Sequence Divergence Estimates Research Articles

Phylogenetic Relationships among Members of the Coregoninae Inferred from Direct Sequencing of PCR-Amplified Mitochondrial DNA

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for eight members of the Coregoninae (Salmonidae) from North America in an effort to elucidate phylogenetic relationships in the subfamily. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Direct estimates of mitochondrial DNA (mtDNA) sequence divergence among taxa ranged from 0.0% between Arctic cisco (Coregonus autumnalis) from the Mackenzie River, Canada, and cisco (C. artedi) from the Laurentian Great Lakes to 5.8% between the inconnu (Stenodus leucichthys) and the round whitefish (Prosopium cylindraceum). As has been noted in other fish species and vertebrates in general, third position silent substitutions predominated over any other type of nucleotide change. No amino acid replacement substitutions were found among any of the eight taxa examined. Comparison of mtDNA sequence divergence estimates from this and other studies suggests that the radiation of the genera within the Coregoninae occurred relatively recently (2–6 million yr B.P.). Cladistic analysis of the mtDNA sequence data yields a hypothesis of relationships that supports previous genetic and morphological classifications of coregonines.

Temporal Stability of Nuclear Gene (Allozyme) and Mitochondrial DNA Genotypes among Red Drums from the Gulf of Mexico

Abstract Allelic variation in nine polymorphic nuclear genes and restriction-site variation in mitochondrial DNA (mtDNA) were assayed among 194 adult red drums Sciaenops ocellatus from the northern Gulf of Mexico, Data were combined with those of previous studies in order to examine patterns of temporal genetic variation among four year-classes (1984–1987) and individuals spawned prior to 1984, Tests of heterogeneity among year-classes in both nuclear gene allele frequencies and mtDNA haplotype frequencies were nonsignificant, and estimated fixation (F ST) values were 0.009 (nuclear genes) and 0.002 (mtDNA). Estimates of Nei's unbiased genetic distance (nuclear genes) and nucleotide sequence divergence (mtDNA) among year-classes also indicated the absence of temporal genetic differentiation, Estimates of average heterozygosity (nuclear genes) and nucleon and nucleotide sequence diversities (mtDNA) indicated that levels of genome-wide variation within and among year-classes of red drum are equivalent to (o...

Population differentiation of the malaria vector Anopheles aquasalis using mitochondrial DNA.

Populations of the malaria vector Anopheles aquasalis from Venezuela, Trinidad, and Brazil were analyzed using restriction enzyme digestion of mitochondrial DNA (mtDNA). The five enzymes surveyed yielded 12 mtDNA haplotypes. Three restriction endonuclease profiles (Bcl I, Eco RI, and Hind III) differentiated the Venezuelan and Trinidadian A. aquasalis from two Brazilian populations. Estimates of mtDNA sequence divergence between the Venezuelan/Trinidadian populations and each Brazilian population (0.023-0.032), as well as divergence between the two Brazilian populations (0.030), were within the range of interspecific distances calculated for members of anopheline species complexes. Ribosomal DNA (rDNA) restriction profiles of the A. aquasalis populations examined were identical.

Molecular insights into the relationships and biogeography of West Indian anoline lizards

The realization that the present day positions of continents and island arcs are a result of continental drift led to the proposal that the extant West Indian fauna reflect an ancient (Cretaceous) land connection between the proto-Antilles and North and South America. Movements of the Antillean islands throughout the Cenozoic are hypothesized to have further fragmented the fauna present on the proto-Antilles when it separated from the mainland 70–80 million years ago. This proposed vicariant origin of the West Indian fauna challenged the previous theory that some or most of the fauna arrived in the Antilles by overwater dispersal from mainland soruces. The virtual absence of appropriate fossils in the West Indies has hampered testing these alternative hypotheses for the origin of the present day West Indian fauna. We present evidence from two types of molecular data, one providing indirect estimates of amino acid sequence divergence for the protein serum albumin, and the other direct DNA sequence information from a mitochondrial ribosomal RNA gene. Our new data provide insights into the origin and relationships of two enigmatic lizard genera, Chamaeleolis and Chamaelinorops, and suggest they are recent derivatives within the genus Anolis. These data, along with molecular data presented elsewhere, strongly implicate an origin by overwater dispersal for most of the Antillean vertebrate fauna.

