Does genetic variation and gene flow vary with rarity in obligate seeding Persoonia species (Proteaceae)?

Theory predicts that genetic variation is a determinant of persistence, and that the abundance and distribution of variation is strongly dependent on genetic drift and gene flow. Small, isolated populations are expected to be less diverse and more differentiated than large, inter-connected populations. Thus rare species may be more at risk of extinction. We used 389 putative AFLP loci to compare genetic variation and structuring in two pairs of closely-related common (large populations geographically widespread) and rare (small populations spatially restricted) Persoonia species. We genotyped 15–22 adult plants, from four populations, covering the geographic range of each species. Although genetic diversity was low for all four species (for long-lived outcrossing perennials), we found significantly more diversity within populations of the rare species than within those of the common species. AMOVA revealed significant levels of structure both among species (21%) and populations (15%). The proportion of inter-population variation within species did not vary consistently with rarity (Pair 1 rare 21.1% versus common 16.5%; Pair 2 rare 15.8% versus common 20.6%). However populations of the rare species were more differentiated than common species with similar geographic separation, suggesting greater gene flow between populations of the common species. Therefore, even relatively small genetically isolated populations of rare Persoonia species were more diverse than large populations of common Persoonia species. We hypothesise that common Persoonia species have undergone a rapid range expansion from a narrow gene pool, while genetic diversity is maintained in the soil seed-bank of rare remnants.     

Patterns of geographic distribution have a considerable influence on population genetic structure in one common and two rare species of Rhododendron (Ericaceae)

Genetic diversity is essential for species to sustain their populations and evolutionary potential. In order to develop effective conservation strategies for rare species, it is necessary to understand differences in patterns of genetic diversity between common and rare species. Data about population genetic structure is important to design effective conservation strategies for rare species. In this study, we compared the genetic diversity and population genetic structure of a common species, Rhododendron weyrichii, to those of two rare species, Rhododendron sanctum and Rhododendron amagianum, with different geographic distributions. We analyzed five microsatellite loci in 16 populations of R. weyrichii, 9 populations of R. sanctum, and 6 populations of R. amagianum. As expected, the level of genetic diversity indicated by allelic richness and gene diversity was lower for the rare species R. sanctum than for the common species R. weyrichii. However, there was no statistically significant difference in genetic diversity between R. weyrichii and the other rare species, R. amagianum. Analyses of the isolation-by-distance pattern, neighbor-joining trees, and Bayesian clustering indicated that R. sanctum had a strong population genetic structure whereas R. amagianum exhibited very weak genetic structure among populations and that there was moderate population genetic structure for R. weyrichii. Therefore, the degree and pattern of population genetic structure in each species was unrelated to its rarity and instead merely reflected its geographic distribution.     

Genetic diversity and population size: island populations of the common shrew, Sorex araneus

Populations of many species are currently being fragmented and reduced by human interactions. These processes will tend to reduce genetic diversity within populations and reduce individual heterozygosities because of genetic drift, inbreeding and reduced migration. Conservation biologists need to know the effect of population size on genetic diversity, as this is likely to influence a population's ability to persist. Island populations represent an ideal natural experiment with which to study this problem. In a study of common shrews (Sorex araneus) on offshore Scottish islands, 497 individuals from 13 islands of different sizes and 6 regions on the mainland were trapped and genotyped at eight microsatellite loci. Previous genetic work had revealed that most of the islands in this study were highly genetically divergent from one another and the mainland. We found that most of the islands exhibited lower genetic diversity than the mainland populations. In the island populations, mean expected heterozygosity, mean observed heterozygosity and mean allelic richness were significantly positively correlated with log island size and log population size, which were estimated using habitat population density data and application of a Geographic Information System.     

Genetic variation in lowland and mountain populations of Tofieldia calyculata and their ability to survive within low levels of genetic diversity

