Population Structure of the Chagas Disease Vector Triatoma infestans in an Urban Environment

Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and 2011. We assessed the clustering of subpopulations and the effect of distance, sampling year, and city block location on genetic distance among pairs of insects. Despite evidence of genetic similarity, the majority of city blocks are characterized by one dominant insect genotype, suggesting the existence of barriers to dispersal. Our analyses show that streets represent an important barrier to the colonization and dispersion of T. infestans in Arequipa. The genetic data describe a T. infestans infestation history characterized by persistent local dispersal and occasional long-distance migration events that partially parallels the history of urban development.     

Genetic analysis of Phytophthora infestans populations in the Nordic European countries reveals high genetic variability

Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). The pathogen is highly adaptable and to get an overview of the genetic variation in the Nordic countries, Denmark, Finland, Norway and Sweden we have analyzed 200 isolates from different fields using nine simple-sequence repeat (SSR) markers. Forty-nine alleles were detected among the nine SSR loci and isolates from all four Nordic countries shared the most common alleles across the loci. In total 169 multilocus genotypes (based on seven loci) were identified among 191 isolates. The genotypic diversities, quantified by a normalized Shannon's diversity index (H(s)), were 0.95 for the four Nordic countries. The low F(ST) value of 0.04 indicates that the majority of variation is found within the four Nordic countries. The large number of genotypes and the frequency distribution of mating types (60% A1) support the hypothesis that sexual reproduction is contributing notably to the genetic variation of P. infestans in the Nordic countries.     

An Ephemeral Sexual Population of Phytophthora infestans in the Northeastern United States and Canada

Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50∶50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified.     

Patterns of allozyme variation in Nordic Pilosella

Patterns of allozyme variation have been investigated in 101 clones representing most of the morphological variation (and taxa) found in the amphi-apomictic genus Pilosella Hill. in the Nordic countries. Levels of variation were very high, both within narrowly defined taxa and within the whole data-set, but the correlation between a morphology-based taxonomy and patterns of allozyme variation was very weak. Almost all enzyme bands were found in more than one taxon and the differences between broadly defined species in terms of the frequency of bands were generally small. Cluster analyses did not perfectly recover any taxon but there were some tendencies for samples of some broadly defined taxa (e.g. P. officinarum s. l., and P. cymosa ssp. cymosa) to cluster together. It is concluded that there is considerable gene-flow among virtually all Nordic morpho-types of Pilosella and this is considered an argument for applying a very broad species concept in this genus.Financial support for the present study has been recieved from Stiftelsen Harald E. Johanssons minnesfond at the Royal Swedish Academy of Sciences.     

Dynamics of Introduced Populations of Phragmidium violaceum and Implications for Biological Control of European Blackberry in Australia

Phragmidium violaceum causes leaf rust on the European blackberry (Rubus fruticosus L. aggregate). Multiple strains of this pathogen have been introduced into southern Australia for the biological control of at least 15 taxa of European blackberry, a nonindigenous, invasive plant. In climates conducive to leaf rust, the intensity of disease varies within and among infestations of the genetically variable host. Genetic markers developed from the selective amplification of microsatellite polymorphic loci were used to assess the population genetic structure and reproductive biology of P. violaceum within and among four geographically isolated and diseased infestations of the European blackberry in Victoria, Australia. Despite the potential for long-distance aerial dispersal of urediniospores, there was significant genetic differentiation among all populations, which was not associated with geographic separation. An assessment of multilocus linkage disequilibrium revealed temporal and geographic variation in the occurrence of random mating among the four populations. The presence of sexual spore states and the results of genetic analyses indicated that recombination, and potentially random migration and genetic drift, played an important role in maintaining genotypic variation within populations. Recombination and genetic differentiation in P. violaceum, as well as the potential for metapopulation structure, suggest the need to release additional, genetically diverse strains of the biocontrol agent at numerous sites across the distribution of the Australian blackberry infestation for maximum establishment and persistence.     

