Population structure in the endangered Mauna Loa silversword, Argyroxiphium kauense (Asteraceae), and its bearing on reintroduction

Reintroduction of populations of endangered species is a challenging task, involving a number of environmental, demographic and genetic factors. Genetic parameters of interest include historical patterns of genetic structure and gene flow. Care must be taken during reintroduction to balance the contrasting risks of inbreeding and outbreeding depression. The Mauna Loa silversword, Argyroxiphium kauense, has experienced a severe decline in population size and distribution in the recent past. Currently, three populations with a total of fewer than 1000 individuals remain. We measured genetic variation within and among the remnant populations using seven microsatellite loci. We found significant genetic variation remaining within all populations, probably related to the recent nature of the population impact, the longevity of the plants, and their apparent self-incompatibility. We also found significant genetic differentiation among the populations, reinforcing previous observations of ecological and morphological differentiation. With respect to reintroduction, the results suggest that, in the absence of additional data to the contrary, inbreeding depression may not be a substantial risk as long as propagules for the founding of new populations are adequately sampled from within each source population before additional inbreeding takes place. The results further suggest that if mixing of propagules from different source populations is not required to increase within-population genetic variation in the reintroduced populations, it may best be avoided.     

Molecular genetic variation following a population crash in the endangered Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae)

The endangered Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), has experienced a severe decline in distribution and abundance because of predation by alien ungulates. The small remnant natural population on the Mauna Kea volcano contains only 46 individuals. By contrast, the Haleakala silversword, A. sandwicense ssp. macrocephalum, consists of a large, vigorous population exceeding 60 000 individuals. Molecular genetic variation in the two populations was assessed using random amplified polymorphic DNA (RAPD) loci. Despite its severe crash in size, the Mauna Kea population did not differ significantly from the Haleakala population in the number of detectably polymorphic loci or in heterozygosity. The lack of substantial reduction in genetic variation, at least as measured with RAPD loci, suggests that the Mauna Kea population may not yet have gone through multiple generations at very small size.     

Genetic analysis of a documented population bottleneck: introduced Bennett's wallabies (Macropus rufogriseus rufogriseus) in New Zealand

Few bottlenecks of wild populations are sufficiently well-documented to constitute models for testing theories about the impact of bottlenecks on genetic variation, and subsequent population persistence. Relevant details of the Bennett's wallaby (Macropus rufogriseus rufogriseus) introduction into New Zealand were recorded (founder number, source and approximate bottleneck duration) and suggest this may provide a rare opportunity to examine the efficacy of tests designed to detect recent bottlenecks in wild populations. We first assessed the accuracy of historic accounts of the introduction using genetic diversity detected in mitochondrial DNA (mtDNA) and at five microsatellite loci. Phylogenetic analyses of mtDNA D-loop sequence haplotypes were consistent with the reported origin of the founders as Tasmania, rather than one of the Bass Strait islands in which Bennett's wallabies are also found. Microsatellite allele frequencies from the Tasmanian source population were then used to seed bottleneck simulations encompassing varying sizes and numbers of generations, in order to assess the severity of bottleneck consistent with diversity observed in the New Zealand population. The results suggested that the founder number was unlikely to have been as small as the three animals suggested by the account of the introduction. Nonetheless, the bottleneck was probably severe; in the range of three to five pairs of wallabies for one to three generations. It resulted in significantly reduced levels of allelic diversity and heterozygosity relative to the source population. This bottleneck is only detectable under the infinite allele model (IAM) and not under the stepwise mutation model (SMM) or the two-phase model (TPM), and possible explanations for this are discussed.     

Increase of heterozygosity in a growing population of lesser kestrels

The lesser kestrel (Falco naumanni) suffered a sharp population decline over much of its European distribution range in the middle of the twentieth century. Still declining in some areas, the species has recently experienced a notable population recovery in certain regions. We examined the genetic diversity variation in a growing population of lesser kestrels from Central Spain over a 6-year period (2000-2005). The population studied showed a rapid demographic expansion, increasing in the number of both breeding pairs and colonies. Annual average heterozygosity and allelic diversity increased and genetic similarity between potential mates decreased over the study period. Several immigrants regularly arrived in the study area and introduced new alleles into the local population, pointing to immigration as the main cause contributing to the observed genetic recovery.     