Loss of genetic diversity is expected to be a reason behind the decline of populations of many rare species. To what extent this is true for populations at the range periphery remains to be explored. Alpine species with peripheral lowland populations are an ideal but little-known model system to address this issue. We used 17 microsatellite markers to investigate the genetic diversity and structure of populations of Tofieldia calyculata, a common species in central European mountains, but highly endangered in lowlands. We showed that lowland populations have lower genetic diversity than mountain populations and that the two groups of populations are not clearly differentiated genetically. The species probably survived the last glaciation in refugia in the margins of the Alps and the western Carpathians and some lowland populations likely originated by postglacial colonisation. Some lowland populations may be relictual, but our data did not unequivocally confirm this. Low genetic diversity of lowland populations is likely the result of the reduction of population sizes, limited gene flow, and selfing. Based on data from herbarium specimens from extinct lowland populations, within-population genetic diversity has not changed over the last century suggesting that, under suitable habitat conditions, these populations are able to survive with low levels of genetic diversity. This idea is also supported by the presence of large viable extant populations with very low genetic diversity. Comparisons between modern and historic collection also showed that a large proportion of genetic diversity was lost, due mainly to the extinction of whole populations. Our results provided detailed insight into the recent past of the populations of Tofieldia calyculata, but the genetic diversity of the populations before the twentieth century remains unknown due to the poor quality of old DNA from herbaria samples. Overall, the study indicates that despite reduced genetic diversity, the lowland populations harbour some unique alleles and, with the current levels of genetic diversity, have a chance to survive in the long-term, and thus deserve conservation.

     

Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation

The genetic consequences of small population size and isolation are of central concern in both population and conservation biology. Organisms with a metapopulation structure generally show effective population sizes that are much smaller than the number of mature individuals and this can reduce genetic diversity especially in small sized and isolated subpopulations. Here, we examine the association between heterozygosity and the size and spatial isolation of natal colonies in a metapopulation of lesser kestrels (Falco naumanni). For this purpose, we used capture-mark-recapture data to determine the patterns of immigration into the studied colonies, and 11 highly polymorphic microsatellite markers that allowed us to estimate genetic diversity of locally born individuals. We found that individuals born in smaller and more isolated colonies were genetically less diverse. These colonies received a lower number of immigrants, supporting the idea that both reduced gene flow and small population size are responsible for the genetic pattern observed. Our results are particularly intriguing because the lesser kestrel is a vagile and migratory species with great movement capacity and dispersal potential. Overall, this study provides evidence of the association between individual heterozygosity and the size and spatial isolation of natal colonies in a highly mobile vertebrate showing relatively frequent dispersal and low genetic differentiation among local subpopulations.     

The importance of rare species: a trait‐based assessment of rare species contributions to functional diversity and possible ecosystem function in tall‐grass prairies

The majority of species in ecosystems are rare, but the ecosystem consequences of losing rare species are poorly known. To understand how rare species may influence ecosystem functioning, this study quantifies the contribution of species based on their relative level of rarity to community functional diversity using a trait‐based approach. Given that rarity can be defined in several different ways, we use four different definitions of rarity: abundance (mean and maximum), geographic range, and habitat specificity. We find that rarer species contribute to functional diversity when rarity is defined by maximum abundance, geographic range, and habitat specificity. However, rarer species are functionally redundant when rarity is defined by mean abundance. Furthermore, when using abundance‐weighted analyses, we find that rare species typically contribute significantly less to functional diversity than common species due to their low abundances. These results suggest that rare species have the potential to play an important role in ecosystem functioning, either by offering novel contributions to functional diversity or via functional redundancy depending on how rare species are defined. Yet, these contributions are likely to be greatest if the abundance of rare species increases due to environmental change. We argue that given the paucity of data on rare species, understanding the contribution of rare species to community functional diversity is an important first step to understanding the potential role of rare species in ecosystem functioning.     

Distribution of genetic diversity among disjunct populations of the rare forest understory herb, Trillium reliquum

We assessed genetic diversity and its distribution in the rare southeastern US forest understory species, Trillium reliquum. In all, 21 loci were polymorphic (PS=95.5%) and the mean number of alleles per polymorphic locus was 3.05. However, genetic diversity was relatively low (Hes=0.120) considering the level of polymorphism observed for this outcrossing species. A relatively high portion of the genetic diversity (29.7%) was distributed among populations. There was no relationship between population size and genetic diversity, and we did not detect significant inbreeding. These results are best explained by the apparent self-incompatibility of this species, its longevity and clonal reproduction. To address questions regarding the history of T. reliquum's rarity, we compared results for T. reliquum with that of its more common and partially sympatric congener, T. cuneatum. Despite shared life history traits and history of land use, we observed significant genetic differences between the two species. Although T. cuneatum contains slightly lower polymorphism (Ps=85%), we detected significantly higher genetic diversity (Hes=0.217); most of its genetic diversity is contained within its populations (GST=0.092). Our results suggest that not only is there little gene flow among extant T. reliquum populations, but that rarity and population isolation in this species is of ancient origins, rather than due to more recent anthropogenic fragmentation following European colonization. The Chattahoochee River was identified as a major barrier to gene exchange.     

