The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. III. Techniques and potential applications

Assembly-free quantification of vagrant DNA inserts

Inserts of DNA from extranuclear sources, such as organelles and microbes, are common in eukaryote nuclear genomes. However, sequence similarity between the nuclear and extranuclear DNA, and a history of multiple insertions, make the assembly of these regions challenging. Consequently, the number, sequence and location of these vagrant DNAs cannot be reliably inferred from the genome assemblies of most organisms. We introduce two statistical methods to estimate the abundance of nuclear inserts even in the absence of a nuclear genome assembly. The first (intercept method) only requires low-coverage (<1×) sequencing data, as commonly generated for population studies of organellar and ribosomal DNAs. The second method additionally requires that a subset of the individuals carry extranuclear DNA with diverged genotypes. We validated our intercept method using simulations and by re-estimating the frequency of human NUMTs (nuclear mitochondrial inserts). We then applied it to the grasshopper Podisma pedestris, exceptional for both its large genome size and reports of numerous NUMT inserts, estimating that NUMTs make up 0.056% of the nuclear genome, equivalent to >500 times the mitochondrial genome size. We also re-analysed a museomics data set of the parrot Psephotellus varius, obtaining an estimate of only 0.0043%, in line with reports from other species of bird. Our study demonstrates the utility of low-coverage high-throughput sequencing data for the quantification of nuclear vagrant DNAs. Beyond quantifying organellar inserts, these methods could also be used on endosymbiont-derived sequences. We provide an R implementation of our methods called "vagrantDNA" and code to simulate test data sets.

Taenia asiatica: Historical overview of taeniasis and cysticercosis with molecular characterization

Asian Taenia is a human-infecting Taenia tapeworm known as Taenia asiatica following morphological examination of adult and larval stages of the tapeworm by Eom and Rim (1993). The life cycle of T. asiatica differs from that of T. saginata in its intermediate host (pigs versus cattle) as well as in the infected organs (liver versus muscle). T. asiatica can be differentiated from T. solium and T. saginata by examination of morphological characteristics such as the scolex, mature and gravid proglottids in the adult stage, and the scolex and bladder surface in the larval stage. T. asiatica has been identified in Korea, Taiwan, the Philippines, China, Thailand, Indonesia, Vietnam, Japan, Lao PDR, Nepal and India. The molecular tools employed for T. asiatica identification have been developed to differentiate T. asiatica from other human-infecting Taenia tapeworms based on genetic information such as nucleotide sequence of mitochondrial genes, nuclear ribosomal genes and nuclear genes that lead to development of the subsequent molecular techniques, such as PCR-RFLP, PCR-RAPD, BESST-base, LAMP and qPCR. Investigation of the phylogenetic relationships among human Taenia species revealed that T. asiatica is a sister species with T. saginata, which is genetically more similar than other Taenia species in terms of the nucleotide sequences of cox1, nad1 and 28S rDNA. The mitochondrial genomes of human Taenia tapeworms comprise 13,703bp (T. asiatica), 13,670bp (T. saginata) and 13,709bp (T. solium), and contain 36 genes including 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Sequence differences in the full genome of T. asiatica and T. saginata mitochondria is 4.6%, while T. solium differs by 11%. Hox gene orthology in T. asiatica was established by comparative analysis with Platyhelminthes Hox genes. T. asiatica Hox revealed six Hox orthologs including two lab/Hox1, two Hox3, one Dfd/Hox4 and one Lox/Lox4. Hybridization between T. asiatica and T. saginata was definitely observed in these species which are sympatrically endemic in the regions of Korea, Thailand, China and Lao PDR. Comparative analyses of T. asiatica, T. saginata and T. solium genomes were also reported with genome features. Taenia asiaticus nomen novum was proposed for T. asiaticaEom and Rim, 1993 which is a homonym of T. asiatica Linstow, 1901 (Davaineidae).

Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing

Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps. A comparison is made between libraries sequenced directly from native DNA and the same samples sequenced from libraries generated with nine overlapping mtDNA amplicons on the Oxford Nanopore MinION™ device. The native and amplicon library preparation methods and alternative base calling strategies were assessed to establish error rates and identify trends of discordance between the two library preparation approaches. For the complete mtGenome, 16 569 nucleotides, an overall error rate of approximately 1.00% was observed. As expected with mtDNA, the majority of error was detected in homopolymeric regions. The use of a modified basecaller that corrects for ambiguous signal in homopolymeric stretches reduced the error rate for both library preparation methods to approximately 0.30%. Our study indicates that direct mtDNA sequencing from native DNA on the MinION™ device provides comparable results to those obtained from common mtDNA sequencing methods and is a reliable alternative to approaches using PCR-enriched libraries.

Study on a 65-mer peptide mimetic enzyme with GPx and SOD dual function

Excessive reactive oxygen species (ROS) levels are harmful to the body. The peroxidase, GPx, and the superoxide dismutase, SOD, are important antioxidant enzymes for preventing ROS-induced damage. Se-CuZn-65P is an enzyme mimetic with dual GPx and SOD antioxidant function. However, currently, its production is mainly based on the cysteine auxotrophic expression technique, which is inefficient, expensive, and time consuming. In this study, we combined protein engineering and the chemical mutation method to synthesize Se-CuZn-65P. The DNA sequence encoding the 65 amino acid peptide with the desired sequence transformations to incorporate the SOD and the GPx catalytic sites was cloned and expressed in a soluble protein expression vector. The protein yield increased up to 152 mg/L, which is 10 times higher than in previous studies. The SOD and GPx activity of Se-CuZn-65P was high (1181 U/mg and 753 U/μmol, respectively). The binding constant of glutathione was 5.6 × 10⁴  L·mol^-1 , which shows that Se-CuZn-65P efficiently catalyzed hydrogen peroxide reduction by glutathione. Mitochondrial damage experiments confirmed the double protective role of the Se-CuZn-65P peptide and demonstrated functional synergy between the SOD and the GPx domains, which indicates its potential to be used in the treatment of ROS-related diseases. Our research may give a new thought to increase the yield of mimic.

EVOLUTION OF ASEXUALITY IN THE COSMOPOLITAN MARINE CLAM LASAEA

The marine clam genus Lasaea is unique among marine bivalves in that it contains both sexual and asexual lineages. We employed molecular tools to infer intrageneric relationships of geographically restricted sexual versus cosmopolitan asexual forms. Polymerase chain reaction primers were used to amplify and sequence homologous 624 nucleotide fragments of COIII from polyploid, asexual, direct-developing individuals representing northeastern Pacific, northeastern Atlantic, Mediterranean, southern Indian Ocean, and Australian populations. DNA sequences also were obtained from the two known diploid congeners, the Australian sexual, indirect developer, Lasaea australis, and an undescribed meiotic Australian direct developer. Estimated tree topologies did not support monophyly for polyploid asexual Lasaea lineages. A robust dichotomy was evident in all phylogenetic trees and each of the two main branches included one of the diploid meitoic Australian congeners. Lasaea australis clustered with two of the direct-developing, polyploid asexual haplotypes, one from Australia, the other from the northeastern Atlantic. Monophyly is supported for the diploid Australian direct-developing lineage together with the remaining polyploid asexual lineages from the northeastern Pacific, northeastern Atlantic, Mediterranean, and southern Indian Ocean. These results indicate that asexual Lasaea lineages are polyphyletic and may have resulted from multiple hybridization events. The high degree of genetic divergence of asexual lineages from co-clustering meiotic congeners (16%-22%) and among geographically restricted monophyletic clones (9%-11%) suggests that asexual Lasaea lineages may be exceptionally long lived.

