Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system,influence of marine currents,and footprints of postglacial recolonization routes

Understanding the factors that contribute to population genetic divergence across a species' range is a long‐standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present‐day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic‐Mediterranean refugia after the last glacial period, with leading‐edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long‐distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life‐history and major geographic features interact to shape the distribution of genetic diversity.     

Insights into the genetic relationships among plants of <Emphasis Type="Italic">Beta</Emphasis> section <Emphasis Type="Italic">Beta</Emphasis> using SNP markers

Key message

Using a much higher number of SNP markers and larger sample sizes than all the previous studies, we characterized the genetic relationships among wild and cultivated plants of section Beta.

Abstract

We analyzed the genetic variation of Beta section Beta, which includes wild taxa (Beta macrocarpa, B. patula, B. vulgaris subsp. adanensis and B. vulgaris subsp. maritima) and cultivars (fodder beet, sugar beet, garden beet, leaf beet, and swiss chards), using 9724 single nucleotide polymorphism markers. The analyses conducted at the individual level without a priori groups confirmed the strong differentiation of B. macrocarpa and B. vulgaris subsp. adanensis from the other taxa. B. vulgaris subsp. maritima showed a complex genetic structure partly following a geographical pattern, which confounded the differences between this taxon and the cultivated varieties. Cultivated varieties were structured into three main groups: garden beets, fodder and sugar beets, and leaf beets and swiss chards. The genetic structure described here will be helpful to correctly estimate linkage disequilibrium and to test for statistical associations between genetic markers and environmental variables.

     

Genetic evidence for the origin of Californian wild beets (genus Beta)

The genus Beta L. is a morphologically and genetically variable group composed of wild, weedy, and domesticated forms that are used for sugar production or as vegetables. In this study, we have evaluated genetic variation in 64 germplasm accessions of wild and domesticated beets and examined the origin of wild beet accessions in California using allozyme analysis. UPGMA analysis showed overall that domesticated and wild beets form genetically coherent groups. Wild beets in California have two different origins, from European Beta vulgaris or from Beta macrocarpa. Population-level patterns of allozyme variation for wild California beets related to B. vulgaris suggest that those populations evolved from naturalized populations of the cultivated B. vulgaris ssp. vulgaris which had hybridized to varying degrees with the sea beets B. vulgaris ssp. maritima. Wild California beets related to B. macrocarpa are essentially genetically identical to European accessions. In addition, we found substantial evidence for hybridization and introgression of B. vulgaris alleles in one B. macrocarpa accession in California. The obligate outcrosser B. vulgaris exhibits more allelic diversity than the self-compatible B. macrocarpa. Beta vulgaris ssp. maritima exhibits more genetic diversity than domesticated B. vulgaris ssp. vulgaris. Received: 2 November 1998 / Accepted: 29 April 1999     

Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima

We present draft genome assemblies of Beta patula, a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related Beta vulgaris ssp. maritima (sea beet). Evidence‐based reference gene sets for B. patula and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon B. vulgaris ssp. vulgaris (sugar beet). Large syntenic regions were identified, and a display tool for automatic genome‐wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research.     

Characterization of nematode resistance genes in the section Procumbentes genus Beta: response to two populations of Heterodera schachtii

Three species of the section Procumbentes genus Beta, nine monosomic additions, and five translocation lines were tested for resistance to two Heterodera schachtii populations. Nematode population 129-v (129-virulent) was selected for virulence to resistance gene(s) transferred from chromosome 1 of Beta procumbens to the diploid resistant sugar beet KWS-NR1. This population is considered to be a pathotype. The unselected sib population 129-av (129-avirulent) was reared continuously on fodder rape, Brassica napus cv Velox. Monosomic additions with chromosome 1 from the three species of the section Procumbentes were susceptible to population 129-v, regardless of the origin of the alien chromosome. Translocations with a gene(s) for resistance from chromosome 7 of B. procumbens and B. webbiana were also susceptible to the pathotype. However, a monosomic addition with chromosome 7 of B. webbiana was resistant to population 129-v. The three wild beets of the section Procumbentes, Beta procumbens, Beta webbiana and Beta patellaris, also were highly resistant to the two populations. The results indicate the existence of just two different major genes for resistance to H. schachtii in the entire Procumbentes section.     

