Low Levels Of Genetic Diversity Research Articles

Geographic distance, landscape heterogeneity and migratory connectivity influence population genetic structure of farmland-dependent wintering birds and their conservation

Understanding the drivers of population structure is a conservation priority for declining species. However, the relative extent to which landscape features in wintering areas and migration route drive population genetic structure for birds is still unclear. The eastern great bustard (Otis tarda dybowskii) is an endangered and declining steppe bird which is heavily dependent on farmland for overwintering. We used noninvasive fecal sampling and molecular genetics to quantify genetic diversity and explore the extent of genetic differentiation among 145 individuals from 7 wintering populations across this subspecies' non-breeding distribution. Genetic analyses revealed low to moderate but significant genetic differentiation, showing three genetic clusters consistent with three migration routes. Landscape genetic analysis based on variance partitioning revealed that 67.4 % of the observed genetic variability was explained through isolation by distance (IBD), and in contrast, 56.5 % was explained by landscape heterogeneity. The low level of genetic diversity and significant population differentiation we discovered, combined with small population size, put the eastern great bustard at risk of inbreeding depression. Our results strengthen evidence for strong migratory connectivity in this subspecies, with significant genetic clustering correlated to known migration routes. The construction of secure nature reserves and improvement of wintering habitats can help to reduce threats on the wintering grounds, and thus associated demographic impacts on tightly connected breeding populations.

Assessment of Genetic Variation of Genus Paracaryum (Boraginaceae) By Rapd Markers

The present study reveals the genetic diversity of Iranian Paracaryum based on morphological and molecular characters of 12 species from 11 provinces of Iran. A total of 118 reproducible bands were generated by 10 of 30 random amplified polymorphic DNA (RAPD) primers, with an average of 11.8 bands per primer and 49% polymorphism. The largest number of effective alleles (Ne), Shannon Index (I) and genetic diversity (H) higher level of Shannon Index (I) and genetic diversity (H) were shown by Paracaryum persicum. Our data depicted the highest similarity between Paracaryum cyclhymenium and P. persicum and the lowest between P. sintenisii and P. bungei. P. bungei showed a relatively low level of genetic variation. Finally, the Neighbor Joining (NJ) trees based on RAPD markers data divided the populations into two different clusters, indicating their genetic difference, which is discussed in detail. Bangladesh J. Plant Taxon. 29(1): 31-41, 2022 (June)

Variation of Residual Sexuality Rates along Reproductive Development in Apomictic Tetraploids of Paspalum.

Most apomictic plants are facultative, maintaining the ability to reproduce sexually at different frequencies depending on the taxa, ploidy, and reproductive stage. In this context, Paspalum species are good model systems for studies evaluating the varying levels of apomixis expression. We aimed to identify, in apomictic tetraploid Paspalum species, the degree of apomixis and residual sexuality in three stages of reproductive development, and if their expression varies along them in order to predict their realized impact on the genetic diversity of future generations. Three main stages in the reproductive development (i.e., ovule, seed, and progeny) were studied in tetraploids from populations of P. cromyorhizon and P. maculosum. Mature ovules were studied using cytoembryological analysis, seeds by flow cytometry, and progeny tests with molecular markers. The expression of sexuality and apomixis was compared in each stage. We observed a decline in expression of sexual reproduction through the consecutive stages, jointly with an increase of apomixis expression. Both species showed at least one tetraploid plant capable of producing progeny by sexual means. These small rates of sexually originated progeny prove the ability of apomictic plants to produce low levels of genetic variation through rare events of sexuality. This study also demonstrates the importance of analyzing different reproductive stages in order to get a whole picture of the reproductive outcomes in plant evolution.

