the hypothesis that bears expanded northward from a Pleistocene refugium located in the American Southwest and northern Mexico and that major highways were not yet affecting gene flow. The potential vulnerability of the species to climate change, transportation infrastructure, and the US–Mexico border wall highlights conservation challenges and opportunities for binational collaboration.

Population Genetic Characteristics and Mating Type Frequency of Venturia effusa from Pecan in South America

Scab, caused by the plant-pathogenic fungus Venturia effusa, is a major disease of pecan in South America, resulting in loss of quantity and quality of nut yield. Characteristics of the populations of V. effusa in South America are unknown. We used microsatellites to describe the genetic diversity and population structure of V. effusa in South America, and determined the mating type status of the pathogen. The four hierarchically sampled orchard populations from Argentina (AR), Brazil (BRC and BRS), and Uruguay (UR) had moderate to high genotypic and gene diversity. There was evidence of population differentiation (F_st = 0.196) but the correlation between geographic distance and genetic distance was not statistically significant. Genetic differentiation was minimal between the UR, BRC, and BRS populations, and these populations were more clearly differentiated from the AR population. The MAT1-1 and MAT1-2 mating types occurred in all four orchards and their frequencies did not deviate from the 1:1 ratio expected under random mating; however, multilocus linkage equilibrium was rejected in three of the four populations. The population genetics of South American populations of V. effusa has many similarities to the population genetics of V. effusa previously described in the United States. Characterizing the populations genetics and reproductive systems of V. effusa are important to establish the evolutionary potential of the pathogen and, thus, its adaptability-and can provide a basis for informed approaches to utilizing available host resistance and determining phytosanitary needs.

Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers

Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (F_IS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.

Finding the adaptive needles in a population-structured haystack: a case study in a New Zealand mollusc

Genetic adaptation to future environmental conditions is crucial to help species persist as the climate changes. Genome scans are powerful tools to understand adaptive landscapes, enabling us to correlate genetic diversity with environmental gradients while disentangling neutral from adaptive variation. However, low gene flow can lead to both local adaptation and highly structured populations, and is a major confounding factor for genome scans, resulting in an inflated number of candidate loci.

Here, we compared candidate locus detection in a marine mollusc (Onithochiton neglectus), taking advantage of a natural geographical contrast in the levels of genetic structure between its populations. O. neglectus is endemic to New Zealand and distributed throughout an environmental gradient from the subtropical north to the subantarctic south. Due to a brooding developmental mode, populations tend to be locally isolated. However, adult hitchhiking on rafting kelp increases connectivity among southern populations.

We applied two genome scans for outliers (Bayescan and PCAdapt) and two genotype–environment association (GEA) tests (BayeScEnv and RDA). To limit issues with false positives, we combined results using the geometric mean of q‐values and performed association tests with random environmental variables. This novel approach is a compromise between stringent and relaxed approaches widely used before, and allowed us to classify candidate loci as low confidence or high confidence.

Genome scans for outliers detected a large number of significant outliers in strong and moderately structured populations. No high‐confidence GEA loci were detected in the context of strong population structure. However, 86 high‐confidence loci were associated predominantly with latitudinally varying abiotic factors in the less structured southern populations. This suggests that the degree of connectivity driven by kelp rafting over the southern scale may be insufficient to counteract local adaptation in this species.

Our study supports the expectation that genome scans may be prone to errors in highly structured populations. Nonetheless, it also empirically demonstrates that careful statistical controls enable the identification of candidate loci that invite more detailed investigations. Ultimately, genome scans are valuable tools to help guide further research aiming to determine the potential of non‐model species to adapt to future environments.

