Population genetic structure and levels of inbreeding depression in the Mediterranean island endemic Cyclamen creticum (Primulaceae)

The variation and evolution of reproductive traits in island plants have much attention from conservation and evolutionary biologists. However, plants on islands in the Mediterranean region have very little attention. In the present study, we examine the floral biology and mating system of Cyclamen creticum , a diploid perennial herb endemic to Crete and Karpathos. Our purpose is to quantify (1) variation and covariation of floral traits related to the mating system, (2) the ability of the species to self in the absence of pollinators and its relative performance on selfing and outcrossing and (3) generic diversity within and among populations. Pollen/ovule ratios were indicative of a xenogamous species. A controlled pollination experiment showed that the species is self-compatible but is unable to set seed, in the absence of pollinators, probably due to stigma-anther separation. A multiplicative estimate of inbreeding depression based on fruit maturation, seed number and percentage seed germination gave δ= 0.38 Population genetic diversity was high, 54.76% polymorphic loci, a mean of 1.78 alleles per locus and a mean observed heterozygosity of 0.053. F -statistics nevertheless indicated high inbreeding rates (mean F ^is= 0.748) in natural populations, and low levels of population differentiation (mean F^is= 0.168). C. creticum thus appears to have a mixed-mating system with high levels of (pollinator) mediated inbreeding (either by facilitated selfing, geitonogamy or biparental inbreeding) in natural populations.     

High genetic diversity detected in the endemic Primula apennina Widmer (Primulaceae) using ISSR fingerprinting

Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population percentage of polymorphic band (PPB = 75.92%, H _S = 0.204, H _pop = 0.319) and at species level (PPB = 96.95%, H _T = 0.242, H _sp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and Bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.     

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.     

RAPD-based evaluation of genetic diversity among populations of the Iranian endemic species Rhabdosciadium aucheri Boiss. (Apiaceae)

Molecular Biology Reports - Rhabosciadium aucheri is an Iranian endemic herbaceous species that grows in the west, center, and south regions of Iran. In the present study, genetic variation of 70...     

High genetic diversity in southwest Asian populations of Philaenus spumarius (Hemiptera: Auchenorrhyncha)

The genus Philaenus is one of the best investigated among Auchenorrhyncha, and several morphological, ecological, karyological, and molecular data have led to a designation of up to 10 species, distributed mainly in the Mediterranean and south-western Asia. The only widespread Palaearctic species, P. spumarius, is known to be structured phylogeographically as it consists of two highly divergent mitochondrial clades (northeast, NE and southwest, SW), with several subclades. This study contributes to the species phylogeography through the study of the genetic diversity and affinity of P. spumarius populations from southwestern Asia. Mitochondrial DNA (cytochrome B) show a high level of genetic diversity within Turkish and Iranian populations, the majority of which belong to the SW clade, and only single populations from northeastern Turkey are found to be substantially highly divergent lineages within the NE clade. One of the NE populations also showed significant differences in the distribution and amount of heterochromatin compared to other populations. According to the results of this study and previous phylogenetic and phylogeographic works on this species, we conclude that Southwestern Asia is probably the place of origin of the Philaenus spumarius.     

High genetic divergence characterizes populations of the endemic plant Lithophragma maximum (Saxifragaceae) on San Clemente Island

Narrowly-ranging species frequently harbor less genetic variability relative to widespread relatives and face graver extinction threats due to the heightened impacts of stochastic events on ecological and genetic diversity. In this study, we examined the impact of historical and current threats to the maintenance of genetic variation in Lithophragma maximum (Saxifragaceae), a perennial herb endemic to San Clemente Island, California. This species exists as small populations confined to canyons along 4 km of the southeast coastline of the island. In 15 populations analyzed with 10 microsatellite markers, we identified an average of 2.05 alleles per locus and 58.7% polymorphic loci. Significant departures from Hardy–Weinberg equilibrium existed in six populations; five of these exhibited heterozygote deficiency. Bayesian inference of genetic structure indicated a significant amount of structure among populations and canyons and infrequent gene flow even over very short distances. We also identified a significant and positive correlation between genetic and geographic distances, indicative of isolation by distance. There was no evidence of recent bottlenecks in any of the sampled populations, but older bottlenecks were detected in two populations. These results suggest that populations of L. maximum have historically been small and isolated, which is likely due to the rugged habitat in which this species occurs and limited pollen and seed dispersal. Given the high degree of structure observed across populations, we suggest that conservation efforts should focus on preserving populations in multiple canyons, maintaining large population sizes to preserve genetic variation, and controlling the spread of invasive species in areas where L. maximum occurs.     