High Levels of Genetic Diversity in Salix viminalis of the Czech Republic as Revealed by Microsatellite Markers

Willows (Salix spp.) grown as short rotation coppice are recognised as an important bioenergy crop, and breeding programmes are underway in several countries, including the Czech Republic. The basket willow Salix viminalis is one of the few willow species that is widespread in the Czech Republic and thus a potential source of diversity, but the most extensive germplasm collection available shows evidence of redundancy. To investigate levels of variation in natural populations of this species for use in crop improvement programmes, a set of 38 microsatellite markers was used to assess genetic diversity and population structure among 84 S. viminalis individuals collected from seven Czech rivers (the Odra, Be?va, Morava, Dyje, Jihlava, Sázava and Vltava), covering a wide geographic distribution. The markers detected 6.95 alleles per locus on average with 92?% of the sampled individuals having a unique multilocus genotype giving a high clonal richness measure among all samples (R?=?0.952). Three sets of putative clones (with identical genotypes as determined by the markers used here) were also identified. Significant levels of genetic diversity were revealed within all sampling sites. With the exception of sites on the Odra and Morava, pairwise F _ST (0.02?C0.1) values indicated moderate differentiation between sites. Principal coordinates analysis revealed some separation of the Dyje individuals from all others. This was in agreement with the population structure results derived from Bayesian analyses using STRUCTURE software. These results provide the first evidence that potentially useful levels of genotypic variation are present within natural S. viminalis populations in the Czech Republic.     

Grain aphid population structure: no effect of fungal infections in a 2-year field study in Denmark

1 Sitobion avenae (F.) is a serious pest in Danish cereal crops. To understand the population genetic structure, aphids were sampled in seven different winter wheat (Triticum sativum Lamarck) fields throughout Denmark. The aphids were genotyped with seven microsatellite markers. In total, 2075 aphids were collected and 1203 of these were genotyped. 2 The Danish S. avenae populations displayed very high genotypic diversity, high percentages of unique genotypes and low linkage disequilibria; this is likely to be a result of genetic recombination encompassed by their holocyclic lifestyle. The populations showed very limited differentiation and no sign of isolation by distance. Almost all the genetic variation was ascribed within the populations rather than between populations, probably due to a high migration rate at approximate 10% per generation. 3 Seasonal changes in clonal diversity and distribution of asexual summer generations of S. avenae within the infestation period in a single winter wheat field were followed over two consecutive years by weekly sampling from 60 plots each of 20 × 20 m. Clonal diversity was high in all samples with no dominant clonal lineages and no significant difference in the genotypic diversity between weeks or between years. However, a temporal genetic differentiation effect, throughout the infestation, suggests that selective factors or high temporal migration play an important role in shaping the genetic structure S. avenae. 4 Analyses of fungal infected and uninfected aphids were performed to test whether some clonal linage were more often infected by fungi from the Entomophthorales under field conditions. In total, 54 progeny from aphids with Entomophthorales were genotyped and compared with 422 uninfected aphid genotypes. The Entomophthorales‐infected aphid genotypes did not cluster out together, suggesting that these fungal pathogens did not affect the population differentiation or clonal distribution of S. avenae in a Danish agroecosystem. 5 Our findings indicate that S. avenae populations can be controlled using conservation biological control     

AFLP reveals cryptic population structure in migratory European red admirals (Vanessa atalanta)

1. The genetic differentiation in a migratory butterfly, the red admiral (Vanessa atalanta), was investigated to discern patterns of migratory routes used across Europe. AFLP profiles showed significant differences between almost all sampled locations, but there was no clear pattern of isolation‐by‐distance. 2. Using the software STRUCTURE 2.2, we found two distinct genotype clusters present in different frequencies at all study sites. The frequencies of these genotypic clusters varied significantly between years within the same site. Remarkably few individuals were of mixed ancestry, indicating that some isolating mechanisms are present. Twenty‐seven mtDNA haplotypes were identified but they showed no geographic structure, nor were they related to either of the two genotype clusters identified in the AFLP data. 3. Most field observations of migrating red admirals suggest a regular north–south migration pattern in Europe. Our data indicate both long‐distance migration and a more variable pattern in orientation, since the composition of the two genotypic clusters shows dramatic variation between sites and years in the northern part of the distribution range.     

