Article

Low genetic diversity in small leading edge populations of a European paleoendemic Ramonda serbica (Gesneriaceae) in Bulgaria

Authors:
  • Institute of Molecular Biology "Roumen Tsanev" , Bulgarian Academy of Sciences
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... In a study on the genetic variability of three populations of R. serbica from Albania and three populations of R. nathaliae from North Macedonia using RAPD markers, Daskalova et al. (2012) could not clearly distinguish the two species. More recently, Petrova et al. (2018) studied five populations of R. serbica in Bulgaria using ISSR markers. They showed that this species has low genetic variability and significant differentiation among populations. ...
... two distinct genetic clusters were identified in Bulgaria, and the existence of which was suggested to be a consequence of isolation between refugial populations (Petrova et al., 2014). Finally, Petrova et al. (2018) have shown that the genetic diversity of R. serbica populations in Bulgaria is very low. The authors hypothesize that this is the result of both post-glacial fragmentation and a particularly pronounced lack of genetic connectivity for the Bulgarian populations, which are on the periphery of the species range. ...
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The genus Ramonda includes three Paleoendemic and Tertiary relict species that survived in refugial habitats of the Balkan Peninsula (R. nathaliae and R. serbica) and the Iberian Peninsula (R. myconi). They are all “resurrection plants,” a rare phenomenon among flowering plants in Europe. Ramonda myconi and R. nathaliae are diploids (2n = 2x = 48), while R. serbica is a hexaploid (2n = 6x = 144). The two Balkan species occur in sympatry in only two localities in eastern Serbia, where tetraploid potential hybrids (2n = 4x = 96) were found. This observation raised questions about the existence of gene flow between the two species and, more generally, about the evolutionary processes shaping their genetic diversity. To address this question, genetic markers (AFLP) and an estimate of genome size variation were used in a much larger sample and at a larger geographic scale than previously. The combination of AFLP markers and genome size results suggested ongoing processes of interspecific and interploidy hybridization in the two sites of sympatry. The data also showed that interspecific gene flow was strictly confined to sympatry. Elsewhere, both Ramonda species were characterized by low genetic diversity within populations and high population differentiation. This is consistent with the fact that the two species are highly fragmented into small and isolated populations, likely a consequence of their postglacial history. Within sympatry, enormous variability in cytotypes was observed, exceeding most reported cases of mixed ploidy in complex plant species (from 2x to >8x). The AFLP profiles of non-canonical ploidy levels indicated a diversity of origin pathways and that backcrosses probably occur between tetraploid interspecific hybrids and parental species. The question arises whether this diversity of cytotypes corresponds to a transient situation. If not, the question arises as to the genetic and ecological mechanisms that allow this diversity to be maintained over time.
... Similar to observations in other species, this may be due to similar selection pressure from different locations, or insufficient interference of geographic factors towards gene follow among populations [38]. Evolutionary forces such as natural selection, genetic drift, gene flow, breeding system, geographic range together with historical processes of colonization and migration are reflected in genetic variation and structure of plant populations [8,39]. ...
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The genus Ramonda includes three preglacial paleoendemic species surviving as the rare resurrection angiosperms of the Northern hemisphere in refugia habitats in the Balkan (Ramonda nathaliae and Ramonda serbica) and Iberian Peninsulas (Ramonda myconi). This study focuses on: assessing genome size and base composition, determining chromosome number and ploidy level in several populations, evaluating inter- and intraspecific variations in DNA content and chromosome number as well as looking for the possible hybridization in the sympatric zones of Balkan species. R. nathaliae and R. myconi are diploid species (2n=2x = 48) while R. serbica is hexaploid (2n=6x = 144). The mean 2C DNA values ranged from 2.30 pg for R. nathaliae to 2.59 pg for R. myconi compared to 7.91 pg for R. serbica. The base composition for R. nathaliae was 42.1% GC, for R. myconi 39.9% and for R. serbica 41.2%. In one population of R. serbica the DNA content ranged from 2C = 7.65 to 11.82 pg, revealing different ploidy levels among its individuals. In sympatric populations genome size was intermediary (∼5 pg) between the diploid and hexaploid classes which indicates the hybridization ability between R. serbica and R. nathaliae. It appears that polyploidization is the major evolutionary mechanism in the genus Ramonda.
