Microsatellite loci for population and parentage analysis in the Amazon River dolphin (Inia geoffrensis de Blainville, 1817)

We developed specific primers for microsatellite DNA regions for the Amazon River dolphin or boto Inia geoffrensis, for use in population and conservation genetic studies. We also tested their transferability for two other species, Pontoporia blainvillei (sister taxon of I. geoffrensis) and Sotalia guianensis. A total of 12 microsatellite loci were polymorphic for the boto. An additional 25 microsatellite loci previously isolated from other cetacean species were also tested in the boto. The 26 polymorphic microsatellite loci indicate they will be excellent markers for studies of population structure and kinship relations of the boto.     

Characterization of microsatellite loci in Tursiops aduncus

We describe the cloning and characterization of five highly polymorphic microsatellite loci cloned from aduncus dolphins (Tursiops aduncus) from Western Australia. Five polymorphic microsatellite loci were isolated and tested on up to 350 animals, showing 7–23 alleles and expected heterozygosity values from 0.68 to 0.89. We also tested the loci on striped dolphins and franciscana dolphins, where we also found high levels of polymorphism (9–16 alleles in 102 striped, and 4–5 alleles in 13 franciscana dolphins). Considering that the cetacean genome is highly conserved, the characterized markers are likely to be useful in a number of cetacean population studies.     

Isolation and characterization of twelve polymorphic microsatellite markers in bottlenose dolphins (Tursiops truncatus)

We developed polymerase chain reaction primers for 12 dinucleotide microsatellite loci in the bottlenose dolphin, Tursiops truncatus. Seven markers were obtained after hybridization screening, and five following random genome sequencing. Orthologous positions were computed for nine markers on the bovine genome and for seven on the human genome. The markers are distributed across chromosomes and found in different types of DNA regions. All 12 loci are polymorphic for Tursiops. Five loci were also polymorphic in the related species Stenella frontalis and the more distantly related river dolphin, Inia geoffrensis, indicating these markers will be informative across the Delphinidae and other cetacean taxa.     

Isolation and characterisation of microsatellite loci in the papillose woolly bat, <Emphasis Type="Italic">Kerivoula papillosa</Emphasis> (Chiroptera: Vespertilionidae)

The papillose woolly bat (Kerivoula papillosa) is one of the most well known species of an understudied bat genus that may be particularly vulnerable to disturbance and fragmentation events. We describe 22 novel microsa tellite loci, 17 of which are polymorphic in K. papillosa, and one of which is polymorphic in a related species K. pellucida. When tested in a single population, none of the markers significantly deviated from Hardy-Weinberg expectations, showed the presence of null alleles or exhibited linkage disequilibrium. These markers will be useful in determining impacts of forest fragmentation on this species.     

Isolation and characterization of microsatellite loci in the finless porpoise (Neophocaena phocaenoides)

Eight dinucleotide microsatellite loci were isolated from the finless porpoise (Neophocaena phocaenoides). Analysis of 30 individuals showed the number of alleles ranged from four to 21 with observed heterozygosity ranging from 0.300 to 0.833, and expected heterozygosity ranging from 0.437 to 0.932. Cross‐species amplification was tested in four other cetacean species. These microsatellite markers would be valuable tools for population genetic studies of finless porpoises and other cetacean species.     

Polymorphic microsatellite markers for the ant Plagiolepis pygmaea

Detailed studies on kin structure, mating patterns and dispersal in social insects require highly polymorphic markers, of which the most commonly used today are DNA microsatellites. Here we characterize 10 polymorphic microsatellite markers for the ant Plagiolepis pygmaea. We also investigated the within‐genus applicability of the markers on P. xene, a social parasite of the source species. In addition, we tested amplification of the markers in three species of the genera Formica and Lasius. Eight of the markers also amplified in P. xene and were polymorphic. Seven markers amplified in at least one other formicine ant.     

Using Massive Parallel Sequencing for the Development,Validation, and Application of Population Genetics Markers in the Invasive Bivalve Zebra Mussel (Dreissena polymorpha)

The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process.     

A set of polymorphic dinucleotide and tetranucleotide microsatellite markers for the Indo-Pacific humpback dolphin (Sousa chinensis) and cross-amplification in other cetacean species

Eleven dinucleotide and five tetranucleotide polymorphic microsatellite loci were presented for the Indo-Pacific humpback dolphin Sousa chinensis, a species categorized as ‘data deficiency’ in the IUCN Red List. These markers were developed to allow future population studies, such as characterization of population structure and genetic diversity that are important for the species’ conservation. The number of alleles ranged from 2 to 9 with observed heterozygosity ranging from 0.167 to 0.917, and expected heterozygosity ranging from 0.159 to 0.913. Test of these loci in five additional cetacean species found that 10–13 loci have successful cross-amplifications.     