Analysis of Population Genetic Diversity and Genetic Structure of Schizothorax biddulphi Based on 20 Newly Developed SSR Markers

To protect the germplasm resources of Schizothorax biddulphi, we developed and used 20 pairs of polymorphic microsatellite primers to analyze the genetic diversity and structure of populations. A total of 126 samples were collected from the Qarqan River (CEC), Kizil River (KZL), and Aksu River (AKS) in Xinjiang, China. The results showed that 380 alleles were detected in 20 pairs of primers and the average number of alleles was 19.0. The effective allele numbers and Nei’s gene diversity ranged from 1.1499 to 1.1630 and 0.0962 to 0.1136, respectively. The Shannon index range suggested low levels of genetic diversity in all populations. The genetic distance between the CEC and AKS populations was the largest, and the genetic similarity was the smallest. There was a significant genetic differentiation between CEC and the other two populations. The UPGMA clustering tree was constructed based on population genetic distance, and the clustering tree constructed by individuals showed that the AKS population and KZL population were clustered together, and the CEC population was clustered separately. Also, the group structure analysis also got the same result. It can be seen that although the three populations of S. biddulphi do not have high genetic diversity, the differentiation between the populations was high and the gene flow was limited, especially the differentiation between the CEC population and the other two populations. This study not only provided genetic markers for the research of S. biddulphi but the results of this study also suggested the need for enhanced management of S. biddulphi populations.

Molecular Assessment of Genetic Diversity and Genetic Structure of Rhanterium epapposum Oliv. in Scarce Populations in Some Regions of Western Saudi Arabia.

Rhanterium epapposum Oliv. is a perennial medicinal shrub growing mainly in desert habitats in the Arabian Peninsula. In western Saudi Arabia, the remaining few populations of this species are exposed to many threats, including overcutting, overgrazing, and recently, increasing human activities. These threats are predicted to be exacerbated by the advancement of aridification caused by climate change. The conservation and recovering of the diminished populations of R. epapposum necessitate measurement of their genetic diversity and genetic differentiation. To accomplish this objective, we tested 150 simple sequence repeat (SSR) primer pairs, with which 40 polymorphic loci were identified. These polymorphic loci were used to determine the population genetics of 540 plant accessions sampled from a total of 45 populations of R. epapposum located in 8 sites in western Saudi Arabia: Wadi Khurieba, Wadi Al Khamas, Gebel Al Twaal, Al Asaafer, Wadi ALHamda, Wadi Al Nassayeif, Wadi Qaraba, Wadi Kuliayah, and Wadi Dahban. Low levels of genetic diversity were found in all populations (the values of the PPL ranged between 52.5 and 15) along with a declined value of HT (0.123) and a considerable inbreeding value (F = 0.942), which confirmed a noticeable shortage of heterozygotes. High genetic differentiation among the populations and a low value of gene flow are indicative of high isolation among the R. epapposum populations, which has caused a severe deficiency in gene migration. The data obtained herein inspire several recommendations for conservation and retrieval of the existing populations, including seed banks, restoration of diminished populations, and monitoring and prevention of cutting and grazing activities at threatened sites. All of these measures are urgently required to avoid imminent extinction.

Tusk anomalies in narwhals (Monodon monoceros) from Greenland

The elongated, spiraled tusk of male narwhals (Monodon monoceros) grows continuously throughout the life of the whale and is most likely a secondary sexual trait used in male–male hierarchical competition and possibly in female mate choice. Sex determination in narwhals is typically based on the presence (male) or absence (female) of an erupted tusk, but anomalies such as females with tusks, tuskless males or double-tusked whales occur, although infrequently. In this study, we collected reproductive data and recorded the presence or absence of a tusk in narwhals from the Inuit hunt in Greenland (1993 and 2010–19) with the purpose of estimating the frequency of tusk anomalies. We found that of the 173 whales, 2.9% displayed tusk anomalies. Tusked females constituted 1.5% of sampled females, tuskless males 2.8% of sampled males and double-tusked males 0.9% of sampled males. Biological information on a tusked female, a tuskless male and a double-tusked male was collected and is presented here. The tusked female was sexually mature, and 18 ovarian scars (indicating pregnancies) documented a long reproductive lifespan. The complete female tusk was estimated to be between 146 and 151 cm in length. The tuskless male was sexually maturing, as indicated by body dimensions, and the double-tusked male was sexually immature, with the two tusks measuring <90 cm in length. Although narwhals exhibit extremely low levels of genetic diversity, tusk anomalies persist in the populations, perhaps facilitated by the reproductive ability of whales with tusk anomalies.

