Relative contribution of inbreeding depression and eroded adaptive diversity to extinction risk in small populations of shore campion

Population Genetics, Genetic Structure, and Inbreeding of Commiphora gileadensis (L.) C. Chr Inferred from SSR Markers in Some Mountainous Sites of Makkah Province

Commiphora gileadensis (L.) C. Chr is a perennial plant existing mainly in the southern and western mountains of the Arabian Peninsula. In the Makkah province, the remaining populations are threatened by many factors such as overcutting, overgrazing, and urban developments. These dangers are expected to be aggravated by the progression of aridification factors arising from climate change. To overcome the decline in remaining populations of this valuable species, a timely evaluation of the population's genetic variables and genetic structure is vital for the conservation of existing C. gileadensis populations. In this study, we used 61 SSR primers to achieve this objective. Only 50 loci showed polymorphisms, which led to further analysis of the population genetics for 600 genotypes that were collected from 50 populations of C. gileadensis found in 10 different sites in the Makkah region: Gebel Al Muliesaa, Wadi Albathna, Wadi Houra, Wadi Albaidaa, Wadi Elebiedia, Gebel Kniethl, Wadi Sayaa, Wadi Elbarasa, Wadi Alfawara, and Wadi Alkharar. The results showed an obvious decrease in genetic diversity variables in all studied populations. The range of PPL was between 8 and 40; additionally, the low H_T value of 0.804 and the high value of inbreeding, F_is = 0.238, reflected a severe lack of heterozygotes. High levels of F_ST and G_ST and low gene flow indicate considerable segregation among the C. gileadensis populations, which creates a barrier to gene migration. Our data suggest the need for conservation planning for C. gileadensis in order to avoid the species' forthcoming extinction. Efforts should be largely oriented around managing water consumption, prohibiting overcutting and overgrazing, and establishing appropriate seed banks.

Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States

Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.

Molecular Assessment of Genetic Diversity and Genetic Structure of Rhanterium epapposum Oliv. in Scarce Populations in Some Regions of Western Saudi Arabia

Rhanterium epapposum Oliv. is a perennial medicinal shrub growing mainly in desert habitats in the Arabian Peninsula. In western Saudi Arabia, the remaining few populations of this species are exposed to many threats, including overcutting, overgrazing, and recently, increasing human activities. These threats are predicted to be exacerbated by the advancement of aridification caused by climate change. The conservation and recovering of the diminished populations of R. epapposum necessitate measurement of their genetic diversity and genetic differentiation. To accomplish this objective, we tested 150 simple sequence repeat (SSR) primer pairs, with which 40 polymorphic loci were identified. These polymorphic loci were used to determine the population genetics of 540 plant accessions sampled from a total of 45 populations of R. epapposum located in 8 sites in western Saudi Arabia: Wadi Khurieba, Wadi Al Khamas, Gebel Al Twaal, Al Asaafer, Wadi ALHamda, Wadi Al Nassayeif, Wadi Qaraba, Wadi Kuliayah, and Wadi Dahban. Low levels of genetic diversity were found in all populations (the values of the PPL ranged between 52.5 and 15) along with a declined value of H_T (0.123) and a considerable inbreeding value (F = 0.942), which confirmed a noticeable shortage of heterozygotes. High genetic differentiation among the populations and a low value of gene flow are indicative of high isolation among the R. epapposum populations, which has caused a severe deficiency in gene migration. The data obtained herein inspire several recommendations for conservation and retrieval of the existing populations, including seed banks, restoration of diminished populations, and monitoring and prevention of cutting and grazing activities at threatened sites. All of these measures are urgently required to avoid imminent extinction.