Phylogenetic relationships between cultivated and wild species of the genusBeta revealed by DNA “fingerprinting”

Forty-one accessions of the genusBeta representing wild and cultivated species of all sections were analyzed by DNA fingerprinting. Four sugar beet minisatellite DNA probes revealed characteristic banding patterns with Southern-hybridizedBeta DNA restricted withHindIII. A total of 111 polymorphic RFLP bands were scored across all accessions. Cluster analysis based on genetic similarity estimates for all 820 combinations of accessions revealed the following results. (1) All accessions could unambiguously be identified by a characteristic RFLP banding pattern. (2) The sugar beet cultivars examined displayed a low level of genetic diversity; they showed high similarity toB. Vulgaris ssp.maritima but low genetic similarity to the other wild species of section I. (3) In most cases, the present taxonomic classification of the genusBeta was confirmed. Species of sections II, III, and IV were clearly distinguishable from those of section I except forB. Macrocarpa, which showed high similarity to wild species of section II. In a second experiment, 108 single-copy RFLP probes from sugar beet were Southern hybridized withB. procumbens DNA. A surprisingly low degree of homology (34%) was found. The results are discussed with regard to the taxonomic classification of the genusBeta.     

Allozyme variation in the sympatric ferns Culcita macrocarpa and Woodwardia radicans at the northern extreme of their ranges

Isozymes were used to study genetic variation in the clonal ferns Culcita macrocarpa and Woodwardia radicans in the northwestern Iberian Peninsula, their northern distributional limit. Despite their high chromosome numbers, both species were isozymic diploids. In C. macrocarpa all 18 resolved loci were monomorphic, with the same allele in all ramets from all populations. In W. radicans only two of the 16 interpreted loci were polymorphic, with two alleles per locus; ramet-level genotypes showed Hardy-Weinberg equilibrium, indicating an intergametophytic mating system; the number of genets distinguished was 1–3 per population; and among-population variation was low (F _ST = 0.231), suggesting effective gene flow (i.e. spore exchange). More generally, the very low (W. radicans, H _T = 0.012) or zero (C. macrocarpa) genetic diversity detected in the present study may be due to genetic drift associated with the reduction of populations in the last glaciation, and to founder effects in the subsequent Holocene expansion.     

Distribution and evolution of two satellite DNAs in the genus Beta

Summary EcoRI monomers of a highly repetitive DNA family of Beta vulgaris have been cloned. Sequence analysis revealed that the repeat length varies between 157–160 bp. The percentage of AT-residues is 62% on average. The basic repeat does not show significant homology to the BamHI sequence family of B. vulgaris that was analyzed by us earlier. Both the EcoRI and BamHI sequences are investigated and compared to each other with respect to their genomic organization in the genus Beta. Both repeats were found to be tandemly arranged in the genome of B. vulgaris in a satellite-like manner. The EcoRI satellite DNA is present in three sections (Beta, Corollinae and Nanae) of the genus, whereas the BamHI satellite DNA exists only in the section Beta. The distribution of the EcoRI and BamHI satellite families in the genus is discussed with respect to their evolution.     

Genetic diversity and differentiation in six species of the genus Rhinanthus (Orobanchaceae)

The intricate genus Rhinanthus L. contains many taxonomically unresolved taxa. The assessment of genetic diversity may clarify the differentiation and taxonomic relationships between species and help to determine their mating system, which is important for understanding the future prospects of populations and species. Isozymes were used to assess the mating system, genetic diversity, and differentiation in R. rumelicus, R. osiliensis, R. wagneri, R. alectorolophus, and R. angustifolius from sect. Cleistolemus and R. minor from sect. Rhinanthus. Genetic diversity at species level was found to be higher in widespread R. angustifolius and R. rumelicus compared with insular endemic R. osiliensis. Positive inbreeding coefficient revealed dominant inbreeding in endemic R. osiliensis and R. wagneri. We also detected a significant departure from Hardy–Weinberg equilibrium in some populations of R. rumelicus and R. angustifolius. The common R. alectorolophus and R. minor and several populations of R. rumelicus and R. angustifolius displayed a mixed mating mode. Six studied species divided into three distinct clusters. Rhinanthus alectorolophus was the most differentiated taxon among the investigated species. The species of sect. Cleistolemus formed two distinct groups. The first cluster consisted only of R. alectorolophus while another comprised R. rumelicus, R. osiliensis, R. wagneri, and R. angustifolius, indicating their close affinity. Thus, our isozyme results call into question the monophyly of section Cleistolemus and the taxonomic position of R. alectorolophus.     

Microsatellites from the vairone Leuciscus souffia (Pisces: Cyprinidae) and their application to closely related species

Eleven microsatellites were isolated from the vairone Leuciscus souffia (Risso 1826), an endangered fish that inhabits river systems in and around the Alps in Europe. The level of genetic diversity was assessed in 29 individuals of the subspecies L. s. souffia, and their variability was further estimated in seven individuals of a different subspecies, L. s. muticellus. Eight of these microsatellite loci were also applied to seven closely related cyprinid species. Availability of the reported microsatellite loci will facilitate the investigation of population genetic structure of these species with applications for the development of conservation strategies and phylogeographical approaches.     

