Showing papers by "John C. Avise published in 1998"
TL;DR: There is rather poor equivalency of taxonomic rank across some of the vertebrates, by the yardstick of genetic divergence in this mtDNA gene, as well as genetic distances in allozymes.
Abstract: 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.
679 citations
TL;DR: 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.
Abstract: 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.
633 citations
TL;DR: Comparisons of genetic–distance trends across the vertebrate classes reveal that 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 phylo geographic variety into many of today's sister species.
Abstract: 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.
586 citations
TL;DR: The early history and explosive growth of phylogeography is traced, and predictions about future challenges for the field that centre on several facets of genealogical concordance are made.
Abstract: Last year marked the 10th anniversary of the birth of phylogeography as a formal discipline. However, the field’s gestation began in the mid-1970s with the introduction of mitochondrial (mt) DNA analyses to population genetics, and to the profound shift toward genealogical thought at the intraspecific level (now formalized as coalescent theory) that these methods prompted. This paper traces the early history and explosive growth of phylogeography, and closes with predictions about future challenges for the field that centre on several facets of genealogical concordance.
378 citations
TL;DR: 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.
Abstract: ▪ Abstract 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 bounda...
182 citations
TL;DR: Molecular phytogenies of species‐rich Sebastes rockfishes from the northeastern Pacific Ocean were used to test predictions of null theoretical models that assume random temporal placements of phylogenetic nodes, and statistical tests of the nodal placements in the Sebastes phylogeny suggest that speciation events in the rockfishing were temporally nonrandom, with significant clustering of cladogenetic events in time.
Abstract: The concept of species flocks has been central to previous interpretations of patterns and processes of explosive species radiations within several groups of freshwater fishes. Here, molecular phytogenies of species-rich Sebastes rockfishes from the northeastern Pacific Ocean were used to test predictions of null theoretical models that assume random temporal placements of phylogenetic nodes. Similar appraisals were conducted using molecular data previously published for particular cichlid fishes in Africa that epitomize, by virtue of a rapid and recent radiation of species, the traditional concept of an intralacustrine "species flock." As gauged by the magnitudes of genetic divergence in cytochrome b sequences from mitochondrial DNA, as well as in allozymes, most speciation events in the Sebastes complex were far more ancient than those in the cichlids. However, statistical tests of the nodal placements in the Sebastes phylogeny suggest that speciation events in the rockfishes were temporally nonrandom, with significant clustering of cladogenetic events in time. Similar conclusions also apply to an ancient complex of icefishes (within the Notothenioidei) analyzed in the same fashion. Thus, the rockfishes (and icefishes) may be interpreted as ancient species flocks in the marine realm. The analyses exemplified in this report introduce a conceptual and operational approach for extending the concept of species flocks to additional environmental settings and evolutionary timescales.
117 citations
TL;DR: The studies compiled in this volume highlight the scope and imaginative uses of genetic information for conservation challenges in the marine realm.
Abstract: Author(s): Avise, JC | Abstract: Techniques for DNA and protein assay make possible genetic studies on any species. In recent years, molecular methods have been applied to a number of conservation-relevant genetic issues for marine organisms ranging from zooplankton to whales. To introduce these symposium proceedings, I will mention some of the unusual challenges and opportunities afforded by marine taxa for genetic research in conservation. Marine organisms often are less accessible for behavioral and natural history observation than are their terrestrial counterparts. Many marine organisms have exceptional dispersal and migratory capabilities. Species' ranges can be vast. Life histories may include high fecundities and explosive reproductive potentials. Many marine species of conservation concern are harvested commercially or illegally and thus economic, social, jurisdictional, and forensic matters often arise in population management, in addition to biological considerations. For a diversity of marine taxa, molecular markers have uncovered previously unknown aspects of behavior, natural history, and population demography that can inform conservation and management decisions. The studies compiled in this volume highlight the scope and imaginative uses of genetic information for conservation challenges in the marine realm.
113 citations
TL;DR: 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, consistent with a monogamous mating system in which both females and males had a single mate during a male brooding period.
Abstract: 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.
109 citations
TL;DR: No simple explanation can account for the great variety of population genetic patterns across loci displayed by American oysters, and this study provides an empirical demonstration that different sequences of DNA within the same organismal pedigree can have quite different phylogeographic histories.
Abstract: 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.
100 citations
TL;DR: Microsatellite markers are developed and employ to assess genetic paternity and maternity of progeny cohorts in a population of redbreast sunfish, a species in which males build and tend nests where heteromorphic males specialized for parasitism or for parental care coexist in high frequency.
Abstract: Despite a great diversity of reproductive behaviors in fishes, few studies have examined the genetic consequences of alternative reproductive tactics. Here we develop and employ microsatellite markers to assess genetic paternity and maternity of progeny cohorts in a population of redbreast sunfish (Lepomis auritus), a species in which males build and tend nests. Nearly 1000 progeny from 25 nests, plus nest-attendant males and nearby adults, were genotyped at microsatellite loci that displayed more than 18 alleles each. The genetic data demonstrate that multiple females (at least two to six) spawned in each nest, their offspring were spatially dispersed across a nest, and more than 90% of the young were sired by the attendant male. However, about 40% of the nests also showed genetic evidence of low-level reproductive parasitism, and two nests were tended by males that had fathered none of the sampled offspring. Genetically deduced reproductive behaviors in this population of redbreast sunfish contrast with those reported previously in bluegill sunfish (L. macrochirus) wherein heteromorphic males specialized for parasitism or for parental care coexist in high frequency. Thus, nest-parasitic reproductive behaviors in fishes appear to be evolutionary labile.
