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Biomedical subjects

J C Avise

Publications and source records attributed to J C Avise.

At least 37 records · Page 2Linked to original sources
PubMed2000

The genetic mating system of spotted sunfish (Lepomis punctatus): mate numbers and the influence of male reproductive parasites.

In nest-building fish species, mature males often exhibit one of two alternative reproductive behaviours. Bourgeois males build nests, court females, and guard their eggs. Parasitic cuckolders attempt to steal fertilizations from bourgeois males and do not invest in parental care. Previous evidence from the bluegill sunfish (Lepomis macrochirus) suggests that adult males are morphologically specialized for these two tactics. Here, we used microsatellite markers to determine genetic parentage in a natural population of the spotted sunfish (L. punctatus) that also displayed both bourgeois and parasitic male morphs. As gauged by relative investments in gonadal vs. somatic tissues, between 5 and 15% of the mature adult males were parasites. Multi-locus genotypes were generated for more than 1400 embryos in 30 nests, their nest-guardian males, and for other adults in the population. Progeny in approximately 57% of the nests were sired exclusively by the guardian male, but the remaining nests contained embryos resulting from cuckoldry as well. Overall, the frequency of offspring resulting from stolen fertilizations was only 1.3%, indicating that the great majority of paternity is by bourgeois nesting males. With regard to maternity, 87% of the nests had at least three dams, and computer simulations estimate that about 7.2 dams spawned per nest.

Alleles↗
PubMed2000

Genetic parentage in large half-sib clutches: theoretical estimates and empirical appraisals.

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.

Animals↗
PubMed1999

Proposal for a standardized temporal scheme of biological classification for extant species.

With respect to conveying useful comparative information, current biological classifications are seriously flawed because they fail to (i) standardize criteria for taxonomic ranking and (ii) equilibrate assignments of taxonomic rank across disparate kinds of organisms. In principle, these problems could be rectified by adopting a universal taxonomic yardstick based on absolute dates of the nodes in evolutionary trees. By using procedures of temporal banding described herein, a simple philosophy of biological classification is proposed that would retain a manageable number of categorical ranks yet apply them in standardized fashion to time-dated phylogenies. The phylogenetic knowledge required for a time-standardized nomenclature arguably may emerge in the foreseeable future from vast increases in multilocus DNA sequence information (coupled with continued attention to phylogeny estimation from traditional systematic data). By someday encapsulating time-dated phylogenies in a familiar yet modified hierarchical ranking scheme, a temporal-banding approach would improve the comparative information content of biological classifications.

Animals↗
PubMed1999

Species realities and numbers in sexual vertebrates: perspectives from an asexually transmitted genome.

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.

Animals↗
PubMed1999

Clustered microsatellite mutations in the pipefish Syngnathus typhle.

Clustered mutations are copies of a mutant allele that enter a population's gene pool together due to replication from a premeiotic germline mutation and distribution to multiple successful gametes of an individual. Although the phenomenon has been studied in Drosophila and noted in a few other species, the topic has received scant attention despite claims of being of major importance to population genetics theory. Here we capitalize upon the reproductive biology of male-pregnant pipefishes to document the occurrence of clustered microsatellite mutations and to estimate their rates and patterns from family data. Among a total of 3195 embryos genetically screened from 110 families, 40% of the 35 detected de novo mutant alleles resided in documented mutational clusters. Most of the microsatellite mutations appeared to involve small-integer changes in repeat copy number, and they arose in approximately equal frequency in paternal and maternal germlines. These findings extend observations on clustered mutations to another organismal group and motivate a broader critique of the mutation cluster phenomenon. They also carry implications for the evolution of microsatellites with respect to mutational models and homoplasy among alleles.

Animals↗
PubMed1998

Speciation durations and Pleistocene effects on vertebrate phylogeography.

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.

Amphibians↗
PubMed1998

Pleistocene phylogeographic effects on avian populations and the speciation process.

Pleistocene biogeographic events have traditionally been ascribed a major role in promoting speciations and in sculpting the present-day diversity and distributions of vertebrate taxa. However, this paradigm has recently come under challenge from a review of interspecific mtDNA genetic distances in birds: most sister-species separations dated to the Pliocene. Here we summarize the literature on intraspecific mtDNA phylogeographic patterns in birds and reinterpret the molecular evidence bearing on Pleistocene influences. At least 37 of the 63 avian species surveyed (59%) are sundered into recognizable phylogeographic units, and 28 of these separations (76%) trace to the Pleistocene. Furthermore, use of phylogroup separation times within species as minimum estimates of 'speciation durations' also indicates that many protracted speciations, considered individually, probably extended through time from Pliocene origins to Pleistocene completions. When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier. Whether the Pleistocene was exceptional in these regards compared with other geological times remains to be determined.

