Characterization of microsatellite markers in the squid,Loligo bleekeri (Cephalopoda: Loliginidae)

Loligo bleekeri has a long spawning season and the size of mature males changes during the season: dimorphic (large/small) early in the spawning season and monomorphic (small) later in the spawning season. To understand how copulatory behaviours relate to the dimorphism, we developed five polymorphic microsatellite loci in L. bleekeri. The level of polymorphism ranged from 10 to 22 alleles with expected heterozygosities ranging from 0.79 to 0.93, suggesting that the novel polymorphic loci should be useful for parentage analysis of L. bleekeri.     

Spatial patterns in the biology of the chokka squid, Loligo reynaudii on the Agulhas Bank, South Africa

Although migration patterns for various life history stages of the chokka squid (Loligo reynaudii) have been previously presented, there has been limited comparison of spatial variation in biological parameters. Based on data from research surveys; size ranges of juveniles, subadults and adults on the Agulhas Bank were estimated and presented spatially. The bulk of the results appear to largely support the current acceptance of the life cycle with an annual pattern of squid hatching in the east, migrating westwards to offshore feeding grounds on the Central and Western Agulhas Bank and the west coast and subsequent return migration to the eastern inshore areas to spawn. The number of adult animals in deeper water, particularly in autumn in the central study area probably represents squid spawning in deeper waters and over a greater area than is currently targeted by the fishery. The distribution of life history stages and different feeding areas does not rule out the possibility that discrete populations of L. reynaudii with different biological characteristics inhabit the western and eastern regions of the Agulhas Bank. In this hypothesis, some mixing of the populations does occur but generally squid from the western Agulhas Bank may occur in smaller numbers, grow more slowly and mature at a larger size. Spawning occurs on the western portion of the Agulhas Bank, and juveniles grow and mature on the west coast and the central Agulhas Bank. Future research requirements include the elucidation of the age structure of chokka squid both spatially and temporally, and a comparison of the statolith chemistry and genetic characterisation between adults from different spawning areas across the Agulhas Bank.     

Isolation and characterization of polymorphic microsatellites in the Trinidadian guppy (Poecilia reticulata)

We isolated microsatellite loci for the Trinidadian guppy Poecilia reticulata from the Oropuche and Caroni drainages in Trinidad, using a modified enrichment protocol that provided 93% enriched libraries. The eight loci presented here are polymorphic, and have between seven and 18 alleles in 33–48 individuals initially screened. Observed heterozygosities in this sample range from 0.28 to 0.88. These loci significantly increase the number of polymorphic microsatellite markers available for paternity and population analysis in this species.     

The locomotory function of the fins in the squid Loligo pealei

Kinematic data of high spatial and temporal resolution, acquired from image sequences of adult long-finned squid, Loligo pealei, during steady swimming in a flume, were used to examine the role of fins and the coordination between fin and jet propulsion in squid locomotion. Fin shape and body outlines were digitized and used to calculate fin wave speed, amplitude, frequency, angle of attack, body deformation, speed, and acceleration. L. pealei were observed to have two fin gait patterns with a transition at 1.4-1.8 mantle lengths per second (Lm s-1) marked by alternation between the two patterns. Fin motion in L. pealei exhibited characteristics of both traveling waves and flapping wings. At low speeds, fin motion was more wave-like; at high speeds, fin motion was more flap-like and was marked by regular periods during which the fins were wrapped tightly against the mantle. Fin cycle frequencies were dependent on swimming speed and gait, and obvious coordination between the fins and jet were observed. Fin wave speed, angle of attack, and body acceleration confirmed the role of fins in thrust production and revealed a role of fins at all swimming speeds by a transition from drag-based to lift-based thrust when fin wave speed dropped below swimming speed. Estimates of peak fin thrust were as high as 0.44-0.96 times peak jet thrust in steady swimming over the range of swimming speeds observed. Fin downstrokes generally contributed more to thrust than did upstrokes, especially at high speeds.     

