A literature review is conducted on the phylogenetic discontinuities in mtDNA sequences of 252 taxonomic species of vertebrates. About 140 of these species (56%) were subdivided clearly into two or more highly distinctive matrilineal phylogroups, the vast majority of which were localized geographically. However, only a small number (two to six) of salient phylogeographic subdivisions (those that stand out against mean within-group divergences) characterized individual species. A previous literature summary showed that vertebrate sister species and other congeners also usually have pronounced phylogenetic distinctions in mtDNA sequence. These observations, taken together, suggest that current taxonomic species often agree reasonably well in number (certainly within an order-of-magnitude) and composition with biotic entities registered in mtDNA genealogies alone. In other words, mtDNA data and traditional taxonomic assignments tend to converge on what therefore may be "real" biotic units in nature. All branches in mtDNA phylogenies are nonanastomose, connected strictly via historical genealogy. Thus, patterns of historical phylogenetic connection may be at least as important as contemporary reproductive relationships per se in accounting for microevolutionary unities and discontinuities in sexually reproducing vertebrates. Findings are discussed in the context of the biological and phylogenetic species concepts.

Geographic patterns in mtDNA variation are compiled for 22 species of freshwater and terrestrial turtles in the southeastern United States, and the results are employed to evaluate phylogeographic hypotheses and principles of genealogical concordance derived previously from similar analyses of other vertebrates in the region. The comparative molecular findings are interpreted in the context of intraspecific systematics for these taxa, the historical geology of the area, traditional nonmolecular zoogeographic information, and conservation significance. A considerable degree of phylogeographic concordance is registered with respect to (a) the configuration of intraspecific mtDNA subdivisions across turtle species, (b) the principal molecular partitions and traditional morphology-based taxonomic boundaries, (c) genetic patterns in turtles versus those described previously for freshwater fishes and terrestrial vertebrates in the region, and (d) intraspecific molecular subdivisions versus the boundaries between major zoogeographic provinces as identified by composite ranges of species in the Testudines. Findings demonstrate shared elements in the biogeographic histories of a diverse regional biota. Such phylogeographic concordances (and discordances) have ramifications for evolutionary theory as well as for the pragmatic efforts of taxonomy and conservation biology.

The musk turtle (Sternotherus minor) is common throughout the southeastern United States. In 1955 a morphologically atypical form confined to the Black Warrior River System in Alabama was discovered and accorded full species status as S. depressus, the 'flattened musk turtle.' Questions remain about the taxonomic status and evolutionary history of the flattened musk turtle because (1) the geographic distribution of S. depressus is nested within the range of S. minor; (2) the flattened shell might be a recently evolved anti-predator adaptation; and (3) reports exist of intergrades between S. depressus and S. minor. We generated and employed sequence data from mitochondrial DNA to address the phylogenetic distinctiveness and phylogeographic position of S. depressus relative to all other musk and mud turtles (Kinosternidae) in North America. The flattened musk turtle forms a well-supported monophyletic group separate from S. minor. Genetic divergence observed between S. depressus and geographic populations of S. minor is no less than that distinguishing many kinosternid congeners from one another. These molecular genetic findings bolster rationale for the taxonomic recognition of S. depressus and, hence, for special efforts to protect this federally threatened species.

Previous studies have revealed considerable genetic variation, geographic localization, and genealogical depth for mitochondrial DNA (mtDNA) haplotypes within each of several species of freshwater turtles in the south-eastern United States of America. Here we report a notable exception to such phylogeographic patterns. In control-region sequences of 66 snapping turtles (Chelydra serpentina) collected from 10 south-eastern states, a single mtDNA haplotype predominated and the two rare variants detected were nearly identical to the common genotype. This pattern of low mtDNA variation and a lack of appreciable geographic population structure is extremely unusual for a widely distributed animal species. For purposes of taxonomy and conservation, these findings suggest the presence of only one 'evolutionarily significant unit' for C. serpentina in this otherwise phylogeographically rich region of the country. Possible explanations for this phylogeographic pattern in the snapping turtle are considered.

Due to the phenomenon of male pregnancy, the fish family Syngnathidae (seahorses and pipefishes) has historically been considered an archetypal example of a group in which sexual selection should act more strongly on females than on males. However, more recent work has called into question the idea that all species with male pregnancy are sex-role reversed with respect to the intensity of sexual selection. Furthermore, no studies have formally quantified the opportunity for sexual selection in any natural breeding assemblage of pipefishes or seahorses in order to demonstrate conclusively that sexual selection acts most strongly on females. Here, we use a DNA-based study of parentage in the Gulf pipefish Syngnathus scovelli in order to show that sexual selection indeed acts more strongly on females than on males in this species. Moreover, the Gulf pipefish exhibits classical polyandry with the greatest asymmetry in reproductive roles (as quantified by variances in mating success) between males and females yet documented in any system. Thus, the intensity of sexual selection on females in pipefish rivals that of any other taxon yet studied.