High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis

Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (F(ST) = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories.     

Microsatellite polymorphism and population subdivision in natural populations of European sea bass Dicentrarchus labrax (Linnaeus, 1758)

Polymorphism of microsatellite markers was used to study the genetic variability and structure in natural populations of European sea bass Dicentrarchus labrax. The data consisted of six microsatellite loci analysed for 172 individuals from three samples collected in the Golfe-du-Lion (France) and one sample collected in the Golfo-de-Valencia (Spain). Our goals were (i) to assess the level of genetic variability as revealed by these markers, (ii) to estimate the genetic differentiation among natural populations within a restricted area, and (iii) to evaluate how microsatellite loci fit the predictions of the two most widely used mutation models (the infinite allele model and the stepwise mutation model). As expected, our results indicate that the genetic polymorphism is very high when compared with previously used genetic markers, the mean expected heterozygosity per locus ranging between 0.69 and 0.93. We also found that all loci but one fitted the infinite allele model better. Using this model as a lower limit, we could extrapolate from the observed diversity effective population sizes on the order of 35 000 individuals. Our results also suggest that there may be a slight genetic differentiation between the two gulfs (F_ST= 0.007, P < 0.05), indicating that the corresponding populations are likely to be dynamically independent. This finding for a species with high dispersal abilities, if confirmed, has important beatings on fish-stock assessment.     

Genetic structure, conservation genetics and evidence of speciation by range expansion in shy and white-capped albatrosses

Six variable microsatellite loci were used to examine genetic structuring in the closely related shy albatross (Thalassarche cauta) and white-capped albatross (T. steadi). First, levels of genetic differentiation between the species, and among three populations within each species, were analysed using amova, FST and RST. We found high levels of genetic structuring and detected many unshared alleles between the species, which provide strong evidence against any contemporary gene flow between them. Within each species, shy albatross populations were found to be genetically distinct whereas white-capped albatross populations were undifferentiated, which implies that dispersal events are much rarer in the former than in the latter. These results formed the basis for the recommendation that the three white-capped albatross populations (as a whole) and each shy albatross population be treated as separate units for conservation. Second, levels of genetic diversity and allelic patterns in shy and white-capped albatrosses were assessed for whether they support earlier mtDNA results suggesting that shy albatrosses arose through range expansion of white-capped albatrosses. All measures indicated lower genetic diversity within shy albatrosses than within white-capped albatrosses and upheld the hypothesis that shy albatrosses were founded by white-capped albatrosses.     

Taxon size predicts rates of rarity in vascular plants

We surveyed rarity in the vascular plants of the continental U.S.A. and Canada and the vascular plants of Hawaii to test the hypothesis that rates of rarity are independent of taxonomic group size. We demonstrated that taxonomic groups of plants with few species consistently contained fewer than the expected numbers of rare species. This pattern was apparent at the levels of genus, family, order and class. We also found that the pattern remained when we examined rates of rarity by comparing sister taxa that share a common ancestor. This pattern may arise from either differential speciation and extinction patterns or taxonomic bias in species designations (lumping and splitting). The pattern of lineages with few species demonstrating reduced rates of rarity is opposite to that previously observed in mammals and birds. If the protection of representatives from a diversity of lineages is a conservation objective, plant conservation is facilitated by the fact that relatively few species-poor lineages contain rare species.     

The population genetic approach delineates the species boundary of reproductively isolated corymbose acroporid corals

In this study, we used a population genetic approach with microsatellite markers to attempt to clarify the species boundary of Acropora corals. Species in this taxon are usually difficult to distinguish with the usual molecular phylogenetic approach. We used Acropora sp. 1 and Acropora digitifera as the target species to shed light on the species boundary of Acropora at the population level. These species are morphologically and ecologically similar but are reproductively isolated by differences of a few months in their spawning seasons. We could not distinguish these species using a phylogenetic analysis of the mitochondrial control region, as previously reported in other Acropora species. In contrast, a population genetic approach clearly distinguished these species both sympatrically and allopatrically. Our results suggest that recent speciation and shared ancestral polymorphisms could partly explain the para- and polyphyly of several Acropora species.     

