Genetic relationships among some new cat populations sampled in Europe: A spatial autocorrelation analysis

The allelic frequencies of nine Mendelizing genetic characteristics that control coat colour, tabby and length and some skeletal abnormalities have been studied in four feral domestic cat populations, two in the north of Catalonia (Girona and Roses & L’Estartit, northeastern Spain) and two Adriatic Italian populations (Rimini and Venice). Using different genetic and multivariate analyses (Nei’s and Cavalli-Sforza and Edwards’s genetic distances, phenograms and cladograms using different algorithms, strict consensus trees, canonical population, principal coordinates and nonmetric multidimensional scaling analyses), I show the genetic relationships between these populations and other Western European cat populations previously studied. In the Western European area comprising Catalonia, Italy, France and Great Britain, I found significant spatial structure for thet ^b, l andW alleles and for the average correlogram for the seven alleles studied as a whole using a spatial autocorrelation analysis. The genetic distance matrices between these European cat populations also showed a significant correlation with the geographical distance between these populations using Mantel’s test. These analyses showed that in each of these countries, local cat populations have characteristic genetic profiles which were different to neighbouring populations in nearby countries. At least in this area of Western Europe, the geographical distances between cat populations (although the gene flow can be relatively high) is an important factor which can explain differences in allele frequencies between these populations.     

Genetic analysis of resistance to six virus diseases in a multiple virus-resistant maize inbred line

Key message

Novel and previously known resistance loci for six phylogenetically diverse viruses were tightly clustered on chromosomes 2, 3, 6 and 10 in the multiply virus-resistant maize inbred line, Oh1VI.

Abstract

Virus diseases in maize can cause severe yield reductions that threaten crop production and food supplies in some regions of the world. Genetic resistance to different viruses has been characterized in maize populations in diverse environments using different screening techniques, and resistance loci have been mapped to all maize chromosomes. The maize inbred line, Oh1VI, is resistant to at least ten viruses, including viruses in five different families. To determine the genes and inheritance mechanisms responsible for the multiple virus resistance in this line, F₁ hybrids, F₂ progeny and a recombinant inbred line (RIL) population derived from a cross of Oh1VI and the virus-susceptible inbred line Oh28 were evaluated. Progeny were screened for their responses to Maize dwarf mosaic virus, Sugarcane mosaic virus, Wheat streak mosaic virus, Maize chlorotic dwarf virus, Maize fine streak virus, and Maize mosaic virus. Depending on the virus, dominant, recessive, or additive gene effects were responsible for the resistance observed in F₁ plants. One to three gene models explained the observed segregation of resistance in the F₂ generation for all six viruses. Composite interval mapping in the RIL population identified 17 resistance QTLs associated with the six viruses. Of these, 15 were clustered in specific regions of chr. 2, 3, 6, and 10. It is unknown whether these QTL clusters contain single or multiple virus resistance genes, but the coupling phase linkage of genes conferring resistance to multiple virus diseases in this population could facilitate breeding efforts to develop multi-virus resistant crops.     

Microsatellite DNA analysis reveals lower than expected genetic diversity in the threatened leopard cat (<Emphasis Type="Italic">Prionailurus bengalensis</Emphasis>) in South Korea

To optimize conservation efforts, it is necessary to determine the risk of extinction by collecting reliable population information for a given species. We developed eight novel, polymorphic microsatellite markers and used these markers in conjunction with twelve existing markers to measure genetic diversity of South Korean populations of leopard cat (Prionailurus bengalensis), a species for which population size and habitat area data are unknown in the country, to assess its conservation status. The average number of alleles and the observed heterozygosity of the species were 3.8 and 0.41, respectively, and microsatellite diversity was lower than the average genetic diversity of 57 populations of 12 other felid species, and lower than that of other mammal populations occurring in South Korea, including the raccoon dog (Nyctereutes procyonoides), water deer (Hydropotes inermis), and endangered long-tailed goral (Naemorhedus caudatus). Furthermore, analysis of genetic structure in the national leopard cat population showed no clear genetic differentiation, suggesting that it is not necessary to divide the South Korean leopard cat population into multiple management units for the purposes of conservation. These results indicate that the genetic diversity of the leopard cat in South Korea is unexpectedly low, and that the risk of local extinction is, as a result, substantial. Thus, it is necessary to begin appropriate conservation efforts at a national level to conserve the leopard cat population in South Korea.     

Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom

Recent studies have suggested that diatom viruses are an important factor affecting diatom population dynamics, which in turn are important in considering marine primary productivity. The marine planktonic diatom Chaetoceros tenuissimus Meunier is a cosmopolitan species and often causes blooms off the western coast of Japan. To date, two viruses, C. tenuissimus DNA virus (CtenDNAV) type I and CtenRNAV type I, have been identified that potentially affect C. tenuissimus population dynamics in the natural environment. In this study, we successfully isolated and characterized two additional novel viruses (CtenDNAV type II and CtenRNAV type II). This paper reports the basic characteristics of these new viruses isolated from surface water or sediment from the Hiroshima Bay, Japan. The physiological and morphological characteristics of the two new viruses were similar to those of the previously isolated viruses. However, the amino acid sequences of the structural proteins of CtenDNAV type II and CtenRNAV type II were clearly distinct from those of both type I viruses, with identity scores of 38.3% and 27.6%, respectively. Our results suggest that at least four genetically distinct viruses sharing the same diatom host are present in western Japan and affect the population dynamics of C. tenuissimus. Moreover, the result that CtenRNAV type II lysed multiple diatom species indicates that RNA viruses may affect various diatom populations in the natural environment.     

Genetic Diversity and Population Structure in Polygonum cespitosum: Insights to an Ongoing Plant Invasion

Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America), via the analyses of 516 individuals, and asked the following questions: 1) Do populations have differing levels of within-population genetic diversity? 2) Do populations form distinct genetic clusters? 3) Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering) and pairwise F _ST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources) in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further contribute to the invasive success of P. cespitosum in its introduced range.     

Trophic Garnishes: Cat–Rat Interactions in an Urban Environment

Background

Community interactions can produce complex dynamics with counterintuitive responses. Synanthropic community members are of increasing practical interest for their effects on biodiversity and public health. Most studies incorporating introduced species have been performed on islands where they may pose a risk to the native fauna. Few have examined their interactions in urban environments where they represent the majority of species. We characterized house cat (Felis catus) predation on wild Norway rats (Rattus norvegicus), and its population effects in an urban area as a model system. Three aspects of predation likely to influence population dynamics were examined; the stratum of the prey population killed by predators, the intensity of the predation, and the size of the predator population.

Methodology/Principal Findings

Predation pressure was estimated from the sizes of the rat and cat populations, and the characteristics of rats killed in 20 alleys. Short and long term responses of rat population to perturbations were examined by removal trapping. Perturbations removed an average of 56% of the rats/alley but had no negative long-term impact on the size of the rat population (49.6±12.5 rats/alley and 123.8±42.2 rats/alley over two years). The sizes of the cat population during two years (3.5 animals/alley and 2.7 animals/alley) also were unaffected by rat population perturbations. Predation by cats occurred in 9/20 alleys. Predated rats were predominantly juveniles and significantly smaller (144.6 g±17.8 g) than the trapped rats (385.0 g±135.6 g). Cats rarely preyed on the larger, older portion of the rat population.

Conclusions/Significance

The rat population appears resilient to perturbation from even substantial population reduction using targeted removal. In this area there is a relatively low population density of cats and they only occasionally prey on the rat population. This occasional predation primarily removes the juvenile proportion of the rat population. The top predator in this urban ecosystem appears to have little impact on the size of the prey population, and similarly, reduction in rat populations doesn''t impact the size of the cat population. However, the selected targeting of small rats may locally influence the size structure of the population which may have consequences for patterns of pathogen transmission.     

Distribution of Gene Frequency as a Test of the Theory of the Selective Neutrality of Polymorphisms

The variation in gene frequency among populations or between generations within a population is a result of breeding structure and selection. But breeding structure should affect all loci and alleles in the same way. If there is significant heterogeneity between loci in their apparent inbreeding coefficients F=s_p²/p(1-p), this heterogeneity may be taken as evidence for selection. We have given the statistical properties of F and shown how tests of heterogeneity can be made. Using data from human populations we have shown highly significant heterogeneity in F values for human polymorphic genes over the world, thus demonstrating that a significant fraction of human polymorphisms owe their current gene frequencies to the action of natural selection. We have also applied the method to temporal variation within a population for data on Dacus oleae and have found no significant evidence of selection.     