Molecular characterization of mahogany tree (Swietenia macrophylla King, Meliaceae) in the remnant natural forest of Ecuador

ABSTRACT The Swietenia macrophylla King (Meliaceae) mahogany tree is widely spread in the neotropics. In Ecuador, it has a wide distribution range from the coastal zone to the Amazon. The mahogany tree is an endangered species due the overexploitation of the high commercial value of its wood. This study is aimed to characterize the Simple Sequence Repeat (SSR) variability of 123 trees selected from six provinces of Ecuador. The results showed that the natural mahogany population had a low level of genetic diversity (A = 6.9; Ho = 0.39; He = 0.43) and a significant heterozygous deficit inbreeding coefficient (F = 0.16). The probability of identity (PI) of the 12 microsatellite markers was low 4.3 × 10−9 and the cumulative exclusion probability of 99.99%. Additionally, the relatedness coefficient among individuals was −0.010 (se = 0.004). The genetic diversity among populations was moderate (ΦST = 8%). In addition, the structure analysis showed two genetic groups; however, it was possible to distinguish admixture within the entire range evaluated. These results show the need to establish strategies that allow the recovery and increase of the genetic diversity in natural populations, especially with the selection of trees to harvest seeds, as well as crossing the tree genetic pool to recombine their diversity.

Population Genetic Analyses of Phytophthora cinnamomi Reveals Three Lineages and Movement Between Natural Vegetation and Avocado Orchards in South Africa.

Phytophthora cinnamomi is the causal agent of root rot, canker, and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses to forestry and agricultural industries, but also threatens the health of various plants in natural ecosystems. In this study, 380 isolates of P. cinnamomi from four avocado production areas and two regions of natural vegetation in South Africa were investigated using 15 microsatellite markers. These populations were found to have a low level of genetic diversity and consisted of isolates from three lineages. Shared genotypes were detected between isolates from avocado orchards and natural vegetation, indicating the movement of isolates between these areas. The population from the Western Cape natural vegetation had the highest level of genotypic diversity and number of unique alleles, indicating this could be the point of introduction of P. cinnamomi to South Africa. Index of association analysis suggested that five of six populations were under linkage disequilibrium, suggesting a clonal mode of reproduction, whereas genotypes sampled from a recently established avocado orchard in the Western Cape were derived from a randomly recombining population. This study provided novel insights on the genetic diversity and spread of P. cinnamomi in South Africa. It also reported on the predominance of triploidy in natural occurring populations and provided evidence for recombination of P. cinnamomi for the first time. The presence of two dominant genotypes in all avocado production areas in South Africa highlight the importance of considering them in disease management and resistance breeding programs.

Genomic Data Reveals Profound Genetic Structure and Multiple Glacial Refugia in Lonicera oblata (Caprifoliaceae), a Threatened Montane Shrub Endemic to North China.

Characterizing genetic diversity and structure and identifying conservation units are both crucial for the conservation and management of threatened species. The development of high-throughput sequencing technology provides exciting opportunities for conservation genetics. Here, we employed the powerful SuperGBS method to identify 33, 758 high-quality single-nucleotide polymorphisms (SNP) from 134 individuals of a critically endangered montane shrub endemic to North China, Lonicera oblata. A low level of genetic diversity and a high degree of genetic differentiation among populations were observed based on the SNP data. Both principal component and phylogenetic analyses detected seven clusters, which correspond exactly to the seven geographic populations. Under the optimal K = 7, Admixture suggested the combination of the two small and geographically neighboring populations in the Taihang Mountains, Dongling Mountains, and Lijiazhuang, while the division of the big population of Jiankou Great Wall in the Yan Mountains into two clusters. High population genetic diversity and a large number of private alleles were detected in the four large populations, while low diversity and non-private alleles were observed for the remaining three small populations, implying the importance of these large populations as conservation units in priority. Demographic history inference suggested two drastic contractions of population size events that occurred after the Middle Pleistocene Transition and the Last Glacial Maximum, respectively. Combining our previous ecological niche modeling results with the present genomic data, there was a possible presence of glacial refugia in the Taihang and Yan Mountains, North China. This study provides valuable data for the conservation and management of L. oblata and broadens the understanding of the high biodiversity in the Taihang and Yan Mountains.