High genetic diversity and low structure in an endemic long-lived tree,Yucca capensis (Asparagaceae)

• Endemic species distributed in fragmented habitats are highly vulnerable to extinction because they may have low genetic diversity. However, some life-history traits can mitigate the effect of genetic drift on populations. We analysed the level and distribution of genetic variation and ancestral population size of Yucca capensis, a long-lived endemic plant of the Baja California Peninsula, Mexico. Its populations are scattered across a habitat that is suffering accelerated transformation.
• We used six nuclear microsatellites to genotype 224 individuals from 17 locations across the entire species' geographic range. We estimated polymorphisms, heterozygosity and genetic structure. We also evaluated the ancestral and recent effective size and time since the population started to change.
• We found high heterozygosity, high polymorphism and low differentiation among locations, suggesting a panmictic population across the range. We also detected a large ancestral effective population size, which suffered a strong reduction in the Mid-Holocene.
• Despite changes in environmental conditions caused by habitat modification, the high diversity and low differentiation in Y. capensis may result from its large ancestral effective size and life-history traits, such as plant longevity, clonal growth and mating system, which reduce the rate of loss of genetic variation. However, the dependence on a specialist pollinator that displays short flight range can reduce gene flow among the plant populations and could, shortly, lead them into an extinction vortex.

     

Factors affecting levels of genetic diversity in natural populations.

Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic polymorphism is virtually absent. Instead, we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered ''normal'', and inbreeding effects, which may hasten loss of variability due to drift. To account for species with large population sizes but low variability we advance three hypotheses. First, it is known that certain metapopulation structures can result in effective population sizes far below the census size. Second, there is increasing evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis provides extra opportunities to mutate. Such a mechanism would undermine the simple relationship between heterozygosity and effective population size. Third, the fact that related species that differ greatly in variability implies that large amounts of variability can be gained or lost rapidly. We argue that such cases are best explained by rapid loss through a genome-wide selective sweep, and suggest a mechanism by which this could come about, based on forced changes to a control gene inducing coevolution in the genes it controls. Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities. Circumstances can even be envisioned in which the process could provide intrinsic impetus to speciation.     

High levels of genetic divergence and inbreeding in populations of cupuassu (Theobroma grandiflorum)

Theobroma grandiflorum (cupuassu) is an important fruit tree native to the Brazilian Amazon. Establishing the genetic diversity and structure of populations is critical to define long-term strategies for cupuassu conservation presently threatened by rapid deforestation. Three natural populations collected at the putative center of diversity, three groups of accessions established at a germplasm collection, and one derived from commercial plantings were analyzed. The genetic diversity was assessed using 21 polymorphic microsatellite loci originally developed for Theobroma cacao, disclosing a total of 113 alleles. The estimated genetic diversity parameters averaged over cupuassu populations (A = 3.53 alleles per locus; H _e = 0.426; H _o = 0.346) were lower than the values reported for other Neotropical tree species. The three natural populations presented a positive and significant fixation index (f), ranging from 0.133 to 0.234. Cupuassu apparently adhered to a general pattern of genetic diversity structure of some Neotropical tree species occurring at low densities, with a low intrapopulation genetic diversity and important levels of endogamy, possibly due to biparental inbreeding derived from the presence of spatial genetic structure in the populations. A high level of genetic divergence was detected among the natural populations (θ _p = 0.301), a strong differentiation caused by limited gene flow, and suggesting that human interference in spreading and/or stimulating plantings might have had a smaller effect than expected. The approximate location of the T. grandiflorum center of diversity could not be confirmed by analyzing natural populations from the putative region.     