The locomotory function of the fins in the squid Loligo pealei

Kinematic data of high spatial and temporal resolution, acquired from image sequences of adult long-finned squid, Loligo pealei, during steady swimming in a flume, were used to examine the role of fins and the coordination between fin and jet propulsion in squid locomotion. Fin shape and body outlines were digitized and used to calculate fin wave speed, amplitude, frequency, angle of attack, body deformation, speed, and acceleration. L. pealei were observed to have two fin gait patterns with a transition at 1.4-1.8 mantle lengths per second (L_m s^-1) marked by alternation between the two patterns. Fin motion in L. pealei exhibited characteristics of both traveling waves and flapping wings. At low speeds, fin motion was more wave-like; at high speeds, fin motion was more flap-like and was marked by regular periods during which the fins were wrapped tightly against the mantle. Fin cycle frequencies were dependent on swimming speed and gait, and obvious coordination between the fins and jet were observed. Fin wave speed, angle of attack, and body acceleration confirmed the role of fins in thrust production and revealed a role of fins at all swimming speeds by a transition from drag-based to lift-based thrust when fin wave speed dropped below swimming speed. Estimates of peak fin thrust were as high as 0.44-0.96 times peak jet thrust in steady swimming over the range of swimming speeds observed. Fin downstrokes generally contributed more to thrust than did upstrokes, especially at high speeds.     

Isolation and characterization of highly polymorphic microsatellites in tea (Camellia sinensis)

Relatively little is known about the diversity and origins of tea. The highest value tea products are sold on the basis of their region of origin but there are currently no methods available to verify the claims made on packages. We have developed 15 microsatellite loci for tea. These have been evaluated for polymorphism in a set of tea clones to determine their usefulness for authentication purposes. The majority of the microsatellites developed proved to be highly polymorphic both between and within different geographical origins and offer the potential to investigate the population genetics and genetic origins of tea.     

Determining the daily spawning cycle of the chokka squid, Loligo reynaudii off the South African Coast

The study investigated the duration and peak of the daily spawning cycle of the chokka squid Loligo reynaudii, and the possibility of estimating the spawning frequency by means of classification and grouping (by age) of post-ovulatory follicles. Post-ovulatory follicles were classified into three types: new, intermediate or old, based in part on the degree of resorption of the follicles determined from histological sections. Ovulation in this species appears to be a rapid process, seen by the occurrence of both mature oocytes and post-ovulatory follicles in partially spent ovaries. Results suggest that chokka squid present a diel timing of spawning, with successive periods of egg accumulation at night, interrupted by periods of active spawning during the day. The ovarian cycle for this species appears typical of serial spawners. During the spawning phase ovaries go through ripe, partially spent and recovering stages by undergoing a process of maturation, ovulation and redeveloping, where a new batch of advanced oocytes is recruited. The cycle typically appears to last between 24 and 36 h, and may depend on a number of factors such as environmental conditions and the presence of predators. The short-lived (about 14 h) nature of the post-ovulatory follicles precludes the calculation of the exact spawning interval and does not allow us to accurately predict the spawning frequency. Together with the degree of oviduct fullness they do however give a good indication of imminent or recent spawning.     

Isolation and characterization of microsatellites in European alpine marmots (Marmota marmota)

For future investigations of the mating system of a highly social mammal (Marmota marmota), we identified 16 new microsatellites using an enrichment protocol. Five loci were revealed to be polymorphic. The polymorphism was rather low (two to six alleles among 24 individuals). However, these markers, added to the other six published microsatellites for M. marmota and Spermophilus citellus, will help to assess dispersal patterns and test for genetic monogamy in alpine marmots from the European Alps.     

Polymorphic microsatellite DNA markers for the Patagonian squid,Loligo gahi (Cephalopoda)

Squid populations are being put under rapidly increasing commercial fishing pressure worldwide. The same species are known to be susceptible to extreme population fluctuations, so detailed knowledge of population substructuring and genetic diversity is essential for rational management. We present a set of microsatellite DNA loci suitable for population genetic analysis of Loligo gahi, the squid species subject to the most detailed monitoring and fishery control (around the Falkland Islands), with the future aim of generating management‐related information to aid conservation of this valuable natural resource.     

