Isolation and characterization of microsatellite loci in Shortia rotundifolia (Diapensiaceae), an endangered relict plant on the Ryukyu Islands and Taiwan

Ten microsatellite loci were isolated and characterized for Shortia rotundifolia, a relict temperate plant on the subtropical Ryukyu Islands and Taiwan. The number of alleles ranged from 2 to 21. The expected (H _E) and observed (H _O) heterozygosities were 0.027–0.877 and 0.027–0.622, respectively, from 74 individuals on Iriomotejima Island of Ryukyus. One locus exhibited significantly fewer heterozygotes than expected under Hardy–Weinberg equilibrium (P < 0.05). These primers amplifying microsatellites in this species may provide a useful tool for population genetics to establish conservation strategy.     

Genetic and clonal diversity in Korean populations ofVitex rotundifolia (Verbenaceae)

Vitex rotundifolia L.f. is a woody perennial and has sexual and asexual modes of reproduction. Allozyme study was conducted on 550 plants in 13 Korean populations. The levels of genetic variability and divergence within and among populations, respectively, are considerably lower and higher than the mean values for woody plants with similar life history tralts. Mean percentage of polymorphic loci (P _P), mean number of alleles per locus (A _P), and mean genetic diversity (He _P) within populations ofV. rotundifolia were: 16.7%, 1.21, and 0.047. On average, about 79% of the total variation inV. rotundifolia was common to all populations (meanG _ST=0.208). In addition, significant differences in allele frequencies among populations were found in all polymorphic loci examined (P<0.001). On the other hand, levels of genotypic diversity within and among populations were moderate. About 44% (18/41) of multilocus genotypes were “local genotypes” (genotypes occurring in only one population), whereas only one “widespread genotype” (genotypes occurring in more than 75% of the populations) were detected. The mean number of multilocus genotypes per population (G) and mean genotypic diversity index (D _G) were 8.4 and 0.74, respectively. Most common multilocus genotypes found in populations were homozygous for five polymorphic loci. The abundance of ramets of these genets is responsible for the low levels of expected heterozygosity within populations. The results indicate that clonal reproduction may act as an enhancer of genetic drift by reducing effective size of local populations ofV. rotundifolia.     

Genetic structure and functioning of alien ship rat populations from a Corsican micro-insular complex

The detrimental effects of the introduced ship rat on bird species on the Lavezzi Mediterranean archipelago has led to the decision to eradicate the rodent from the main island, Lavezzu (73 ha), as well as from several neighbouring islets. A genetic study using eight microsatellite markers has revealed some of the dynamics of this rat population. First, it has been shown that the rat population was genetically stable (no departure from Hardy-Weinberg equilibrium and no linkage disequilibrium) and as suggested by paleontological data, established for a long time. This information is encouraging in term of viability of the eradication campaign in the long term, even if rare immigration events cannot be excluded. Second, this study shows that rats are likely to swim between the main island and the islets quite regularly since no clear genetic differentiation has been detected between them. This result is quite surprising since the ship rat is not known for its swimming abilities. Third, a cryptic genetic structure has been detected on the main island, with the north peninsula differentiated from the rest. This result correlates the observation of particular predation behaviours only observed in this part of the island. Finally, evolutionary hypotheses (e.g., dispersal limitation, emergence of family groups, local adaptation) are discussed to explain the genetic patterns observed and the population functioning inferred. These results should be of particular interest to wildlife managers concerned with rat eradications, and also provide clear insights into the study of other biological invasions.     

Seed migration and the structure of plant populations

Summary We use chemical typing to compare sub-populations of thyme (Thymus vulgaris L.) growing in the channels of several ravines where seed migration is expected from sub-populations on the plateu to associated basin subpopulations. The results indicate that seed migration does occur. However, there is little effective gene flow between sub-populations. We discuss the implications of restricted gene flow for population dynamics and structure.     