Animals↗
PubMed1998

Microsatellite evidence for monogamy and sex-biased recombination in the Western Australian seahorse Hippocampus angustus.

Four polymorphic microsatellite loci were used to assess biological parentage of 453 offspring from 15 pregnant males from a natural population of the Western Australian seahorse Hippocampus angustus. Microsatellite genotypes in the progeny arrays were consistent with a monogamous mating system in which both females and males had a single mate during a male brooding period. Multilocus genotypes implicated four females in the adult population sample as contributors of eggs to the broods of collected males, but there was no evidence for multiple mating by females. Based on genotypic data from the progeny arrays, two loci were linked tightly and the recombination rate appeared to be approximately 10-fold higher in females than in males. The utility of linked loci for parentage analyses is discussed.

Animals↗
PubMed1998

A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene.

Mitochondrial cytochrome b (cytb) is among the most extensively sequenced genes to date across the vertebrates. Here, we employ nearly 2,000 cytb gene sequences from GenBank to calculate and compare levels of genetic distance between sister species, congeneric species, and confamilial genera within and across the major vertebrate taxonomic classes. The results of these analyses parallel and reinforce some of the principal trends in genetic distance estimates previously reported in a summary of the multilocus allozyme literature. In particular, surveyed avian taxa on average show significantly less genetic divergence than do same-rank taxa surveyed in other vertebrate groups, notably amphibians and reptiles. Various biological possibilities and taxonomic "artifacts" are considered that might account for this pattern. Regardless of the explanation, by the yardstick of genetic divergence in this mtDNA gene, as well as genetic distances in allozymes, there is rather poor equivalency of taxonomic rank across some of the vertebrates.

Amphibians↗
PubMed1998

Population structure in the American oyster as inferred by nuclear gene genealogies.

Multiple haplotypes from each of three nuclear loci were isolated and sequenced from geographic populations of the American oyster, Crassostrea virginica. In tests of alternative phylogeographic hypotheses for this species, nuclear gene genealogies constructed for these haplotypes were compared to one another, to a mitochondrial gene tree, and to patterns of allele frequency variation in nuclear restriction site polymorphisms (RFLPs) and allozymes. Oyster populations from the Atlantic versus the Gulf of Mexico are not reciprocally monophyletic in any of the nuclear gene trees, despite considerable genetic variation and despite large allele frequency differences previously reported in several other genetic assays. If these populations were separated vicariantly in the past, either insufficient time has elapsed for neutral lineage sorting to have achieved monophyly at most nuclear loci, or balancing selection may have inhibited lineage extinction, or secondary gene flow may have moved haplotypes between regions. These and other possibilities are examined in light of available genetic evidence, and it is concluded that no simple explanation can account for the great variety of population genetic patterns across loci displayed by American oysters. Regardless of the source of this heterogeneity, this study provides an empirical demonstration that different sequences of DNA within the same organismal pedigree can have quite different phylogeographic histories.

Animals↗
PubMed1997

Phylogenetic assessment of length variation at a microsatellite locus.

Sixty-six haplotypes at a locus containing a simple dinucleotide (CA)n microsatellite repeat were isolated by PCR-single-strand conformational polymorphism from populations of the horseshoe crab Limulus polyphemus. These haplotypes were sequenced to assess nucleotide variation directly. Thirty-four distinct sequences (alleles) were identified in a region 570 bp long that included the microsatellite motif. In the repeat region itself, CA-number varied in integer values from 5 to 11 across alleles, except that a (CA)8 class was not observed. Differences among alleles were due also to polymorphisms at 22 sites in regions immediately flanking the microsatellite repeats. Nucleotide substitutions in these regions were used to estimate phylogenetic relationships among alleles, and the gene phylogeny was used to trace the evolution of length variation and CA repeat numbers. A low correlation between size variation and genealogical relationships among alleles suggests that absolute fragment size (as normally scored in microsatellite assays) is an unreliable indicator of historical affinities among alleles. This finding on the molecular fine structure of microsatellite variation suggests the need for caution in the use of repeat counts at microsatellite loci as secure indicators of allelic relationships.