Subtle population structuring within a highly vagile marine invertebrate, the veined squid Loligo forbesi, demonstrated with microsatellite DNA markers

Microsatellite DNA markers were applied for the first time in a population genetic study of a cephalopod and compared with previous estimates of genetic differentiation obtained using allozyme and mitochondrial DNA (mtDNA) markers. Levels of genetic variation detected with microsatellites were much higher than found with previous markers (mean number of alleles per locus=10.6, mean expected heterozygosity ( H _E)=0.79; allozyme H _E=0.08; mtDNA restriction fragment length polymorphism (RFLP) H _E=0.16). In agreement with previous studies, microsatellites demonstrated genetic uniformity across the population occupying the European shelf seas of the North East Atlantic, and extreme genetic differentiation of the Azores population ( R _ST/ F _ST=0.252/0.245; allozyme F _ST=0.536; mtDNA F _ST=0.789). In contrast to other markers, microsatellites detected more subtle, and significant, levels of differentiation between the populations of the North East Atlantic offshore banks (Rockall and Faroes) and the shelf population ( R _ST=0.048 and 0.057). Breakdown of extensive gene flow among these populations is indicated, with hydrographic (water depth) and hydrodynamic (isolating current regimes) factors suggested as possible barriers to migration. The demonstration of genetic subdivision in an abundant, highly mobile marine invertebrate has implications for the interpretation of dispersal and population dynamics, and consequent management, of such a commercially exploited species. Relative levels of differentiation indicated by the three different marker systems, and the use of measures of differentiation (assuming different mutation models), are discussed.     

Isolation and characterization of 10 highly polymorphic di- and trinucleotide microsatellite markers in the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae)

We describe the isolation of ten polymorphic microsatellite loci from the mayfly Ameletus inopinatus. Loci had di‐ or trinucleotide repeat motifs and were highly variable with three to 17 alleles (mean = 7.15). Observed heterozygosity ranged from 0.143 to 0.905. One locus (Ami_202) showed significant deviation from Hardy–Weinberg equilibrium in one population, but no evidence for null alleles. One locus (Ami_73) was significantly linked with three other loci. The remaining nine loci should prove highly informative for population genetic studies.     

Cloning of highly polymorphic microsatellites in the horse

We have isolated equine microsatellites by screening a genomic library with (TG)n and (TC)n probes. TG microsatellites were found to be more abundant than TC repeats, with an estimated frequency of one per 100,000bp. Sequence analysis of eight TG-positive clones revealed varying structures of the repeat regions; perfect stretches of TG repeats, imperfect stretches of TG repeats and compound regions of TG and TC repeats. Five loci were analysed by PCR and showed extensive polymorphism; three to seven alleles and heterozygosities of 0.40-0.76 were observed when screening 20-30 unrelated individuals. The high degree of polymorphism, their abundance and the possibility of automating the typing procedure make these loci ideal for standardized paternity testing in the horse. Furthermore, we demonstrate that single hairs can be used as starting material for the PCR analysis.     

Isolation and characterization of microsatellites in a perennial Apiaceae,Eryngium alpinum L.

In order to investigate the genetic structure in an endangered Alpine plant (Eryngium alpinum L.), we developed microsatellites. Two different approaches were used: an enrichment protocol and the classical technique of hybridization on nylon membranes. We identified 25 loci, 13 of which revealed to be polymorphic. The polymorphism was rather low (2–6 alleles; H_E = 0.49 ± 0.16), probably due to the short size of microsatellites (6–10 dinucleotide repeats) and to the fine spatial scale investigated. However, these markers are expected to provide a new insight about the genetic processes at work within and among E. alpinum populations.     

Species‐specific microsatellite loci for the European squid (Loligo vulgaris)

A microsatellite dinucleotide‐enriched library was obtained from the European squid (Loligo vulgaris) and five species‐specific dinucleotide markers were optimized. These markers are highly polymorphic with average expected heterozygosity ranging from 0.706 to 0.927 and allele number ranging from 7 to 17. This set of primers is suitable for population genetic studies.     