Distribution and characteristics of <i>Ashworthius sidemi</i> Schulz, 1933 (Nematoda, Trichostrongylidae) in wild ungulates in Belarus

The material was collected during the period 2018‒2021 by dissection of internal organs of European bisons, red deers, European roe deers and elks. The found helminths were identified morphologically and using molecular genetic tools. Analysis of 16 ND4 mDNA sequences of A. sidemi revealed low level of genetic diversity which may indicate that Ashworthius sidemi in Belarus spread from one source.

Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming

Simple SummaryThe pikeperch Sander lucioperca (Linnaeus, 1758) is an important fish species in the development of European aquaculture. The aquaculture of a fish species can be facilitated by knowing the genetic variability within and among populations. Here, we assessed the genetic background of 8 wild populations along with 13 broodstocks (i.e., from fish farms) of pikeperch through a combination of genetic markers. We underlined that current broodstocks have a genetic diversity similar to wild populations. When focusing on genetic differentiation, we highlight that European pikeperch populations are divided into two groups: one predominantly present in Northern Europe and around the Baltic Sea and another mainly in Central Europe. Broodstocks appear to contain fish of a single origin with only a few exceptions. Ultimately, we have proposed baseline information about genetic diversity of pikeperch along with a genetic tool that can help pikeperch producers manage and improve their fish stock.The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions.

Effect of Continuous Iron Pollution on Morphology and DNA Profile of Pleurotus tuber-regium

Aims: Iron, the fourth most abundant micronutrient in the soil has been classified as a metal of environmental concern, the study was to assess the effect of continuous iron pollution on growth and the molecular profile of Pleurotus tuber-regium.
 Study design: Experimental research design.
 Place and Duration of Study: The Bells University of Technology, between December 2019 and October 2020.
 Methodology: P. tuber-regium sclerotia procured locally were seeded into 1 kg soil polluted with 20, 40, 60, and 80 mg kg-1 FeSO4 respectively. Watering was done with the respective Fe solutions for 59 days at the rate of 100ml/48hrs. The Stipe length, pileus diameter, fruitbody weight, and days for fruitbody emergence were recorded for each treatment. The concentration of iron in soil and mushroom was determined by Atomic Absorption Spectrophotometer (AAS). DNA extracted from the fruitbodies was subjected to Random Amplified Polymorphic DNA (RAPD) analysis using five RAPD primers and a cluster analysis was performed.
 Results: Fruiting was achieved in all soils (0, 20, 40, 60, 80 mg kg-1) after 23±0.5, 17±1.0, 50±2.5, 58±1.0, and 59±2.0 days respectively. Iron had no significant effect on stipe length while pileus diameter and fruitbody weight increased only at 20mg kg-1. Iron concentration in the soil and mushroom increased as Fe pollution was increased. The bioaccumulation factor was higher in contaminated soil and was between 0.78 and 1.08. The RAPD primers amplified 53 band sizes ranging from 100 - 700 bp and the DNA was clustered in a major group. The percentage polymorphism was 16.9% indicating a low level of genetic variation.
 Conclusion: The result indicated that continuous Fe pollution at the stated concentrations did not have any significant effect on the DNA profile of Pleurotus tuber-regium but the morphological growth of the mushroom was enhanced at low iron contamination levels.

Genetic insights into an Apennine population of the Italian red deer

The red deer Cervus elephus has been a common species in Italy until the Middle Ages and the Renaissance, when its distribution range started to considerably decrease, due to gradual deforestation and hunting pressure. Afterwards, the red deer has been reintroduced to many regions of the world, including Italy. In the Italian Apennines, the Acquerino-Cantagallo Natural Reserve (ACQUERINO) hosts one of the largest peninsular red deer populations, originated from a series of successful reintroductions. In this study, we meant to detect the level of genetic variability of Acquerino-Cantagallo Natural Reserve deer population and to investigate the genetic relationships with the other Italian and European populations. We identified five mitochondrial DNA control region (D-loop) haplotypes, four falling in lineage A and one falling in lineage C, derived from at least two maternal lineages, confirming that ACQUERINO population should be the result of multiple reintroductions. Haplotype diversity (H = 0.50) and nucleotide (π = 0.004) diversity were low, but included into the deer range values. ACQUERINO population showed low levels of genetic diversity when compared to other European and Mediterranean populations, confirming that this expanding population may have been generated from a low number of founders.