Molecular diversity and allergenic profiles of Alternaria spp. from desert environments in Arizona

This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis was performed for all isolates. Strains representative of the sampled genotypic diversity (n = 125) were further characterized according their sporulation pattern and the capability to produce allergens. Morphological characterization assigned the majority of the strains to the Alternaria alternata and Alternaria tenuissima morpho-groups with only two isolates assigned to the Alternaria arborescens morpho-group. AFLP fingerprinting differentiated the A. arborescens morpho-groups, but could not distinguish between the A. alternata and A. tenuissima morpho-groups. Western blot analysis showed that a large number of allergenic proteins were produced by strains. These proteins were not specific for any morpho-group nor source of isolation. A hierarchical analysis of molecular variance was performed on the AFLP data to quantify molecular variation and partition this variation among sampled locations and habitat. No statistically significant differentiation among locations and habitat was detected indicating a lack of population structure across environments.     

Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei

Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products.     

Microsatellite markers reveal two admixed genetic groups and an ongoing displacement within the French population of the invasive plant pathogen Phytophthora infestans

Potato late blight is an example of a re‐emerging disease of plants. Phytophthora infestans was first introduced into Europe during the 19th century, where it caused the Irish potato famine. During the 20th century several additional introduction events have been suspected, especially in the mid‐70s due to the import of large quantities of potato needed after the shortage caused by drought in 1976. Here, we investigate the genetic population structure of Phytophthora infestans, at the first stages of a recent invasion process in France. A total of 220 isolates was collected from 20 commercial fields of the potato susceptible cultivar Bintje, during two consecutive years (2004 and 2005). Clustering analyses based on eight recently developed microsatellite markers reveal that French P. infestans populations are made of two differentiated genetic clusters of isolates (F_ST = 0.19). This result suggests multiple introductions of P. infestans into France, either through the introduction of a composite population of isolates or through the successive introduction of isolates having differentiated genetic backgrounds. Both clusters identified have a strong clonal structure and are similar regarding genetic diversity and mating type composition. The maintenance of differentiation between the two genetic clusters should result from the low or non‐existent contribution of sexual reproduction in French P. infestans populations.     

Disentangling complex genomic signals to understand population structure of an exploited,estuarine‐dependent flatfish

Interpreting contemporary patterns of population structure requires an understanding of the interactions among microevolutionary forces and past demographic events. Here, 4,122 SNP‐containing loci were used to assess structure in southern flounder (Paralichthys lethostigma) sampled across its range in the US Atlantic Ocean (Atlantic) and Gulf of Mexico (Gulf) and relationships among components of genomic variation and spatial and environmental variables were assessed across estuarine population samples in the Gulf. While hierarchical amova revealed significant heterogeneity within and between the Atlantic and Gulf, pairwise comparisons between samples within ocean basins demonstrated that all significant heterogeneity occurred within the Gulf. The distribution of Tajima''s D estimated at a genome‐wide scale differed significantly from equilibrium in all estuaries, with more negative values occurring in the Gulf. Components of genomic variation were significantly associated with environmental variables describing individual estuaries, and environment explained a larger component of variation than spatial proximity. Overall, results suggest that there is genetic spatial autocorrelation caused by shared larval sources for proximal nurseries (migration/drift), but that it is modified by environmentally driven differentiation (selection). This leads to conflicting signals in different parts of the genome and creates patterns of divergence that do not correspond to paradigms of strong local directional selection.     