The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): a microsatellite analysis

The reintroduction of wild boar from central Europe after World War II has contributed substantially to the range expansion of this species in Italy, where indiscriminate hunting in earlier times resulted in extreme demographic reduction. However, the genetic impact of such processes is not well-understood. In this study, 105 individuals from Italian and Hungarian wild boar populations were characterized for nine autosomal microsatellite loci. The Hungarian samples, and two central Italian samples from protected areas (parks) where reintroduction is not documented, were assumed to be representative of the genetic composition of the source and the target populations in the reintroduction process, respectively. Animals hunted in the wild in the Florence area of Tuscany (Italy) were then studied to identify the effects of reintroduction. The results we obtained can be summarized as follows: (i) none of the populations analysed shows genetic evidence of demographic decline; (ii) the three parental populations from Italy and Hungary are genetically distinct; however, the low level of divergence appears in conflict with the naming of the Italian and the European subspecies (Sus scrofa majori and Sus scrofa scrofa, respectively); in addition, the Italian groups appear to be as divergent from each other as they are from the Hungarian population; (iii) most of the individuals hunted near Florence are genetically intermediate between the parental groups, suggesting that hybridization has occurred in this area, the average introgression of Hungarian genotypes is 13%, but approximately 45% of the genetic pool of these individuals can not be directly attributed to any of the parental populations we analysed; (iv) analysis of microsatellite loci, though in a limited number, is an important tool for estimating the genetic effect of reintroduction in the wild boar, and therefore for the development of conservation and management strategies for this species.     

Low genetic variability of the koala Phascolarctos cinereus in south-eastern Australia following a severe population bottleneck

Genotyping of koalas at CA-repeat microsatellite loci has revealed significant differences in the levels of allelic diversity ( A ) and expected heterozygosity ( H¯ _E) between populations from north-eastern and south-eastern Australia. In the 10 populations studied, allelic diversity ranged from 8.0 in the Nowendoc population to 1.7 in the Kangaroo Is. population, and values of H¯ _E ranged from 0.831 in the Nowendoc population to 0.331 in the Kangaroo Is. population. Data from pooled populations revealed koalas from the north-eastern region had significantly higher levels of allelic diversity ( A = 11.5 ± 1.4) than those from south-eastern Australia ( A = 5.3 ± 1.0). Furthermore significantly higher heterozygosity levels were found in the north-eastern ( H¯ _E= 0.851) vs. the south-eastern ( H¯ _E= 0.436) regions of Australia. Following a near-extinction bottleneck in the 1920s, mainland Victorian and Kangaroo Is. koalas have been involved in an extensive program of relocations. The source populations of the relocated animals were islands in Westernport Bay, which were founded by very few individuals in the late 1800s and early 1900s. The significantly lower levels of variation between south-eastern Australian populations suggests that human intervention has had a severe effect on levels of genetic diversity in this region, and this may have long-term genetic consequences.     

Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki)

The genetic population structure of coastal cutthroat trout ( Oncorhynchus clarki clarki ) in Washington state was investigated by analysis of variation in allele frequencies at six highly polymorphic microsatellite loci for 13 anadromous populations, along with one outgroup population from the Yellowstone subspecies ( O. clarki bouvieri) (mean heterozygosity = 67%; average number of alleles per locus = 24). Tests for genetic differentiation revealed highly significant differences in genotypic frequencies for pairwise comparisons between all populations within geographical regions and overall population subdivision was substantial ( F _ST = 0.121, R _ST = 0.093), with 44.6% and 55.4% of the among-population diversity being attributable to differences between streams ( F _SR = 0.054) and between regions ( F _RT = 0.067), respectively. Analysis of genetic distances and geographical distances did not support a simple model of isolation by distance for these populations. With one exception, neighbour-joining dendrograms from the Cavalli-Sforza and Edwards' chord distances and maximum likelihood algorithms clustered populations by physiogeographic region, although overall bootstrap support was relatively low (53%). Our results suggest that coastal cutthroat trout populations are ultimately structured genetically at the level of individual streams. It appears that the dynamic balance between gene flow and genetic drift in the subspecies favours a high degree of genetic differentiation and population subdivision with the simultaneous maintenance of high heterozygosity levels within local populations. Results are discussed in terms of coastal cutthroat trout ecology along with implications for the designation of evolutionarily significant units pursuant to the US Endangered Species Act of 1973 and analogous conservation units.     