Genetic Diversity and Population Genetic Structure of Setosphaeria turcica From Sorghum in Three Provinces of China Using Single Nucleotide Polymorphism Markers

Setosphaeria turcica is a heterothallic fungus that is the causal agent of northern leaf blight (NLB), which is a devastating foliar disease of sorghum and maize. Despite of its adversary to crop production, little is known about the genetic diversity and population genetic structure of this pathogen from sorghum. In this study, we explored the utilization of single nucleotide polymorphism (SNP) molecular markers and three mating type-specific primers to analyze the genetic diversity, population genetic structure, and mating type distribution of 87 S. turcica isolates that had been collected in sorghum production areas from three provinces, including Henan, Shaanxi, and Shanxi in China. The populations are featured with moderate genetic diversity and relatively equal mating type distribution of MAT1-1 and MAT1-2. The genetic differentiation was significant (p < 0.05) among different populations except those from Henan and Shanxi provinces that showed particularly frequent gene flow between them. Neither the maxinum likelihood phylogenetic tree, nor principal coordinate analysis, nor genetic structure analysis was able to completely separate the three populations. The relatively low genetic distance and high genetic identification were also observed among the three populations. Nevertheless, the genetic variation within populations was the major source of variation as revealed by AMOVA analysis. The findings of this study have improved our current understanding about the genetic diversity, population genetic structure, and the distribution of mating type of S. turcica, which are useful for unraveling the epidemiology of NLB and developing effective disease management strategies.

Resprouters Versus Reseeders: Are Wild Rooibos Ecotypes Genetically Distinct?

Aspalathus linearis (Burm. F.) R. Dahlgren (Fabaceae) or rooibos, is a strict endemic species, limited to areas of the Cederberg (Western Cape) and the southern Bokkeveld plateau (Northern Cape) in the greater Cape Floristic Region (CFR) of South Africa. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and genetics, and these ecotypes are broadly distinguished into two main groups, namely, reseeders and resprouters, based on their fire-survival strategy. No previous assessment of genetic diversity or population structure using microsatellite markers has been conducted in A. linearis. This study aimed to test the hypothesis that wild rooibos ecotypes are distinct in genetic variability and that the ecotypes found in the Northern Cape are differentiated from those in the Cederberg that may be linked to a fire-survival strategy as well as distinct morphological and phytochemical differences. A phylogeographical and population genetic analyses of both chloroplast (trnLF intergenic region) and newly developed species-specific nuclear markers (microsatellites) was performed on six geographically representative wild rooibos populations. From the diversity indices, it was evident that the wild rooibos populations have low-to-moderate genetic diversity (He: 0.618-0.723; Ho: 0.528-0.704). The Jamaka population (Cederberg, Western Cape) had the lowest haplotype diversity (H = 0.286), and the lowest nucleotide diversity (π = 0.006) even though the data revealed large variations in haplotype diversity (h = 0.286-0.900) and nucleotide diversity (π = 0.006-0.025) between populations and amongst regions where wild rooibos populations are found. Our data suggests that populations of rooibos become less diverse from the Melkkraal population (Suid Bokkeveld, Northern Cape) down towards the Cederberg (Western Cape) populations, possibly indicative of clinal variation. The largest genetic differentiation was between Heuningvlei (Cederberg, Western Cape) and Jamaka (FST = 0.101) localities within the Cederberg mountainous region, and, Blomfontein (Northern Cape) and Jamaka (Cederberg) (FST = 0.101). There was also a significant isolation by distance (R2 = 0.296, p = 0.044). The presence of three main clusters is also clearly reflected in the discriminant analysis of principal components (DAPC) based on the microsatellite marker analyses. The correct and appropriate management of wild genetic resources of the species is urgently needed, considering that the wild Cederberg populations are genetically distinct from the wild Northern Cape plants and are delineated in accordance with ecological functional traits of reseeding or resprouting, respectively. The haplotype divergence of the ecotypes has also provided insights into the genetic history of these populations and highlighted the need for the establishment of appropriate conservation strategies for the protection of wild ecotypes.