Isolation and characterization of polymorphic microsatellites in Iris ensata (Iridaceae)

• Premise of the study: Microsatellite primers were developed in Iris ensata (Iridaceae) to provide polymorphic markers for further studies into population genetics. • Methods and Results: Thirteen polymorphic microsatellite loci were isolated from I. ensata. These loci were successfully amplified in two natural populations of I. ensata from eastern China (Longwangshan, Zhejiang Province) and northeastern China (Jinchuan, Jilin Province). There was no significant linkage disequilibrium found for any pair of loci. These loci contained between two and 12 alleles per locus across all 48 individuals of I. ensata. The number of alleles per locus varied from two to 10 at the population level and the observed and expected heterozygosities ranged from 0.167 to 0.958 and from 0.284 to 0.853, respectively. • Conclusions: These loci showed high levels of polymorphism and could be used to study the population genetic structure, genetic relationships, and phylogeography of I. ensata.     

Isolation and characterization of microsatellites in giant freshwater prawn Macrobrachium rosenbergii

Microsatellite loci were characterized in a freshwater prawn from enriched genomic library using six biotinylated probes: (AG)₁₀, (TG)₁₀, (CAA)₁₀, (CAG)₁₀, (GAT)₁₀ and (TAC)₁₀. Primers for DNA amplification were designed and synthesized for 20 loci. Ten loci were polymorphic with the number of alleles ranging from five to 17 alleles per locus and the observed heterozygosity ranging from 0.27 to 0.83 per locus. Developed microsatellite primers should prove useful for selective breeding programs and population genetic studies of freshwater prawn.     

Isolation and characterization of 15 polymorphic microsatellites in the Plethodontid salamander Ensatina eschscholtzii

We developed 15 new polymorphic microsatellites for the plethodontid salamander Ensatina eschscholtzii. Loci were isolated from a genomic library from Ensatina eschscholtzii xanthoptica enriched for (AAAG)(n) repetitive elements. The number of alleles per locus ranged from 4 to 20 (mean 9) in the sampled population. Observed heterozygosity ranged from 0.37 to 1. None of the loci deviated from Hardy-Weinberg equilibrium or showed significant linkage disequilibrium after a Bonferroni correction for multiple comparisons. All loci amplified in the six other subspecies of the Ensatina eschscholtzii complex. These new markers will prove useful in measuring gene flow and population structure as well as patterns of mating and sperm use in Ensatina.     

Isolation and characterization of polymorphic microsatellite loci in the plural cooperatively breeding superb starling,Lamprotornis superbus

Superb starlings (Lamprotornis superbus) are separate nesting plural cooperative breeders endemic to East Africa that show high levels of reproductive conflict and low reproductive skew. I isolated 31 polymorphic microsatellite loci from the superb starling genome and characterized them in approximately 31 individuals. The numbers of alleles per locus ranged from two to 16 and observed heterozygosities ranged from 0.03 to 0.88. Many of these loci amplified in other passerine species including the European starling, Sturnus vulgaris, and a variety of other starlings and mockingbirds.     

Microsatellites reveal high levels of gene flow among populations of the California squid Loligo opalescens

Information on the extent of genetic differentiation among populations of the squid Loligo opalescens is crucial for the conservation of this commercially utilized species. We analysed six highly variable microsatellite loci in 11 collections of L. opalescens from different locations and spawning seasons to estimate the relative influence of two major evolutionary forces, gene flow and genetic drift. Microsatellite allele frequency patterns suggest that gene flow prevents population differentiation in L. opalescens. Tests for genetic differentiation showed homogeneity of the samples with an overall FST/RST of 0.0028/-0.0013. Genetic uniformity among samples from different year classes indicates that allele frequency patterns in L. opalescens are relatively stable over time. However, a more complete and detailed picture of fine-scale allele frequency shifts in this species will require a systematic microsatellite analysis of local populations over consecutive spawning cycles.