The Genetics and Ecology of Post-Fire Eucalyptus globulus Recruitment in an Isolated Stand in Central Portugal

Eucalyptus globulus Labill. is a widespread forest tree species, reported as naturalized across the introduced range, often showing abundant natural regeneration after wildfires. This paper studies a post-fire cohort of seedlings derived from a small, isolated E. globulus stand in central Portugal. The aim is to better understand the genetic dynamics and dispersal mechanisms of naturally established E. globulus populations in the introduced range. The seedling density at 55 m from adult trees was 12,000 ha−1, the farthest seedling being registered at 101 m. Post-fire expansion occurred in a southward direction, in accordance with predominant wind. Seedlings had significantly lower levels of genetic diversity (Ae = 5.8.; He = 0.8) than adult trees (Ae = 6.5; He = 0.8). Crossings were strongly unbalanced, with only eight trees contributing to the sampled seedlings, and one single tree contributing to 52% of these seedlings. Moreover, the co-ancestry amongst seedlings more than doubled (from θ = 0.03 to 0.076), and the population status number was around one third of the value registered for the adult population (from Ns = 16.2 to 6.6). Despite its isolation, external pollen was detected in the stand, and appears to have travelled at least 700 m, contributing to 22% of the offspring. Overall, the seedling cohort is much less diverse than the parent trees, with expected lower resilience and persistence to environmental stresses.

Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico

Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of the oil spill: Ceratoscopelus warmingii (N = 65, SNP = 1804), Diaphus dumerilii (N = 42, SNP = 2577), and Lepidophanes guentheri (N = 44, SNP = 3462). Fishes were sampled in 2011, and then again in 2015, and 2016, and genotyped using single nucleotide polymorphisms (SNP) markers. An additional 22 C. warmingii samples collected in 2014 from the western North Atlantic were used to assess genetic connectivity between these two regions. Overall, all three species were characterized by low levels of genetic diversity and high inbreeding coefficients, and within two of the three species (C. warmingii and L. guentheri), little (if any) evidence of population genetic structure was found within northern GOM waters. Conversely, significant intra-GOM genetic population structure was found for D. dumerilii, highlighting the need for a more robust population genetic survey of these fishes within the GOM to understand how populations of these fishes may respond to future environmental perturbations. In addition, significant genetic population structure was also found between sub-populations of C. warmingii from the northern GOM and western North Atlantic; with evidence of a mixture of two genetic populations co-occurring within the western North Atlantic. Given the potential for future environmental perturbations caused by expanding oil and gas extraction and climate change on GOM mesopelagic communities, rigorous population genetic assessments are required to understand the population dynamics of fishes and to safeguard the genetic diversity and resilience of this functionally important group of deep-sea fishes.

Genetic diversity and population structure of Cinnamomum balansae Lecomte inferred by microsatellites.

Cinnamomum balansae Lecomte (Lauraceae), an economically important forest tree, is distributed in the tropical forests of central and northern Vietnam, which has been threatened in recent decades due to the destruction of its habitat and over-exploitation. The genetic diversity and population structure of the species have not been fully evaluated. We used a set of 15 microsatellites to analyze 161 adult trees from 9 different populations, representing the geographical distribution of C. balansae. Ninety-two different alleles were identified. Here our results showed a low genetic diversity level with an average H o = 0.246 and H e = 0.262, and a high level of genetic differentiation (F ST = 0.601). The bottleneck tests indicated evidence of a reduction in the population size of the two populations (TC and CP). Additionally, all three clustering methods (Bayesian analysis, principal coordinate analysis, and Neighbor-joining tree) were identified in the two genetic groups. The Mantel test showed a significant positive correlation between genetic distance and geographic distance (R 2 = 0.7331). This study will provide a platform for the conservation of C. balansae both in ex-situ and in-situ plans.