Historical Dynamics of Semi-Humid Evergreen Forests in the Southeast Himalaya Biodiversity Hotspot: A Case Study of the Quercus franchetii Complex (Fagaceae)

The Oligocene and Miocene are key periods in the formation of the modern topography and flora of East Asian and Indo-China. However, it is unclear how geological and climatic factors contributed to the high endemism and species richness of this region. The Quercus franchetii complex is widespread in the southeast Himalaya fringe and northern Indo-China with a long evolutionary history. It provides a unique proxy for studying the diversity pattern of evergreen woody lineages in this region since the Oligocene. In this study, we combined chloroplast (cpDNA) sequences, nuclear microsatellite loci (nSSRs), and species distribution modeling (SDM) to investigate the impacts of geological events on genetic diversity of the Q. franchetii complex. The results showed that the initial cpDNA haplotype divergence was estimated to occur during the middle Oligocene (30.7 Ma), which might have been raised by the tectonic activity at this episode to the Miocene. The nSSR results revealed two major groups of populations, the central Yunnan-Guizhou plateau (YGP) group and the peripheral distribution group when K = 2, in responding to the rapid YGP uplift during the late Miocene, which restricted gene flow between the populations in core and marginal areas. SDM analysis indicated that the distribution ranges of the Q. franchetii complex expanded northwards after the last glacial maximum, but the core distribution range in YGP was stable. Our results showed that the divergence of Q. franchetii complex is rooted in the mid-Oligocene. The early geological events during the Oligocene, and the late Miocene may play key roles to restrict seed-mediated gene flow among regions, but the pollen-mediated gene flow was less impacted. The uplifts of the YGP and the climate since LGM subsequently boosted the divergence of the populations in core and marginal areas.

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide F_ST  ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.

A comprehensive analysis of genetic diversity of EBV reveals potential high-risk subtypes associated with nasopharyngeal carcinoma in China

Epstein-Barr virus (EBV), a widespread oncovirus, is associated with multiple cancers including nasopharyngeal carcinoma (NPC), gastric cancer and diverse lymphoid malignancies. Recent studies reveal that specific EBV strains or subtypes are associated with NPC development in endemic regions. However, these NPC specific subtypes were only identified in a portion of infected individuals due possibly to the limited samples size studied or the complicated population structures of the virus. To identify additional high-risk EBV subtypes, we conducted a comprehensive genetic analysis of 22 critical viral proteins by using the largest dataset of 628 EBV genomes and 792 sequences of single target genes/proteins from GenBank. The phylogenetic, principal component and genetic structure analyses of these viral proteins were performed through worldwide populations. In addition to the general Asia-Western/Africa geographic segregation, population structure analysis showed a 'Chinese-unique' cluster (96.57% isolates from China) was highly enriched in the NPC patients, compared to the healthy individuals (89.6% vs. 44.5%, P < 0.001). The newly identified EBV subtypes, which contains four Chinese-specific NPC-associated amino acid substitutions (BALF2 V317M, BNRF1 G696R, V1222I and RPMS1 D51E), showed a robust positive association with the risk of NPC in China (Odds Ratio = 4.80, 20.00, 18.24 and 32.00 for 1, 2, 3 and 4 substitutions, respectively, P _trend <0.001). Interestingly, the coincidence of positively selected sites with NPC-associated substitutions suggests that adaptive nonsynonymous mutation on critical proteins, such as BNRF1, may interact with host immune system and contribute to the carcinogenesis of NPC. Our findings provide a comprehensive overview of EBV genetic structure for worldwide populations and offer novel clues to EBV carcinogenesis from the aspect of evolution.

Genetic imprints of Brosimum alicastrum Sw. in Mexico

PREMISE

The mechanisms generating the geographical distributions of genetic diversity are a central theme in evolutionary biology. The amount of genetic diversity and its distribution are controlled by several factors, including dispersal abilities, physical barriers, and environmental and climatic changes. We investigated the patterns of genetic diversity and differentiation among populations of the widespread species Brosimum alicastrum in Mexico.

METHODS

Using nuclear DNA microsatellite data, we tested whether the genetic structure of B. alicastrum was associated with the roles of the Trans-Mexican Volcanic Belt and the Isthmus of Tehuantepec as geographical barriers to gene flow and to infer the role of past events in the genetic diversity patterns. We further used a maximum-likelihood population-effects mixed model (MLPE) to identify the main factor affecting population differentiation in B. alicastrum.

RESULTS

Our results suggested that Mexican B. alicastrum is well differentiated into three main lineages. Patterns of the genetic structure at a finer scale did not fully correspond to the current geographical barriers to gene flow. According to the MLPE mixed model, isolation by distance is the best model for explaining the genetic differentiation of B. alicastrum in Mexico.

