Fifteen microsatellite loci for the jungle perch, Kuhlia rupestris

We developed and optimized 15 polymorphic microsatellite loci in the jungle perch, Kuhlia rupestris. Loci were screened in a single population (n = 24) from Fraser Island, Queensland, Australia. Number of alleles per locus ranged from 3 to 19 and observed heterozygosity from 0.25 to 1. No significant linkage disequilibrium was detected between any pair of loci. Genotype proportions for these loci in the population sampled were in Hardy–Weinberg equilibrium.     

Isolation and characterization of polymorphic microsatellite loci in Aleurodicus dispersus (Hemiptera, Aleyrodidae)

Ten microsatellite markers were isolated and characterized from Aleurodicus dispersus, the spiraling whitefly, an exotic pest species that is considered to be one of the most serious agricultural pests on Hainan Island, China. The polymorphism of these loci was examined in individual whiteflies from Hainan Island and from the Canary Islands. All loci were polymorphic, with two to four alleles per locus. Mean observed and expected heterozygosity values were 0.773 and 0.585, respectively. These microsatellite markers provide powerful tools for ecological, epidemiological and population genetic studies on this highly invasive insect. Thirty insects were collected and studied at each location. There were no differences between the two locations.     

Characterization of 10 microsatellite loci in the spiny‐tailed iguana Ctenosaura hemilopha

Ten microsatellite loci were developed for the Baja California spiny‐tailed iguana Ctenosaura hemilopha, using an enriched genomic DNA library. In the Cerralvo Island population, seven loci were polymorphic and presented moderate levels of variation. Number of alleles ranged from two to eight (average 4.43), and observed heterozygosity from 0.150 to 0.857 (average 0.492). Polymorphism was detected at six loci on C. hemilopha individuals from the southern Baja California Peninsula. These markers will be useful to study familiar relationships and behaviour on the Cerralvo Island population.     

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.     

Microsatellite DNA loci identify individuals and provide no evidence for multiple paternity in wild tuatara (Sphenodon: Reptilia)

Six new microsatellite DNA loci are isolated from a genomic library of the sphenodontid reptile tuatara (Sphenodon) and presented here as a tool for identifying individuals for future paternity and kinship studies. These loci, in combination with four previously published loci, are sufficient to discriminate between clutch-mate siblings from Stephens Island and Brothers Island populations. These populations represent high and low levels of genetic diversity in tuatara populations respectively. An estimate of minimum number of fathers of each clutch found no evidence for multiple paternity in any clutch. These newly isolated loci complete the development of an array of genetic tools for use in tuatara to enhance ongoing conservation and management of wild, translocated and captive populations.     

Development and characterization of microsatellite markers for Hibiscus glaber Matsum. ex Nakai, an endemic tree species of the oceanic Bonin Islands, Japan

Polymorphic microsatellite markers were developed for Hibiscus glaber, an endemic tree of the Bonin Islands. Eighty-seven of the 208 sequences from an enriched library were unique and containing microsatellites. Ten loci were proved to be highly polymorphic among 78 individuals from the Nishi-jima Island. Total exclusionary powers for the first and the second parents were 99.989% and 99.999%, respectively. Nine loci also amplified single fragment from genomic DNA of H. tiliaceus, a related and widespread congener. Our markers can be reliably used for the estimation of current gene flow within/among populations of the two woody Hibiscus species.     

Development of nuclear microsatellite markers for the Japanese conifers Tsuga diversifolia and T. sieboldii (Pinaceae)

Nuclear microsatellite markers were developed for the two Tsuga species native to the Japanese Archipelago, Tsuga diversifolia and T. sieboldii, and a population with genetic affinities to T. diversifolia on Ulleung Island, Korea. Tsuga diversifolia and T. sieboldii are widespread dominant trees of temperate and subalpine forests in Japan but to date no genetic markers have been developed for these species. Fifteen polymorphic loci were developed and characterized, of which 14 are reliably amplified in each taxon. Across both species and the Ulleung Island population, the number of alleles per locus ranged from 3 to 26 (average = 13.93) and observed heterozygosity ranged from 0.005 to 0.935 (average = 0.535). In addition, all 15 loci were successfully amplified in a single accession of the Chinese species, T. chinensis. These markers will be useful for investigating the species’ biogeography, range‐wide genetic diversity, conservation genetic issues and potential for hybridisation.     

Isolation and characterization of microsatellite loci in Ainsliaea faurieana (Asteraceae), an endemic plant species on Yakushima Island, Japan, and cross-species amplification in closely related taxa

Fourteen microsatellite loci were isolated and characterized for Ainsliaea faurieana, an endemic perennial plant species on Yakushima Island. In an analysis of 37 individuals from Yakushima Island, the observed number of alleles ranged from two to six. The expected and observed heterozygosities were 0.109-0.811 and 0.000-0.27, respectively. The inbreeding coefficient was 0.489-1.000. The interspecific applicability of these microsatellites was evaluated by analysing three closely related taxa from the Ryukyu Islands. All primer pairs for the 14 loci tested successfully amplified in all taxa.     