EVOLUTIONARY ASSOCIATIONS OF BROOD PARASITIC FINCHES (VIDUA) AND THEIR HOST SPECIES: ANALYSES OF MITOCHONDRIAL DNA RESTRICTION SITES

The species-specific associations of the African brood parasitic finches Vidua with their estrildid finch host species may have originated by cospeciation with the host species or by later colonizations of new hosts. Predictions of these alternative models were tested in two species groups of brood parasites (indigobirds, paradise whydahs) and their hosts. Phylogenetic analyses suggested that the brood parasites and their hosts did not speciate in parallel. The parasitic indigobirds share mitochondrial haplotypes with each other, and species limits in both indigobirds and paradise whydahs do not correspond with their gene trees. Different parasite species within a region are more closely related to each other than any is to parasites that are associated with its same host species in other regions of Africa. There is little genetic difference between parasite species D̂_i,j < 0.001 in the indigobirds, D̂_i,j = 0.01 in the whydahs). Genetic distances D̂_i,j between the parasite species are less than the genetic distances between their corresponding host species in all parasite-host comparisons, and average only 7.2% as large in the indigobirds as in their hosts and 42% as large in the paradise whydahs as in their hosts. A phylogenetic model that allows ancestral haplotype polymorphisms to be retained in descendant species was compared to a constraint model of species monophyly requiring all but the one ancestral haplotype to be independently derived within each species. The constraint model increases the length of the indigobird tree by 50% over that of the model of retained ancestral polymorphisms; the difference is statistically significant. Both phylogenetic and distance analyses indicate that the brood parasites have become associated with their host species through host switches and independent colonizations of the hosts, rather than through parallel cospeciation with them. The molecular genetic results are supported by recent discoveries of additional host species that are associated with the indigobirds in the field and by variation in the species-specific song behaviors of the brood parasites.

DEVELOPMENT OF THE HYBRID SWARM BETWEEN PECOS PUPFISH (CYPRINODONTIDAE: CYPRINODON PECOSENSIS) AND SHEEPSHEAD MINNOW (CYPRINODON VARIEGATUS): A PERSPECTIVE FROM ALLOZYMES AND mtDNA

A comparison of allozyme and mtDNA frequencies was used for insight into a situation in the Pecos River, Texas where contact between the endemic pupfish (Cyprinodon pecosensis) and an introduced congener (C. variegatus) has resulted in rapid, geographically extensive genetic introgression. Temporal changes in mean frequencies of diagnostic allozyme markers indicate that the clinal pattern of introduced genetic material (Echelle and Connor 1989) is slowly decreasing in amplitude. Significant rank concordance in diagnostic allele frequencies among sites and across sampling years indicates directional influences upon temporal allele frequency change. These observations are consistent with the theory of gene flow in neutral clines. Levels of introgression indicated by each of four allozyme loci and mtDNA were roughly equivalent. The early history of the hybrid swarm is explained by genetic swamping, possibly mediated by selection for C. variegatus or C. variegatus × C. pecosensis, at a time when the normally abundant endemic species had been catastrophically depleted. High frequencies of an introduced GPI-A allele in all samples of intergrades suggests that the introduced genome originated with a single founding event.

ANALYSIS OF MITOCHONDRIAL DNA POLYMORPHISMS AMONG CHANNEL ISLAND DEER MICE

Mitochondrial DNA (mtDNA) from 131 deer mice, Peromyscus maniculatus, collected on the eight California Channel Islands and from seven southern California mainland locations, was isolated and analyzed for restriction endonuclease fragment polymorphisms. A total of 26 mtDNA genotypes were distinguishable among the deer mice sampled. All of the island samples had mtDNA restriction-fragment patterns not found among the mainland samples. Distributions of specific restriction-fragment patterns provide evidence for at least four separate colonization events to the Channel Islands. The estimated percentage of sequence divergence between all mtDNA's in this study was less than 1%, suggesting that colonization of the islands occurred fairly recently, probably within the last 500,000 years. Levels of mtDNA heterogeneity were much lower within island populations than within mainland populations.