Anthropogenic fragmentation increases risk of genetic decline in the threatened orchid Platanthera leucophaea

Protecting biodiversity requires an understanding of how anthropogenic changes impact the genetic processes associated with extinction risk. Studies of the genetic changes due to anthropogenic fragmentation have revealed conflicting results. This is likely due to the difficulty in isolating habitat loss and fragmentation, which can have opposing impacts on genetic parameters. The well-studied orchid, Platanthera leucophaea, provides a rich dataset to address this issue, allowing us to examine range-wide genetic changes. Midwestern and Northeastern United States. We sampled 35 populations of P. leucophaea that spanned the species' range and varied in patch composition, degree of patch isolation, and population size. From these populations we measured genetic parameters associated with increased extinction risk. Using this combined dataset, we modeled landscape variables and population metrics against genetic parameters to determine the best predictors of increased extinction risk. All genetic parameters were strongly associated with population size, while development and patch isolation showed an association with genetic diversity and genetic structure. Genetic diversity was lowest in populations with small census sizes, greater urbanization pressures (habitat loss), and small patch area. All populations showed moderate levels of inbreeding, regardless of size. Contrary to expectation, we found that critically small populations had negative inbreeding values, indicating non-random mating not typically observed in wild populations, which we attribute to selection for less inbred individuals. The once widespread orchid, Platanthera leucophaea, has suffered drastic declines and extant populations show changes in the genetic parameters associated with increased extinction risk, especially smaller populations. Due to the important correlation with risk and habitat loss, we advocate continued monitoring of population sizes by resource managers, while the critically small populations may need additional management to reverse genetic declines.

The effects of pollination, herbivory and autonomous selfing on the maintenance of flower colour variation in Silenelittorea

Intraspecific flower colour variation has been generally proposed to evolve as a result of selection driven by biotic or abiotic agents. In a polymorphic population of Silene littorea with pink- and white-flowered plants, we studied pollinators, analysed flower colour perception and tested for differences in pollinator visitation. We also experimentally analysed pollinator limitation in fruit and seed set, and the degree of autonomous selfing. The incidence of florivory and leaf herbivory was compared over 3-4 years. Silene littorea is mainly pollinated by bees and butterflies. Pollinators preferred pink flowers, which did not show pollinator limitation. On the contrary, white flowers showed pollinator limitation in fruit set. White-flowered plants had less floral display and higher levels of florivory than pink plants. Flower colour morphs of S. littorea can reproduce in the absence of pollinators by autonomous selfing, setting 20% and 12% of fruit and seeds in the pink morph and 27% and 20% in the white morph, respectively. Fruit set of white flowers produced by autonomous selfing did not differ from open-pollinated flowers. In conclusion, S. littorea is pollinated by insects of different orders that more frequently visit pink flowers, which is reflected in pollinator limitation of fruit set in white flowers. Moreover, this species has a mixed mating system in which both colour morphs can reproduce in the absence of pollinators by autonomous selfing, although white flowers mainly produce fruits by autogamy. We suggest that reproductive assurance by autonomous selfing helps to maintain flower colour polymorphism in this population.

Population viability analysis of small population: a case study for Asian elephant in China

Small populations are at risk of extinction from deterministic and stochastic factors. Less than 250 Asian elephants (Elephas maximus) remain in China, and are distributed in a few isolated areas; yet, population viability analyses of this endangered population have not been conducted. Here, the current genetic status of the Pu'Er-Mengyang Asian elephant populations in China was analyzed, and the risk of extinction was predicted over the next 500 years. Factors affecting the viability of this population were determined through simulations. The genetic diversity of the population was very low (mean allele number: 3.1; expected heterozygosity: 0.463), even though a recent population bottleneck was not detected. The effective population size was approximately 24.1 adult elephants. Enough adult breeding individuals exist to maintain population viability. VORTEX simulation model showed that this population would not go extinct in the next 500 years. However, illegal poaching and harvesting could negatively affect population size. A sensitivity analysis showed that the mean stochastic growth rate of the study population is sensitive to sex ratio, number of breeding females, mortality of females of different age classes, carrying capacity, and lethal equivalents. Based on our results, we suggest that action should be taken to alleviate inbreeding and any further loss of genetic diversity, by connecting fragmented elephant habitat or by translocating individual elephants. In addition, human-elephant conflict should be mitigated using various modern approaches, including crop guarding techniques, and by encouraging farmers to switch to crops and income sources not vulnerable to elephant raids.