We report perhaps the first genic-level molecular documentation of a mammalian-like 'X-linked' mode of sex determination in molluscs. From family inheritance data and observed associations between sex-phenotyped adults and genotypes in Busycon carica, we deduce that a polymorphic microsatellite locus (bc2.2) is diploid and usually heterozygous in females, hemizygous in males, and that its alleles are transmitted from mothers to sons and daughters but from fathers to daughters only. We also employ bc2.2 to estimate near-conception sex ratio in whelk embryos, where gender is indeterminable by visual inspection. Statistical corrections are suggested at both family and population levels to accommodate the presence of homozygous bc2.2 females that could otherwise be genetically mistaken for hemizygous males. Knobbed whelks were thought to be sequential hermaphrodites, but our evidence for genetic dioecy supports an earlier hypothesis that whelks are pseudohermaphroditic (falsely appear to switch functional sex when environmental conditions induce changes in sexual phenotype). These findings highlight the distinction between gender in a genetic versus phenotypic sense.

An approach applied previously to avian biotas is extended in this paper to other vertebrate classes to evaluate Pleistocene phylogeographic effects and to estimate temporal spans of the speciation process (speciation durations) from mitochondrial (mt) DNA data on extant taxa. Provisional molecular clocks are used to date population separations and to bracket estimates of speciation durations between minimum and maximum values inferred from genetic distances between, respectively, extant pairs of intraspecific phylogroups and sister species. Comparisons of genetic-distance trends across the vertebrate classes reveal the following: (i) speciation durations normally entail at least two million years on average; (ii) for mammals and birds, Pleistocene conditions played an important role in initiating phylogeographic differentiation among now-extant conspecific populations as well as in further sculpting pre-existing phylogeographic variety into many of today's sister species; and (iii) for herpetofauna and fishes, inferred Pleistocene biogeographic influences on present-day taxa differ depending on alternative but currently plausible mtDNA rate calibrations.

Nearly all of the 906 embryos from a male-tended nest of the sand goby (Pomatoschistus minutus) were genotyped at two hypervariable microsatellite loci to document conclusively the number of mothers and their relative genetic contributions to the nest. The true number of mothers determined by this nearly exhaustive genetic appraisal was compared to computer simulation treatments based on allele frequencies in the population, assumptions about reproductive skew, and statistical sampling strategies of progeny subsets. The "ground-truthed" appraisal and the theoretical estimates showed good agreement, indicating that for this nest a random sample of approximately 20 offspring would have sufficed for assessing the true number of biological parents (but not necessarily their relative genetic contributions). Also, a general dilocus matrix procedure is suggested for organizing and interpreting otherwise cumbersome data sets when extremely large numbers of full-sib and half-sib embryos from a nest are genotyped at two or more hypervariable loci.

Alternative mating strategies are common in nature and are generally thought to increase the intensity of sexual selection. However, cuckoldry can theoretically decrease the opportunity for sexual selection, particularly in highly polygamous species. We address here the influence of sneaking (fertilization thievery) on the opportunity for sexual selection in the sand goby Pomatoschistus minutus, a marine fish species in which males build and defend nests. Our microsatellite-based analysis of the mating system in a natural sand goby population shows high rates of sneaking and multiple mating by males. Sneaker males had fertilized eggs in approximately 50% of the assayed nests, and multiple sneakers sometimes fertilized eggs from a single female. Successful males had received eggs from 2 to 6 females per nest (mean = 3.4). We developed a simple mathematical model showing that sneaking in this polygynous sand goby population almost certainly decreases the opportunity for sexual selection, an outcome that contrasts with the usual effects of cuckoldry in socially monogamous animals. These results highlight a more complex and interesting relationship between cuckoldry rates and the intensity of sexual selection than previously assumed in much of the literature on animal mating systems.

Molecular markers have proved extremely useful in resolving mating patterns within individual populations of a number of species, but little is known about how genetic mating systems might vary geographically within a species. Here we use microsatellite markers to compare patterns of sneaked fertilization and mating success in two populations of sand goby (Pomatoschistus minutus) that differ dramatically with respect to nest-site density and the documented nature and intensity of sexual selection. At the Tvärminne site in the Baltic Sea, the microsatellite genotypes of 17 nest-tending males and mean samples of more than 50 progeny per nest indicated that approximately 35% of the nests contained eggs that had been fertilized by sneaker males. Successful nest holders mated with an average of 3.0 females, and the distribution of mate numbers for these males did not differ significantly from the Poisson expectation. These genetically deduced mating-system parameters in the Tvärminne population are remarkably similar to those in sand gobies at a distant site adjoining the North Sea. Thus, pronounced differences in the ecological setting and sexual selection regimes in these two populations have not translated into evident differences in cuckoldry rates or other monitored patterns of male mating success. In this case, the ecological setting appears not to be predictive of alternative male mating strategies, a finding of relevance to sexual selection theory.