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Climate change causes species ranges to shift geographically as individuals colonise new suitable temperature zones or fail to reproduce where climate conditions fall below tolerance levels. Little is known about the potential loss of genetic diversity in such dynamic ranges. We investigated the level and distribution of neutral genetic diversity in shifting metapopulations during three scenarios of temperature increase projected for this century and at various degrees of weather variability. We used an individual-based and spatially explicit metapopulation model in which temperature zones were simulated to move across a fragmented landscape following different climate change scenarios. Although the connectivity between habitat patches allowed the species, modelled after the middle spotted woodpecker Dendrocopos medius, to move along with the shifting temperature range, existing neutral genetic diversity was lost under all three temperature increase scenarios. This was independent of the loss of individuals. The explanation for this effect is that only a part of the original genetic variation moved into the newly colonised habitat. Under increased weather variability the number of individuals and the number of alleles per locus were persistently lower. However, the pattern of changes in allele distributions under temperature zone shifts was the same under all weather variability levels. Genetic differentiation between populations had a tendency to increase at metapopulation range margins, but decreased again when population sizes increased in time. Increased weather variability led to increased variation around the mean genetic differentiation across the metapopulation. Our results illustrate the usefulness of more realistic models for studying the effects of climate change on metapopulations. They indicate that biodiversity monitoring indices based on species occurrence and abundance are not a good proxy for the trend in the level of genetic diversity. Further, the results underline the importance of conserving areas where species have existed for a long time as modern refugia for genetic diversity.
Article
Zieria prostrata (Rutaceae) is known from only four headlands within a 3-km stretch of coastline in New South Wales, Australia. The species was presumed to have occurred at a headland 24 km south of its present range. We used random amplified polymorphic DNA analysis to assess patterns of genetic variation within and among the extant populations. The analysis also included an individual reputedly rescued from the now extinct population. A high level of population divergence was revealed by principal coordinate analysis and an analysis of molecular variance (AMOVA; 37% among populations). Our genetic findings provide implications for the conservation management of the species. First, the loss of any one population would lead to a severe loss of genetic variation. Second, an adequate ex situ collection must sample the full range of genetic diversity from all populations. Third, the consequences of mixing populations may be an important conservation consideration if further translocations proceed. Fourth, the individual apparently sampled prior to its population extinction is genetically similar to individuals from one of the extent sites. This degree of similarity was unexpected and, after further investigation, led to the conclusion that prior existence of the species at the site is doubtful. Subsequently, a planned reintroduction program was abandoned. So far, of these four management implications, only the last has had a direct management outcome. These implications that failed to lead to practical management outcomes did so because the same management recommendations could be obtained without genetic research. Clearly, the challenge for more effective conservation managers. This may be best achieved by assessing the outcomes of genetic studies already conducted.
Article
Investigating diversity in asexual organisms using molecular markers involves the assignment of individuals to clonal lineages and the subsequent analysis of clonal diversity. Assignment is possible using a distance matrix in combination with a user-specified threshold, defined as the maximum distance between two individuals that are considered to belong to the same clonal lineage. Analysis of clonal diversity requires tests for differences in diversity and clonal composition between populations. We developed two programs, genotype and genodive for such analyses of clonal diversity in asexually reproducing organisms. Additionally, genotype can be used for detecting genotyping errors in studies of sexual organisms.
Article
Remnant population dynamics permit many plant species to persist timespans extending from decades up to several millenia. The regional-scalepersistence of these plant species strictly depends on the persistence of localpopulations within the region. This type of dynamics can explain the existenceof preglacial relict species in the Mediterranean today. We studied thepopulation dynamics of the long-lived iteroparous herb Ramondamyconi, a preglacial relict species with a fragmented distributioninMediterranean mountains, to evaluate the regional-scale persistence of thespecies. Demographic data were collected from 5 populations placed at LaCerdanya Pyrenean region for up to 6 years. The main life-history features ofthis species are the great longevity of adult plants and the high mortality ofseedlings. Matrix population models were used to investigate its demography.Overall, the population growth rate () ranged from a low of 0.79 to ahigh of 1.06. However, did not differ significantly from theequilibrium point, as indicated by their confidence intervals, except for onepopulation in one year. Despite the small between-year variation in ,variation in climatic conditions at La Cerdanya from year to year explained animportant part of such variation. Elasticity analyses were performed toevaluatethe relative importance of demographic parameters for population growth. Stasistransitions made the greatest contribution to . Finally, the long-termdynamics of R. myconi populations were analysed byincorporating environmental stochasticity into the models. Projectionsindicatedthat local R. myconi populations tend to decline over timebut with a long time to extinction, so the persistence ofR. myconi all over La Cerdanya is determined by thepersistence of its remnant local populations.
Article
Compared with populations near the core of aspecies' range, edge populations tend to becharacterized by low density and high temporalvariation. Based on empirical studiesquantifying this pattern, we show thateffective population size (N e)could be 2 to 30 times greater near the coreof the species' range than near the edge ofthe range. Hence, the rate of genetic driftmay be 2 to 30 times greater near the edge ofthe range. Despite these strong spatialpatterns in N e, empirical findingsindicate that peripheral populations sometimeshave less but sometimes have more geneticdiversity than core populations. Our analysisindicates that this variation can be explainedby uncertainty in spatial patterns ofmigration rates. Nevertheless, our analysis:(1) provides a framework or null hypothesis forempirically assessing how spatial patterns ofmigration or selection influence large-scalespatial patterns of genetic diversity, (2)highlights the potential importance ofcontemporary processes, such as spatialpatterns in N e (cf. historicalphenomena, such as range expansion) in thedevelopment and maintenance of large-scalespatial patterns in genetic diversity, and (3) provides new context for understanding the conservation value and vulnerability of peripheralpopulations. The conservation ofecological/evolutionary processes requiresunderstanding large scale spatial patterns ofdemographic and genetic processes such as thatdescribed here.