A Family of Differentially Amplified Repetitive DNA Sequences in the Genus Beta Reveals Genetic Variation in Beta vulgaris Subspecies and Cultivars

Members of a highly abundant restriction satellite family have been isolated from the wild beet species Beta nana. The satellite DNA sequence is characterized by a conserved RsaI restriction site and is present in three of four sections of the genus Beta, namely Nanae, Corollinae, and Beta. It was not detected in species of the evolutionary old section Procumbentes, suggesting its amplification after separation of this section. Sequences of eight monomers were aligned revealing a size variation from 209 to 233 bp and an AT content ranging from 56.5% to 60.5%. The similarity between monomers in B. nana varied from 77.7% to 92.2%. Diverged subfamilies were identified by sequence analysis and Southern hybridization. A comparative study of this repetitive DNA element by fluorescent in situ hybridization and Southern analyses in three representative species was performed showing a variable genomic organization and heterogeneous localizations along metaphase chromosomes both within and between species. In B. nana the copy number of this satellite, with some 30,000 per haploid genome, is more than tenfold higher than in Beta lomatogona and up to 200 times higher than in Beta vulgaris, indicating different levels of sequence amplification during evolution in the genus Beta. In sugar beet (B. vulgaris), the large-scale organization of this tandem repeat was examined by pulsed-field gel electrophoresis. Southern hybridization to genomic DNA digested with DraI demonstrated that satellite arrays are located in AT-rich regions and the tandem repeat is a useful probe for the detection of genetic variation in closely related B. vulgaris cultivars, accessions, and subspecies. Received: 24 May 1996 / Accepted: 13 September 1996     

猕猴桃属十个种的染色体倍性鉴定

猕猴桃属(Actinidia)植物全世界有66种,约有118个种下分类单位(也有新的划分方法将其划分为54种21变种),其中大部分为中国特有。在猕猴桃杂交育种中,不同倍性之间选配不当会出现杂交失败、后代不育等现象,因此倍性鉴定是猕猴桃常规育种亲本选择的前提条件之一。但到目前为止,不少猕猴桃种或亚种的染色体倍性研究并不十分清楚,因而限制了这些资源的进一步开发利用。该研究针对广西植物研究所猕猴桃种质资源圃收集的目前倍性尚不明确的白萼、白花柱果、二色花、临桂、卵圆叶、桃花、宛田、长果、融水和五瓣猕猴桃等10个种类的猕猴桃,使用酸解法制备染色体标本,通过显微镜观察确定其倍性。这10个种类大多为广西特有,其中蕴藏着独特的优良园艺性状,具有很高的生产和开发价值。该研究结果表明这10个种类猕猴桃的染色体倍性均为二倍体(2n=2x=58)。该研究结果进一步丰富了猕猴桃种质资源多样性数据库,为这些猕猴桃资源的合理开发利用奠定了基础。     

Patellaria: A new genus in the Chenopodiaceae

Comparative taxonomic studies within the genus Beta have shown that the section Patellares is distinct and should be regarded as a new genus, Patellaria, with the type Patellaria webbiana. The transference of Beta patellaris to this genus requires a new specific name, P. cordata.     

Ploidy level,genetic diversity,and differentiation in two closely related mosses,Scorpidium cossonii and S. revolvens (Calliergonaceae)

As ploidy level and mating system can affect genetic diversity and differentiation, we conducted population genetic analyses of two closely related mosses, Scorpidium cossonii (Schimp.) Hedenäs, and S. revolvens (Sw. ex Anonymo) Rubers which differ in ploidy level and sexual system. We collected 315 specimens in total from five populations of S. cossonii and four populations of S. revolvens in the Swiss Alps. Ploidy level, genetic diversity within populations, and genetic differentiation between populations and species were estimated using nine microsatellite markers. In each S. cossonii sample, each locus bore only one allele, while in S. revolvens, seven out of the nine loci were fixed or nearly fixed for two alleles per locus per individual. These findings are consistent with a gametophytic haploid S. cossonii and allodiploid S. revolvens. The haploid and dioicous S. cossonii was genetically more diverse than the (allo)diploid and monoicous S. revolvens. Differences in genetic diversity between the two species may be explained by different mating systems, different population sizes, and different population histories. Genetic differentiation among populations of S. cossonii was higher than among those of S. revolvens. The low genetic differentiation among populations of the monoicous species was not unexpected, since monoicous species frequently produce sporophytes, long-distance spore dispersal is more likely and leads to low differentiation.     