CONCLUSIONS

We propose that the differentiation patterns might reflect (1) an ancient differentiation that occurred in Central and South America, (2) the effects of past climatic changes, and (3) the functions of some physical barriers to gene flow. This study provides insights into the possible mechanisms underlying the geographic genetic variation of B. alicastrum along a moisture gradient in tropical lowland forests.

Whole genome genotyping reveals discrete genetic diversity in north-east Atlantic maerl beds

Maerl beds are vital habitats for a diverse array of marine species across trophic levels, but they are increasingly threatened by human activities and climate change. Furthermore, little is known about the genetic diversity of maerl-forming species and the population structure of maerl beds, both of which are important for understanding the ability of these species to adapt to changing environments and for informing marine reserve planning. In this study, we used a whole genome genotyping approach to explore the population genomics of Phymatolithon calcareum, a maerl-forming red algal species, whose geographical distribution spans the north-east Atlantic, from Norway to Portugal. Our results, using 14,150 genome-wide SNPs (single nucleotide polymorphisms), showed that P. calcareum maerl beds across the north-east Atlantic are generally structured geographically, a pattern likely explained by low dispersal potential and limited connectivity between regions. Additionally, we found that P. calcareum from the Fal Estuary, south-west England, is genetically distinct from all other P. calcareum sampled, even from The Manacles, a site located only 13 km away. Further analysis revealed that this finding is not the result of introgression from two closely related species, Phymatolithon purpureum or Lithothamnion corallioides. Instead, this unique diversity may have been shaped over time by geographical isolation of the Fal Estuary maerl bed and a lack of gene flow with other P. calcareum populations. The genomic data presented in this study suggest that P. calcareum genetic diversity has accumulated over large temporal and spatial scales, the preservation of which will be important for maximizing the resilience of this species to changes in climate and the environment. Moreover, our findings underline the importance of managing the conservation of maerl beds across western Europe as distinct units, at a site-by-site level.

Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range

The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.

Microsatellite-Based Genetic Characterization of the Indigenous Katjang Goat in Peninsular Malaysia

Simple Summary

Genetic characterization is one of the tools to assess the genetic diversity of livestock breeds towards the goals of conservation and sustainable use. This research aimed to assess the genetic diversity, population, genetic relationship, and structure of the Malaysian indigenous Katjang goat breed, which has been reported to be at risk of extinction by the Food and Agriculture Organization of the United Nations (FAO). Through assessment from microsatellite DNA markers, this breed was found to have low genetic diversity and showed evidence of high inbreeding. This breed might also have undergone population bottlenecks in the past. Through combined data analysis with other breeds and populations, available through data from published research, the Katjang goat population was found to have interconnection and form the centre of the network; it was also found to be the centroid of the multidimensional scaling plot. The findings of this research help in the understanding of the current genetic diversity of this breed and the need for its conservation.

Abstract

The Katjang goat is the only indigenous domestic goat breed in Malaysia. Following a national baseline survey from 2001 to 2002, this breed was reported to the FAO as being at risk of extinction. In this study, 36 microsatellite markers were screened, and 25 polymorphic markers were used to analyze the genetic structure of the Katjang goat breed in Peninsular Malaysia. A sample set of data derived from another 10 populations from three published research studies was used as an outgroup for an inter-population genetic study. The analysis showed that the mean value of the observed heterozygosity was 0.29 ± 0.14, and the expected heterozygosity was 0.72 ± 0.14, which indicated low genetic diversity. The inbreeding coefficient, F_IS, was high, at 0.46. Significant (p < 0.01) deviations from the Hardy Weinberg equilibrium were noted for all loci. The bottleneck analysis using the Wilcoxon Rank test under the two-phase model of mutation was significant (p < 0.01) for heterozygosity excess, which suggested that the Katjang breed had undergone significant population reduction in the past. Through combined analysis of data from publicly available research, almost the entire population of Katjang goats represent the centroid and are grouped together on a multidimensional scaling plot, except for the Terengganu population. Network analysis revealed that the goat population from Pahang formed the centrality of the network.

