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Biomedical subjects

S A Karl

Publications and source records attributed to S A Karl.

11 recordsLinked to original sources
PubMed2000

Evolution of poecilogony and the biogeography of North American populations of the polychaete Streblospio.

Invertebrate interspecific developmental patterns can be highly variable and, taxonomically, are considered only weakly constrained. Intraspecifically, some invertebrate species possess multiple developmental modes-a condition known as poecilogony. Closer examination of most putative poecilogenous species, however, has not supported poecilogony, but rather has uncovered hidden or cryptic species. The polychaete Streblospio benedicti is a well-known, poecilogenous species found along the coast of North America. We collected mitochondrial cytochrome subunit I DNA sequence data from 88 individuals taken from 11 locations along the Atlantic, Gulf, and Pacific Coasts of the United States to provide a phylogenetic framework from which to interpret intraspecific variation in larval life history and brooding structure morphology in this species. Our results are consistent with a recent revision of the species into two separate species: S. benedicti, a pouched brooding form distributed along the Atlantic and Pacific Coasts, and S. gynobranchiata, a branchiate brooding form in the Gulf of Mexico. Contrary to the redescription, S. benedicti is paraphyletic because the pouched brooding population in Vero Beach, Florida shows strong genetic affinity with Gulf of Mexico populations (S. gynobranchiata). However, S. benedicti is a true poecilogenous species, with both lecithotrophic and planktotrophic individuals possessing identical mitochondrial DNA haplotypes. Crossbreeding experiments further support the molecular phylogeny with reproductive isolation demonstrated between, but not within, the major phylogenetic clades consistent with the previously described species. The genetic break near Vero Beach, Florida, corresponds to a well-known phylogeographic boundary, but the estimated time of separation for the Streblospio spp., approximately 10 million years before present, predates all other known phylogeographic subdivisions in this area. This suggests that biogeographic sundering in this region is a recurrent event. Divergence times within the major Streblospio spp. clades are recent and indicate that changes in larval life history as well as brooding structure morphology are highly plastic and can evolve rapidly.

Animals↗
PubMed1999

The bounded complexity of DNA computing.

This paper proposes a new approach to analyzing DNA-based algorithms in molecular computation. Such protocols are characterized abstractly by: encoding, tube operations and extraction. Implementation of these approaches involves encoding in a multiset of molecules that are assembled in a tube having a number of physical attributes. The physico-chemical state of a tube can be changed by a prescribed number of elementary operations. Based on realistic definitions of these elementary operations, we define complexity of a DNA-based algorithm using the physico-chemical property of each operation. We show that new algorithms for Hamiltonian path are about twice as efficient as Adleman's original one and that a recent algorithm for Max-Clique provides a similar increase in efficiency. Consequences of this approach to tube complexity and DNA computing are discussed.

Algorithms↗
PubMed1999

Three dimensional DNA structures in computing.

We show that 3-dimensional graph structures can be used for solving computational problems with DNA molecules. Vertex building blocks consisting of k-armed (k = 3 or 4) branched junction molecules are used to form graphs. We present procedures for the 3-SAT and 3-vertex-colorability problems. Construction of one graph structure (in many copies) is sufficient to determine the solution to the problem. In our proposed procedure for 3-SAT, the number of steps required is equal to the number of variables in the formula. For the 3-vertex-colorability problem, the procedure requires a constant number of steps regardless of the size of the graph.

Animals↗
PubMed1998

Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci.