Taxonomic notes on the Oreochromis niloticus subspecies-complex (Pisces: Cichlidae), with a description of a new subspecies

Relationships among the seven recognized subspecies of the widespread African cichlid Oreochromis niloticus (L.) were investigated using restriction endonuclease analysis of mitochondrial DNA. Changes in nomenclature are based on estimates of sequence divergence and concordant results from phenetic, cladistic, and maximum likelihood analyses of molecular character sets. Oreochromis niloticus cancellatus and O. n. filoa are reassigned to O. cancellatus as O. c. cancellatus and O. c. filoa, respectively. The tilapiine fishes of Lake Tana, Ethiopia, previously assigned to O. n. cancellatus, are here described as Oreochromis niloticus tana subsp.nov. in recognition of their distinctive molecular phenotypes.

DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations.

Throughout its natural range, the brown trout Salmo trutta L. exhibits a complex pattern of morphological and life-history variation. This has led to considerable taxonomic confusion, hampering the understanding of the evolutionary history of the species. To document the phylogenetic relationships among morphologically and geographically remote brown trout populations across western Europe, we determined the DNA sequence variation in segments of the mitochondrial control region for 151 individuals representing 24 populations. DNA was prepared for double-stranded sequencing by the polymerase chain reaction (PCR). Twenty-one variable nucleotide positions within a 640-bp fragment surveyed defined 12 genotypes differing by a mean of 7 nucleotide substitutions (range 1-12). Five major phylogenetic assemblages differing by mean sequence divergence estimates of 0.96 to 1.44% were identified. These groupings exhibited a strong spatial partitioning but lacked congruence with either ecological or morphological differentiation. Complete mitochondrial DNA (mtDNA) monomorphism across all Atlantic basin populations contrasted with the high interdrainage genetic diversity observed in more southerly populations. This study exemplified the usefulness of mitochondrial DNA sequence analysis for estimating phylogenetic relationships within S. trutta populations.

Mitochondrial DNA reveals formation of nonhybrid frogs by natural matings between hemiclonal hybrids.

The European water frog Rana esculenta (RL), a natural hybrid between R. ridibunda (RR) and R. lessonae (LL), reproduces by hybridogenesis: haploid gametes usually contain an intact chromosome set of R. ridibunda (R); the lessonae nuclear genome (L) is lost from the germ line. Hybridity is restored in the next generation, via fertilization by syntopic R. lessonae. Matings between two hybrids (RL x RL) usually give inviable R. ridibunda (RR) progeny. The adult R. ridibunda subpopulation of Trubeschloo, a gravel pit in northern Switzerland, consists only of females. Fragment patterns for mitochondrial DNA (mtDNA) of these R. ridibunda were identical with those of syntopic R. esculenta and of local populations of R. lessonae; they differed from the patterns in eastern European populations of R. lessonae and of R. ridibunda mtDNAs (3.7% and 9.3% estimated sequence divergence, respectively). In contrast, mtDNAs of two R. ridibunda from an introduced Swiss population with both sexes, although different (2.7% divergence) from each other, were typical R. ridibunda rather than R. lessonae mtDNAs. These data, together with unisexuality, demonstrate conclusively that the all-female R. ridibunda population at Trubeschloo originated from matings between two R. esculenta. The formation of independently reproducing R. ridibunda populations via such hybrid x hybrid matings is precluded because progeny of these matings are unisexual. Recombination in the regenerated fertile R. ridibunda females, followed by matings with R. lessonae, nevertheless provides a mechanism for meiotic reshuffling of genetic material in ridibunda haplotypes that is not typically available in hemiclonal lineages.

Geographic mitochondrial DNA variation in the rock hyrax, Procavia capensis.