High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction

The maintenance of genetic diversity is thought to be fundamental for the conservation of threatened species. It is therefore important to understand how genetic diversity is affected by the re-introduction of threatened species. We use establishment history and genetic data from the remnant and re-introduced populations of a New Zealand endemic bird, the hihi Notiomystis cincta, to understand genetic diversity loss and quantify the genetic effects of re-introduction. Our data do not support any recent bottleneck events in the remnant population. Furthermore, all genetic diversity measures indicate the remnant hihi population has retained high levels of genetic diversity relative to other New Zealand avifauna with similar histories of decline. Genetic diversity (N(A) , alleles per locus, allelic richness, F(IS) and H(S) ) did not significantly decrease in new hihi populations founded through re-introduction when compared to their source populations, except in the Kapiti Island population (allelic richness and H(S) ) which had very slow post-re-introduction population growth. The N(e) /N(c) ratio in the remnant population was high, but decreased in first-level re-introductions, which together with significant genetic differentiation between populations (F(ST) & Fisher's exact tests) suggest that extant populations are diverging as a result of founder effects and drift. Importantly, simulations of future allele loss predict that the number of alleles lost will be higher in populations with a slow population growth, fewer founding individuals and with nonrandom mating. Interestingly, this species has very high levels of extra-pair paternity which may reduce reproductive variance by allowing social and floater males to reproduce a life history trait that together with a large remnant population size may help maintain higher levels of genetic diversity than expected.     

Anagenetic speciation in Ullung Island, Korea: genetic diversity and structure in the island endemic species, Acer takesimense (Sapindaceae)

Anagenetic speciation is an important mode of speciation in oceanic islands; one-fourth of the endemic plants are estimated to have been derived via this process. Few studies, however, have critically examined the genetic consequences of anagenesis in comparison with cladogenesis (involved with adaptive radiation). We hypothesize that endemic species originating via anagenetic speciation in a relatively uniform environment should accumulate genetic variation with limited populational differentiation. We undertook a population genetic analysis using nine nuclear microsatellite loci of Acer takesimense, an anagenetically derived species endemic to Ullung Island, Korea, and its continental progenitor A. pseudosieboldianum on the Korean Peninsula. Microsatellite data reveal a clear genetic distinction between the two species. A high F value in the cluster of A. takesimense was found by Bayesian clustering analysis, suggesting a strong episode of genetic drift during colonization and speciation. In comparison with A. pseudosieboldianum, A. takesimense has slightly lower genetic diversity and possesses less than half the number of private and rare alleles. Consistent with predictions, weak geographical genetic structure within the island was found in A. takesimense. These results imply that anagenetic speciation leads to a different pattern of specific and genetic diversity than often seen with cladogenesis.     

High levels of genetic diversity in populations of Iris aphylla L. (Iridaceae), an endangered species in Poland

We used RAPDs (Random Amplified Polymorphic DNAs) to investigate genetic diversity and its partition within and between three populations of Iris aphylla in Poland. Analysis of Molecular Variance (AMOVA) of 84 distinct RAPD multiband genotypes revealed higher variation within populations (77.2%) than genetic differentiation between them (22.8%, P  < 0.002). Values of genetic diversity indices ( H ) were similar in all three sites (0.21–0.24). The differentiation of the populations corresponded to low average gene flow ( Nm  = 0.81). Our results indicated that genetic diversity was independent of population size. We concluded that although sexual reproduction and gene flow between populations of I. aphylla were very limited, they preserved high levels of genetic diversity. Relatively large number of seeds, which migrated in the past to populations, as well as patterns of reproduction and life history of I. aphylla may explain this situation.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 65–72.     

Mandible asymmetry and genetic diversity in island populations of the common shrew, Sorex araneus

Mandibles from 13 island and six mainland populations of common shrews from the west coast of Scotland were subjected to geometric morphometric analysis in order to investigate the relationship between genetic diversity and fluctuating asymmetry. Although population mean shape fluctuating asymmetry (FA) and size FA were significantly inversely correlated with population genetic diversity this result was substantially due to one island. Sanda, the smallest island with by far the lowest genetic diversity, also had the highest FA. When Sanda was removed from the analysis, the relationship was not significant. There was no relationship between genetic diversity and FA at the individual level, whether measured as mean locus heterozygosity or d(2). In general, if genetic variation affects FA at all, the effect is weak and may only be of biological interest in very small populations.     