Evolutionary history of the oriental fire-bellied toad (Bombina orientalis) in Northeast China

The evolutionary history of a species is generally affected by the combination of geological events and climate fluctuations. By analyzing the population features, genetic structure and the effective population historical dynamics of existing species, the population evolutionary history can be reestablished. In recent years, geological evidence shows that the Yilan-Yitong fault zone located in Northeast Asia experienced strong and frequent geological changes in the late Quaternary period. Species population history has been shaped by the combination of the complex climatic conditions of the Quaternary and Pleistocene glacial interglacial cycles and palaeogeological events in Northeast Asia and it has become a research focus for evolutionary biology researchers. In this study, mitochondrial and microsatellite molecular markers were used to reveal the population features, genetic structure, and the effective population historical dynamics of the Oriental fire-bellied toad (Bombina orientalis). The results showed that the strong seismic activity of the Yilan-Yitong fault zone in the late Quaternary period was the main reason for the population differentiation of Oriental fire-bellied toad in northeast China. The Quaternary Pleistocene glacial interglacial cycles led to the significant bottleneck effect of the western population located in the Maoer mountain area. As a result, the western population has low genetic diversity. Recent gene flow between eastern and western populations and historical evidence of population expansion proved that the dispersal behavior of the western populations was the main cause of the low genetic diversity and mitochondrial and nuclear discordance. Human economic activity may be the mainly driving factor. These evidences showed that the comprehensive influence of geology, climate, human activities and other factors should be considered in the process of exploring the evolutionary history of species.

Genetic Variability and Molecular Evolution of Maize Yellow Mosaic Virus Populations from Different Geographic Origins

Maize yellow mosaic virus (MaYMV) hosted in various gramineous plants was assigned to the genus Polerovirus (family Luteoviridae) in 2018. However, little is known about its genetic diversity and population structure. In this study, 509 sugarcane leaf samples with mosaic symptoms were collected in 2017 to 2019 from eight sugarcane-growing provinces in China. Reverse-transcription PCR results revealed that four positive-sense RNA viruses were found to infect sugarcane, and the incidence of MaYMV among samples from Fujian, Sichuan, and Guangxi Provinces was 52.1, 9.8, and 2.5%, respectively. Based on 82 partial MaYMV sequences and 46 whole-genome sequences from different host plants, phylogenetic analysis revealed that MaYMV populations are very closely associated with their source geographical regions (China, Africa, and South America). Pairwise identity analysis showed significant variability in genome sequences among MaYMV isolates with genomic nucleotide identities of 91.1 to 99.9%. In addition to codon mutations, insertions or deletions also contributed to genetic variability in individual coding regions, especially in the readthrough protein (P3-P5 fusion protein). Low gene flow and significant genetic differentiation of MaYMV were observed among the three geographical populations, suggesting that environmental adaptation is an important evolutionary force that shapes the genetic structure of MaYMV. Genes in the MaYMV genome were subject to strong negative or purification selection during evolution, except for the movement protein (MP), which was under positive selection pressure. This finding suggests that the MP may play an important role in MaYMV evolution. Taken together, our findings provide basic information for the development of an integrated disease management strategy against MaYMV.

Ocean Currents Drove Genetic Structure of Seven Dominant Mangrove Species Along the Coastlines of Southern China

