We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

N 2 fixation by diazotrophic bacteria associated with the roots of the smooth cordgrass, Spartina alterniflora, is an important source of new nitrogen in many salt marsh ecosystems. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are unknown. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified nifH sequence segments was used in previous studies to examine the stability and dynamics of the Spartina rhizosphere diazotroph assemblages in the North Inlet salt marsh, near Georgetown, S.C. In this study, plugs were taken from gel bands from representative DGGE gels, the nifH amplimers were recovered and cloned, and their sequences were determined. A total of 59 sequences were recovered, and the amino acid sequences predicted from them were aligned with sequences from known and unknown diazotrophs in order to determine the types of organisms present in the Spartina rhizosphere. We recovered numerous sequences from diazotrophs in the ␥ subdivision of the division Proteobacteria (␥-Proteobacteria) and from various anaerobic diazotrophs. Diazotrophs in the ␣-Proteobacteria were poorly represented. None of the Spartina rhizosphere DGGE band sequences were identical to any known or previously recovered environmental nifH sequences. The Spartina rhizosphere diazotroph assemblage is very diverse and apparently consists mainly of unknown organisms.

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Effective sustainable management of marine fisheries requires that assessed management units (that is, fish stocks) correspond to biological populations. This issue has long been discussed in the context of Atlantic bluefin tuna (ABFT, Thunnus thynnus) management, which currently considers two unmixed stocks but does not take into account how individuals born in each of the two main spawning grounds (Gulf of Mexico and Mediterranean Sea) mix in feeding aggregations throughout the Atlantic Ocean. Using thousands of genome‐wide molecular markers obtained from larvae and young of the year collected at the species’ main spawning grounds, we provide what is, to the best of our knowledge, the first direct genetic evidence for “natal homing” in ABFT. This has facilitated the development of an accurate, cost‐effective, and non‐invasive tool for tracing the genetic origin of ABFT that allows for the assignment of catches to their population of origin, which is crucial for ensuring that ABFT management is based on biologically meaningful stock units rather than simply on catch location.

Genetic diversity in mtDNA was assd within the unisexual (all female) hybridogenetic fish Poecdiopsis monacha-occidentalis and the two sexual species from which it arose. Results confirm that P. monacha was the maternal ancestor and that paternal leakage of P. occidentals mtDNA has not occurred. Of particular interest is the high level of de novo mutational divergence within one hybridogenetic lineage that on the basis of independent zoogeographic considerations, protein electrophoretic data, and tissue gaftng analysis is of monophyletic (single hybridization) origin. Using a conventional mtDNA clock calibration, we estimate that this unisexual clade might be >100,000 generations old. Contrary to conventional belief, this result shows that some unisexual vertebrate lineages can achieve a substantial evolutionary age.Clonally reproducing organisms are believed to have short evolutionary life-spans due to a presumed lack of sufficient genotypic diversity for adaptive change to variable environments (1-3) or to an accumulation of deleterious mutations and gene combinations that cannot be purged in the absence of recombination (2,4). However, many unisexual (all female) vertebrate populations are not devoid of genetic variation, and some clearly enjoy short-term ecological success relative to their sexual progenitors (5). Can such unisexual lineages also persist over long evolutionary time scales?Genetic studies reveal that virtually all unisexual vertebrates arose recently from hybridization involving congeneric sexual species (for reviews, see ref. 6). Clonal diversity within a unisexual "biotype" (a particular combination of two or more heterospecific genomes) results primarily from multiple, independent, hybrid origins; however, additional variation can accrue within independent lineages after their inception via polyploidization and mutation (5).Inferences concerning the evolutionary age of unisexual organisms must avoid confounding postformational processes that are indicative of an old lineage with genetic diversity arising from multiple hybrid origins. However, incomplete sampling of the sexual ancestors and incomplete assessment of diversity in the unisexual populations often defeat attempts to discriminate multiple origins from postformation processes. For example, unisexual lineages often are marked by unique alleles not observed in samples of their sexual relatives (7-11). Although unique alleles might represent postformational mutations, most authors interpret them as "orphan alleles," variants that exist in unsampled sexual populations or that might have existed in extinct sexual progenitors (12). With this conservative approach, postformational mutations could be overlooked and potential evidence for antiquity could be discounted.The present study avoids this dilemma by focusing on postformational mtDNA and allozyme mutations within a monophyletic lineage of the unisexual fish Poeciliopsis monacha-occidentalis (hereafter MO). The MO biotype arose in northwestern Mexico (Fig. 1A) via crosses be...

A karyotype analysis by several staining techniques was carried out on triplicate samples of the shortnose sturgeon, Acipenser brevirostrum. The chromosome number was found to be 2n = 372 +/- 6. A representative karyotype of 374 chromosomes was composed of 178 metacentrics/submetacentrics and 196 telocentrics/acrocentrics and microchromosomes. The signals of fluorescent in situ hybridization (FISH) with a HindIII satellite DNA probe were visible on 14 chromosomes. The signals obtained with a PstI satellite DNA probe appeared on 12 chromosomes. The FISH with a 5S rDNA probe revealed fluorescent signals on 6 chromosomes. These last results, compared with 2 signals in species with about 120 chromosomes and 4 in species with 240, support the hypothesis that A. brevirostrum is a hexaploid species, probably of hybrid origin. Based on these results, we propose a model explaining speciation events occurring in sturgeons by hybridization, genome duplication, and diploidization.

Abstract. The deep sea is the largest ecosystem on Earth. Recent exploration has revealed that it supports a highly diverse and endemic benthic invertebrate fauna, yet the evolutionary processes that generate this remarkable species richness are virtually unknown. Environmental heterogeneity, topographic complexity, and morphological divergence all tend to decrease with depth, suggesting that the potential for population differentiation may decrease with depth. To test this hypothesis, we use mitochondrial DNA (16S rRNA gene) to examine patterns of population differentiation in four species of protobranch bivalves (Nuculoma similis, Deminucula atacellana, Malletia abyssorum, and Ledella ultima) distributed along a depth gradient in the western North Atlantic. We sequenced 268 individuals from formalinfixed samples and found 45 haplotypes. The level of sequence divergence among haplotypes within species was similar, but shifted from between populations at bathyal depths to within populations at abyssal depths. Levels of population structure as measured by ⌽ ST were considerably greater in the upper bathyal species (N. similis ϭ 0.755 and D. atacellana ϭ 0.931; 530-3834 m) than in the lower bathyal/abyssal species (M. abyssorum ϭ 0.071 and L. ultima ϭ 0.045; 2864-4970 m). Pairwise genetic distances among the samples within each species also decreased with depth. Population trees (UPGMA) based on modified coancestry coefficients and nested clade analysis both indicated strong population-level divergence in the two upper bathyal species but little for the deeper species. The population genetic structure in these protobranch bivalves parallels depth-related morphological divergence observed in deep-sea gastropods. The higher level of genetic and morphological divergence, coupled with the strong biotic and abiotic heterogeneity at bathyal depths, suggests this region may be an active area of species formation. We suggest that the steep, topographically complex, and dynamic bathyal zone, which stretches as a narrow band along continental margins, plays a more important role in the evolutionary radiation of the deep-sea fauna than the much more extensive abyss.Key words. Deep sea, depth gradient, mollusks, phylogeography, population divergence, population structure. The deep ocean (below 200 m) is an enormous and complex ecosystem covering two-thirds of the planet. The fauna inhabiting this remote environment is highly endemic and surprisingly rich (Hessler and Sanders 1967). Although numerous studies have explored evolutionary processes in shallowwater systems (e.g

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