Limited genetic structure of Gulf Menhaden (Brevoortia patronus), as revealed by microsatellite markers developed for the genus Brevoortia (Clupeidae)

Long-term sustainable management of wild populations should be based on management actions that account for the genetic structure among populations. Knowledge of genetic structure and of the degree of demographic exchange between discreet [sic] populations allows managers to better define management units. However, adequate gene loci for population assessments are not always available. In this study, variable co-dominant DNA loci in the heavily exploited marine genus Brevoortia were developed with a microsatellite-enriched DNA library for the Gulf Menhaden (Brevoortia patronus). Microsatellite marker discovery was followed by genetic characterization of 4 endemic North American Brevoortia species, by using 14 novel loci as well as 5 previously described loci. Power analysis of these loci for use in species identification and genetic stock structure was used to assess their potential to improve the stock definition in the menhaden fishery of the Gulf of Mexico. These loci could be used to reliably identify menhaden species in the Gulf of Mexico with an estimated error rate of α=0.0001. Similarly, a power analysis completed on the basis of observed allele frequencies in Gulf Menhaden indicated that these markers can be used to detect very small levels of genetic divergence (Fst≈0.004) among simulated populations, with sample sizes as small as n=50 individuals. A cursory analysis of genetic structure among Gulf Menhaden sampled throughout the Gulf of Mexico indicated limited genetic structure among sampling locations, although the available sampling did not reach the target number (n=50) necessary to detect minimal values of significant structure.

Demographic assessment of the blue crab (Callinectes sapidus) in Chesapeake Bay using extractable lipofuscins as age markers

The blue crab (Callinectes sapidus) plays an important economic and ecological role in estuaries and coastal habitats from the Gulf of Mexico to the east coast of North America, but demographic assessments are limited by length-based methods. We applied an alternative aging method using biochemical measures of metabolic byproducts (lipofuscins) sequestered in the neural tissue of eyestalks to examine population age structure. From Chesapeake Bay, subsamples of animals collected from the 1998–99 (n=769) and 1999–2000 (n=367) winter dredge surveys were collected and lipofuscin was measured. Modal analysis of the lipofuscin index provided separation into three modes, whereas carapace-width data collected among the same individuals showed two broad modes. Lipofuscin modal analysis indicated that most adults (carapace width >120 mm) were <2 years old. The results indicate that use of extractable lipofuscin can provide a more accurate and better resolved estimation of demographic structure of blue crab populations in the field than size alone.

Nuclear and mitochondrial DNA markers for specific identification of istiophorid and xiphiid billfishes

Independent molecular markers based on mitochondrial and nuclear DNA were developed to provide positive identification of istiophorid and xiphiid billfishes (marlins, spearfishes, sailfish, and swordfish). Both classes of markers were based on amplification of short segments (<1.7 kb) of DNA by the polymerase chain reaction and subsequent digestion with informative restriction endonucleases. Candidate markers were evaluated for their ability to discriminate among the different species and the level of intraspecific variation they exhibited. The selected markers require no more than two restriction digestions to allow unambiguous identification, although it was not possible to distinguish between white marlin and striped marlin with any of the genetic characters screened in our study. Individuals collected from throughout each species’ range were surveyed with the selected markers demonstrating low levels of intraspecific character variation within species. The resulting keys provide two independent means for the forensic identification of fillets and for specific identification of early life history stages.

Origin of immature loggerhead sea turtles (Caretta caretta) at Hutchinson Island, Florida: evidence from mtDNA markers

Loggerhead sea turtles (Caretta caretta) are migratory, long-lived, and slow maturing. They are difficult to study because they are seen rarely and their habitats range over vast stretches of the ocean. Movements of immature turtles between pelagic and coastal developmental habitats are particularly difficult to investigate because of inadequate tagging technologies and the difficulty in capturing significant numbers of turtles at sea. However, genetic markers found in mitochondrial DNA (mtDNA) provide a basis for predicting the origin of juvenile turtles in developmental habitats. Mixed stock analysis was used to determine which nesting populations were contributing individuals to a foraging aggregation of immature loggerhead turtles (mean 63.3 cm straight carapace length [SCL]) captured in coastal waters off Hutchinson Island, Florida. The results indicated that at least three different western Atlantic loggerhead sea turtle subpopulations contribute to this group: south Florida (69%), Mexico (20%), and northeast Florida-North Carolina (10%). The conservation and management of these immature sea turtles is complicated by their multinational genetic demographics.

Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker-based analysis reveals cattle-specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY(cattle) = 2.66 +/- 0.53% and Q(cattle) = 0.69 +/- 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai-Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak-cattle hybridization is primarily driven to produce F-1 hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make-up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.

Use of allozyme markers to determine the genetic structure of hatchery population of Thai pangas, Pangasius hypophthalmus of Jessore, Bangladesh

Genetic structure of hatchery population of Thai pangas (Pangasius hypophthalmus) of Jessore region, Bangladesh has been investigated from 1 January 2004 to 31 December 2004. Samples for this study were collected from five fish hatcheries viz. Asrom, Banchte Shekha, Chowdhury, Maola and Rezaul Haque. The enzymes were encoded by 15 gene loci: Adh-1*, Est-1*, G3pdh-2*, Gpi-1*, Gpi-2*, Idhp-1*, Idhp-2*, Ldh-1*, Ldh-2*, Mdh-1*, Mdh-2*, Pgm*, Sdh-1*, Sdh-2* and Sod*. Among them four (Est-1*, G3pdh-2*, Gpi-2*and Pgm*) were found to be polymorphic in different populations but only Gpi-2* was polymorphic in all the sampled populations. The mean proportion of polymorphic loci per population was the highest (26.7%) in Banchte Shekha hatchery while the mean proportion of heterozygous loci was 13.33% per individual in Banchte Shekha and Maola hatcheries. The UPGMA dendrogram of Nei's (1972) genetic distances indicated a relationship between the genetic distance and geographical difference. High genetic variability in stocks of Thai pangas was observed in the Banchte Shekha and Maola hatcheries and less variability was found in the other three hatcheries.

A markov chain Monte Carlo method for estimating population mixing using Y-chromosome markers: Mixing of the Han people in China

We present a new approach for estimating mixing between populations based on non-recombining markers, specifically Y-chromosome microsatellites. A Markov chain Monte Carlo (MCMC) Bayesian statistical approach is used to calculate the posterior probability

Co-expression of CD173 (H2) and CD174 (Lewis Y) with CD44 suggests that fucosylated histo-blood group antigens are markers of breast cancer-initiating cells

Histo-blood group antigens CD173 (H2) and CD174 (Lewis Y) are known to be developmentally regulated carbohydrate antigens which are expressed to a varying degree on many human carcinomas. We hypothesized that they might represent markers of cancer-initiating cells (or cancer stem cells, CSC). In order to test this hypothesis, we examined the co-expression of CD173 and CD174 with stem cell markers CD44 and CD133 by flow cytometry analysis, immunocytochemistry, and immunohistochemistry on cell lines and tissue sections from breast cancer. In three breast cancer cell lines, the percentage of CD173(+)/CD44(+) cells ranged from 17% to > 60% and of CD174(+)/CD44(+) from 21% to 57%. In breast cancer tissue sections from 15 patients, up to 50% of tumor cells simultaneously expressed CD173, CD174, and CD44 antigens. Co-expression of CD173 and CD174 with CD133 was also observed, but to a lesser percentage. Co-immunoprecipitation and sandwich ELISA experiments on breast cancer cell lines suggested that CD173 and CD174 are carried on the CD44 molecule. The results show that in these tissues CD173 (H2) and CD174 (LeY) are associated with CD44 expression, suggesting that these carbohydrate antigens are markers of cancer-initiating cells or of early progenitors of breast carcinomas.