Development of microsatellite markers in heterostylous Hedyotis chrysotricha (Rubiaceae)

? Premise of the study: Microsatellite primers were developed for a heterostylous herb, Hedyotis chrysotricha to investigate the effect of habitat fragmentation on its genetic diversity and population structure. ? Methods and Results: Twelve primer sets were developed and their polymorphisms were tested on 47 individuals from two island populations of H. chrysotricha in Thousand Island Lake of China. The number of alleles per locus ranged from five to 10, with an average of seven alleles. Expected heterozygosity per locus ranged from 0.284 to 0.821 and observed heterozygosity ranged from 0.191 to 0.851. ? Conclusions: We showed that all of the 12 microsatellite markers developed for H. chrysotricha are polymorphic within populations, which should provide a powerful tool for assessing population structure and genetic diversity across fragmented and continuous populations, and for studying the genetic effects of habitat fragmentation on this species.     

Characterization of 10 microsatellite loci in an avian louse, Degeeriella regalis (Phthiraptera: Ischnocera: Philopteridae)

We isolated and characterized 10 polymorphic microsatellite loci in an ischnoceran louse, Degeeriella regalis, which parasitizes the threatened Galápagos hawk (Buteo galapagoensis) and other falconiform birds. The loci were screened across 30 individuals from two island populations in the Galápagos Islands. The number of alleles per locus ranged from two to 28. Polymorphic information content ranged from 0.14 to 0.94 and observed heterozygosity ranged from 0 to 0.67. These markers will be valuable in comparative population genetics studies in this species, which is the focus of a long-term population and disease ecology research program.     

Characterization of microsatellite markers for the tanoak tree,Lithocarpus densiflorus

We describe the development of 19 primers for amplification of microsatellite loci for tanoak, Lithocarpus densiflorus (Hook. & Arn.). A population from Soquel State Demonstration Forest, Santa Cruz County, California (n = 20), and eight individuals from four additional coastal populations and one interior (Sierra Nevada) population were used to investigate polymorphism. The total number of alleles per locus ranged from two to 10. Observed heterozygosity in the Soquel population ranged from 0.05 to 0.70, with two loci being fixed.     

Microsatellite markers for the tetraploid halophyte Suaeda maritima (L.) Dumort. (Chenopodiaceae) and cross-species amplification in related taxa

We developed 12 polymorphic microsatellite markers for the tetraploid halophyte Suaeda maritima (Chenopodiaceae). Population genetic parameters were estimated for three populations from different habitats (coastal and inland), using the program Tetrasat. Between two and 15 alleles per locus were observed. Mean expected heterozygosities (H(E) ) and Shannon-Wiener Diversity Indices (H') per locus and population ranged from zero to 0.852, and from zero to 2.990, respectively. The two inland populations were less diverse than the coastal one at most of the loci. All markers cross-amplified in the closely related Suaeda salsa, and all but one were transferable to Suaeda spicata and Suaeda salinaria.     

Isolation and characterization of polymorphic microsatellite loci for the Skyros wall lizard Podarcis gaigeae (Squamata: Lacertidae)

Fifteen polymorphic markers were developed from a microsatellite-enriched library for the lizard Podarcis gaigeae. The loci were checked for variability in 68 individuals from a population on the island of Skyros, Greece. The number of alleles ranged from 3 to 23 per locus and expected heterozygosity from 0.29 and 0.94. Most markers were also polymorphic in three closely related Podarcis species, namely P. erhardi, P. taurica and P. milensis. The markers will be used to examine gene flow and differentiation of island and mainland populations of P. gaigeae.     

Seventeen polymorphic microsatellite markers developed for the Javelin goby, Synechogobius hasta (Gobiidae)

Synechogobius hasta is an important commercial marine fish with distinctive features of rapid growth and short lifespan. We isolated and characterized 17 microsatellite markers for S. hasta using a (GT)(13)-enriched genomic library. Polymorphism was assessed in 48 individuals from a single population collected from the northern coastal waters of the Yellow Sea. The number of alleles per locus ranged from 2 to 23, with a mean of 11.3. The observed and expected heterozygosities ranged from 0.130 to 1.000 and from 0.123 to 0.939, with means of 0.758 and 0.774, respectively. Fourteen of 17 loci conformed to Hardy-Weinberg equilibrium and no significant linkage disequilibrium between locus pairs was detected. These microsatellite markers will be useful for population genetic structure analyses.     