Factors affecting the persistence of endangered Ganges River dolphins (Platanista gangetica gangetica)

The Ganges-Brahmaputra-Meghna and Karnaphuli (GBMK) River Basin in Nepal, India, and Bangladesh is among the world's most biodiverse river basins. However, human-induced habitat modification processes threaten the ecological structure of this river basin. Among the GBMK's diverse flora and fauna of this freshwater ecosystem, the endemic Ganges River dolphin (Platanista gangetica gangetica; GRD) is one of the most charismatic species in this freshwater ecosystem. Though a >50% population size reduction has occurred since 1957, researchers and decision-makers often overlook the persistence (or evolutionary potential) of this species in the highly fragmented GBMK. We define the evolutionary potential as the ability of species/populations to adapt in a changing environment by maintaining their genetic diversity. Here, we review how evolutionary trap mechanisms affect the dynamics and viability of the GRD (hereafter Ganges dolphin) populations after rapid declines in their population size and distribution. We detected six potential trap mechanisms that might affect the Ganges dolphin populations discretely or in combination: (a) habitat modification; (b) occurrence of finite and geographically restricted local populations; (c) ratio of effective to estimate population size; (d) increasing risk of inbreeding depression in genetically isolated groups; (e) at-risk behavioral attributes; and (f) direct fisheries-dolphin interactions. Because evolutionary traps appear most significant during low water season, they adversely affect demographic parameters, which reduce evolutionary potential. These traps have already caused local extirpation events; therefore, we recommend translocation among populations, including restoring and preserving essential habitats as immediate conservation strategies. Integrative evolutionary potential information based on demographic, genetic, and environmental data is still lacking. Thus, we identify gaps in the knowledge and suggest integrative approaches to understand the future of Ganges dolphins in South Asian waterways.

Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth

According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.

Reduced Genetic Diversity and Increased Dispersal in Guigna (Leopardus guigna) in Chilean Fragmented Landscapes

Landscape fragmentation is often a major cause of species extinction as it can affect a wide variety of ecological processes. The impact of fragmentation varies among species depending on many factors, including their life-history traits and dispersal abilities. Felids are one of the groups most threatened by fragmented landscapes because of their large home ranges, territorial behavior, and low population densities. Here, we model the impacts of habitat fragmentation on patterns of genetic diversity in the guigna (Leopardus guigna), a small felid that is closely associated with the heavily human-impacted temperate rainforests of southern South America. We assessed genetic variation in 1798 base pairs of mitochondrial DNA sequences, 15 microsatellite loci, and 2 sex chromosome genes and estimated genetic diversity, kinship, inbreeding, and dispersal in 38 individuals from landscapes with differing degrees of fragmentation on Chiloé Island in southern Chile. Increased fragmentation was associated with reduced genetic diversity, but not with increased kinship or inbreeding. However, in fragmented landscapes, there was a weaker negative correlation between pairwise kinship and geographic distance, suggesting increased dispersal distances. These results highlight the importance of biological corridors to maximize connectivity in fragmented landscapes and contribute to our understanding of the broader genetic consequences of habitat fragmentation, especially for forest-specialist carnivores.