海南岛中华蜜蜂遗传多样性的微卫星DNA分析

为了解海南岛中华蜜蜂Apis cerana cerana的遗传多样性和遗传结构及其与大陆种群的关系, 本研究应用10个微卫星DNA标记对海南岛11个地点627个蜂群的627头工蜂样本和大陆2个地点102个蜂群的102头工蜂样本进行了分析。结果表明： 海南岛中华蜜蜂遗传多样性较高, 单个位点检测到等位基因5～17个; 各种群平均等位基因数为4.5～7.0个, 平均杂合度为0.59～0.65。海南岛中华蜜蜂在10个位点上表现出相似遗传结构, 文昌和屯昌种群在AT101位点的等位基因频率较特殊。岛内 岛外中华蜜蜂的遗传分化系数F_ST范围为0.06～0.13; 文昌、 屯昌种群分别同海南岛内其他9个种群的F_ST（0.06～0.12）大于这9个种群间的FST（0～0.05）。海南岛中华蜜蜂同邻近大陆种群发生了明显的遗传分化; 除文昌、 屯昌种群发生中等程度的分化外, 海南岛内其他种群之间遗传分化较小。本研究结果对海南岛中华蜜蜂资源的保护和合理利用具有重要的指导意义。     

Polymorphic microsatellite loci for population studies of the Japanese scallop,Patinopecten yessoensis

Fifteen microsatellite loci were developed to examine the population structure of Japanese scallop, Patinopecten yessoensis. These markers were tested in samples from two geographically distant populations: the Sakhalin Island (Russia) and Dalian City (China). The mean numbers of alleles, observed and expected heterozygosities between the two populations were summarized by locus, but none of them show significant divergence between the two populations. Most loci conformed to Hardy–Weinberg expectation with the exception of loci HLJX‐06, HLJX‐12, HLJX‐13 and HLJX‐28, which had heterozygote deficits.     

黑头酸臭蚁微卫星标记的分离与开发(英文)

【目的】本研究旨在分离黑头酸臭蚁Tapinoma melanocephalum基因组微卫星标记,确定这些微卫星位点的多态性。【方法】使用454 GS-FLX焦磷酸测序技术开发来自中国华南陆地和岛屿的11个黑头酸臭蚁地理种群基因组微卫星位点。从随机设计的100对微卫星引物中筛选出10对引物,用于确定黑头酸臭蚁4个地理种群［东澳岛(DAD)、荷包岛(HBD)、梅州(MZ)和山咀(SJ)］10个微卫星位点的多态性,分析种群遗传多样性和种群分化。【结果】从11个黑头酸臭蚁地理种群基因组中成功开发和分离10对微卫星引物。在DAD, HBD, MZ和SJ 4个地理种群中,10个微卫星位点中7个有高多态性,这10个位点均显著偏离Hardy-Weinberg平衡;每个位点的等位基因数量(A)是3.50~9.00个,每个地理种群每个位点等位基因丰富度(A_R)在1.992~12.938之间。岛屿地理种群(DAD和HBD)的AR和预期杂合度(H_E)与大陆地理种群(MZ和SJ)的相比差异不显著。4个地理种群均显示高水平遗传分化(F_ST=0.15969);HBD和MZ种群与其他配对地理种群相比,遗传分化较高(F_ST=0.185),基因流较低,说明这两个种群基因流被限制。此外,遗传变异来自种群内个体之间。【结论】筛选新的微卫星位点能够为研究黑头酸臭蚁种群结构和繁殖结构提供有效工具,以深入了解其传播机制。     

Closing the gap: Avian lineage splits at a young,narrow seaway imply a protracted history of mixed population response

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β‐fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide‐ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island—South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.     

Geographic Microsatellite Variability in Central American Howling Monkeys

In 1997, we began to assess the genetic variability and the potential conservation risk of the increasing human impact on the howling monkeys of Ometepe Island in southern Nicaragua. We captured and collected blood from 29 howling monkeys (Alouatta palliata) at two geographically separated localities in a single area (San Ramon) on Ometepe Island, Nicaragua, during two field seasons. We also collected blood from a community of 10 Alouatta pigra in the Scotland Half Moon region in Belize. We extracted DNA from the blood and analyzed 12 microsatellite loci. The number of alleles per locus (allele variability) is less for most (but not all) loci in the Ometepe versus the Belize sample and less than earlier published reports of mixed geographic samples from Central America. The results are noteworthy in that both the Ometepe Island sample and the Belize sample possess greater allelic heterozygosity for most loci than reported in other Central American howling monkey populations. The Ometepe and Belize groups also demonstrated differences in allele frequencies at each geographic location. There appeared to be adequate gene flow in both locations despite extensive fragmentation due to agriculture and other human land usage.     

PERMANENT GENETIC RESOURCES: Fifteen polymorphic microsatellite DNA loci from Hawaii's Metrosideros polymorpha (Myrtaceae: Myrtales), a model species for ecology and evolution

We developed 15 polymorphic microsatellite loci from the Hawaiian tree Metrosideros polymorpha. These loci were screened against two varieties from several populations and from 23 individuals from one mid-elevation population on Hawaii Island. Loci were variable with the number of alleles per locus ranging from three to 24. Polymorphic information content ranged from 0.222 to 0.941, and observed heterozygosity ranged from 0.261 to 0.955.     