Restriction-fragment-length polymorphisms in mitochondrial DNA (mtDNA) were used to evaluate geographic population genetic structure in the rock hyrax, Procavia capensis, a species which occurs widely, though restricted to rocky habitat, throughout South Africa. Ten restriction endonucleases were employed to assay mtDNAs from 55 specimens representing 10 localities. Haplotypes showed strong geographic patterning, and estimates of nucleotide sequence divergence indicate two major clades thought to be dispersing along separate routes. The divergence time of approximately 2 Myr between clades is relatively high for intraspecific variation. We speculate that the marked genetic break distinguishing the northwestern populations from those constituting the south/central clade may be indicative of two species in what has conventionally been regarded as P. capensis.

Mitochondrial DNA evolution at a turtle's pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines.

Evidence is compiled suggesting a slowdown in mean microevolutionary rate for turtle mitochondrial DNA (mtDNA). Within each of six species or species complexes of Testudines, representing six genera and three taxonomic families, sequence divergence estimates derived from restriction assays are consistently lower than expectations based on either (a) the dates of particular geographic barriers with which significant mtDNA genetic clades appear associated or (b) the magnitudes of sequence divergence between mtDNA clades in nonturtle species that otherwise exhibit striking phylogeographic concordance with the genetic partitions in turtles. Magnitudes of the inferred rate slowdowns average eightfold relative to the "conventional" mtDNA clock calibration of 2%/Myr sequence divergence between higher animal lineages. Reasons for the postulated deceleration remain unknown, but two intriguing correlates are (a) the exceptionally long generation length most turtles and (b) turtles' low metabolic rate. Both factors have been suspected of influencing evolutionary rates in the DNA sequences of some other vertebrate groups. Uncertainities about the dates of cladogenetic events in these Testudines leave room for alternatives to the slowdown interpretation, but consistency in the direction of the inferred pattern, across several turtle species and evolutionary settings, suggests the need for caution in acceptance of a universal mtDNA-clock calibration for higher animals.

Phylogenetic relationships among Middle American pocket gophers ( genus Orthogeomys) based on mitochondrial DNA sequences

Relationships among members representing each of the three subgenera of the Middle American rodent genus Orthogeomys (Rodentia: Geomyidae) were studied by comparing DNA sequence data from two regions of the mitochondrial genome. Results from 527 by from the 16 S rDNA region and a 402-bp fragment of the cytochrome b gene indicate that the three subgenera are well differentiated genetically, with the subgenus Orthogeomys being distantly related to Macrogeomys and Heterogeomys, and Macrogeomys appearing as the most derived. Within the subgenus Macrogeomys, O. heterodus and O. cherriei form a distinct clade, as do O. dariensis and O. cavator. As with previous protein-electrophoretic studies, the placement of O. underwoodi could not be determined definitively within the subgenus Macrogeomys. We interpret our inability to determine phylogenetic relationships among these three clades as evidence for a rapid phyletic radiation within this subgenus. Sequence divergence estimates indicate that the Macrogeomys radiation took place following the time of completion of the Panamanian land bridge (1.9–2.9 mya). Additionally, the near identity of sequences of a newly described species, O. thaeleri, with those of O. dariensis (percentage sequence divergence = 0.3%) suggests that the two may be conspecific.

Phylogenetics of the Cotton Genus (Gossypium): Character-State Weighted Parsimony Analysis of Chloroplast-DNA Restriction Site Data and Its Systematic and Biogeographic Implications