Microsatellite loci for euglossine bees (Hymenoptera: Apidae)

The Neotropical Euglossini (Hymenoptera: Apidae) are important pollinators of many flowering plants, particularly orchids. Lack of highly polymorphic genetic markers for euglossine species has limited the study of their social organization and inbreeding. We therefore developed microsatellite markers for two species, Eulaema nigrita (11 loci) and Euglossa cordata (nine loci), most of which were highly polymorphic in the source species and in a range of related euglossine bees.     

Conserved Microsatellites in Ants Enable Population Genetic and Colony Pedigree Studies across a Wide Range of Species

Broadly applicable polymorphic genetic markers are essential tools for population genetics, and different types of markers have been developed for this purpose. Microsatellites have been employed as particularly polymorphic markers for over 20 years. However, PCR primers for microsatellite loci are often not useful outside the species for which they were designed. This implies that a new set of loci has to be identified and primers developed for every new study species. To overcome this constraint, we identified 45 conserved microsatellite loci based on the eight currently available ant genomes and designed primers for PCR amplification. Among these loci, we chose 24 for in-depth study in six species covering six different ant subfamilies. On average, 11.16 of these 24 loci were polymorphic and in Hardy-Weinberg equilibrium in any given species. The average number of alleles for these polymorphic loci within single populations of the different species was 4.59. This set of genetic markers will thus be useful for population genetic and colony pedigree studies across a wide range of ant species, supplementing the markers available for previously studied species and greatly facilitating the study of the many ant species lacking genetic markers. Our study shows that it is possible to develop microsatellite loci that are both conserved over a broad range of taxa, yet polymorphic within species. This should encourage researchers to develop similar tools for other large taxonomic groups.     

Development and characterization of ten novel microsatellite markers from olive ridley sea turtle (Lepidochelys olivacea)

Olive ridleys, one of the widely distributed marine turtle species has undergone declines in recent years due to multiple anthropogenic factors warranting conservation efforts for which assessment of genetic variability in existing populations become critical. Here we describe development of ten new microsatellite markers from a short sequence repeat-enriched partial genomic DNA library, which are found to be highly informative for genetic studies. Eight of these markers when tested on 83 olive ridley turtles revealed high allelic diversity (4–27 alleles per marker), and high observed and expected heterozygosity estimates that ranged from 0.29 to 0.82 and 0.62 to 0.94, respectively. Two microsatellites were monomorphic in the tested olive ridley samples, but were found to be informative/polymorphic when tested on related marine turtle species. More importantly, nine of the new markers showed robust cross-species amplifications in three related species Dermochelys coriacea, Chelonia mydas and Eretmochelys imbricata. Thus, this study describes ten new microsatellite markers and also demonstrates their potential as efficient genetic markers in studies related to parentage analysis, population structure, phylogeography and species relationships of olive ridleys and other marine turtle species.     

The functional significance of colouration in cetaceans

Cetaceans show many of the classic mammalian colouration patterns, such as uniform colouration, countershading, and prominent patches of colour, all within one relatively small taxon. We collated all the functional hypotheses for cetacean colouration that have been put forward in the literature and systematically tested them using comparative phylogenetic analyses. We found that countershading is a mechanism by which smaller cetacean species may avoid being seen by their prey. We discovered that prominent markings are associated with group living, fast swimming, and ostentatious behaviour at the surface, suggesting that they function in intraspecific communication. White markings on several parts of the body seem to be involved in the capture of fish, squid, and krill. Therefore, several different selection pressures have shaped the great diversity of skin colouration seen in extant cetaceans, although background matching, disruptive colouration and interspecific communication do not appear to be involved.     

云南普通野生稻遗传多样性和亲缘关系

野生稻（Oryza rufipogon）是稻属的重要组成部分,具有许多优良性状,是水稻遗传改良的天然基因库。本研究通过对形态学性状的观测,及ISSR和RAPDUPGMA聚类分析,将云南普通野生稻划分为4个类型,即元江类型、景洪紫杆直立型、景洪绿杆直立型和景洪匍匐型。在供试材料中筛选到具有多态性的ISSR和RAPD引物各11个,ISSR引物扩增出多态带113条,多态性条带比率（PPB）为82．26％,RAPD引物共扩增出多态性条带76条,PPB值为76．77％,两种分子标记的分析结果呈极显著正相关（r=0.951）。此外UPGMA聚类结果表明,云南普通野生稻不同类型与其它地区普通野生稻之间的遗传亲缘关系差异明显。     

Development and characterization of microsatellite markers for the invasive weed Mikania micrantha (Asteraceae)

Mikania micrantha is a successful invasive weed in many parts of the world. Twelve polymorphic microsatellite loci were isolated and characterized from an AC-enriched genomic library of this species. Twenty-eight individuals from one population in Dongguan were tested for polymorphism. The average allele number of these microsatellites was three per locus, ranging from two to five. The expected and observed heterozygosities ranged from 0.275 to 0.742, and from 0.250 to 1.000, respectively. These microsatellite markers can be applied to study the population genetics in the native and invasive ranges of this species, and to trace its invasion history.     