Diversity of sexual systems within different lineages of the genus Silene

Species and populations can be categorized by their sexual systems, depending on the spatial distribution of female and male reproductive structures within and among plants. Although a high diversity of sexual systems exists in Silene, their relative frequency at the genus and infrageneric level is unknown. Here, we carried out an extensive literature search for direct or indirect descriptions of sexual systems in Silene species. We found descriptions of sexual systems for 98 Silene species, where 63 and 35 correspond to the phylogenetically supported subgenera Silene and Behenantha, respectively. Hermaphroditism was the commonest sexual system (58.2 %), followed by dioecy (14.3 %), gynodioecy (13.3 %) and gynodioecy-gynomonoecy (i.e. hermaphroditic, female and gynomonoecious plants coexisting in the same population; 12.2 %). The presence of these sexual systems in both subgenera suggests their multiple origins. In 17 species, the description of sexual systems varied, and in most cases these differences corresponded to variations within or among populations. Interestingly, the poorly studied gynodioecy-gynomonoecy sexual system showed similar frequency to dioecy and gynodioecy in both subgenera. In addition, the incidence of gynodioecy-gynomonoecy was analysed in the species of section Psammophilae (Silene littorea, S. psammitis, S. adscendens and S. cambessedesii), in a survey of 26 populations across the distribution area of the species. The four species showed gynomonoecy-gynodioecy in most populations. Hermaphrodites were the most frequent morph, with a low number of females and gynomonoecious plants in all populations. The frequency of sexual morphs varied significantly among the studied populations but not among species. Female plants generally produced smaller numbers of flowers than hermaphroditic or gynomonoecious plants, and the percentages of female flowers per population were low. All these findings suggest that the gynodioecious-gynomonoecious sexual system in section Psammophilae is closer to hermaphroditism or gynomonoecy than gynodioecy.

Splitting or lumping? A conservation dilemma exemplified by the critically endangered dama gazelle (Nanger dama)

Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions.

Nuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487-489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction.

Joint effects of population size and isolation on genetic erosion in fragmented populations: finding fragmentation thresholds for management

Size and isolation of local populations are main parameters of interest when assessing the genetic consequences of habitat fragmentation. However, their relative influence on the genetic erosion of local populations remains unclear. In this study, we first analysed how size and isolation of habitat patches influence the genetic variation of local populations of the Dupont's lark (Chersophilus duponti), an endangered songbird. An information-theoretic approach to model selection allowed us to address the importance of interactions between habitat variables, an aspect seldom considered in fragmentation studies, but which explained up to 65% of the variance in genetic parameters. Genetic diversity and inbreeding were influenced by the size of local populations depending on their degree of isolation, and genetic differentiation was positively related to isolation. We then identified a minimum local population of 19 male territories and a maximum distance of 30 km to the nearest population as thresholds from which genetic erosion becomes apparent. Our results alert on possibly misleading conclusions and suboptimal management recommendations when only additive effects are taken into account and encourage the use of most explanatory but easy-to-measure variables for the evaluation of genetic risks in conservation programmes.

Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology

There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines.

The roles of female and hermaphroditic flowers in the gynodioecious-gynomonoecious Silene littorea: insights into the phenology of sex expression

Some gynodioecious species have intermediate individuals that bear both female and hermaphroditic flowers. This phenomenon is known as a gynodioecious-gynomonoecious sexual system. Gender expression in such species has received little attention in the past, and the phenologies of male and female functions have also yet to be explored. In this study, we examined variations in gender patterns, their effects on female reproductive success and sex expression in depth throughout the flowering period in two populations. The studied populations of Silene littorea contained mostly gynomonoecious plants and the number of pure females was very low. The gynomonoecious plants showed high variability in the total proportion of female flowers. In addition, the proportion of female flowers in each plant varied widely across the flowering season. Although there was a trend towards maleness, our measures of functional gender suggested that most plants transmit their genes via both pollen and ovules. Fruit set and seed set were not significantly different among populations; in contrast, flower production significantly varied between the two populations - and among plants - with consequent variation in total seed production. Conversely, gender and sex expression were similar in both populations. Plants with higher phenotypic femaleness did not have higher fruit set, seed set or total female fecundity. The mating environment fluctuated little across the flowering period, but fluctuations were higher in the population with low flower production. We therefore conclude that the high proportion of gynomonoecious individuals in our studied populations of S. littorea may be advantageous for the species, providing the benefits of both hermaphroditic and female flowers.