ABsTRAcr. Total genomic DNAs from 61 accessions of 40 species of Gossypium were surveyed for restriction site variation in the maternally inherited plastid genome using 25 endonucleases. One hundred thirty-five of the 202 restriction site variants detected were potentially synapomorphous and served as binary characters for phylogeny estimation. Two cladistic methods were employed: Wagner parsimony analysis, which resulted in four equally most-parsimonious topologies requiring 161 steps (CI = 0.84), and a novel character-state weighting approach that models the relative probabilities of restriction site losses versus gains. This latter technique, which is theoretically preferable to both Dollo and Wagner parsimony analysis in that it optimizes against parallel site gains, resulted in two optimal phylogenetic estimates (a subset of the Wagner topologies) that differ only in the placement of G. longicalyx. In general, maternal cladistic relationships are congruent with both cytogenetic groupings and geographic clustering. Three major monophyletic clades among diploid species correspond to three continents: Australia (C-, G-genome), the Americas (D-genome), and Africa (A-, E-, and F-genome). African B-genome diploids are placed as sister to the New World D-genome species, albeit by a single homoplasious character state. Substantial agreement is also evident between the cpDNA phylogeny and traditional taxonomic treatments, although there is considerable disagreement at lower infrageneric ranks, particularly among the American and Australian cottons. These discrepancies are discussed, as is the possibility that inconsistency may reflect, at least in part, reticulation events among diploids, which may have occurred in at least three cases. An area cladogram suggests that Gossypium originated in either Africa or Australia. Because paleocontinental reconstructions, palynological evidence and cpDNA sequence divergence estimates concur in suggesting that the two primary clades diverged during the mid to upper Oligocene, the initial cladogenetic event most likely involved long-distance, intercontinental dispersal. Two colonizations of the New World are indicated, a relatively early long-distance dispersal from Africa leading to the evolution of the D-genome diploids, and a second, later dispersal of the maternal, A-genome ancestor of the allopolyploids. American diploid species are hypothesized to have originated in northwestern Mexico, with later radiations into other regions. The radiation of Gossypium in Australia is suggested to have proceeded from the westernmost portion of the continent. The maternal phylogenetic hypothesis and area cladogram suggest the possibility that New World allopolyploids originated following a trans-Pacific transfer of an ancestral A-genome taxon to the Pacific coast of Mesoamerica or South America.

Phylogenetic relationships among the subfamily Coregoninae as revealed by mitochondrial DNA restriction analysis

Mitochondria1 DNA (mtDNA) restriction analysis was used to assess phylogenetic patterns among 21 taxa of the subfamily Coregoninae. The genus Prosopium formed a very distinct group differing by 10% (sequence divergence estimate) from other species. Coregonus and Stenodus species were closely related, diverging by sequence divergence estimates of less than 5.6%. These species split into two major sister groups. One comprised all ‘true whitefish’ (subgenus Coregonus) and four cisco species (subgenus Leucichrhys). The most distant species within this assemblage was the Acadian whitefish (C. huntsmani). The other group included all other cisco species and also the Inconnu (Stenodus leucichthys). These results supported a polyphyletic origin of the ciscoes, and did not support Stenodus as a sister taxon of the genus Coregonus. The levels of sequence divergence observed suggested that most extant coregonines radiated during the Pleistocene.

Genetic studies in marine fishes. IV. An analysis of population structure in the red drum ( Sciaenops ocellatus) using mitochondrial DNA

Variation in mitochondrial DNA (mtDNA) was examined among 397 individuals representing 13 geographic samples of red drum ( Sciaenops ocellatus). Five of the samples were from the Atlantic coast of the southeastern United States, and eight were from the northern Gulf of Mexico. Seventy-six mtDNA haplotypes were found: eight haplotypes were found in 13 or more individuals, ten were found in four to 12 individuals, 22 were found in two to three individuals, and 36 were found in only one individual each. Mitochondrial DNA nucleon diversity values within samples ranged from 0.850 to 1.000; the value over all fish surveyed was 0.943. These data indicate that red drum have at least “normal” levels of genetic variability. Estimates of the percentage nucleotide sequence divergence among the 76 mtDNA haplotypes ranged from 0.137 to 1.962, with a mean (±SE) of 0.803 ± 0.006. Heterogeneity in the frequencies of four haplotypes was detected between pooled samples from the Atlantic vs. pooled samples from the Gulf. No heterogeneity was detected among samples from the Atlantic or among samples from the Gulf. F ST values (a measure of the variance in mtDNA haplotype frequencies) over the four heterogeneous haplotypes ranged from 0.019 to 0.137 (mean F ST = 0.057), and the effective number of female migrants ( N e m) per generation using Wright's island model ranged from 1.58 to 12.91 (mean N e m = 4.14). The average percentage nucleotide sequence divergence within samples ranged from 0.494 to 0.734, with a mean (±SE) of 0.574 ± 0.021. The percentage nucleotide sequence divergence among pairwise comparisons of samples ranged from 0.498 to 0.713, with a mean (±SE) of 0.571 ± 0.005. Parsimony and phenetic analyses of individuall mtDNA haplotypes and of sample localities revealed no strong evidence for geographic cohesion of haplotype or sample groupings. A matrix correlation (Mantel) test also revealed no significant association between matrices of mtDNA sequence divergence and geographic distance among sample localities. Collectively, these data indicate that the red drum population is weakly subdivided, with semi-isolated subpopulations occurring along the southeastern Atlantic coast and in the northern Gulf of Mexico. The large number of rare or unique mtDNA haplotypes found in the study may prove useful in evaluating the success of red drum stocking programs.