Microsatellite loci in the Canary Islands endemic ground beetle Trechus flavocinctus and their applicability to cave‐dwelling related species

Six polymorphic microsatellite markers have been developed for the Canary endemic ground beetle Trechus flavocinctus, and the performance of primer pairs amplifying these loci in closely related taxa (including two cave‐obliged species) has been tested. The number of alleles in T. flavocinctus samples taken from three distant localities in two islands ranged from four to 14 per locus. Observed heterozygosities were from 0.333 to 0.933. These markers could be useful tools to study the population structure and the genetic consequences of island and cave colonization by ground beetles.     

虾夷扇贝（Patinopecten yessoensis）5个群体的遗传多样性

虾夷扇贝为20世纪80年代初从日本引入我国并逐渐开展养殖的双壳贝类,目前已在我国北方地区大面积养殖。实验采用微卫星分子遗传标记技术对大连獐子岛底播增殖放流群体（CC）、黄海北部海区采集的野生群体（HQ）、日本青森养殖群体（JX）、俄罗斯远东日本海沿岸养殖群体（RX）及大连大长山岛养殖上壳白化群体（ZB）等5个虾夷扇贝群体的遗传多样性进行研究。其中HQ群体为本课题组2005年在黄海北部采集的野生群体,本研究筛选出一个该群体的特异性遗传标记。用8个微卫星位点进行扩增,共获得45个等位基因,每个位点的等位基因数处于3—9之间,大小为100—340bp,平均有效等位基因数为3．1535,基因型数为3—21个,PIC（PolymorphismInformationContent）值处于0．0322-0．5944之间。5个群体的平均观测杂合度分别为0．3292、0．3048、0．3167、0．2708、0．3042,平均期望杂合度分别为0．4595、0．4002、0．3838、0．3620、0．3885,群体间的多态性差异不显著。根据群体间遗传相似性系数、遗传距离及UPGMA聚类分析发现,CC和HQ群体亲缘关系最近,JX和RX群体的亲缘关系较近,ZB群体与JX和RX群体的亲缘关系较近。通过Hardy—Weinberg平衡及F-检验发现,5个群体都不同程度的偏离平衡,表明各群体基因频率和基因型频率的稳定性较低,且5个群体均处于不同程度的杂合子缺失状态,群体间的遗传分化程度较高,但遗传变异主要来自群体内的个体间。     

Development and Application of Microsatellites in Carcinus maenas: Genetic Differentiation between Northern and Central Portuguese Populations

Carcinus maenas, the common shore crab of European coastal waters, has recently gained notoriety due to its globally invasive nature associated with drastic ecological and economic effects. The native ubiquity and worldwide importance of C. maenas has resulted in it becoming one of the best-studied estuarine crustacean species globally. Accordingly, there is significant interest in investigating the population genetic structure of this broadly distributed crab along European and invaded coastlines. Here, we developed polymerase chain reaction (PCR) primers for one dinucleotide and two trinucleotide microsatellite loci, resulting from an enrichment process based on Portuguese populations. Combining these three new markers with six existing markers, we examined levels of genetic diversity and population structure of C. maenas in two coastal regions from Northern and Central Portugal. Genotypes showed that locus polymorphism ranged from 10 to 42 alleles (N = 135) and observed heterozygosity per locus ranged from 0.745 to 0.987 with expected heterozygosity ranging from 0.711 to 0.960; values typical of marine decapods. The markers revealed weak, but significant structuring among populations (global F_ST = 0.004) across a 450 km (over-water distance) spatial scale. Combinations of these and existing markers will be useful for studying population genetic parameters at a range of spatial scales of C. maenas throughout its expanding species range.     

Microsatellite markers for Spergularia media (L.) C. Presl. (Caryophyllaceae) and their cross-species transferability

We developed 11 polymorphic microsatellite markers for Spergularia media (Caryophyllaceae), a perennial halophyte of coastal salt meadows and continental areas of western Eurasia. The number of alleles per locus observed in a single population of 20 individuals from the German North Sea coast ranged from 3 to 20. Observed and expected heterozygosities ranged from 0.200 to 0.850 and from 0.278 to 0.936 respectively. Observed heterozygosities were lower than expected heterozygosities at all loci, presumably as a consequence of inbreeding. All markers cross-amplified in the closely related S. salina. Of these, nine were polymorphic in the heterologous species. Only two primer pairs generated PCR products in S. diandra.     