Mangrove forest ecosystems, which provide important ecological services for marine environments and human activities, are being destroyed worldwide at an alarming rate. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes on the distribution of mangroves and patterns of population genetic differentiation. Seven mangrove species (Acanthus ilicifolius, Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, Kandelia obovata, Lumnitzera racemosa, and Rhizophora stylosa), which are predominant along the coastlines of South China, were genotyped at nuclear (nSSR) and chloroplast (cpSSR) microsatellite markers. We estimated historical and contemporary gene flow, the genetic diversity and population structure of seven mangrove species in China. All of these seven species exhibited few haplotypes, low levels of genetic diversity (H E = 0.160-0.361, with the exception of K. obovata) and high levels of inbreeding (F IS = 0.104-0.637), which may be due to their marginal geographical distribution, human-driven and natural stressors on habitat loss and fragmentation. The distribution patterns of haplotypes and population genetic structures of seven mangrove species in China suggest historical connectivity between populations over a large geographic area. In contrast, significant genetic differentiation [F ST = 0.165-0.629 (nSSR); G ST = 0.173-0.923 (cpSSR)] indicates that populations of mangroves are isolated from one another with low levels of contemporary gene flow among populations. Our results suggest that populations of mangroves were historically more widely inter-connected and have recently been isolated, likely through a combination of ocean currents and human activities. In addition, genetic admixture in Beibu Gulf populations and populations surrounding Hainan Island and southern mainland China were attributed to asymmetric gene flow along prevailing oceanic currents in China in historical times. Even ocean currents promote genetic exchanges among mangrove populations, which are still unable to offset the effects of natural and anthropogenic fragmentation. The recent isolation and lack of gene flow among populations of mangroves may affect their long-term survival along the coastlines of South China. Our study enhances the understanding of oceanic currents contributing to population connectivity, and the effects of anthropogenic and natural habitat fragmentation on mangroves, thereby informing future conservation efforts and seascape genetics toward mangroves.

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two types of genomic variation in population genomics studies.

Fine-scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus

The genetic structure of animal populations has considerable behavioural, ecological and evolutionary implications and may arise from various demographic traits. Here, we use observational field data and molecular genetics to determine the genetic structure of an invasive population of monk parakeets, Myiopsitta monachus, at a range of spatial scales, and investigate the demographic processes that generate the observed structure. Monk parakeets construct large nests that can house several pairs occupying separate chambers; these nests are often aggregated within nesting trees. We determined patterns of relatedness within compound nests, within nesting trees and between trees. Spatial autocorrelation analyses of pairwise genetic relatedness revealed fine-scale genetic structure with relatives of both sexes spatially clustered within, but not beyond, nesting trees. In addition, males were more related to males sharing their compound nests than to other males occupying the same nesting tree. By contrast, males and females within compound nests were not significantly more closely related than elsewhere in the same tree, and we found no evidence for inbreeding. Adults showed high breeding site fidelity between years despite considerable disturbance of nest sites. Natal dispersal was female-biased, but dispersal distances were relatively short with some natal philopatry observed in both sexes. Sibling coalitions, typically of males, were observed amongst both philopatric and dispersing birds. Our results show significant clustering of kin within compound nests and nesting trees resulting from limited and coordinated natal dispersal, with subsequent breeding site fidelity. The resulting genetic structure has implications for social behaviour in this unusual parrot species.

Resistance and resilience of genetic and phenotypic diversity to "black swan" flood events: A retrospective analysis with historical samples of guppies

Rare extreme "black swan" disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called "50-year floods") can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events - perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods - one in 2005 and another in 2016. For each river, we selected four sites and used archived "historical" samples to compare levels of genetic and phenotypic diversity before vs. after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) colour. We found that genetic diversity and population structure was mostly "resistant" to even these extreme floods; whereas the larger impacts on phenotypic diversity were short-lived, suggesting additional "resilience". We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances.

Population genetic structure underlying the geographic variation in beetle structural colour with multiple transition zones

We studied the population genetic structure underlying the geographic variation in the structural colour of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colours of different reflectance wavelengths perceived as red, green and indigo. These forms occur parapatrically in an area of Japan. The colour variation was not related to variation in climatic factors. Using single nucleotide polymorphisms (SNPs) from restriction-site-associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red and east/red) by a combination of genetic clusters (west, south and east) and three colour forms. There were three transition zones for the colour forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colours. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident colour changes, which implies regionally specific selection on the different colours. In a genomewide association study, we identified four SNPs that were associated with the red/green or indigo colour and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different colour range. These loci may have controlled the transitions between different combinations of colours. Our study demonstrates that geographic colour variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colours, and the effects of different colour loci.