Genetic diversity and population genetic structure of six dromedary camel (camelus dromedarius) populations in Saudi Arabia

Camels are an integral and essential component of the Saudi Arabian heritage. The genetic diversity and population genetic structure of dromedary camels are poorly documented in Saudi Arabia so this study was carried out to investigate the genetic diversity of both local and exotic camel breeds. The genetic diversity was evaluated within and among camel populations using 21 microsatellite loci. Hair and blood samples were collected from 296 unrelated animals representing 4 different local breeds, namely Majaheem (MG), Maghateer (MJ), Sofr (SO), and Shaul (SH), and two exotic breeds namely Sawahli (SL) and Somali (SU). Nineteen out of 21 microsatellite loci generated multi-locus fingerprints for the studied camel individuals, with an average of 13.3 alleles per locus. Based on the genetic analyses, the camels were divided into two groups: one contained the Saudi indigenous populations (MG, MJ, SH and SO) and the other contained the non-Saudi ones (SU and SL). There was very little gene flow occurring between the two groups. The African origin of SU and SL breeds may explain their close genetic relationship. It is anticipated that the genetic diversity assessment is important to preserve local camel genetic resources and develop future breeding programs to improve camel productivity.     

Genetic diversity and fine-scale genetic structure in Hancornia speciosa Gomes (Apocynaceae)

We studied the genetic diversity and spatial genetic structure (SGS) of adult and juvenile individuals in a population of Hancornia speciosa in Central-West Brazil. For this, we sampled and mapped 113 adults and 100 juveniles in an area of 2.5 ha. Genomic DNA was obtained from leaves and seven microsatellite loci were used to genotype all individuals. The studied population showed high genetic diversity (H_e) but with significant inbreeding (f) for both life stages most likely due to biparental inbreeding. Spatial genetic structure was weak for both life stages and the values of S_P were low and neighborhoods (Nb) was high for both generations showing a potential long-distance gene dispersal.     

Genetic diversity and genetic structure of Northern Goshawk (Accipiter gentilis) populations in eastern Japan and Central Asia

Japanese goshawk was classified as a vulnerable species in the Red Data Book. There have been possibilities of a decrease of genetic diversity accompanied by habitat loss and genetic pollution due to hybridization with escaping imported goshawks. In this paper, genetic diversity, gene flow and conservation of Northern Goshawk (Accipiter gentilis) in Japan are discussed and compared with that in Central Asia. We used 11 newly developed microsatellite markers and also adopted six previously published markers. Genetic diversity was shown to be maintained with 0.58 as mean heterozygosity and 3.95 as mean allelic richness. The degree of genetic differentiation across all populations was low (Nei’s genetic differentiation index = 0.036, Wright’s genetic differentiation index = 0.039), possibly due to gene flow via adjacent regions (average number of migrants = 4.26; 0.68–20.30). However, it is possible that slight differentiation resulted from the short divergence time and/or inflow of escaping imported individuals. We recommend that goshawks in eastern Japan should be managed as a single unit. They do not appear to be under threat genetically at present, but there is the potential for rapid loss of genetic diversity. For future conservation, investigations of dispersal routes and actual conditions of gene flow are also recommended. To prevent further inflow of escaping goshawks into natural populations, it is desirable to reduce importation of goshawks and to enact a regulation obliging purchasers to register imported goshawks. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogeography of island canary (Serinus canaria) populations

Island canaries (Serinus canaria) are characterised as a species living exclusively on North Atlantic islands, mainly on the Azores, Madeira and Canary Islands. Although they are very common in their habitats, their behaviour and breeding system has only recently been studied systematically. To advance the understanding of their ecology and to see if the rather isolated archipelagos are already promoting a genetic differentiation, we investigated their phylogeographic relationship as revealed by mtDNA sequences of the cytochrome b gene and investigated whether this measure corresponds to morphological characteristics within the islands. Genetic distances were very low throughout the distribution range of the species. Although the variation of genetic distances within the population of Pico (Azores) was larger than that on Madeira and Canary Islands, the genetic distances between island populations were very low throughout which prevented a clear phylogeographic differentiation. Moreover, morphological measurements did not reveal a consistent pattern to reliably separate the populations, although the measures of beak length and body weight revealed a clear island-specific differentiation. These data lead to the assumption that the colonisation of the Atlantic islands by the canaries occurred very recently, while there is no persisting gene flow between the populations.     