Genetic variation in lowland and mountain populations of Tofieldia calyculata and their ability to survive within low levels of genetic diversity

Genetic variation in lowland and mountain populations of Tofieldia calyculata and their ability to survive within low levels of genetic diversity

Genetic monitoring of the Critically Endangered Araripe Manakin reveals low diversity and declining effective population size

Abstract Genetic information is still underestimated in conservation policies, seldom being monitored or included in management strategies. Monitoring changes in genetic diversity over time in endangered species is useful to anticipate possible risks associated with reduced genetic variation. The Araripe Manakin (Antilophia bokermanni) is a Critically Endangered species, probably with a historically low level of genetic diversity and currently facing demographic population decline. This is the first study to present a fine-scale spatio-temporal genetic monitoring for the Araripe Manakin. Using microsatellite loci, genotyped at two time periods (2003–2004 and 2015–2017), we conclude that genetic diversity has been relatively stable in this short-term assessment, with limited signs of population structure between time frames, and no current population structure within past or present species distribution. However, we also detect signs of genetic bottleneck and evidence that suggest that mating is not presently random. Our results corroborate that the species is a resilient bird, but habitat loss and degradation are jeopardizing Araripe Manakin’s persistence. The species comprises a unique small population, and restoration of habitat quality and connectivity should continue to maintain its viability. Nonetheless, given the low genetic diversity observed, we further identify some challenges and recommend solutions for the implementation of genetic information in the current conservation effort of the Araripe Manakin.

Heterozygosity, genetic similarity and extra‐pair paternity variation in two populations of rock sparrow Petronia petronia: a within and between populations comparison

Extra‐pair paternity (EPP) has been broadly reported in socially monogamous bird species and it has been hypothesized that females engage in extra‐pair copulations to increase the genetic variability of the offspring and to reduce the risk of inbreeding and genetic incompatibilities. This hypothesis makes two predictions: within populations, females should engage with more dissimilar/heterozygous males and, among populations, females should pursue more frequently EPP in populations characterized by a lower genetic variability and a higher homozygosity. However, support is still unclear throughout literature, and usually involves the study of a single population. We compared a peripheral population of rock sparrow Petronia petronia living at the marginal distribution of the species and characterized by a high EPP level (> 50%) (Italian Alps) with a population located in the centre of the species' distribution (central Spain), to understand if variations in EPP could be linked to differences in mean heterozygosity and genetic similarity both between and within populations. EPP in the Spanish population was 18.1%, three times lower than that observed in the Alpine one (51.2%), and this difference remained fairly constant across different years. Supporting the between populations prediction, we found lower heterozygosity and reduced allelic richness in the Alpine population compared to the Spanish one. In contrast, social and extra‐pair males, as well as within and extra‐pair offspring, did not significantly differ in terms of genetic similarity and heterozygosity within brood in either population. Social and extra‐pair males did not differ in tarsus size, body weight or yellow badge size, suggesting that females were not choosing extra‐pair partners based on heterozygosity, genetic similarity or phenotypic quality. Although based on a limited sample in the within population analysis, our results indicate that EPP may evolve in response to a low level of genetic variability in the population.

Genome-wide SNPs reveal the fine-scale population structure of Laodelphax striatellus in China using double-digest restriction site-associated DNA sequencing

The small brown planthopper (SBPH), Laodelphax striatellus (Fallén) is one of the most destructive rice pests and has caused serious economic losses in China. To clarify the genetic differentiation and population genetic structure of this insect pest, we investigated the genomic polymorphisms, genetic differentiation, and phylogeography of 31 SBPH populations from 28 sampling sites from three climatic zones of China using double-digest restriction site-associated DNA sequencing (ddRADseq). In total, 2,813,221,369 high-quality paired-end reads from 306 individuals and 1925 single nucleotide polymorphisms (SNPs) were obtained. Low levels of genetic diversity and significant genetic differentiation were observed among the SBPH populations, and three genetic clusters were detected in China. Neutrality tests and bottleneck analysis provided strong evidence for recent rapid expansion with a severe bottleneck in most populations. Our work provides new insights into the genetics of the SBPH and will contribute to the development of effective management strategies for this pest.