Isolation of microsatellite loci in the Capricorn silvereye,Zosterops lateralis chlorocephalus (Aves: Zosteropidae)

The Capricorn silvereye (Zosterops lateralis chlorocephalus) is ideally suited to investigating the genetic basis of body size evolution. We have isolated and characterized a set of microsatellite markers for this species. Seven out of 11 loci were polymorphic. The number of alleles detected ranged from two to five and observed heterozygosities between 0.12 and 0.67. One locus, ZL49, was found to be sex‐linked. This moderate level of diversity is consistent with that expected in an isolated, island population.     

Sicilian provinces: population subdivisions revealed by surname frequencies

The Sicilian population has a complex history of colonization and invasions that have influenced the genetic composition of the nine provinces of the island. Because surnames are patrilineally inherited, they simulate a Y-chromosome nonrecombinant genetic locus. We used surname data and a specific sampling strategy to describe the major subdivisions in each province and for the whole island of Sicily. The high number of families per surname in two provinces can be related to inbreeding as a result of founder events. Each province shows a major division, which, according to local historical events, likely represents cultural and probably genetic differences between east and west, between north and south, or between the inner regions and the coastal area. On the island level surnames reproduce the same separation, obtained by others with genes, of the eastern area from the western area. The separation is attributed to Greek influence in the east and to Phoenician-Carthaginian-Norman influence in the west. This separation crosses the two central provinces of Agrigento and Caltanissetta.     

Microsatellite loci development in endangered pamphagid grasshoppers endemic to the Canary Islands (Orthoptera)

The five recognized endemic pamphagid species (Orthoptera) of the Canary Islands have restricted and fragmented ranges due to habitat decline. Seven polymorphic microsatellite markers have been developed for Acrostira tamarani, and the performance of primer pairs amplifying these loci in related taxa has been tested. The number of alleles in A. tamarani samples taken from two distant localities in the island of Gran Canaria ranged from two to eight per locus. Observed heterozygosities were from 0.151 to 0.559. Up to four primer pairs amplified in related species with moderate heterozigosities (maximum of 0.687 and 10 alleles for Ata67 locus in Purpuraria erna). These markers could be useful tools to study the population structure and management of endemic threatened pamphagids of the Canary archipelago.     

Isolation and characterization of microsatellite DNA loci from the golden cuttlefish,Sepia esculenta Hoyle (Cephalopoda)

The first microsatellite markers were isolated from the golden cuttlefish, Sepia esculenta Hoyle. Eleven primer sets were designed to amplify the marker sequences via polymerase chain reaction. The 45–50 individuals from one wild population in the coastal waters of Ehime Prefecture, Japan were used to screen polymorphism in the 11 microsatellite loci. All the microsatellite loci were polymorphic, with the range of alleles from seven to 27 per locus. The observed and expected heterozygosities ranged from 0.380 to 0.980 and from 0.654 to 0.940, respectively. These marker loci except for one locus showing significant deviation from Hardy–Weinberg equilibrium will be useful for the assessment of genetic variation and population structure of this species.     

Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago

We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatellite loci. The number of alleles per locus ranged from 3 to 33 and the observed heterozygosity per population ranged from 0.01 in Mare to 0.74 in Ile des Pins. The genetic diversity was lowest in the most recent islands, the Loyautes, and highest in the oldest island, Grande Terre, as well as the nearby small Ile des Pins. Significant departures from panmixia were observed for some loci-population combinations (per population FIS = 0-0.03 on Grande-Terre and Ile des Pins, and 0-0.67 on Loyautes). A strong genetic differentiation among all islands was observed (FST = 0.22), and the amount of differentiation increased with geographic distance in Iles Loyaute and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average FIS that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occurred extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum.     

Analysis of Microsatellite DNA Polymorphisms in Rockfish Sebastes thompsoni and Application to Population Genetics Studies

Population differentiation and relationships among 6 natural rockfish populations collected from northern coastal seas around Japan were assayed using microsatellite DNA loci. Seven loci examined were polymorphic in all populations. The number of alleles per locus ranged from 6.7 to 9.3, and the average of observed and expected heterozygosity ranged from 0.63 to 0.68, and from 0.66 to 0.69, respectively. The observed genotype frequencies at each locus were almost in agreement with Hardy-Weinberg expectations with two exceptions (P < .05). The allele frequencies of 16 population pairs were significantly different (P < .05). Genetic distance (D _A ) between 6 populations ranged from 0.03 to 0.08. According to a neighbor-joining tree generated from the D _A values, the 6 populations fell into 3 clusters. These clusters were correlated with the geographical positions of each population; larval dispersions due to water current were also found to have an effect on these results. Received May 2, 2000; accepted July 17, 2000.     