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.     

Genetic structure among and within populations of the serpentine endemic Heteropappus hispidus ssp. leptocladus (Compositae)

Heteropappus hispidus ssp. leptocladus is an edaphic endemic taxon that is confined to serpentine and limestone-derived soils and is allopatrically distributed in three regions of western Japan. In this study, we attempted to detect genomic signatures of seven H. hispidus ssp. leptocladus populations along with eight other subspecies populations using eight nuclear microsatellite loci. The Mantel test supported an isolation by distance model across all H. hispidus populations, thus implying the possibility of parallel evolution for each subspecies. Results from AMOVA recognized relatively larger differentiations in geographic distribution compared to intraspecific taxonomy. Relationships indicated by neighbor-joining phylogenetic tree analysis and population structure generally did not reflect an intraspecific taxonomy. Populations from limestone-derived soil harbored a homogeneous genetic structure with neighboring populations from serpentine-derived soils. These results suggest that the edaphic ecotype may have derived allopatrically while a lack of edaphic constraint existed between serpentine and limestone soils.     

Low levels of allozyme differentiation betweenPyxidanthera (pyxie-moss) taxa (Diapensiaceae)

TwoPyxidanthera morphs of questionable taxonomic rank are described in the eastern United States. We analyzed leaf samples from ninePyxidanthera populations (four of each morph and one with intermediate morphology) for 13 allozyme loci. Our results do not support differentiation of the two morphs at the species level. Mean genetic identity among populations was high ( = 0.97), and typical of that found for conspecific populations. The proportion of total genetic diversity found among populations was low (G_ST = 0.079). Several low frequency alleles were confined to each of the morphs, being found in some of the populations of each morph, but not all.     

Genetic structure of wild populations of the endangered Desert Pupfish complex (Cyprinodontidae: Cyprinodon)

Data from 10 microsatellite DNA loci were used to describe the genetic structure of the two extant species (Cyprinodon macularius and C. eremus) of the endangered Desert Pupfish complex of southwestern United States and northwestern Mexico. Variation at microsatellite loci was significantly correlated (Mantel test) with that of previous mtDNA results, both for the complex and for the relatively wide-ranging C. macularius alone. Both species showed unusually high levels of microsatellite diversity for non-marine fish (H _e = 0.84–0.93; A_R = 11.9–17.0). There was evidence (R _ST > F _ST) that the two extant populations of C. eremus have been isolated sufficiently long for mutation to contribute significantly to genetic divergence, whereas divergence among the nine assayed populations of C. macularius could be attributed to genetic drift alone. Correspondingly, 10% of the diversity in C. eremus was attributable to differences between the two populations, whereas, for C. macularius, only 2.7% was attributable to among-population variation. Within C. macularius, a small (0.8%), but statistically significant, portion was attributable to differences between populations in the Salton Sea area and those on the lower Colorado River delta. The two populations of C. eremus and five groups of populations of C. macularius are recommended as management units for conservation genetics management of the two species.     

Spatial genetic structure within two populations of a self-incompatible perennial,Chionographis japonica var.japonica (Liliaceae)

Intrapopulational spatial genetic structure was examined in two populations ofChionographis japonica var.japonica, a self-incompatible perennial, by spatial autocorrelation analysis of enzyme polymorphism. Although most spatial autocorrelation indices (Moran'sI) in the shortes distance class were significantly positive, most in the other distance classes did not significantly deviate from the values expected from random distributions of genotypes in both populations. This contrasts with a spatial genetic pattern previously reported for a population of the predominantly selfing congener,C. japonica var.kurohimensis, indicating that pollen-mediated gene flow highly impedes genetic substructuring within populations of outcrossingC. japonica var.japonica. Genetic similarity in very proximate distance found in outcrossingC. japonica var.japonica is probably due to restricted dispersal of seeds.     