Dispersal limitations, rather than bottlenecks or habitat specificity, can restrict the distribution of rare and endemic rainforest trees

Despite their narrow distribution, Australian rainforests still contain considerable levels of diversity and include many ancient, but often rare, lineages. Very little is known about the general biology of rainforest species, yet their long-term management depends on a better understanding of the main factors leading to rarity. For instance, are they highly endemic taxa, at the early stages of expansion, nearing the end of a period of decline, or persisting at low numbers over the long term? In this study we combine molecular, environmental, and ecological data to identify the factors responsible for the narrow distribution of a paleoendemic rainforest tree: Elaeocarpus sedentarius (Elaeocarpaceae). Between-population and between-generation comparisons of genetic diversity across all known populations of E. sedentarius show evidence of mutation-drift equilibrium rather than evidence of a recent bottleneck. Similarly, floristic and environmental data negate the hypothesis of rarity as a consequence of highly specialized habitat requirements. Instead, genetic structure and the available ecological data support the hypothesis of dispersal limitation as the main cause of endemism and that the species may have attained genetic equilibrium without realizing its full niche potential. We suggest that these factors are likely to explain narrow endemism in a broader range of taxa.     

Fragmentation and Genetic Diversity in Romnalda (Dasypogonaceae), a Rare Rain forest Herbaceous Genus from New Guinea and Australia

Rain forests are expected to be amongst the ecosystem types most affected by fragmentation due to their high species diversity, high endemism, complexity of interactions, and contrast with surrounding altered matrix. Due to their shorter life cycles and dependence on canopy cover, rain forest understory herbs are expected to indicate the effects of recent fragmentation more rapidly than canopy trees. This study investigated all four known species of the genus Romnalda , all of which are rare rain forest herbaceous species, to investigate the possible effects of habitat fragmentation and isolation on genetic diversity and gene flow. Allozymes were used as genetic markers and regional remnant vegetation maps were used to compare landscape fragmentation. We found that R. strobilacea populations in a highly fragmented landscape were genetically depauperate compared with those of its congeneric species that are found within continuous rain forest habitats and that allelic diversity decreased with decreasing population size but not geographic distance in R. strobilacea . Given the similarity among the species, our results indicate that all Romnalda species are potentially susceptible to loss of genetic diversity due to habitat fragmentation within relatively short timeframes. The results indicate that populations are not highly genetically differentiated and there is little evidence of genetic provenance where the species have restricted geographic ranges. Thus, species recovery programs would be better to focus on maintaining population size and genetic diversity rather than population differentiation.     

Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef

Connectivity underpins the persistence and recovery of marine ecosystems. The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem and managed by an extensive network of no‐take zones; however, information about connectivity was not available to optimize the network's configuration. We use multivariate analyses, Bayesian clustering algorithms and assignment tests of the largest population genetic data set for any organism on the GBR to date (Acropora tenuis, >2500 colonies; >50 reefs, genotyped for ten microsatellite loci) to demonstrate highly congruent patterns of connectivity between this common broadcast spawning reef‐building coral and its congener Acropora millepora (~950 colonies; 20 reefs, genotyped for 12 microsatellite loci). For both species, there is a genetic divide at around 19°S latitude, most probably reflecting allopatric differentiation during the Pleistocene. GBR reefs north of 19°S are essentially panmictic whereas southern reefs are genetically distinct with higher levels of genetic diversity and population structure, most notably genetic subdivision between inshore and offshore reefs south of 19°S. These broadly congruent patterns of higher genetic diversities found on southern GBR reefs most likely represent the accumulation of alleles via the southward flowing East Australia Current. In addition, signatures of genetic admixture between the Coral Sea and outer‐shelf reefs in the northern, central and southern GBR provide evidence of recent gene flow. Our connectivity results are consistent with predictions from recently published larval dispersal models for broadcast spawning corals on the GBR, thereby providing robust connectivity information about the dominant reef‐building genus Acropora for coral reef managers.     

POPULATION GENETICS OF RESURGENCE: WHITE-TAILED DEER IN KENTUCKY

Abstract: White-tailed deer (Odocoileus virginianus) in Kentucky represent an example of successful wildlife restoration. Eliminated from all but a few remnant areas by the early part of the twentieth century, the species is once again widely distributed and abundant as a result of intensive restocking efforts since the 1940s. Seven DNA microsatellite markers were used to survey the extent and pattern of genetic variation in 322 deer from multiple localities throughout the commonwealth. Six genetically homogeneous regions and 1 heterogeneous region were identified across Kentucky. High levels of allelic diversity were detected with no apparent reduction in heterozygosity, disproportionate loss of rare alleles, or shift in modal allele frequency class as might be expected if the severe historical population size reduction generated a concomitant genetic bottleneck. These results are consistent with predictions of founder-flush models: that rapid population growth may minimize the loss of genetic variability associated with a population bottleneck. Nevertheless, comparisons of our data to that derived from other imperiled taxa suggest that species demographics can also play an important role in determining the genetic consequences of population size reduction and subsequent recovery. Our data also illuminate the critical role of deer from Land Between the Lakes (LBL) as the initial source population from which all extant Kentucky deer are descended. While generally supporting current regional management perspectives, our results argue for recognition of the LBL herd as a distinct management island of genetic and historical value.     