Variable resistance to spinetoram in populations of Thrips palmi across a small area unconnected to genetic similarity

The melon thrips, Thrips palmi, is an increasingly important pest of vegetables in northern China. Some populations have developed resistance in the field to the insecticide spinetoram. Understanding the origin and dispersal of insecticide-resistant populations can shed light on resistance management strategies. In this study, we tested susceptibility of seven greenhouse populations of T. palmi to spinetoram collected from a small area of about 300 km2 in Shandong Province and examined population genetic structure across the area based on a segment of mitochondrial cox1 gene and 22 microsatellite loci to infer the possible origin and dispersal of insecticide resistance. Levels of resistance to spinetoram differed among seven populations, which included one population with high resistance (LC50 = 759.34 mg/L), three populations with medium resistance (LC50 ranged from 28.69 to 34.79 mg/L), and three populations with low resistance (LC50 ranged from 7.61 to 8.97 mg/L). The populations were genetically differentiated into two groups unrelated to both levels of resistance and geographic distance. The molecular data indicated high levels of gene flow between populations with different levels of resistance to spinetoram and low gene flow among populations with the same level of resistance, pointing to a likely separate history of resistance evolution. Resistance levels of two tested populations to spinetoram decreased 23 and 4.6 times after five generations without any exposure to the pesticide. We therefore suspect that resistance of T. palmi most likely evolved in response to local applications of the insecticide. Our study suggests that the development of resistance could be avoided or resistance even reversed by reducing usage of spinetoram.

Population genetic structure and marker-trait associations in East and West African Striga hermonthica with varying phenotypic response to Fusarium oxysporum f. sp. strigae isolates Foxy-2 and FK3

To examine the genetic basis for the variable susceptibility of Striga hermonthica from differing zones of sub-Saharan Africa to Fusarium oxysporum f. sp. strigae (Fos) isolates Foxy-2 and FK3, 10 S. hermonthica populations from Eastern and Western Africa were phenotyped for their susceptibility response to Foxy-2 and FK3, and then genotyped with 22 simple sequence repeat (SSR) markers. There is low genetic differentiation between East African and West African S. hermonthica populations (i.e. the proportion of the total genetic variance contained in the subpopulation relative to the total genetic variance, F_ST  = 0.012, P < 0.05), but intermediate genetic differentiation (F_ST  = 0.143, P < 0.01) underlies the S. hermonthica groups that are differentiated by their phenotypic responses to Fos isolates. An expressed sequence tag SSR (EST-SSR) marker Y53 (P < 0.01) and a genomic SSR marker E1009 (P < 0.05) were associated with the S. hermonthica class susceptible to Foxy-2 and FK3 (group A). A divergent S. hermonthica class, consisting of groups with intermediate susceptibility to Foxy-2 (group B) and susceptibility to either FK3 (group C) or Foxy-2 (group D), showed no marker-trait association, instead demonstrated linkage disequilibrium decay. Owing to point substitutions and insertion-deletion mutations, the unique, protein-coding nucleotide sequence at the E1009 locus in group A was partly dissimilar to group B, but was totally distinct from groups C and D. These findings implied that the inconsistent effectiveness of a Fos isolate is better explained by genomic variation in S. hermonthica, rather than by S. hermonthica sampling zones.

Global patterns of population genetic differentiation in seed plants

Evaluating the factors that drive patterns of population differentiation in plants is critical for understanding several biological processes such as local adaptation and incipient speciation. Previous studies have given conflicting results regarding the significance of pollination mode, seed dispersal mode, mating system, growth form and latitudinal region in shaping patterns of genetic structure, as estimated by F_ST values, and no study to date has tested their relative importance together across a broad scale. Here, we assembled a 337-species data set for seed plants from publications with data on F_ST from nuclear markers and species traits, including variables pertaining to the sampling scheme of each study. We used species traits, while accounting for sampling variables, to perform phylogenetic multiple regressions. Results demonstrated that F_ST values were higher for tropical, mixed-mating, non-woody species pollinated by small insects, indicating greater population differentiation, and lower for temperate, outcrossing trees pollinated by wind. Among the factors we tested, latitudinal region explained the largest portion of variance, followed by pollination mode, mating system and growth form, while seed dispersal mode did not significantly relate to F_ST . Our analyses provide the most robust and comprehensive evaluation to date of the main ecological factors predicted to drive population differentiation in seed plants, with important implications for understanding the basis of their genetic divergence. Our study supports previous findings showing greater population differentiation in tropical regions and is the first that we are aware of to robustly demonstrate greater population differentiation in species pollinated by small insects.