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen

Pest and pathogen losses jeopardise global food security and ever since the 19^th century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.     

Host-associated genetic differentiation in rice grasshopper, Oxya japonica, on wild vs. cultivated rice

Rice grasshopper, Oxya japonica, is one of the most important pests in south China, mainly inhabiting fields of wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa). In this study, we used AFLP marker to investigate the genetic diversity and population structure of rice grasshoppers collected from south China, with emphasis on testing the hypothesis that there was significant genetic differentiation among grasshopper populations associated with different hosts (i.e. wild vs. cultivated rice). Seven populations consisting of 104 individuals were sampled from Hainan Island and the mainland of south China. Eight primer combinations produced 564 reliable bands, of which 563 were polymorphic. O. japonica showed considerable genetic variation at population level, with gene diversity (H_E) ranging from 0.1103 to 0.2035. Genetic diversity were studied on seven populations, and generally three populations from wild rice had higher levels of genetic diversity (H_E = 0.1635) than the other four populations feeding on cultivated rice (H_E = 0.1327). We observed high population differentiation, with F_st ranging from 0.4172 to 0.7652 among the seven populations. However, Mantel test detected no significant correlation between genetic distance and geographical distance (r = 0.3541; p = 0.0689). By contrast, we found significant genetic differentiation between groups collected from different hosts. These data suggested that the anthropogenic activity in cultivated rice fields (i.e. pesticides, fertilization and cultivation) could have played an important role in shaping the genetic structure of O. japonica.     

Mitochondrial DNA suggests a single maternal origin for the widespread triploid parthenogenetic pest species,Paratanytarsus grimmii,but microsatellite variation shows local endemism

Parthenogenesis is common among invasive pest species, with many parthenogenetic species also showing polyploidy. Parthenogenetic polyploid species often have multiple hybrid origins and the potential to rapidly spread over vast geographical areas. In this study, we examine patterns of mitochondrial and microsatellite variation in a widespread triploid parthenogenetic chironomid pest species, Paratanytarsus grimmii. Based on samples from five countries, including Australia, England, Germany, Japan, and Canada, we found extremely low mitochondrial diversity (<0.14%), with most individuals sharing a common and widespread haplotype. In contrast, microsatellite diversity revealed 41 clonal variants, which were regionally endemic. These findings suggest a single invasive maternal lineage of P. grimmii is likely to have recently spread over a broad geographical range. High levels of genotypic endemism suggest P. grimmii populations have remained relatively isolated after an initial spread, with little ongoing migration. This, in part, can be attributed to rapid genetic differentiation via mutations of common clonal genotypes after P. grimmii spread, but multiple polyploidization and subsequent founder events are also likely to be contributing factors.     

Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region

The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size), genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall F_ST index indicated that 2.7% of the total genetic variation was present among sub-populations. The least differentiation was observed between the two sub-populations of Mbarara south and Luwero in Uganda, while the highest level of differentiation was observed between the Mugamba in Burundi and Malagarasi in Tanzania. An estimated membership of four for the inferred clusters from a model-based Bayesian approach was obtained. Both analyses on distance-based and model-based methods consistently isolated the Mugamba sub-population in Burundi from the others.     

Herbivore host-associated genetic differentiation depends on the scale of plant genetic variation examined