Nitrogen‐fixing tree abundance in higher‐latitude North America is not constrained by diversity

The rarity of nitrogen (N)‐fixing trees in frequently N‐limited higher‐latitude (here, > 35°) forests is a central biogeochemical paradox. One hypothesis for their rarity is that evolutionary constraints limit N‐fixing tree diversity, preventing N‐fixing species from filling available niches in higher‐latitude forests. Here, we test this hypothesis using data from the USA and Mexico. N‐fixing trees comprise only a slightly smaller fraction of taxa at higher vs. lower latitudes (8% vs. 11% of genera), despite 11‐fold lower abundance (1.2% vs. 12.7% of basal area). Furthermore, N‐fixing trees are abundant but belong to few species on tropical islands, suggesting that low absolute diversity does not limit their abundance. Rhizobial taxa dominate N‐fixing tree richness at lower latitudes, whereas actinorhizal species do at higher latitudes. Our results suggest that low diversity does not explain N‐fixing trees' rarity in higher‐latitude forests. Therefore, N limitation in higher‐latitude forests likely results from ecological constraints on N fixation.     

A 'fair go' for coral hybridization

Hybridisation between coral species clearly occurs in vitro, but the evolutionary significance of this cross-fertility is still the subject of much debate. Compelling genetic and reproductive evidence support introgressive hybridization amongst Indo-Pacific members of the scleractinian genus Acropora. Although population genetic analyses indicate that interspecific hybridization events are relatively rare, they are likely be important on evolutionary time scales, creating the capacity for adaptive evolution by increasing genomic diversity and heterozygosity. However, in a recent paper based exclusively on the three endemic Caribbean Acropora species, Vollmer and Palumbi (2002) dispute the occurrence of reticulation in corals. Here we use data from both the Vollmer and Palumbi study and our earlier paper on the same species (van Oppen et al., 2000) to show that reticulation has occurred amongst the Caribbean Acropora species. Furthermore, conclusions based on the limited Caribbean Acropora fauna cannot simply be extrapolated to Indo-Pacific corals, and it is inappropriate to view some coral species as 'immortal mules'.     

The tales of two geckos: does dispersal prevent extinction in recently fragmented populations?

Although habitat loss and fragmentation threaten species throughout the world and are a major threat to biodiversity, it is apparent that some species are at greater risk of extinction in fragmented landscapes than others. Identification of these species and the characteristics that make them sensitive to habitat fragmentation has important implications for conservation management. Here, we present a comparative study of the population genetic structure of two arboreal gecko species (Oedura reticulata and Gehyra variegata) in fragmented and continuous woodlands. The species differ in their level of persistence in remnant vegetation patches (the former exhibiting a higher extinction rate than the latter). Previous demographic and modelling studies of these two species have suggested that their difference in persistence levels may be due, in part, to differences in dispersal abilities with G. variegata expected to have higher dispersal rates than O. reticulata. We tested this hypothesis and genotyped a total of 345 O. reticulata from 12 sites and 353 G. variegata from 13 sites at nine microsatellite loci. We showed that O. reticulata exhibits elevated levels of structure (FST=0.102 vs. 0.044), lower levels of genetic diversity (HE=0.79 vs. 0.88), and fewer misassignments (20% vs. 30%) than similarly fragmented populations of G. variegata, while all these parameters were fairly similar for the two species in the continuous forest populations (FST=0.003 vs. 0.004, HE=0.89 vs. 0.89, misassignments: 58% vs. 53%, respectively). For both species, genetic structure was higher and genetic diversity was lower among fragmented populations than among those in the nature reserves. In addition, assignment tests and spatial autocorrelation revealed that small distances of about 500 m through fragmented landscapes are a barrier to O. reticulata but not for G. variegata. These data support our hypothesis that G. variegata disperse more readily and more frequently than O. reticulata and that dispersal and habitat specialization are critical factors in the persistence of species in habitat remnants.