Article
A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance measures the accumulated allele differences per locus. If the rate of gene substitution per year is constant, it is linearly related to the divergence time between populations under sexual isolation. It is also linearly related to geographical distance or area in some migration models. Since D is a measure of the accumulated number of codon differences per locus, it can also be estimated from data on amino acid sequences in proteins even for a distantly related species. Thus, if enough data are available, genetic distance between any pair of organisms can be measured in terms of D. This measure is applicable to any kind of organism without regard to ploidy or mating scheme.
Article
Due to past and current climatic changes, range contractions and range shifts are essential stages in the history of a species. However, unlike range expansions, the molecular consequences of these processes have been little investigated. In order to fill this gap, we simulated patterns of molecular diversity within and between populations for various types of range contractions and range shifts. We show that range contractions tend to decrease genetic diversity as compared with population with stable ranges but quite counterintuitively fast range contractions preserve higher levels of diversity and induce lower levels of genetic differentiation among refuge areas than slow contractions. Contrastingly, fast range shifts lead to lower levels of diversity than slow range shifts. At odds with our expectations, we find that species actively migrating toward refuge areas can only preserve higher levels of diversity in refugia if the contraction is rapid. Under slow range contraction or slow range shift, active migration toward refugia lead to a larger loss of diversity as compared with scenarios with isotropic migration and may thus not be a good evolutionary strategy. These results suggest that the levels of diversity preserved after a climate change both within and between refuge areas will not only depend on the dispersal abilities of a species but also on the speed of the change. It also implies that a given episode of climatic change will impact differently species with different generation times.
Article
Thesis (Ph. D.)--North Carolina State University. Includes bibliographical references (leaves 262-266). Includes vita. microfiches. s
Article
Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd.uchicago.edu/structure.html.
Article
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
Article
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
Article
To investigate phylogenetic relationships in the genus Cucumis, 9 consensus chloroplast simple sequence repeat (ccSSR) primer pairs (ccSSR3, 9, 11, 13, 14, 17, 20, 21, and 23) were employed for DNA fragment length variation and 5 amplified fragments, ccSSR4, 12, 13, 19, and 20, were sequenced using total DNA from 13 accessions representing 7 African Cucumis species (x = 12), 3 Cucumis melo L. (x = 12) accessions, 2 Cucumis sativus L. (x = 7) accessions, and 1 Cucumis hystrix Chakr. (x = 12) accession. A Citrullus lanatus (Thunb.) Matsum. & Nakai (x = 11) accession was used as an outgroup. While fragment length analysis revealed the existence of 3 major species clusters (i.e., a group of African Cucumis species, a group composed of C. melo accessions, and a group containing C. sativus and C. hystrix species), sequence variation analysis identified 2 major species clusters (i.e., a group of African Cucumis species and a group composed of C. melo, C. sativus, and C. hystrix species). Comparative analysis using nuclear DNA (previous studies) and cpDNA sequence substitution data resulted in the placement of C. melo and C. sativus in different cluster groupings. Thus, both nuclear and cytoplasmic DNA should be employed and compared when a putative progenitor or specimens of an ancestral Cucumis species lineage is investigated. In addition, C. ficifolius (2x) and C. aculeatus (4x) of the African Cucumis species clustered together in this study. This result does not agree with reported isozyme analyses, but does agree with previously characterized chromosome homologies between these 2 species. Although African Cucumis species and C. hystrix do not share a close relationship, genetic affinities between C. sativus and C. hystrix are considerable. Combined evidence from previously published studies and data presented herein lend support to the hypothesis that C. hystrix is either a progenitor species of C. sativus or that they at least share a common ancestral lineage.
Contribution à l'étude caryologique des Gésneriacées d'Europe et de leur germination
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Contandriopoulos, J. 1966. Contribution à l'étude caryologique des Gésneriacées d'Europe et de leur germination. -91 Congrès des Sociétés Savantes, Rennes 3: 271-280.
Development of the female x-generation and embryo in Ramonda
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Inferring weak population structure with the assistance of sample group information
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GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update
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Peakall, R. and Smouse, P. E. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and researchan update. -Bioinformatics 28: 2537-2539.
Data from: Low genetic diversity in small leading edge populations of a European paleoendemic Ramonda serbica (Gesneriaceae) in Bulgaria. -Dryad Digital Repository
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Petrova, G. et al. 2018. Data from: Low genetic diversity in small leading edge populations of a European paleoendemic Ramonda serbica (Gesneriaceae) in Bulgaria. -Dryad Digital Repository,  http://dx.doi.org/10.5061/dryad.vq349kt .