HALDANE'S RULE AND SEX BIASSED GENE FLOW BETWEEN TWO HYBRIDIZING FLYCATCHER SPECIES (FICEDULA ALBICOLLIS AND F. HYPOLEUCA, AVES: MUSCICAPIDAE)

The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) hybridize where their geographic ranges overlap. Restriction fragment comparison of 5% of the mitochondrial genome showed a sequence divergence of 10% between these flycatcher species. This degree of sequence divergence between a closely related pair of bird species is unusually high and contrasts with the low level of divergence between F. albicollis and F. hypoleuca in nuclear genes (Nei's D = 0.0006) revealed by enzyme electrophoresis. The low nuclear differentiation is explained by sex biassed gene flow and introgression in nuclear genes (via fertile male hybrids), while the high mitochondrial DNA sequence divergence is preserved by sterility of female hybrids, which prevents mitochondrial introgression. This pattern is in accordance with Haldane's rule and is supported by field data on hybrid fertility. The high mtDNA differentiation could be explained by transfer of mitochondrial DNA from a third species during a past period of hybridization.

POPULATION GENETIC CONSEQUENCES OF DEVELOPMENTAL EVOLUTION IN SEA URCHINS (GENUS HELIOCIDARIS)

Within the sea urchin genus Heliocidaris, changes in early embryonic and larval development have resulted in dramatic differences in the length of time larvae spend in the plankton before settling. The larvae of one species, H. tuberculata, spend several weeks feeding in the plankton before settling and metamorphosing into juveniles. The other species, H. erythrogramma, has modified this extended planktonic larval stage and develops into a juvenile within 3-4 days after fertilization. We used restriction site polymorphisms in mitochondrial DNA to examine the population genetic consequences of these developmental changes. Ten restriction enzymes were used to assay the mitochondrial genome of 29 individuals from 2 localities for H. tuberculata and 62 individuals from 5 localities for H. erythrogramma. Within H. tuberculata, 11 mitochondrial genotypes were identified. A G_ST analysis showed high levels of genetic exchange between populations separated by 1,000 kilometers of open ocean. In contrast, in H. erythrogramma, 13 mitochondrial genotypes differing by up to 2.33% were geographically partitioned over spatial scales ranging from 800 to 3,400 kilometers. Between distant localities, there was complete mitochondrial lineage sorting and large sequence divergence between resulting clades. Over much smaller spatial scales (< 1,000 km), genetic differentiation was due to the differential sorting of very similar genotypes. This pattern of mitochondrial variation suggests that these population differences have arisen recently and may reflect the historical interplay between the restricted dispersal capabilities of H. erythrogramma and the climatic and geological changes associated with Pleistocene Ice Ages.

MITOCHONDRIAL DNA VARIATION IN THE FIELD VOLE (MICROTUS AGRESTIS): REGIONAL POPULATION STRUCTURE AND COLONIZATION HISTORY

Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.

ON THE ORIGIN OF INCIPIENT REPRODUCTIVE ISOLATION: THE CASE OF DROSOPHILA ALBOMICANS AND D. NASUTA

The nasuta subgroup of Drosophila consists of 12 known species classified within the immigrans group. D. nasuta and D. albomicans are two sibling species widely distributed throughout the Indo-Pacific tropics, which, although morphologically indistinguishable, have different meta-phase-chromosome configurations: chromosomes X and 3 are attached in D. albomicans, so that about 60% of its genes are sex-linked. Our experiments show that, at least in the laboratory, there is no sexual, mechanical, or gametic isolation between the two species. There is, however, hybrid "breakdown" expressed in three ways: 1) reduction in the number of F₂ hybrids produced per culture; 2) reduction in the fertility of F₂ (males) and F₃ (males and females) hybrid progenies; and 3) abnormal sex ratios in the progenies of crosses between strains of certain localities. In experimental populations, the karyotypes of both species are still present in substantial frequencies after 20 generations, although the frequencies of the two karyotypes vary depending on the geographic origin of the strains. Our results support the hypothesis that, in allopatry, the evolution of postzygotic isolation precedes that of prezygotic isolation. The mtDNA is polymorphic in both D. nasuta and D. albomicans and fairly similar between them. Assuming typical rates of mtDNA evolution, the two species would have diverged from each other about 500,000 years ago, whereas the African and Indian populations of D. nasuta (considered to be different subspecies by some authors) might have diverged some 350,000 years ago.