Disentangling the impact of demographic factors on population differentiation of an endangered freshwater crayfish (Austropotamobius pallipes) using population density and microsatellite data

1. Habitat fragmentation of stream ecosystems often results in decreased connectivity between populations and lower population sizes. Hence, understanding how habitat fragmentation affects genetic erosion is important for the preservation of freshwater biodiversity, in particular, as small populations suffer from loss of genetic diversity through genetic drift and loss of fitness because of inbreeding, increasing the risk of extinction. 2. Here, we assess the impact of demographic factors on population differentiation in the endangered freshwater crayfish Austropotamobius pallipes by analysing population genetic structure, estimating effective population sizes and comparing levels of polymorphism at five microsatellite loci with density estimates of 10 populations within a small French catchment that has become progressively confined to headwaters over the last six decades. 3. Levels of expected heterozygosity and allelic richness per population were relatively low (0.214–0.396 and 1.6–2.6, respectively). We found strong genetic differentiation between these geographically close populations (F_ST = 0.283), with weak statistical evidence for a pattern of isolation by distance. Estimates of effective population size were low (<150) in most populations, but potentially reached several thousands in three populations. 4. Population density and allelic richness were strongly positively correlated. A robust relationship between population density and heterozygosity values was also noted, but only after discarding two populations for which significant genetic signatures of a recent bottleneck were found; these two populations displayed high expected heterozygosity compared with a very low density. Populations with the highest densities of individuals had the highest effective population size estimates and vice versa. 5. Our results clearly show the importance of demographic factors and genetic drift on A. pallipes populations. Furthermore, analysis of genetic and population density data is a pragmatic and efficient approach to corroborate inferences from genetic data and can be particularly useful in the identification of populations experiencing a bottleneck and therefore in conservation genetics studies aiming at identifying priority populations for conservation.     

Genetic consequences of a single-founder population bottleneck in Trifolium amoenum (Fabaceae)

We investigated the genetic consequences of a single-founder bottleneck in a population of showy Indian clover (Trifolium amoenum), a species presumed to be extinct until rediscovered near Occidental, California, in 1993. Electrophoretic variation was evaluated in the bottlenecked population and in a larger population (Dillon Beach) discovered during the course of this study, as well as in populations of two closely related species, T. albopurpureum var. dichotomum and T. macraei. We found a surprisingly high amount of polymorphism in the single-founder T. amoenum population from Occidental (15% of loci polymorphic; an average of 1.1 alleles per locus). However, this represents a 53% reduction in number of polymorphic loci and a 20% reduction in average number of alleles per locus compared to three Trifolium populations with putatively similar mating systems (the Dillon Beach T. amoenum population and both populations of T. albopurpureum var. dichotomum). Expanding the genetic base of the Occidental T. amoenum population is a priority due to concerns about loss of evolutionary potential and the possibility of deleterious effects associated with inbreeding. However, using seed from the Dillon Beach T. amoenum population may not be beneficial due to distinct, presumably adaptive differences between plants from the two populations and concerns about outbreeding depression.     