Influenza A Virus Migration and Persistence in North American Wild Birds

Wild birds have been implicated in the emergence of human and livestock influenza. The successful prediction of viral spread and disease emergence, as well as formulation of preparedness plans have been hampered by a critical lack of knowledge of viral movements between different host populations. The patterns of viral spread and subsequent risk posed by wild bird viruses therefore remain unpredictable. Here we analyze genomic data, including 287 newly sequenced avian influenza A virus (AIV) samples isolated over a 34-year period of continuous systematic surveillance of North American migratory birds. We use a Bayesian statistical framework to test hypotheses of viral migration, population structure and patterns of genetic reassortment. Our results reveal that despite the high prevalence of Charadriiformes infected in Delaware Bay this host population does not appear to significantly contribute to the North American AIV diversity sampled in Anseriformes. In contrast, influenza viruses sampled from Anseriformes in Alberta are representative of the AIV diversity circulating in North American Anseriformes. While AIV may be restricted to specific migratory flyways over short time frames, our large-scale analysis showed that the long-term persistence of AIV was independent of bird flyways with migration between populations throughout North America. Analysis of long-term surveillance data provides vital insights to develop appropriately informed predictive models critical for pandemic preparedness and livestock protection.     

Ancient geographical gaps and paleo-climate shape the phylogeography of an endemic bird in the sky islands of southern India

Background

Sky islands, formed by the highest reaches of mountain tracts physically isolated from one another, represent one of the biodiversity-rich regions of the world. Comparative studies of geographically isolated populations on such islands can provide valuable insights into the biogeography and evolution of species on these islands. The Western Ghats mountains of southern India form a sky island system, where the relationship between the island structure and the evolution of its species remains virtually unknown despite a few population genetic studies.

Methods and Principal Findings

We investigated how ancient geographic gaps and glacial cycles have partitioned genetic variation in modern populations of a threatened endemic bird, the White-bellied Shortwing Brachypteryx major, across the montane Shola forests on these islands and also inferred its evolutionary history. We used Bayesian and maximum likelihood-based phylogenetic and population-genetic analyses on data from three mitochondrial markers and one nuclear marker (totally 2594 bp) obtained from 33 White-bellied Shortwing individuals across five islands. Genetic differentiation between populations of the species correlated with the locations of deep valleys in the Western Ghats but not with geographical distance between these populations. All populations revealed demographic histories consistent with population founding and expansion during the Last Glacial Maximum. Given the level of genetic differentiation north and south of the Palghat Gap, we suggest that these populations be considered two different taxonomic species.

Conclusions and Significance

Our results show that the physiography and paleo-climate of this region historically resulted in multiple glacial refugia that may have subsequently driven the evolutionary history and current population structure of this bird. The first avian genetic study from this biodiversity hotspot, our results provide insights into processes that may have impacted the speciation and evolution of the endemic fauna of this region.     

Determinants of Genetic Structure in a Nonequilibrium Metapopulation of the Plant Silene latifolia

Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase F _ST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. F _ST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.     

Threatened but understudied: supporting conservation by understanding the genetic structure of the flat-headed cat

The flat-headed cat (Prionailurus planiceps) is a wetland specialist, currently facing habitat loss on a serious scale due to massive destruction of lowland forests and wetlands in Southeast Asia. Despite its ‘endangered’ status in the IUCN Red List, there has virtually been no investigation on the population structure nor on the evolutionary history of the flat-headed cat. To fill this gap, we used full mitochondrial genome sequences, obtained from archival samples, covering the historical distribution of the flat-headed cat. Our data revealed a high genetic differentiation (F _st = 0.81, P?<?0.001) between mitochondrial lineages from Borneo and those from Thai-Malay Peninsula/Sumatra, a split that was dated to ~575 Kya. Such a significant differentiation clearly distinguishes the Bornean flat-headed cat population from all other populations and suggests that there should be a reassessment of the flat-headed cat’s intraspecific taxonomy. However, morphological and nuclear data are required to corroborate our mtDNA results. Until such data become available, we recommend that for future conservation efforts and captive breeding programmes the two genetically distinct flat-headed cat populations are managed separately as two lineages to maintain the original genetic diversity of this endangered species.     

The impact of population structure on genomic prediction in stratified populations

Key message

Impacts of population structure on the evaluation of genomic heritability and prediction were investigated and quantified using high-density markers in diverse panels in rice and maize.