云南普通野生稻遗传多样性和亲缘关系

野生稻(Oryza rufipogon)是稻属的重要组成部分, 具有许多优良性状, 是水稻遗传改良的天然基因库。本研究通过对形态学性状的观测, 及ISSR和RAPD UPGMA聚类分析, 将云南普通野生稻划分为4个类型, 即元江类型、景洪紫杆直立型、景洪绿杆直立型和景洪匍匐型。在供试材料中筛选到具有多态性的ISSR和RAPD引物各11个, ISSR引物扩增出多态带113条, 多态性条带比率(PPB)为82.26%, RAPD引物共扩增出多态性条带76条, PPB值为76.77%, 两种分子标记的分析结果呈极显著正相关(r = 0.951)。此外UPGMA聚类结果表明, 云南普通野生稻不同类型与其它地区普通野生稻之间的遗传亲缘关系差异明显。     

Anonymous nuclear markers for cetacean species

Here we report the development and characterization of 17 anonymous nuclear markers for cetacean species. These markers were isolated from a genomic library built from a common dolphin (genus Delphinus), and tested across several families within Cetacea. An average of 1 SNP per 272 bp was found in 10 anonymous markers screened for polymorphism within the genus Delphinus (total of 6,537 bp sequenced). These markers represent a significant addition to the set of tools used in genetic studies of cetaceans where population and species boundaries have to be inferred in order to implement proper conservation strategies.     

Genetic segregation of random amplified polymorphic DNA in diploid cultivated alfalfa.

Polymerase chain reaction was used, with single 10-mer primers of arbitrary sequence, to amplify random regions of genomic DNA from a diploid cultivated alfalfa backcross population. Segregation of the random amplified polymorphic DNA (RAPD) fragments was analysed to determine if RAPD markers are suitable for use as genetic markers. Of the 19 primers tested, 13 amplified a total of 37 polymorphic fragments, of which 28 (76%) segregated as dominant Mendelian traits. RAPD markers appear useful for the rapid development of genetic information in species like alfalfa where little information currently exists or is difficult to obtain.     

Development of tetranucleotide microsatellite loci for the finless porpoise (<Emphasis Type="Italic">Neophocaena phocaenoides</Emphasis>)

The finless porpoise, Neophocaena phocaenoides, is endemic to the coastal waters of the Indo-Pacific, ranging from the Persian Gulf to Japan. Nine tetranucleotide microsatellite loci were isolated from the finless porpoise (Neophocaena phocaenoides). Polymorphism of each locus was assessed in 39 unrelated individuals from the Yellow Sea and the South China Sea of the Chinese waters. The number of alleles per locus varied from 2 to 11. The ranges of observed and expected heterozygosity were 0.154–0.795 and 0.146–0.839, respectively. Cross-species amplification of these loci was tested in other cetacean species. These microsatellite markers described here will be suitable for population genetic studies of finless porpoises and other cetacean species.     

Microsatellite markers for European Daphnia

We present 32 polymorphic microsatellite markers for species of the European Daphnia longispina group: D. galeata, D. hyalina, D. rosea, D. cucullata and D. curvirostris. Microsatellite markers were either isolated from genomic libraries or optimized based on previously published sequence information of sister taxa. Cross‐species tests revealed that all but one of the polymorphic markers are applicable to more than one species, which allows intra‐ and interspecific genetic studies on, i.e. population structure, hybridization events and introgression.     

Isolation and characterization of novel microsatellite loci for the short‐beaked common dolphin (Delphinus delphis) and cross‐amplification in other cetacean species

Seven tetranucleotide and three dinucleotide microsatellite loci were isolated from the short‐beaked common dolphin (Delphinus delphis). Number of alleles and observed heterozygosity ranged from three to twelve (mean 8.4) and from 0.087 to 0.978 (mean 0.741), respectively. All loci were tested in four other odontocete species and showed polymorphisms in most locus–species combinations. This panel of nuclear markers will be useful for the investigation of population ecology and social interactions in common dolphins and other cetacean species.