Genetic structure of continental and island populations of the Mediterranean endemic Cyclamen balearicum (Primulaceae)

Cyclamen balearicum is a self-compatible perennial herb endemic to the western Mediterranean Basin. This species occurs in five geographically isolated terrestrial islands in southern France and on four Balearic islands. In this study, we compare genetic variability and differentiation within and among 11 terrestrial island populations and 17 true island populations. Of nine readable enzyme loci, five were polymorphic in both terrestrial and true islands. F statistics showed a significant heterozygote deficiency in all populations, probably due to high levels of autonomous selfing, restricted gene flow, and subsequent genetic drift. Genetic diversity was higher in terrestrial islands than on the Balearic islands, suggesting that the Balearic islands were colonized when they were in contact with the continent. Population differentiation was greater among terrestrial islands (Fst = 0.417 and Gst = 0.344) than among true islands (Fst = 0.112 and Gst = 0.093). Furthermore, differentiation among populations on the Basses Cévennes terrestrial island was greater (Fst = 0.254) than among populations on the true island of Mallorca (Fst = 0.163). The greater genetic differentiation among terrestrial islands could have been caused by genetic bottlenecks associated with changes in climate and human land use that may have reduced population sizes more severely in terrestrial islands in southern France than on the Balearic islands.     

Genetic diversity in micronesian island populations of the tropical tree campnosperma brevipetiolata (anacardiaceae)

Tropical plant species have been the focus of considerable attention in regard to their potential economic and social importance in the face of rapidly diminishing biodiversity in the tropics. Pacific Island species represent an even more fragile resource because different island populations are widely scattered and overall population sizes are small. We examined the distribution of genetic variation in Campnosperma brevipetiolata (Anacardiaceae), an upland rainforest tree species that is of potential use for both lumber and reforestation efforts in the Federated States of Micronesia (FSM). Seeds were collected from multiple populations on four island groups in the Caroline Islands (Kosrae, Pohnpei, and Yap in the FSM; and the Republic of Palau) and subjected to an electrophoretic analysis involving four polymorphic genetic loci. We hypothesized that variation on these islands would decrease with increasing distance from the presumed Indo-Malayan source of these island floras. Indeed, we found a trend of decreasing variation from west to east indicated by the mean number of alleles per locus (A = 1.50-1.33), effective number of alleles per locus (A_e = 1.14-1.12) and mean genetic diversity (H_e = 0.123-0.107). We also found little genetic differentiation among the islands (F_pt = 0.174) and among subpopulations within islands (F_sp = 0.047), indicating that either there are high levels of gene flow among the islands by seed dispersal or that these populations have not been established long enough for divergence to have occurred. The lack of divergence among islands observed for Campnosperma brevipetiolata suggests that germplasm sampled from any one island population would be a suitable starting point for plant breeding or reforestation efforts.     

High levels of genetic diversity in marginal populations of the marsh orchid Dactylorhiza majalis subsp. majalis

Because of harsh conditions, suboptimal habitat quality and poor connectivity to other populations, plant populations at the margin of a distribution are expected to be less genetically diverse, but to be more divergent from each other than populations in the centre of a distribution. In northern Europe, northern marginal populations may also be younger than populations further to the south, and may have had less time to accumulate genetic diversity by mutation and gene flow. However, orchids have very small seeds, which are easily dispersed long distances by wind, and orchids are therefore expected to show less differentiation between marginal and central populations than other groups of seed plants. Here, we analysed whether Scandinavian populations of the tetraploid marsh orchid Dactylorhiza majalis subsp. majalis differ from central European populations in genetic diversity patterns. A total of 220 plants from eight central European and ten Scandinavian populations was examined for variation at five nuclear microsatellite loci, nuclear ITS and 13 polymorphic sites in noncoding regions of the plastid genome. The total genetic diversity was slightly lower in Scandinavia than in central Europe, both in plastid and nuclear markers, but the differences were small. Also, the Scandinavian populations were less diverse and somewhat more strongly differentiated from each other than the central European ones. Dactylorhiza majalis subsp. majalis has apparently colonized Scandinavia on multiple independent occasions and from different source areas in the south. Seed flow between Scandinavian populations has still not fully erased the patterns imprinted by early colonization. Our results suggest that marginal populations of orchids may be as important as central ones in preserving genetic diversity through Pleistocene glacial cycles. We also predict that orchids with their light seeds are better adapted than many other plants to respond to future climate changes by dispersing into new suitable areas.     