Among vertebrates, cichlid fishes are the paradigmatic example of adaptive radiation and ecological specialization. In turn, molecular genetic studies of cichlids have focused primarily on more recently diverged groups. Here, we present an evolutionary hypothesis of the major lineages of cichlid fishes based on DNA sequence data from two nuclear loci. One marker, Tmo-4C4, is a single-copy locus containing a region of amino acid similarity to the muscle protein TITIN. Flanking sequence from a second, microsatellite, locus Tmo-M27, shows similarity to mammalian RAS guanine nucleotide-releasing factor. We compare and combine data from these loci to evaluate phylogenetic performance. In separate and combined analyses, the sequence data support and clarify previous morphological hypotheses of cichlid major-group relationships. Indian and Malagasy cichlids form a basal, paraphyletic group. Neotropical cichlids are the sister clade to an African assemblage composed of the paraphyletic west and Pan-African lineages and a group of east African rift lake taxa. We use a consensus phylogeny of the Cichlidae to trace evolutionary changes in the microsatellite repeat motif at Tmo-M27. Analysis reveals that the repeat region was nearly lost in the ancestor to cichlids and then amplified extensively in African taxa. Results demonstrate that the two new DNA markers could be widely applied in perciform systematics. Furthermore, the comparative approach can unveil mutational dynamics of simple-sequence repeat loci over long periods of fish evolution. Simple-sequence repeat regions are increasingly being found in introns of important regulatory genes. We address issues involving their function and suggest caution in making assumptions of strict neutrality.

Animals↗
PubMed1997

Reconstructing labroid evolution with single-copy nuclear DNA.

Fifteen per cent of all living fishes are united in a single suborder (Labroidei) and display a dazzling array of behavioural and ecological traits. The labroids are considered monophyletic and members share a pharyngeal jaw apparatus (PJA) modified for crushing and processing prey. Outside of the explicitly functional PJA, there is no corroborative evidence for a monophyletic Labroidei. Here, we report the first molecular phylogenetic analysis of the suborder. Contrary to morphology-based phylogenies, our single-copy nuclear DNA data do not support labroid families as a natural group. Our data indicate that pharyngognathy has evolved independently among labroid families and that characters of the PJA are not reliable markers of perciform evolution. This work 'crushes' conventional views of fish phylogeny and should engender novel concepts of piscine life history evolution.

Animals↗
PubMed1996

Anonymous nuclear DNA markers in the American oyster and their implications for the heterozygote deficiency phenomenon in marine bivalves.

A puzzling population-genetic phenomenon widely reported in allozyme surveys of marine bivalves is the occurrence of heterozygote deficits relative to Hardy-Weinberg expectations. Possible explanations for this pattern are categorized with respect to whether the effects should be confined to protein-level assays or are genomically pervasive and expected to be registered in both protein- and DNA-level assays. Anonymous nuclear DNA markers from the American oyster were employed to reexamine the phenomenon. In assays based on the polymerase chain reaction (PCR), two DNA-level processes were encountered that can lead to artifactual genotypic scorings: (a) differential amplification of alleles at a target locus and (b) amplification from multiple paralogous loci. We describe symptoms of these complications and prescribe methods that should generally help to ameliorate them. When artifactual scorings at two anonymous DNA loci in the American oyster were corrected, Hardy-Weinberg deviations registered in preliminary population assays decreased to nonsignificant values. Implications of these findings for the heterozygote-deficit phenomenon in marine bivalves, and for the general development and use of PCR-based assays, are discussed.

Alleles↗
PubMed1993

PCR-based assays of mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics.

This paper outlines a PCR-based approach for population genetics that offers several advantages over conventional Southern blotting methods for revealing restriction-fragment-length polymorphisms (RFLPs) in nuclear DNA. Primers are constructed from clones isolated from a nuclear DNA library, and these primers subsequently are employed in in vitro syntheses of homologous regions. Amplified products are then screened directly for RFLPs by using gel-staining procedures. Population applications for this PCR-based approach, including potential strengths and weaknesses, are exemplified by two RFLP data sets generated to estimate (a) male-mediated gene flow in the green turtle (Chelonia mydas) and (b) geographic population genetic structure in the American oyster (Crassostrea virginica). Restriction assays of amplified products from 14 or 15 independent primer pairs in each species revealed polymorphisms at several loci that proved highly informative in the population genetic analyses. In general, the Mendelian polymorphisms produced by this PCR-based approach will provide useful genetic markers for population studies, particularly in situations where simpler and less expensive allozyme methods have failed, for whatever reason, to provide adequate information.