Relationship of Hypochaeris salzmanniana (Asteraceae, Lactuceae), an endangered species of the Iberian Peninsula, to H. radicata and H. glabra and biogeographical implications

Hypochaeris salzmanniana DC. (Asteraceae, Lactuceae) is an endangered species on the Iberian Peninsula, known from only eight coastal populations. Most authors have treated it as a variety, subspecies or simply as a synonym of H. glabra L. On the basis of morphological and cytological characters, Talavera recently separated H. salzmanniana (2n = 8) from H. glabra (2n = 10). Material of H. salzmanniana, H. glabra and H. radicata was collected from Spain, Italy, Sicily and Tunisia in order to assess taxonomic status and population relationships. Amplified Fragment Length Polymorphism (AFLP) analysis revealed three well-differentiated species. A close relationship between H. salzmanniana and H. radicata is also confirmed by AFLP analysis and chromosome number (2n = 8), morphology, and rDNA localization (FISH, fluorescence in situ hybridization). Hypochaeris salzmanniana and H. radicata share three fixed diagnostic AFLP fragments out of 348 fragments scored. The population structure of H. salzmanniana reveals distinct groups in southern Spain that are separated geographically. High differentiation among a western (Conil to Zahara), an intermediate (Punta Paloma and Los Algarbes) and an eastern (Algeciras and La Línea) group may reflect ancient separation. Population sizes and genetic compatibility differ greatly among populations and can be used to explain levels of within-population genetic diversity, together with recent documented loss of habitats resulting from tourist developments. Population structures of H. radicata and H. glabra show a similar geographical patterning: strongly differentiated populations from the Betic Cordillera and from the Iberian Massif, which are separated at present by the Guadalquivir river. Geological events at the end of the Tertiary (Tortonian–Messinian Miocene) might help explain patterns of differentiation in these three species of sect. Hypochaeris. © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 146 , 79–95.     

bottlesim: a bottleneck simulation program for long‐lived species with overlapping generations

Population bottlenecks reduce genetic diversity and thus cause great concern in conservation biology. Previous theoretical studies often assume discrete generations in projecting declines in genetic diversity caused by bottlenecks. This assumption creates complexities when applying the models to long‐lived species with overlapping generations. bottlesim is a program for simulating bottlenecks to estimate the impact on genetic diversity; the novelties include an overlapping‐generation model, a wide range of reproductive systems, and flexible population size settings. With these features, bottlesim will be a useful tool for estimating the genetic consequences of bottlenecks, evaluating conservation plans, and performing power analysis.     

Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications

The African antelope Addax nasomaculatus is a rare mammal at high risk of extinction, with no more than 300 individuals in the wild and 1,700 captive animals distributed in zoos around the world. In this work, we combine genetic data and genealogical information to assess the structure and genetic diversity of a captive population located at Parque Lecocq Zoo (N=27), originated from only two founders. We amplified 39 microsatellites previously described in other Artiodactyls but new to this species. Seventeen markers were polymorphic, with 2–4 alleles per locus (mean=2.71). Mean expected heterozygosity (He) per locus was between 0.050 (marker ETH3) and 0.650 (marker D5S2), with a global He of 0.43. The mean inbreeding coefficient of the population computed from pedigree records of all registered individuals (N=53) was 0.222. The mean coancestry of the population was 0.298 and F_IS index was ?0.108. These results reflect the importance of an adequate breeding management on a severely bottlenecked captive population, which would benefit by the incorporation of unrelated individuals. Thanks to the successful amplification of a large number of microsatellites commonly used in domestic bovids, this study will provide useful information for the management of this population and serve as future reference for similar studies in other captive populations of this species. Zoo Biol 30:399–411, 2011. © 2010 Wiley‐Liss, Inc.     

Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae)

Habitat fragmentation may severely affect survival of social insect populations as the number of nests per population, not the number of individuals, represents population size, hence they may be particularly prone to loss of genetic diversity. Erosion of genetic diversity may be particularly significant among social Hymenoptera such as bumblebees (Bombus spp.), as this group may be susceptible to diploid male production, a suggested direct cost of inbreeding. Here, for the first time, we assess genetic diversity and population structuring of a threatened bumblebee species (Bombus sylvarum) which exists in highly fragmented habitat (rather than oceanic) islands. Effective population sizes, estimated from identified sisterhoods, were very low (range 21-72) suggesting that isolated populations will be vulnerable to loss of genetic variation through drift. Evidence of significant genetic structuring between populations (theta = 0.084) was found, but evidence of a bottleneck was detected in only one population. Comparison across highly fragmented UK populations and a continental population (where this species is more widespread) revealed significant differences in allelic richness attributable to a high degree of genetic diversity in the continental population. While not directly related to population size, this is perhaps explained by the high degree of isolation between UK populations relative to continental populations. We suggest that populations now existing on isolated habitat islands were probably linked by stepping-stone populations prior to recent habitat loss.     

Genetic structure of the vairone Telestes souffia in the eastern part of Lake Constance, central Europe

Examination of the genetic structure of the vairone Telestes souffia based on 10 nuclear markers (microsatellites) revealed little-to-moderate genetic differentiation between geographically adjacent populations in the eastern part of Lake Constance in central Europe. Results emphasize the critically endangered status of this freshwater fish in the upper Rhine River system.     

Extinction,reintroduction, and restoration of a lizard meta‐population equilibrium in the missouri ozarks

In this issue of Molecular Ecology, Neuwald & Templeton (2013) report on a 22‐year study of natural populations of Collared Lizards (Crotaphytus collaris) that evolved on isolated on rock outcrops (‘glades’) in the Ozark Mountains in eastern Missouri. This ecosystem was originally maintained by frequent fires that kept the forest understory open, but fire‐suppression was adopted as official policy in about 1945, which led to a loss of native biodiversity, including local extinctions of some lizard populations. Policies aimed at restoring biodiversity included controlled burns and re‐introductions of lizards to some glades, which began in 1984. Populations were monitored from 1984–2006, and demographic and genetic data collected from 1 679 lizards were used to documents shifts in meta‐population dynamics over four distinct phases of lizard recovery: 1–an initial translocation of lizards drawn from the same source populations onto three glades that were likely part of one meta‐population; 2–a period of isolation and genetic drift associated with the absence of fires; 3–a period of rapid colonization and population increase following restoration of fire; and 4–stabilization of the meta‐population under regular prescribed burning. This study system thus provides a rare opportunity to characterize the dynamics of a landscape‐scale management strategy on the restoration of the meta‐population of a reintroduced species; long‐term case studies of the extinction, founding, increase, and stabilization of a well‐defined meta‐population, based on both demographic and population genetic data, are rare in the conservation, ecological, and evolutionary literature.     

Genetic characterization of Bhutanese native chickens based on an analysis of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), domestic Southeast Asian and commercial chicken lines (Gallus gallus domesticus)

The genetic diversity of Bhutanese chickens needs to be understood in order to develop a suitable conservation strategy for these birds in Bhutan. In this, work, we used microsatellite markers to examine the genetic diversity of Bhutanese chickens. Four Bhutanese chicken varieties (Black plumage, Frizzle, Naked neck and Red Junglefowl-like, corresponding to Yuebjha Narp, Phulom, Khuilay and Seim, respectively), two subspecies of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), two varieties of Thai native chickens (Pradhu Hang Dam and Chee; Gallus gallus domesticus) representing the Southeast Asian domestic chicken, and two commercial lines (Broiler and Single Comb White Leghorn) were genotyped with 18 microsatellites that included 16 loci recommended by the FAO/ISAG for investigations of genetic variability in chickens. All loci were polymorphic, with the number of alleles ranging from six (MCW0111) to 23 (MCW0183). Substantial genetic variation was observed in all populations, with the Bhutanese native chicken Yuebjha Narp (Black plumage chicken) showing the lowest genetic variability. Despite extensive intrapopulation variation, the genetic differentiation among 10 populations was moderate. A neighbor-joining tree revealed the genetic relationships involved while principal component analysis showed that Bhutanese native chickens should be given priority in conservation efforts because of their genetic distinctiveness. Chee chickens are especially valuable as a reservoir of predomestic diversity, as indicated by their greater genetic variation and their position in the phylogenetic tree.