Population genetic structure of the short-beaked common dolphin from the Black Sea and the Turkish Straits System

Our study aims to assess the population connectivity, evolutionary history, and conservation status of the short-beaked common dolphin in the Black Sea and Turkish Straits System (TSS). We also include DNA sequences from the Atlantic Ocean and the Mediterranean Sea to provide a regional perspective to our localized study. Analysis of 366 base pairs of mitochondrial DNA D-loop fragments from 37 samples collected from short-beaked common dolphins in the Black Sea, TSS, and Aegean Sea revealed 13 haplotypes, eight of which have not been previously reported. While analysis of samples archived on GenBank revealed 89 different haplotypes across the region. The haplotype network contains two main peripheral groups that include individuals from all locations. Haplotypes from the Atlantic Ocean are scattered across the network and no obvious population separation was detected. Some shared haplotypes potentially indicate multi-directional colonization events of the Mediterranean Sea from the eastern Atlantic Ocean. Moreover, some less widely distributed haplotypes suggest some level of more recent genetic connectivity through the Strait of Gibraltar and the TSS and point out the importance of these straits in the dispersal of short-beaked common dolphins. The haplotype and nucleotide diversity values were lower in the Black Sea, TSS, and western Mediterranean Sea when compared to the Atlantic Ocean, supporting the expansion of Atlantic populations into the Mediterranean and the Black Seas. Differentiation was observed between the Atlantic Ocean, and the Mediterranean Sea, TSS and the Black Sea based on Фst but not between Mediterranean and the Black Seas. For common dolphins, which have high dispersal potential, the protection of open seas and narrow seaways to enhance connectivity may be crucial.

Urban Populations of Aedes aegypti (Diptera: Culicidae) From Central Argentina: Dispersal Patterns Assessed by Bayesian and Multivariate Methods

Aedes aegypti (L.), the main vector of dengue and other arboviruses, was declared eradicated from Argentina in 1964; however, in 1987, it was detected again and nowadays it occurs in most of the country territory. To understand the transmission of vector-borne diseases, knowledge of the dispersal of vector populations is essential to evaluate the risk of pathogen transmission. We conducted a population genetic analysis of Ae. aegypti in 20 neighborhoods from Córdoba, the second largest city in Argentina, using 10 microsatellite loci. High genetic differentiation and the absence of an isolation by distance pattern was found using Weir and Cockerham's θ. Bayesian and multivariate clustering analyses showed that the studied sites included individuals with high membership coefficients (Q) in their populations, individuals with membership in another cluster, and admixed individuals. Individuals with high Q in clusters different from the population in which they were collected strongly suggests that passive transport is important in shaping the Ae. aegypti dispersal pattern in Córdoba city. Knowing the genetic structure of Ae. aegypti populations and their dispersal patterns would contribute to the implementation of vector control programs.

Genetic Diversity of Pseudomonas syringae pv. actinidiae: Seasonal and Spatial Population Dynamics

Pseudomonassyringae pv. actinidiae (Psa) is a gram-negative bacterium responsible for the bacterial canker in Actinidia chinensis var. deliciosa and A. chinensis var. chinensis, a quarantine organism threatening the kiwifruit industry sustainability. The present study aimed to determine the genetic structure of the endophytic and epiphytic populations of Psa isolated from four different Portuguese orchards with distinct abiotic conditions in two consecutive seasons. The results identified several coexisting and highly heterogeneous Psa populations. Moreover, evident changes in population structure occurred between the epiphytic and endophytic populations, and between seasons with a notable decrease in Psa diversity in autumn. This work provided solid evidence that the initial clonal expansion of Psa in Europe was followed by a wide genomic diversification. This perspective is important for the understanding of kiwifruit bacterial canker disease occurrence and Psa evolution, namely when adopting strategies for management of epidemics.