The island syndrome in isolated populations of a tropical forest rodent

I examined population traits of eight isolated populations of a tropical forest rodent (Proechimys semispinosus, the Central American spiny rat) for 1 year in central Panamá. Populations were sampled by monthly live-trapping, and seven traits (density, population growth rate, adult survival, reproductive effort, age structure, sex ratio, and body mass) were compared among populations. I also compared results with published data from nearby mainland populations. Each isolated population showed characteristics typical of island populations when compared with mainland populations, including higher and more stable densities, reduced reproductive effort, and greater body mass. Densities were the highest yet recorded for this species, and biomass of these island populations was among the highest of any tropical rodent yet studied. Population traits varied not only between island and mainland populations but also among island populations. P. semispinosus have traits that allow individuals in a population to rapidly respond to temporal changes in habitat quality or resource abundance. These traits include a high reproductive rate and an ability to adjust reproductive effort to changes in density. P. semispinosus are therefore able to quickly reach and maintain high densities under favorable conditions, thereby allowing close tracking of temporally and spatially varying resources. This flexibility is predicted for habitat generalists and presumably promotes abundance and persistence in temporally and spatially heterogeneous environments. P. semispinosus, often the most abundant and widely distributed species of rodent in forests throughout their geographic range, therefore have traits that are similar to those of generalist rodents in temperate forests.     

Microsatellite markers reveal spatial genetic structure of Tetranychus urticae (Acari: Tetranychidae) populations along a latitudinal gradient in Europe

The genetic structure of populations of the two-spotted spider mite Tetranychus urticae was investigated along a south–north European transect spanning from southern France to The Netherlands. Mites were collected on Urtica dioica in 6 sampling zones. Microsatellite variation at 5 loci revealed considerable genetic variation with an average heterozygozity of 0.49. Significant heterozygote deficiency was found in 7 populations out of the 18 samples analyzed and one of them was completely monomorphic. Tetranychus urticae populations show some level of genetic structuring. First, genetic differentiation between localities (F _ST estimates) was significant for all comparisons. Second, the analysis of molecular variance, AMOVA, indicates that there is an effect, albeit low (9%), of the locality in accounting for allele frequency variance. Geographic distance emerges as a factor responsible for this genetic structure. The results are discussed in relation to the biological features of the species and the known patterns of migration. Related agronomical issues are addressed.     

Genetic structure of Halotydeus destructor and Penthaleus major populations in Victoria (Acari: Penthaleidae)

The redlegged earth mite (Halotydeus destructor) and the blue oat mite (Penthaleus major) are major pests of pastures and crops in southern Australia. Reproductive modes, migration rates and levels of differentiation between populations were investigated using allozyme electrophoresis. Collections were made throughout Victoria and a sample was also obtained from Western Australia. Three enzyme loci were polymorphic in H. destructor (Mdh-1, Mdh-2 and Idh). Genotype frequencies of these loci did not differ between phenotypic males and females, providing no evidence for haplodiploidy. Allele frequencies were in Hardy-Weinberg equilibrium, indicating that H. destructor is diploid and sexual. This was confirmed via crosses between males and females. Allele frequencies differed between Victorian sites, although F statistics indicated little differentiation over all loci. A sample from Western Australia did not differ in allele frequencies from the Victorian sites. Four polymorphic loci were found in P. major (Mdh-1, Mdh-2, Idh and Gpi). Only a few multilocus genotypes occurred in a sample, indicating that P. major is parthenogenic. No male P. major were found in this study. A number of colour morphs were also identified and a genetic association between genital plate colour and clonal type was found in one population of P. major. Two different body colour morphs were associated with different clonal types.     

Influence of age structure of plant populations on damping-off epidemics

Summary Germination synchrony may facilitate damping-off epidemics by creating a high density of uniformly susceptible individuals. We tested the hypothesis that synchronous germination causes increased seed and seedling mortality from damping-off in two legume species attacked by the fungal pathogen, Pythium aphanidermatum. Glycine max exhibited rapid, synchronous germination compared to its progenitor, G. soja, and suffered greater mortality from both pre-and postemergent damping-off in controlled environment experiments. However, when mixed-aged populations of G. max were created experimentally by staggering planting times, a significant increase in damping-off mortality occurred. In G. soja, which typically has mixed-aged populations due to asynchronous germination, experimental populations with an even-aged distribution also suffered increased damping-off mortality. Hence, the relationship between population age structure and damping-off mortality was species-specific. We propose that species differences in the duration of individual seedling susceptibility to disbase interact with population age structure to control the cutcome of damping-off epidemics.     