Phylogeny and molecular epidemiology of Sporothrix schenckii in Japan

Mitochondrial DNA(mtDNA) diversity was investigated in 257 clinical isolants of Sporothrix schenckii obtained from 4 districts in Japan. S. schenckii was classified into 10 types based on Hae III restriction profiles. Phylogeny of types constructed by the method of Fitch and Margoliash [1] on the estimated sequence divergence within mtDNA using the methods of Nei and Li [2], showed that S. schenckii are grouped into 2 clusters, one group consisting of types 1, 2 and 3, and the other group consisting of the other seven types. In addition, types 1, 2, and 5 were correlated with their geographic origin, whereas type 4 was present throughout Japan.

MOLECULAR AND GEOLOGIC EVIDENCE OF SHARED HISTORY BETWEEN HERMIT CRABS AND THE SYMBIOTIC GENUS HYDRACTINIA.

The paleobiogeographic histories of three North Atlantic hermit crab lineages were compared with a single-copy DNA-DNA hybridization phylogeny of their symbiotic hydroid genus Hydractinia to test hypotheses of shared history between these host and symbiont lineages. A survey of the geologic literature suggests that two vicariance events in the Quaternary are responsible for existing range disjunctions of the host hermit crab lineages. The Hydractinia phylogeny revealed two distinct clades, one with a primarily northern and the other with a primarily southern distribution. In two of three cases, hydroids associated with closely related hermits on both sides of the range disjunction appear as sister taxa in the phylogeny. A linear scaling between a measure of hydroid sequence divergence and independent geologic estimates of the timing of the vicariant events believed to have established the hermit crab range disjunctions is consistent with the claim of temporal coincidence of cladogenic and vicariance events. These findings provide evidence for shared history of symbiotic associations in two of the three cases.

Mitochondrial DNA Variation Reveals Genetically Distinct Sympatric Populations of Anadromous and Nonanadromous Atlantic Salmon,Salmo salar

Mitochondrial DNA variation was surveyed among wild anadromous and nonanadromous Atlantic salmon, Salmo salar, which occur in sympatry in Gambo River, Newfoundland. Seventy-one salmon were screened with 18 restriction enzymes, 5 of which revealed nucleotide sequence variation. Nucleotide sequence divergence estimates among the four distinct genotypes detected ranged from 0.2 to 1.0%. Significant heterogeneity in mtDNA genotype frequencies supports the view that exchange of breeding females between groups is infrequent or does not occur, an inference consistent with the observation that the forms use separate spawning sites within the system. Mitochondrial DNA diversity was somewhat greater among the nonanadromous salmon than the anadromous salmon (nucleon diversity (h) = 0.37 and 0.52, respectively). Potential mechanisms for maintaining reproductive isolation include selection of different spawning habitats, different spawning times, and sexual selection based upon the size difference between the two forms.

Association between mitochondrial DNA and morphological evolution in Canada geese

Variation within and between eight subspecies of Canada geese was assessed by restriction fragment analysis of mitochondrial DNA (mtDNA), electrophoresis of proteins encoded by nuclear DNA, and the morphometric analysis of skeletons. Estimates of mtDNA sequence divergence between Canada goose subspecies ranged from 0.04 to 2.54%. Pairwise comparisons of the three data matrices revealed that only mtDNA variation and body size are significantly correlated. Subspecies with northern breeding grounds are small-bodied and display small variations of one mtDNA clone, whereas those breeding further south are largebodied and show small differences in another mtDNA clone. Canada geese exhibit strong geographic differentiation with respect to mtDNA sequence, but weak structuring in protein-encoding nuclear DNA. This finding can be explained by a lower level of gene flow for the mitochondrial genome than for the nuclear genome, which in turn emanates from the maternal inheritance of mtDNA and male-biased dispersal in Canada geese. Despite male-mediated flow of nuclear genes, strong morphometric differentiation persists among Canada geese subspecies.