Spatial genetic structure and clonal diversity of island populations of lady's slipper (Cypripedium calceolus) from the Biebrza National Park (northeast Poland)

Three populations of the rare and endangered plant species Cypripedium calceolus were included in a study of genetic diversity and spatial genetic structure in the Biebrza National Park, northeast Poland. Analysis of 11 allozyme loci indicate that the populations of this species contained high genetic variability (P = 45.5%, A= 1.73). On the other hand, the genetic differentiation (FST = 0.014, P < 0.05) among C. calceolus populations was very low when compared to other species with similar life history characteristics. The observed high rate of gene flow (Nm = 18) may suggest that the populations studied derived from each other in the recent past. Five polymorphic allozyme markers identified 109 multilocus genotypes in three populations and the majority of them (67%) were population-specific. One of the populations studied, characterized by particularly extensive vegetative reproduction, showed the lowest clonal diversity (G/N = 0.15) and heterozygosity (HO = 0.111) values and the highest FIS(0.380), when compared to other two populations (G/N = 0.26-0.27, HO= 0.166-178, FIS = 0.024-0.055). This may indicate that clonal reproduction has an important influence on the genetic structure of C. calceolus populations. The longevity of genets, the out-crossing breeding system and the presence of recruitment from seeds are factors maintaining genetic diversity in C. calceolus.     

High levels of genetic polymorphism in the insular endemic herb Jepsonia malvifolia.

Jepsonia malvifolia is a long-lived perennial herb endemic to the Channel Islands of southern California and Guadalupe Island, Mexico. Twelve populations of J. malvifolia on San Clemente Island were surveyed for their genotype at 21 allozyme loci, revealing high levels of genetic polymorphism. For all individuals across San Clemente Island, 95.2% of loci are polymorphic with A(p) = 2.90 and H(e) = 0.179. Populations averaged 60.2% polymorphic loci with A(p) = 2.42 and H(e) = 0.158. Most variation is found within rather than among populations (G(ST) = 0.101), although differentiation among populations is significant. Genetic identities range from 0.936 to 0.999 with mean I = 0.975. There is no significant relationship between genetic and geographic distance. Gene flow among populations is Nm = 9.5 based on private alleles and Nm = 2.2 based on F(ST). Outcrossing rates based on fixation indices average t = 0.753, indicating a primarily outcrossed mating system. The genetic variation observed is unusually high for an insular endemic herb and indicates that J. malvifolia is unlikely to be endangered by genetic factors.     

High genetic diversity among fossorial lizard populations (Anniella pulchra) in a rapidly developing landscape (Central California)

California is a biodiversity hotspot facing unbridled human population growth, especially in Central California. One of the poorly known, sensitive species in this area is the California legless lizard (Anniella pulchra), a fossorial worm-like reptile. We report mt and nuDNA sequences from 69 museum-vouchered samples of Anniella (A. pulchra and its sister species A. geronimensis) from 48 localities. Our genetic survey reveals substantially more genetic diversity within A. pulchra than previously reported. Our two independently evolving markers (mt and nuDNA) reveal five major lineages of A. pulchra. Two of the five major lineages of A. pulchra correspond to a north-south split found in other widespread California reptiles. These northern and southern clades also correspond to a previous study showing variation in chromosomal number. Unlike most other Californian reptiles, A. pulchra has major genetic lineages that are endemic to Central California including two that are endemic to the San Joaquin Valley and Carrizo Plain. Although A. pulchra is threatened throughout its range, the distinct San Joaquin lineages are seriously imperiled by urban sprawl. Some of the localities for the newly recognized genetic lineages have already been destroyed by development.