MITOCHONDRIAL-DNA RESTRICTION-SITE POLYMORPHISMS IN THE TELEOST FUNDULUS HETEROCLITUS SUPPORT SECONDARY INTERGRADATION

Fundulus heteroclitus is a highly polymorphic fish distributed along the Atlantic coast of North America. Several loci show directional changes in gene frequency with latitude (i.e., clines). Such directional changes have classically been described by two general models: primary and secondary intergradation. Previously, it has not been possible to distinguish between these models for Fundulus heteroclitus on the basis of allelic isozymes or morphological data. However, recent analysis of mitochondrial-DNA (mtDNA) restriction electromorphs helps resolve this issue. Mitochondrial-DNA samples from 48 individuals representing four populations were digested with 17 restriction endonucleases. After electrophoresis, the sizes of the mtDNA fragments were used to analyze the phylogenetic relatedness of fish collected over most of the species range. The analysis clearly identified two major races within the species: a northern and a southern form. The distribution of the mtDNA electromorphs, combined with zoogeographical changes in allelic isozymes and in eggs and adult morphologies (published elsewhere), makes the secondary-intergradation hypothesis most compelling.

DNA EVOLUTION AND COLONIZATION SEQUENCE OF ISLAND LIZARDS IN RELATION TO GEOLOGICAL HISTORY: MTDNA RFLP, CYTOCHROME B, CYTOCHROME OXIDASE, 12S RRNA SEQUENCE, AND NUCLEAR RAPD ANALYSIS

A novel source of nuclear DNA information from random amplified polymorphisms (RAPD) and a wide-range mitochondrial DNA information (cytochrome b, cytochrome oxidase, and 12s rRNA sequence, RFLP from 4-base and 6-base recognition endonucleases) are used to reconstruct the population phylogeny of the western Canary Island lizard, Gallotia galloti, which, for geological reasons, has been subject to dispersal but not vicariance. Interpretation of DNA phylogenies in terms of colonization sequence indicates that G. galloti arose in Tenerife and dispersed westward in two independent pathways: north from north Tenerife to La Palma, and south from south Tenerife to Gomera to Hierro. The direction and timing of colonization by DNA divergence is entirely compatible with geological time and sequence of island origin.

MITOCHONDRIAL DNA HOMOGENEITY IN THE PHENOTYPICALLY DIVERSE REDPOLL FINCH COMPLEX (AVES: CARDUELINAE: CARDUELIS FLAMMEA-HORNEMANNI)

Breeding redpoll finches (Aves: Carduelinae) show extensive plumage and size variability and, in many cases, a plumage polymorphism that is not related to age or sex. This has been ascribed to extreme phenotypic variation within a single taxon or to moderate variability within distinct taxa coupled with hybridization. The predominant view favors the recognition of two largely sympatric species: Carduelis flammea, comprised of four well-marked subspecies-flammea, cabaret, islandica, and rostrata; and C. hornemanni, comprised of two subspecies-hornemanni and exilipes. We studied representative samples of these putative subspecies (except islandica) for variation in mitochondrial DNA (mtDNA). Using 20 informative restriction enzymes that recognized 124 sites (642 base pairs [bp] of sequence or ≈ 3.7% of the molecule), we identified 17 RFLP haplotypes in the 31 individuals surveyed. The haplotypes formed a simple phylogenetic network with most clones diverging by a single site difference from a common haplotype found in almost half of the individuals. Within populations and taxa, levels of mtDNA diversity were similar to those observed in other avian species. The pattern of mtDNA divergence among populations was statistically unrelated to their geographic or traditional taxonomic relationships, and the estimated distance between the two traditionally recognized species was very small relative to those typically observed among avian sister species.