Mitochondrial DNA Variation among Anadromous Populations of Cisco (Coregonus artedii) as revealed by Restriction Analysis

Mitochondrial DNA (mtDNA) restriction analyses were done to test the hypothesis that river populations of anadromous cisco from James-Hudson Bays that exhibit life-history variations are reproductively isolated. MtDNA variation among 141 cisco (Coregonus artedii) from eight rivers was studied with eight hexameric, four multihexameric and one multipentameric restriction enzymes which generated a mean of 78 fragments per fish. Pair-wise sequence divergence estimates among the 19 mtDNA clones resolved were generally low but highly variable (mean: 0.52%, range: 0.08 to 1.03%). UPGMA and Wagner parsimony analysis revealed two major clonal groups which differed in diversity and geographic distribution; the more diversified (nucleon diversity index; 0.70) and less diversified (0.31) groups were twice as abundant in James and Hudson Bays, respectively. This suggests that cisco of James-Hudson Bays are derived from two glacial refugia and that they recolonized the area by two major postglacial routes. The frequency distribution analysis of all defined clones revealed significant stock discreteness among Hudson Bay populations and a lack of population subdivision in James Bay. The genetic structuring and diversity of anadromous cisco in James-Hudson Bay is discussed in relation to historical biogeographical events and to interactions of various life-history stages with the physical oceanographic environment.

Population bottlenecks: influence on mitochondrial DNA diversity and its effect in coregonine stock discrimination

This study was designed to test the hypothesis that anadromous populations of North American whitefish, Coregonus clupeaformis (Mitchill), believed to have suffered more intense population bottlenecks during past glaciation events, should reveal less mitochondrial DNA (mtDNA) variability and population‐genetic structuring than anadromous populations of European whitefish, C. lavaretus (L.). C. clupeaformis exhibited extremely low levels of diversity and population structuring, in terms of number and frequency of clonal lines as well as sequence divergence estimates, as compared with populations of C. lavaretus. These results support the hypothesis that the severity of population bottlenecks related to Pleistocene glaciation events may be largely responsible for the level of mtDNA variability observed. This in turn influences the sampling strategy required to maximize the usefulness of mtDNA analysis in stock discrimination.

RESTRICTION FRAGMENT ANALYSIS OF CHLOROPLAST DNA AND THE SYSTEMATICS OF VIGUIERA AND RELATED GENERA (ASTERACEAE: HELIANTHEAE)

Phylogenetic relationships among 31 species representing variously Helianthus, Helianthopsis, Heliomeris, Simsia, Viguiera, and Tithonia were assessed by chloroplast DNA restriction site mapping. A total of 147 mutations including 92 informative ones was detected using 16 restriction enzymes, with an estimated sequence divergence within the group of 1.4%. Parsimony analysis produced a single most parsimonious tree with a length of 161 steps and a consistency index of 0.91. Statistically significant clades, as assessed by the bootstrap method, correspond to a number of taxa recognized previously, including Helianthus (3 species), Helianthopsis (5 species), and several groups within Viguiera, including sect. Maculatae (4 species), the Baja California group (6 species), sect. Paradosa (2 species) and V. dentata (3 samples). However, species of Viguiera collectively form a highly paraphyletic group relative to species of other genera. Helianthus and Helianthopsis were separated into different clades, supporting their recent segregation. Placement of H. porteri in Helianthus rather than Heliomeris was confirmed; the single sample of the latter genus was most similar to the Baja California group of Viguiera. An expected relationship between Simsia (2 species) and one member of Viguiera ser. Grammatoglossae was confirmed (although not with two other putatively related members of Viguiera) and an unexpected relationship between Simsia and Tithonia was suggested. The presence of Mexican taxa as the more basal groups in the tree points toward a possible Mexican origin for Viguiera and related genera. A molecular clock hypothesis is rejected in many pairwise comparisons involving woody taxa with herbaceous ones, although it could not be rejected in most pairwise comparisons involving taxa of similar habit.