Abstract

Population structure is an important factor affecting estimation of genomic heritability and assessment of genomic prediction in stratified populations. In this study, our first objective was to assess effects of population structure on estimations of genomic heritability using the diversity panels in rice and maize. Results indicate population structure explained 33 and 7.5 % of genomic heritability for rice and maize, respectively, depending on traits, with the remaining heritability explained by within-subpopulation variation. Estimates of within-subpopulation heritability were higher than that derived from quantitative trait loci identified in genome-wide association studies, suggesting 65 % improvement in genetic gains. The second objective was to evaluate effects of population structure on genomic prediction using cross-validation experiments. When population structure exists in both training and validation sets, correcting for population structure led to a significant decrease in accuracy with genomic prediction. In contrast, when prediction was limited to a specific subpopulation, population structure showed little effect on accuracy and within-subpopulation genetic variance dominated predictions. Finally, effects of genomic heritability on genomic prediction were investigated. Accuracies with genomic prediction increased with genomic heritability in both training and validation sets, with the former showing a slightly greater impact. In summary, our results suggest that the population structure contribution to genomic prediction varies based on prediction strategies, and is also affected by the genetic architectures of traits and populations. In practical breeding, these conclusions may be helpful to better understand and utilize the different genetic resources in genomic prediction.     

Genetic diversity and structure in two species of Leavenworthia with self-incompatible and self-compatible populations

Self-fertilization is a common mating system in plants and is known to reduce genetic diversity, increase genetic structure and potentially put populations at greater risk of extinction. In this study, we measured the genetic diversity and structure of two cedar glade endemic species, Leavenworthia alabamica and L. crassa. These species have self-incompatible (SI) and self-compatible (SC) populations and are therefore ideal for understanding how the mating system affects genetic diversity and structure. We found that L. alabamica and L. crassa had high species-level genetic diversity (H_e=0.229 and 0.183, respectively) and high genetic structure among their populations (F_ST=0.45 and 0.36, respectively), but that mean genetic diversity was significantly lower in SC compared with SI populations (SC vs SI, H_e for L. alabamica was 0.065 vs 0.206 and for L. crassa was 0.084 vs 0.189). We also found significant genetic structure using maximum-likelihood clustering methods. These data indicate that the loss of SI leads to the loss of genetic diversity within populations. In addition, we examined genetic distance relationships between SI and SC populations to analyze possible population history and origins of self-compatibility. We find there may have been multiple origins of self-compatibility in L. alabamica and L. crassa. However, further work is required to test this hypothesis. Finally, given their high genetic structure and that individual populations harbor unique alleles, conservation strategies seeking to maximize species-level genetic diversity for these or similar species should protect multiple populations.     

Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India

Background

Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected.

Methodology/Principal Findings

We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F _ST of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India.

Conclusions/Significance

Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.     

Using Dynamic Stochastic Modelling to Estimate Population Risk Factors in Infectious Disease: The Example of FIV in 15 Cat Populations

Background

In natural cat populations, Feline Immunodeficiency Virus (FIV) is transmitted through bites between individuals. Factors such as the density of cats within the population or the sex-ratio can have potentially strong effects on the frequency of fight between individuals and hence appear as important population risk factors for FIV.

Methodology/Principal Findings

To study such population risk factors, we present data on FIV prevalence in 15 cat populations in northeastern France. We investigate five key social factors of cat populations; the density of cats, the sex-ratio, the number of males and the mean age of males and females within the population. We overcome the problem of dependence in the infective status data using sexually-structured dynamic stochastic models. Only the age of males and females had an effect (p = 0.043 and p = 0.02, respectively) on the male-to-female transmission rate. Due to multiple tests, it is even likely that these effects are, in reality, not significant. Finally we show that, in our study area, the data can be explained by a very simple model that does not invoke any risk factor.

Conclusion

Our conclusion is that, in host-parasite systems in general, fluctuations due to stochasticity in the transmission process are naturally very large and may alone explain a larger part of the variability in observed disease prevalence between populations than previously expected. Finally, we determined confidence intervals for the simple model parameters that can be used to further aid in management of the disease.     

Female in the inside,male in the outside: insights into the spatial organization of a European wildcat population

Hybridization between the European wildcat, Felis silvestris silvestris, and the domestic cat, Felis silvestris catus, has been found in several European countries with different landscape structures and in various proportions. In this study, we focus on a local population of European wildcats in forests fragmented by agricultural lands in northeastern France. Our aim is to better understand how the spatial organization of the wildcats in this particular type of environment might impact the proportion of hybridization. We combined radio-tracking and genetics through the use of microsatellite markers in order to assess both the spacing pattern and the level of hybridization of this wildcat population. Hybridization is rare in this wildcat population with only one putative hybrid (most likely backcrossed) detected out of 42 putative wildcats. We found that most females were concentrated inside the forest while males stood in the periphery or outside the forest. Furthermore, many males and females resulted related. Such a spacing pattern might limit contacts between male domestic cats and female wildcats and can be one of the causes that explain the low level of hybridization in the wildcat population in this environment. We could not exclude the possibility of hybrid presence in the neighboring domestic cat populations. Our results yield new insights on the influence that the landscape configuration and the spacing pattern can have on genetic flow between the populations of the two subspecies.     