THE GEOGRAPHY OF MITOCHONDRIAL DNA VARIATION, POPULATION STRUCTURE, HYBRIDIZATION, AND SPECIES LIMITS IN THE FOX SPARROW (PASSERELLA ILIACA)

Geographic variation in mitochondrial DNA (mtDNA) restriction sites was studied in the fox sparrow (Passerella iliaca). Seventy-eight haplotypes were found. Haplotypes fall into four phylogeographic groups that correspond to groups defined by plumage characters. The geographic distribution of these four groups does not appear congruent with mtDNA patterns in other vertebrates. Within each group, there is little geographic variation in mtDNA restriction sites, although there is geographic variation in plumage coloration and body size. The evolution of mtDNA diversity in fox sparrows seems best explained by vicariant events rather than isolation by distance. The mtDNA evidence suggests that Passerella megarhyncha and Passerella schistacea, two nonsister taxa that occur in western North America, have independently undergone bottlenecks. Hybridization is limited between all pairs of taxa except P. megarhyncha and P. schistacea, where mtDNA evidence suggests a narrow contact zone along the interface of the Great Basin and Sierra Nevada/Cascades. Morphometric characters intergrade over a broader area, suggesting that different processes are responsible for the two gradients. The occurrence of limited backcrossing among taxa suggests that cytoplasmic-nuclear incompatibility is lacking. The number of biological species would range from one to four, depending on the degree of hybridization tolerated. The mtDNA and plumage characters suggest four phylogenetic species: P. iliaca, P. megarhyncha, P. unalaschcensis, and P. schistacea.

ASSOCIATIONS BETWEEN MITOCHONDRIAL AND NUCLEAR GENOTYPES IN CUTTHROAT TROUT HYBRID SWARMS

We examined mtDNA and nuclear allozyme genotypes in hybrid populations formed from interbreeding of westslope cutthroat trout (Oncorhynchus clarki lewisi) and Yellowstone cutthroat trout (O. c. bouvieri). These subspecies show substantial genetic divergence (Nei's D = 0.30; mtDNA P = 0.02). Diagnostic alleles at multiple nuclear loci and two distinct mtDNA haplotypes segregate in the hybrids. Nuclear and mtDNA genotypes are largely randomly associated, although there is slight disequilibrium in both nuclear and cytonuclear measures in some samples. Consistent positive gametic disequilibria for three pairs of nuclear loci confirm one previously reported linkage, and indicate two more. Allele frequencies provide no evidence for selection on individual chromosome segments. However, westslope mtDNA haplotype frequencies exceed westslope nuclear allele frequencies in all samples. This may be explained by differences in the frequency of occurrence of reciprocal F₁ matings, by viability, fertility, or sex ratio differences in the progeny of reciprocal matings, or by weak selection on mtDNA haplotypes.

Isolation and characterization of 24 polymorphic microsatellite loci for the study of genetic population structure of the sheepshead Archosargus probatocephalus (Actinopterygii, Perciformes, Sparidae)

Background

The sheepshead (Archosargus probatocephalus) is found in nearshore waters from Nova Scotia, Canada, to Rio Grande do Sul, Brazil. In the southeastern United States two subspecies are recognized based on a number of meristic characters, primarily counts of melanistic pigment bars. The only previous study based on mtDNA control-region sequence found limited divergence between those subspecies and isolation by distance among 15 locations from Florida (Atlantic Ocean) to Texas (Gulf of Mexico). In the same study, using six sparid microsatellite markers, Bayesian analysis showed that the Gulf and Atlantic sheepshead form a single population. To reinvestigate the fine-scale genetic population structure and examine genetic support for the morphologically classified subspecies, a set of species-specific microsatellite markers was needed.

Findings

Here we report on 24 polymorphic microsatellite markers isolated from sheepshead and screened in 57 specimens from the Indian River, Florida. The average number of alleles per locus was 13.1; mean observed and expected heterozygosities were 0.68 and 0.73, respectively. Nine sparid markers screened for the same specimens showed an average of 8.6 alleles per locus; mean observed and expected heterozygosities were 0.46 and 0.55, respectively.

Conclusions

The polymorphic markers reported here can be used to search for genetic evidence for the morphologically defined subspecies, to elucidate the fine-scale genetic population structure of this broadly distributed coastal species, and to provide an opportunity to directly compare results of population delineation between nonspecific and species-specific markers.