<Emphasis Type="Italic">Vanderhorstia papilio</Emphasis>, a new shrimp-associated goby from the Ryukyu Islands,Japan (Perciformes: Gobiidae: Gobiinae), with comments on the limits of the genus

A new gobiid fish, Vanderhorstia papilio, is described based on a single specimen (40.9mm SL) captured from a sandy-mud bottom at a depth of 45m in a protected bay of Iriomote-jima Island, Ryukyu Islands, Japan. It is distinguished from congeners in having the following combination of characters: 11 segmented dorsal-fin rays; 11 segmented anal-fin rays; 27 longitudinal scales; 11 predorsal scales; third spine of first dorsal fin elongate, filamentous, and longer than preceding spine; fifth and ninth branched caudal-fin rays elongate, filamentous, and forming bifurcated caudal fin; fifth and ninth branched caudal-fin rays with a single branch in each; cephalic sensory-papillae row a comprises three widely-spaced papillae; when live or fresh, numerous small yellow spots scattered on head, body, and dorsal fins; dusky yellowish-brown vertical bar below eye; four dark gray-brown saddles on body, in addition to a similarly colored large blotch at midlateral caudal-fin base. The limits and diagnosis of the genus Vanderhorstia are discussed.     

Phylogeography and genetic structure of the Canarian common chaffinch (Fringilla coelebs) inferred with mtDNA and microsatellite loci

The widespread common chaffinch (Fringilla coelebs) inhabits five of the seven Canary Islands. Sequences of the mitochondrial cytochrome b gene (1002 bp) revealed new insights into the systematics and phylogeography of this taxon. Additionally, a set of microsatellite loci were analyzed to examine the structure of these populations. Our results suggest that a new species of the genus Fringilla is present in the Canary Islands, which comprises at least three subspecies, but with a different distribution to that which has been morphologically accepted. The specimens from Gran Canaria are genetically distinct from those of La Gomera and Tenerife (F. c. canariensis), which suggests the existence of an undescribed taxon. Furthermore, nuclear microsatellite data suggest an ongoing incipient speciation process in this population. This study provides both important conservationist implications and a basis for re-evaluating the taxonomic status of the Canarian Fringilla coelebs populations.     

Genetic variation and population structure in Korean populations of sand dune speciesSalsola komarovi (Chenopodiaceae)

Salsola komarovi lljin is a herbaceous annual native to the sand dunes and beaches of Japan, northern China, Sakhalln and Korea. Starch-gel electrophoresis was conducted on leaves and stems collected from 300 plants in eight Korean populations. The mean number of alleles per locus (A _p=1.51), mean expected heterozygosity (He _p=0.116), and total genetic diversity (H _T=0.279) were comparable with those for species with similar life history and ecological traits. A general conformance of genotype frequencies to Hardy-Weinberg expectations (meanF _IS=−0.030) indicates thatS. komarovi is an outcrossing species. Slightly more than 20% of the genetic variation was found among populations (F _ST=0.204). In addition, significant differences in allele frequency were detected between populations at all 11 polymorphic loci (P<0.001). Nei's genetic identities range from 0.885 to 0.985 with a mean of 0.942. However, indirect estimates of the number of migrant per generation (0.97, calculated fromF _ST and 0.31, calculated from seven private alleles) indicate that the levels of gene flow is low among Korean populations. Although the species maintains a moderate level of genetic variation within populations, the small, isolated natural populations of the species have been severely destructed by human activities, particularly in summer season. If this is true, conservation efforts should be focused on those populations that currently maintain the most genetic diversity (e.g., populations of Cheju Island and coast of the southwestern Korean Peninsula).