Genetic structure of Asian populations of Bombus ignitus (Hymenoptera: Apidae)

The genetic structure of seven mainland and island Asian populations of Bombus ignitus was investigated using nine microsatellite markers and the sequences of part of the mitochondrial cytochrome b (cytb) gene. While microsatellite markers showed high genetic variability, no sequence variation was found in the cytb gene fragment analyzed. The number of microsatellite alleles ranged from 9 to 24. Gene diversities per locus per population ranged from 0.378 to 0.992. Analysis of molecular variance (AMOVA) and most pairwise F(ST) values showed significant genetic differentiation between mainland and island populations. Cytb sequences data and microsatellite bottleneck tests indicated that almost all populations were subjected to recent bottlenecks. Our results suggest that B. ignitus populations diverged due to recent bottlenecks and geographic isolation.     

Isolation and characterization of novel microsatellite markers for Cymodocea serrulata (Cymodoceaceae), a seagrass distributed widely in the Indo‐Pacific region

Cymodocea serrulata is a tropical seagrass species distributed widely in the Indo‐Pacific region. We developed 16 novel microsatellite (simple sequence repeat) markers for C. serrulata using next‐generation sequencing for use in genetic studies. The applicability of these markers was attested by genotyping of 40 individuals collected from a natural population in the Philippines. Of the 16 loci, 15 showed polymorphism. For the 15 polymorphic markers, the number of alleles per locus ranged from two to seven, and the observed and expected heterozygosities ranged from 0.131–1.000 and 0.124–0.788, respectively. These markers are useful tools for elucidating genetic diversity, connectivity, and structure in this foundational coastal species.     

Vicariance and marine migration in continental island populations of a frog endemic to the Atlantic Coastal forest

The theory of island biogeography is most often studied in the context of oceanic islands where all island inhabitants are descendants from founding events involving migration from mainland source populations. Far fewer studies have considered predictions of island biogeography in the case of continental islands, where island formation typically splits continuous populations and thus vicariance also contributes to the diversity of island populations. We examined one such case on continental islands in southeastern Brazil, to determine how classic island biogeography predictions and past vicariance explain the population genetic diversity of Thoropa taophora, a frog endemic to the Atlantic Coastal Forest. We used nuclear microsatellite markers to examine the genetic diversity of coastal and island populations of this species. We found that island isolation has a role in shaping the genetic diversity of continental island species, with island populations being significantly less diverse than coastal populations. However, area of the island and distance from coast had no significant effect on genetic diversity. We also found no significant differences between migration among coastal populations and migration to and from islands. We discuss how vicariance and the effects of continued migration between coastal and island populations interact to shape evolutionary patterns on continental islands.     

Genetic relationships of American alligator populations distributed across different ecological and geographic scales

Although much work has been conducted on coastal populations of the American alligator (Alligator mississippiensis), less is known about the population dynamics and genetic structure of populations of alligators confined to inland habitats. DNA microsatellite loci, derived from the American alligator, were used to investigate patterns of genetic variation within and between populations of alligators distributed at coastal and inland localities in Texas. These data were used to evaluate the genetic discreteness of different alligator stocks relative to their basic ecology at these sites. Observed mean heterozygosities across seven loci for both coastal and inland populations ranged from 0.50-0.61, with both inland and coastal populations revealing similar patterns of variation. Measures of F(st) revealed significant population differentiation among all populations; however, analyses of molecular variance (AMOVAs) failed to demonstrate any apparent geographic pattern relative to the population differentiation indicated by F(st) values. Each population contained unique alleles for at least one locus. Additionally, assignment tests based on the distribution of genotypes placed 76% of individuals to their source population. These genetic data suggest considerable subdivision among alligator populations, possibly influenced by demographic and life history differences as well as barriers to dispersal. These results have clear implications for management. Rather than managing alligators in Texas as a single panmictic population, translocation programs and harvest quotas should consider the ecological and genetic distinctiveness of local alligator populations.