Genetic structuring among Alaskan Pacific herring populations identified using microsatellite variation

Five highly variable microsatellite loci were used to investigate population structuring in Pacific herring Clupea pallasi collected from Kodiak Island, two sites in the Bering Sea and four sites within Prince William Sound, Alaska. All loci revealed high levels of variability with heterozygosity estimates ranging from 86 to 97% (mean heterozygosity: 89%). The variation was structured significantly among sites suggesting that the samples investigated were genetically distinct from each other. Genetic divergence was greatest between populations from the Bering Sea and those from Prince William Sound. The Kodiak Island and Point Chalmers samples appeared to be distinct from the Prince William Sound and Bering Sea populations. The observed genetic distance relationships among samples could be explained largely in terms of geographical separation.     

Characterization of polymorphic microsatellite loci from Round Island Petrels (Pterodroma arminjoniana) and their utility in other seabird species

Six microsatellite loci were isolated from the petrels of Round Island, near Mauritius in the Indian Ocean (Pterodroma arminjoniana). Three loci were monomorphic in P. arminjoniana but were found to be polymorphic in other Procellariiforms. Cross-utility of all six loci was tested in 17 Procellariiform and 1 penguin species. In addition, 53 microsatellite loci developed for other species of birds were tested for cross-species amplification in P. arminjoniana. Six of these loci were found to be polymorphic.     

Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy-Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.     

Chloroplast microsatellite markers for the mangrove tree species Bruguiera gymnorrhiza, Kandelia candel, and Rhizophora stylosa, and cross-amplification in other mangrove species

Chloroplast microsatellite (cpSSR) markers were developed for three ecologically and economically important tree species in the mangrove family, Rhizophoraceae: Bruguiera gymnorrhiza, Kandelia candel, and Rhizophora stylosa. Noncoding regions of chloroplast DNA (cpDNA) from each species were separately amplified using universal chloroplast primers. Six, two, and three polymorphic cpSSR loci in B. gymnorrhiza, K. candel, and R. stylosa, respectively, were developed from amplified noncoding cpDNA regions. Characterization of 216, 156, and 253 individuals of B. gymnorrhiza, K. candel, and R. stylosa, respectively, collected from different natural mangrove populations (B. gymnorrhiza, 9; K. candel, 7; R. stylosa, 9) on Iriomote Island in Japan showed that these loci provide cpSSR markers with polymorphisms ranging from two to four alleles per locus and gene diversity between 0.027 and 0.480. These cpSSR markers will be useful for analyzing the maternal lineage distributions and population genetic structures of the three species. Several of these markers may also be useful in similar studies of other mangrove species.     

Development of microsatellite markers for an extremely limited distributed rare diving beetle species,Acilius kishii,and a widely distributed species,Acilius japonicus (Coleoptera: Dytiscidae)

Acilius kishii Nakane, 1963 (Coleoptera: Dytiscidae) is an endangered diving beetle species distributed in only one location, Lake Yashaga‐Ike, Honshu Island, Japan. Acilius japonicus, which is related to A. kishii, is distributed widely in northern Honshu Island and Hokkaido Island in Japan. In this study, we identified 14 microsatellite loci for A. kishii and A. japonicus, including both polymorphic and monomorphic loci, using the next‐generation sequencing method. We observed that 5 and 10 loci showed polymorphisms in 31 and 32 individuals of A. kishii and A. japonicus, respectively. The observed and expected heterozygosities were 0.00–1.00 and 0.00–0.74, respectively. These microsatellite loci could be useful for future conservation genetic studies, including monitoring of genetic diversity and extinction risk of A. kishii.     

Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, <Emphasis Type="Italic">Honckenya peploides</Emphasis>

Codominant marker systems are better suited to analyze population structure and assess the source of an individual in admixture analyses. Currently, there is no codominant marker system using microsatellites developed for the sea sandwort, Honckenya peploides (L.) Ehrh., an early colonizer in island systems. We developed and characterized novel microsatellite loci from H. peploides, using reads collected from whole genome shotgun sequencing on a 454 platform. The combined output from two shotgun runs yielded a total of 62,669 reads, from which 58 loci were screened. We identified 12 polymorphic loci that amplified reliably and exhibited disomic inheritance. Microsatellite data were collected and characterized for the 12 polymorphic loci in two Alaskan populations of H. peploides: Fossil Beach, Kodiak Island (n?=?32) and Egg Bay, Atka Island (n?=?29). The Atka population exhibited a slightly higher average number of alleles (3.9) and observed heterozygosity (0.483) than the Kodiak population (3.3 and 0.347, respectively). The overall probability of identity values for both populations was PID?=?2.892e^?6 and PID_sib?=?3.361e^?3. We also screened the 12 polymorphic loci in Wilhelmsia physodes (Fisch. ex Ser.) McNeill, the most closely related species to H. peploides, and only one locus was polymorphic. These microsatellite markers will allow future investigations into population genetic and colonization patterns of the beach dune ruderal H. peploides on new and recently disturbed islands.