Dynamics of <Emphasis Type="Italic">Vulmar/VulMITE</Emphasis> group of transposable elements in <Emphasis Type="Italic">Chenopodiaceae</Emphasis> subfamily <Emphasis Type="Italic">Betoideae</Emphasis>

Transposable elements are important factors driving plant genome evolution. Upon their mobilization, novel insertion polymorphisms are being created. We investigated differences in copy number and insertion polymorphism of a group of Mariner-like transposable elements Vulmar and related VulMITE miniature inverted-repeat transposable elements (MITEs) in species representing subfamily Betoideae. Insertion sites of these elements were identified using a modified transposon display protocol, allowing amplification of longer fragments representing regions flanking insertion sites. Subsequently, a subset of TD fragments was converted into insertion site-based polymorphism (ISBP) markers. The investigated group of transposable elements was the most abundant in accessions representing the section Beta, showing intraspecific insertion polymorphisms likely resulting from their recent activity. In contrast, no unique insertions were observed for species of the genus Beta section Corollinae, while a set of section-specific insertions was observed in the genus Patellifolia, however, only two of them were polymorphic between P. procumbens and P. webbiana. We hypothesize that Vulmar and VulMITE elements were inactivated in the section Corollinae, while they remained active in the section Beta and the genus Patellifolia. The ISBP markers generally confirmed the insertion patterns observed with TD markers, including presence of distinct subsets of TE insertions specific to Beta and Patellifolia.     

Variation in wild populations of annual beet (Beta,Chenopodiaceae)

Among the morphological variation in wild annual populations of sect.Beta only tepal characters show a geographic pattern, and hence can be used to distinguish different taxa. Two morphological types correspond with taxa already described:B. macrocarpa (incl.B. bourgaei) has a Macaronesian and W. to E. Mediterranean andB. adanensis an E. Mediterranean distribution area. A third type in the Aegean region is not well known yet and possibly has to be included inB. macrocarpa. Both diploid and tetraploid (x = 9) cytotypes are found withinB. macrocarpa, the latter exclusively on the Canary Islands.     

Multispecies genetic structure and hybridization in the Betula genus across Eurasia

Boreal and cool temperate forests are the major land cover of northern Eurasia, and information about continental‐scale genetic structure and past demographic history of forest species is important from an evolutionary perspective and has conservation implications. However, although many population genetic studies of forest tree species have been conducted in Europe or Eastern Asia, continental‐scale genetic structure and past demographic history remain poorly known. Here, we focus on the birch genus Betula, which is commonly distributed in boreal and cool temperate forests, and examine 129 populations of two tetraploid and four diploid species collected from Iceland to Japan. All individuals were genotyped at seven to 18 nuclear simple sequence repeats (nSSRs). Pairwise among the six species ranged from 0.285 to 0.903, and genetic differentiation among them was clear. structure analysis suggested that Betula pubescens is an allotetraploid and one of the parental species was Betula pendula. In both species pairs of B. pendula and B. plathyphylla, and B. pubescens and B. ermanii, genetic diversity was highest in central Siberia. A hybrid zone was detected around Lake Baikal for eastern and western species pairs regardless of ploidy level. Approximate Bayesian computation suggested that the divergence of B. pendula and B. platyphylla occurred around the beginning of the last ice age (36 300 years BP, 95% CI: 15 330–92 700) and hybridization between them was inferred to have occurred after the last glacial maximum (1614 years BP, 95% CI: 561–4710), with B. pendula providing a higher contribution to hybrids.     

How many species of Paradoxurus civets are there? New insights from India and Sri Lanka

Using molecular data and morphological features, we investigated the species limits and genetic diversity among populations of the Asian palm civets of the genus Paradoxurus. Our main objectives were to determine the number of species within Paradoxurus hermaphroditus and to test the validity of the newly proposed species within Paradoxurus zeylonensis. Fragments of two mitochondrial (Cytochrome b, Control Region) and one nuclear (intron 7 of the beta fibrinogen) markers were sequenced from 128 individuals of P. hermaphroditus, P. zeylonensis and Paradoxurus jerdoni. DNA sequences were analysed using phylogenetic and haplotype network methods. Our analyses confirmed that P. hermaphroditus comprises three major clades, which should be recognized as separate species: P. hermaphroditus (Indian and Indochinese regions), Paradoxurus musangus (mainland Southeast Asia, Sumatra, Java and other small Indonesian islands) and Paradoxurus philippinensis (Mentawai Islands, Borneo and the Philippines). Furthermore, we have proposed that there are two subspecies within both P. musangus and P. philippinensis, and there might be at least two or three subspecies within P. hermaphroditus. We found a very low genetic diversity and no geographical structure within P. zeylonensis and did not find any support for splitting P. zeylonensis into several species nor subspecies. Finally, we confirmed that P. jerdoni and P. zeylonensis are sister species.