Animals↗
PubMed1992

Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs.

Population genetic analyses that depend on the assumption of neutrality for allozyme markers are used widely. Restriction fragment length polymorphisms in nuclear DNA of the American oyster evidence a pronounced population subdivision concordant with mitochondrial DNA. This finding contrasts with a geographic uniformity in allozyme frequencies previously thought to reflect high gene flow mediated by the pelagic gametes and larvae. The discordance likely is due to selection on protein electrophoretic characters that balances allozyme frequencies in the face of severe constraints to gene flow. These results raise a cautionary note for studies that rely on assumptions of neutrality for allozyme markers.

Alleles↗
PubMed1992

Global population genetic structure and male-mediated gene flow in the green turtle (Chelonia mydas): RFLP analyses of anonymous nuclear loci.

We introduce an approach for the analysis of Mendelian polymorphisms in nuclear DNA (nDNA), using restriction fragment patterns from anonymous single-copy regions amplified by the polymerase chain reaction, and apply this method to the elucidation of population structure and gene flow in the endangered green turtle, Chelonia mydas. Seven anonymous clones isolated from a total cell DNA library were sequenced to generate primers for the amplification of nDNA fragments. Nine individuals were screened for restriction site polymorphisms at these seven loci, using 40 endonucleases. Two loci were monomorphic, while the remainder exhibited a total of nine polymorphic restriction sites and three size variants (reflecting 600-base pair (bp) and 20-bp deletions and a 20-bp insertion). A total of 256 turtle specimens from 15 nesting populations worldwide were then scored for these polymorphisms. Genotypic proportions within populations were in accord with Hardy-Weinberg expectations. Strong linkage disequilibrium observed among polymorphic sites within loci enabled multisite haplotype assignments. Estimates of the standardized variance in haplotype frequency among global collections (FST = 0.17), within the Atlantic-Mediterranean (FST = 0.13), and within the Indian-Pacific (FST = 0.13), revealed a moderate degree of population substructure. Although a previous study concluded that nesting populations appear to be highly structured with respect to female (mitochondrial DNA) lineages, estimates of Nm based on nDNA data from this study indicate moderate rates of male-mediated gene flow. A positive relationship between genetic similarity and geographic proximity suggests historical connections and/or contemporary gene flow between particular rookery populations, likely via matings on overlapping feeding grounds, migration corridors or nonnatal rookeries.

Animals↗
PubMedDate not supplied

Hybridization among the ancient mariners: characterization of marine turtle hybrids with molecular genetic assays.

Reports of hybridization between marine turtle species (family Cheloniidae) have been difficult to authenticate based solely on morphological evidence. Here we employ molecular genetic assays to document the sporadic, natural occurrence of viable interspecific hybrids between species representing four of the five genera of cheloniid sea turtles. Using multiple DNA markers from single-copy nuclear loci, eight suspected hybrids (based on morphology) were confirmed to be the products of matings involving the loggerhead turtle (Caretta caretta) x Kemp's ridley (Lepidochelys kempii) (N = 1 specimen), loggerhead turtle x hawksbill (Eretmochelys imbricata) (N = 2), loggerhead turtle x green turtle (Chelonia mydas) (N = 4), and green turtle x hawksbill (N = 1). Molecular markers from mitochondrial DNA permitted identification of the maternal parental species in each cross. The species involved in these hybridization events represent evolutionary lineages thought to have separated 10-75 million years ago (mya) and thus may be among the oldest vertebrate lineages capable of producing viable hybrids in nature. In some cases, human intervention with the life cycles of marine turtles (e.g., through habitat alteration, captive rearing, or attempts to establish new breeding sites) may have increased the opportunities for interspecific hybridization.

Animals↗