Revealing cryptic genetic structuring in an urban population of stray cats (Felis silvestris catus)

Urban stray cat populations have previously been shown to be organized in moderately to strongly genetically differentiated colonies. However, the spatial pattern of this genetic differentiation and the possibility that some cryptic genetic structure occurs have not been investigated. Firstly, we combine a pairwise Fst method, a fully Bayesian clustering method and a multivariate analysis to show that the spatial structure of 17 urban stray cat colonies (Nancy, France) does not match the underlying genetic structure. These colonies are structured in two clusters at the uppermost hierarchical level. Additionally, geographic proximity between colonies does not explain their genetic homogeneity. The spatial pattern in genetic differentiation seems more to be a mixture between low global structure and some highly localized structure, comprising isolated colonies. Variations in the local ecological and social constraints on immigration between colonies may explain this pattern. Secondly, we show that the overall current immigration rate is low (8%). Our results suggest that dispersal does not play a major role in the process of homogenization of allelic frequencies. Our study provides a case-study on the use of Bayesian clustering and assignment methods on a real, small data set with numerous fragmented populations; a population structure that is of high relevance in conservation biology.     

Stress tolerance and population stability of rock pool Daphnia in relation to local conditions and population isolation

Small fragmented populations can lose genetic variability, which reduces population viability through inbreeding and loss of adaptability. Current and previous environmental conditions can also alter the viability of populations, by creating local adaptations that determine responses to stress. Yet, most studies on stress tolerance usually consider either the effect of genetic diversity or the local environment, missing a more holistic perspective of the factors contributing to stress tolerance among natural populations. Here, we studied how salinity stress affects population growth of Daphnia longispina, Daphnia magna, and Daphnia pulex from rock pools with varying degrees of population isolation and salinity conditions. Standing variation of in situ rock pool salinity conditions explained more variation in salt tolerance than the standing variation of population isolation or genetic diversity, in both a pulse and a press disturbance experiment. This indicates that the level of stress, which these natural populations experience, influences their response to that stress, which may have important consequences for the conservation of fragmented populations. However, long-term population stability in the field decreased with population isolation, indicating that natural populations experience a variety of stresses; thus, population isolation and genetic diversity may stabilize population dynamics over larger spatiotemporal scales.     

Nuclear and chloroplast microsatellites show multiple introductions in the worldwide invasion history of common ragweed, Ambrosia artemisiifolia

Background

Ambrosia artemisiifolia is a North American native that has become one of the most problematic invasive plants in Europe and Asia. We studied its worldwide population genetic structure, using both nuclear and chloroplast microsatellite markers and an unprecedented large population sampling. Our goals were (i) to identify the sources of the invasive populations; (ii) to assess whether all invasive populations were founded by multiple introductions, as previously found in France; (iii) to examine how the introductions have affected the amount and structure of genetic variation in Europe; (iv) to document how the colonization of Europe proceeded; (v) to check whether populations exhibit significant heterozygote deficiencies, as previously observed.

Principal Findings

We found evidence for multiple introductions of A. artemisiifolia, within regions but also within populations in most parts of its invasive range, leading to high levels of diversity. In Europe, introductions probably stem from two different regions of the native area: populations established in Central Europe appear to have originated from eastern North America, and Eastern European populations from more western North America. This may result from differential commercial exchanges between these geographic regions. Our results indicate that the expansion in Europe mostly occurred through long-distance dispersal, explaining the absence of isolation by distance and the weak influence of geography on the genetic structure in this area in contrast to the native range. Last, we detected significant heterozygote deficiencies in most populations. This may be explained by partial selfing, biparental inbreeding and/or a Wahlund effect and further investigation is warranted.

Conclusions

This insight into the sources and pathways of common ragweed expansion may help to better understand its invasion success and provides baseline data for future studies on the evolutionary processes involved during range expansion in novel environments.     

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation

Key message

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world.

Abstract

Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.