Alleles↗
PubMed1997

Phylogenetics and the origin of species.

A recent criticism that the biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory that considers multiple, sex-defined genealogical pathways through sexual organismal pedigrees. A competing phylogenetic species concept (PSC) also is evaluated from this vantage. Two analytical approaches are employed to capture the composite phylogenetic information contained within the braided assemblages of hereditary pathways of a pedigree: (i) consensus phylogenetic trees across allelic transmission routes and (ii) composite phenograms from quantitative values of organismal coancestry. Outcomes from both approaches demonstrate that the supposed sharp distinction between biological and phylogenetic species concepts is illusory. Historical descent and reproductive ties are related aspects of phylogeny and jointly illuminate biotic discontinuity.

Models, Genetic↗
PubMed1997

Microsatellite analysis of maternity and the mating system in the Gulf pipefish Syngnathus scovelli, a species with male pregnancy and sex-role reversal.

Highly variable microsatellite loci were employed to study the mating system of the sexually dimorphic Gulf pipefish Syngnathus scovelli. In this species, like others in the family Syngnathidae, 'pregnant' males provide all parental care. Gulf pipefish were collected from one locale in the northern Gulf of Mexico, and internally carried broods of 40 pregnant males were analysed genetically. By comparing multilocus microsatellite fingerprints for the inferred mothers against expected genotypic distributions from the population sample, it was determined that: (i) only one male had received eggs from more than a single female; and (ii) on two separate occasions, two different males had received eggs from the same female. Given the high power to detect multiple matings by males, the first finding indicates that only rarely are individual males impregnated by multiple females during the course of a pregnancy. Conversely, given the lower power to detect multiple matings by females due to sampling constraints, the second finding suggests a high frequency of multiple successful matings by females. Thus, this population of Gulf pipefish displays a polyandrous genetic mating system. The relevance of these genetic findings is discussed with regard to the evolution of secondary sex traits in this species, and in other syngnathids.

Animals↗
PubMed1997

Detection and isolation of nuclear haplotypes by PCR-SSCP.

SSCP (single-strand conformational polymorphism) is used widely in the field of human biomedicine, but its potential as a population genetics tool for the recovery of nuclear gene genealogies remains to be realized. We describe and illustrate a use for SSCP in the physical isolation of nuclear haplotypes that circumvents several difficulties associated with more conventional cloning procedures. The DNA sequence can be determined directly from the isolated haplotypes and used for phylogenetic inference. SSCP provides a convenient first step toward generating nuclear genealogies for population studies.

Animals↗
PubMed1996

Molecular documentation of polyembryony and the micro-spatial dispersion of clonal sibships in the nine-banded armadillo, Dasypus novemcinctus.

A battery of allelic markers at highly polymorphic microsatellite loci was developed and employed to confirm genetically, the clonal nature of sibships in nine-banded armadillos. This phenomenon of consistent polyembryony, otherwise nearly unknown among the vertebrates, was capitalized upon to describe the micro-spatial distributions of numerous clonal sibships in a natural population of armadillos. Adult clone mates were significantly more dispersed than were juvenile sibs, suggesting limited opportunities for altruistic behavioural interactions among mature individuals. These results, and considerations of armadillo natural history, suggest that evolutionary explanations for polyembryony in this species may not reside in the kinds of ecological and kin selection theories relevant to some of the polyembryonic invertebrates. Rather, polyembryony in armadillos may be associated evolutionarily with other reproductive peculiarities of the species, including delayed uterine implantation of a single egg.

Alleles↗
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↗
PubMed1996

Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification.

Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For replicate simulated phylads with n extant species, cumulative distribution functions (cdf's) of branching times were calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to those from three published empirical trees. Molecular phylogenies for columbine plants and avian cranes showed statistically significant departures from the null expectations, in directions indicating recent and ancient species' radiations, respectively, whereas a molecular phylogeny for the Drosophila virilis species group showed no apparent historical clustering of branching events. Effects of outgroup choice and phylogenetic frame of reference were investigated for the columbines and found to have a predictable influence on the types of conclusions to be drawn from such analyses. To enable other investigators to statistically test for nonrandomness in temporal cladogenetic pattern in empirical trees generated from data on extant species, we present tables of mean cdf's and associated probabilities under the null model for expected branching times in phylads of varying size. The approaches developed in this report complement and extend those of other recent methods for employing null models to assess the statistical significance of pattern in evolutionary trees.

Animals↗