Herbivore adaptation to plant genetic variation can lead to reproductive isolation and the formation of host-associated lineages (host-associated differentiation, or HAD). Plant genetic variation exists along a scale, ranging from variation among individual plant genotypes to variation among plant species. Along this scale, herbivores may adapt and diverge at any level, yet few studies have examined whether herbivore differentiation exhibits scaling with respect to host variation (e.g., from genotypes to species). Determining at which level(s) herbivore differentiation occurs can provide insight into the importance of plant genetic variation on herbivore evolution. Previous studies have found strong genetic differentiation in the eriophyid mite, Aceria parapopuli, between hybrid Populus hosts and parental Populus species, but minimal neutral-locus differentiation among individual trees of the same species. We tested whether genetic differentiation in A. parapopuli scales with genetic variation in its Populus hosts. Using mite ITS1 sequence data collected among host species and among host populations, two key patterns emerged. (1) We found strong differentiation of A. parapopuli among Populus species, supporting the hypothesis that plant species differences drive reproductive isolation and HAD. (2) We did not find evidence of host-driven genetic differentiation in mites at the level of plant populations, suggesting that this level of plant variation is insufficiently strong to drive differentiation at a neutral locus. In combination with previous studies, we found that HAD occurs at the higher levels of plant genetic variation, but not at lower levels, and conclude that HAD depends on the scale of plant genetic variation examined.     

Highly Diverse Endophytic and Soil Fusarium oxysporum Populations Associated with Field-Grown Tomato Plants

The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates.     

Patterns of Genetic Population Differentiation in Four Species of Amazonian Frogs: A Test of the Riverine Barrier Hypothesis1

Patterns and levels of allozyme variation among populations of Amazonian frogs were used to test the riverine barrier hypothesis of species differentiation. Two frog species were sampled from each of the two main forest habitats on both banks of the Juruá River in the southwestern Brazilian Amazon Basin at various points along its course to contrast different barrier strengths. Scarthyla ostinodactyla and Scinax rubra were sampled from flooded forest (varzea), and Physalaemus petersi and Epipedobates femoralis from non-flooded forest (terra firme). All species showed high levels of within-population genetic variation. Average Nei's (1978) and Rogers’ (1972) genetic distances between sampled sites for all species were high indicating substantial among-population differentiation. The observation of low gene flow between sampled sites within species was further substantiated with Slatkin's (1993) M? analyses. Randomization tests suggested that there was some population structure at a few assayed polymorphic loci that was consistent with the riverine barrier hypothesis. However, it was apparent from the raw allozyme frequency data that these results were largely driven by substantial differentiation at one or a few collecting localities rather than by basin-wide patterns of riverine differentiation. Phenograms using genetic distance matrices supported this interpretation. Patterns of geographic variation are probably more consistent with the idea of this region being a zone of secondary contact.     

Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China

Pyrus betulaefolia Bunge, considered as an intermediate between oriental and occidental pear groups, is one of the most important wild pear species. The number of its populations is decreasing because of habitat destruction, fragmentation, and continuous exploitation, so protection and conservation measures are urgently needed. Assessment of its genetic diversity and phylogeography are imperative for its efficient conservation. Two chloroplast DNA intergenic fragments were used to detect genetic diversity and phylogeography of 320 individuals from 18 wild P. betulaefolia populations. Haplotype variation, genetic differentiation, and historical events of the populations were estimated. The results showed that P. betulaefolia populations sampled in northern China contained a high level of genetic diversity (H _T?=?0.826). A significant isolation-by-distance value (r?=?0.587, P?<?0.001, 1,000 permutations) among all 18 populations indicated a correlation between genetic divergence and geographic distance. Four population groups were identified in a neighbor-joining tree based on the genetic distance. Analyses of molecular variation showed that the genetic variation mainly existed among population groups, representing 64.61 % of the total variation. Phylogeographic analyses indicated that the populations of P. betulaefolia experienced a scenario of rapid range expansion, which probably occurred between 608,000 and 204,580 years ago. Meanwhile, both the restricted gene flow with isolation by distance and allopatric fragmentation were crucial processes responsible for shaping the genetic patterns of P. betulaefolia. The occurrence of specific haplotypes might be ascribed to an ancestral introgression or joint retention of an ancestral polymorphism with other Pyrus species at the northern edge of the distribution of P. betulaefolia. Three populations displaying a high level of haplotype diversity and unique haplotypes were assumed to be relict populations of Quaternary glaciation and should have conservation priority. Three additional large populations should also be preferentially protected by building natural preservation zones.