Mating system shifts on the trailing edge

BACKGROUND

The trailing edges of species ranges are becoming a subject of increasing interest as the environment changes due to global warming. Trailing edge populations are likely to face extinction because of a decline in numbers and an inability to evolve new adaptations with sufficient speed. Discussions of character change in the trailing edge have focused on physiological, exomorphic and phenological traits. The mating pattern within populations has not been part of the discourse, in spite of the fact that the mating pattern may affect the ability of populations to respond to environmental change and to maintain their sizes. In this paper, the case is made that a substantial increase in self-fertilization rates may occur via plastic responses to stress.

SCOPE AND CONCLUSIONS

Small populations on the trailing edge are especially vulnerable to environmental change because of inadequate levels of cross-fertilization. Evidence is presented that a deficiency of cross-seed production is due to inadequate pollinator services and a paucity of self-incompatibility alleles within populations. Evidence also is presented that if plants are self-compatible, self-fertilization may compensate in part for this deficiency through a stress-induced increase in levels of self-compatibility and stress-induced alterations in floral morphology that elevate self-pollination. Whereas increased self-fertility may afford populations the time to adapt to their changing environments, it can be concluded that increased selfing is not a panacea for the ills of environmental change, because it will lead to substantial reductions in genetic diversity, which may render adaptation unlikely.

Pollen limitation and inbreeding depression in an 'old rare' bumblebee-pollinated grassland herb

Habitat fragmentation and reduction of population size have been found to negatively affect plant reproduction in 'new rare' species that were formerly common. This has been attributed primarily to effects of increased inbreeding but also to pollen limitation. In contrast, little is known about the reproduction of 'old rare' species that are naturally restricted to small and isolated habitats and thus may have developed strategies to cope with long-term isolation and small population size. Here we study the effects of pollen source and quantity on reproduction of the 'old rare' bumblebee-pollinated herb, Astragalus exscapus. In two populations of this species, we tested for pollen autodeposition, inbreeding depression and outbreeding depression. Caged plants were left unpollinated or were pollinated with pollen from the same plant, from the same population or from a distant population (50 km). Additionally, we tested for pollen limitation by pollen supplementation in four populations of different size and density. In the absence of pollinators, plants did not produce seed whereas self-pollinated plants did. This indicates a self-compatible breeding system dependent on insect pollination. Both self-pollination and, in one of the two populations, cross-pollination with pollen from plants from the distant population resulted in a lower number of seeds per flower than cross-pollination with pollen from plants from the resident population, indicating inbreeding and outbreeding depression. Pollen addition enhanced fruit set and number of seeds per flower in three of the four populations, indicating pollen limitation. The degree of pollen limitation was lowest in the smallest but densest population. Our results suggest that, similar to 'new rare' plant species, also 'old rare' species may be at risk of inbreeding depression and pollen limitation.

The stabilizing effect of intraspecific genetic variation on population dynamics in novel and ancestral habitats

Recent studies show that intraspecific genetic variation in asexual species may have large effects on community and ecosystem functions, increasing their stability, productivity, and species richness. However, major questions regarding its population-level impact remain empirically unanswered: (a) How does intraspecific genetic diversity affect the ecological characteristics of sexual species, in which recombination can alter the outcome of causal mechanisms such as selection and niche diversification? (b) Does genetic diversity increase population dynamic stability? (c) Is the impact of genetic diversity dependent on the selective environment? To answer these questions, I founded replicate flour beetle (Tribolium castaneum) populations with different degrees of ecologically relevant, heritable trait variation and monitored their dynamics for approximately eight generations. I show that population stability and persistence increased with greater genetic variation but that the stabilizing effect was independent of the selective habitat (different proportions of ancestral and novel resources). Alleles from a single founding strain underwent a selective sweep in the homogeneous ancestral habitat but not in a novel heterogeneous habitat. These results expand current understanding of the ecological impacts of genetic diversity by showing that genetically more diverse sexual populations persist longer and are more stable but that the selective environment determines the mechanistic basis of increased stability.