81 citations
TL;DR: Results suggest that the original null allele (as well as the nonnull class), which was cloned and characterized from the White Sands pupfish, has diversified considerably since its origin and has not recombined frequently with the non null class of alleles.
Abstract: Author(s): Jones, AG; Stockwell, CA; Walker, D; Avise, JC | Abstract: Microsatellite loci were cloned and characterized from the White Sands pupfish (Cyprinodon tularosa), a New Mexico state-listed endangered species. One locus exhibited a high-frequency nonamplifying allele localized to a single population. This null allele was PCR amplified by redesign of one of the original primers and multiple individuals homozygous for null as well as for nonnull alleles were sequenced using the new primer. These molecular dissections revealed that the original failure to amplify some alleles from this microsatellite locus was due to a 4 bp deletion in one of the original PCR priming sites. Furthermore, the reamplifications revealed five distinct size classes of alleles that had been masquerading as the original null. These null alleles did not overlap in length with the nonnull alleles, and they also differed consistently by a linked nucleotide substitution. Results suggest that the original null allele (as well as the nonnull class) has diversified considerably since its origin and has not recombined frequently with the nonnull class of alleles.
TL;DR: The genetic data demonstrated that nests of males frequently contain eggs from multiple females, and the multilocus genotypes of inferred mothers indicated that females mate with multiple males, sometimes over distances greater than one kilometer.
Abstract: Attempts by males to steal fertilizations from other males are common in many species. In some sticklebacks, males also are known to steal eggs from the nests of rivals and to carry them back to their own nests. However the genetic consequences of these nest-raiding behaviors seldom have been investigated. Here we assess genetically the prevalence of sneaked fertilizations and egg stealing, and we describe the mating system in a natural population of the fifteenspine stickleback. Six microsatellite markers were developed and employed to assay a total of 1307 embryos from 28 nests. Guardian males and all nest-holding males in the local area also were genotyped for two to six loci Analysis of male genotypes and those of embryos revealed that five of the 28 nests (18%) contained progeny from sneaked fertilizations, and that four of the 24 nests (17%) with resident males contained stolen egg clutches Comparisons of the composite DNA genotypes of nest-holding males against those of inferred sneakers implicated one nest holder as the sneaker of a nest seven meters from his own. Also, the genetic data demonstrated that nests of males frequently contain eggs from multiple females. The multilocus genotypes of inferred mothers indicated that females mate with multiple males, sometimes over distances greater than one kilometer.
TL;DR: 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.
Abstract: Author(s): Walker, DE; Moler, PE; Buhlmann, KA; Avise, JC | Abstract: 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.
TL;DR: Results suggest that molecular assays of highly polymorphic genetic systems can add considerable power to assessments of biological parentage in natural populations even when neither parent is otherwise known.
Abstract: Genetic data from polymorphic microsatellite loci were employed to estimate paternity and maternity in a local population of nine-banded armadillos (Dasypus novemcinctus) in northern Florida. The parentage assessments took advantage of maximum likelihood procedures developed expressly for situations when individuals of neither gender can be excluded a priori as candidate parents. The molecular data for 290 individuals, interpreted alone and in conjunction with detailed biological and spatial information for the population, demonstrate high exclusion probabilities and reasonably strong likelihoods of genetic parentage assignment in many cases; low mean probabilities of successful reproductive contribution to the local population by individual armadillo adults in a given year; and statistically significant microspatial associations of parents and their offspring. Results suggest that molecular assays of highly polymorphic genetic systems can add considerable power to assessments of biological parentage in natural populations even when neither parent is otherwise known.
Journal Article•
TL;DR: MtDNA phylogeographic patterns in the baurii/subrubrum complex are remarkably similar to those reported previously for two other southeastern kinosternids, Sternotherus minor and S. odoratus.
Abstract: We used restriction assays of mitochondrial (mt) DNA to estimate phylogeographic variation in two sister taxa of muid turtles in the southeastern United States. Extensive mtDNA variation characterized Kinosternon subrubrum and, to a lesser degree, K. baurii. Each of 26 mtDNA haplotypes from the 83 assayed specimens was localized spatially. Collectively, these mtDNA haplotypes demarcated four major matrilineal assemblages, each with a well defined regional distribution: a western group (A) in Missouri and Louisiana, a central group (B) throughout the Gulf coastal states, an eastern group (C) along the Atlantic coastal states north of Florida, and a southern group (D) in peninsular Florida. All assayed samples of K. baurii belonged to the mtDNA C assemblage. The two species in Florida are thus highly distinct in mtDNA genotype, but they exhibit minimal mtDNA divergence along the Atlantic coastal states. These findings raise questions concerning the evolutionary history and taxonomy of these two recognized species. MtDNA phylogeographic patterns in the baurii/subrubrum complex are remarkably similar to those reported previously for two other southeastern kinosternids, Sternotherus minor and S. odoratus.
Book•
01 Jan 1998
TL;DR: Avise as discussed by the authors reviewed discoveries in molecular biology, evolutionary genetics, and human genetic engineering, and discussed the relevance of these findings to issues of concern traditionally reserved for mythology, theology and religious faith.
Abstract: In clear terms, John Avise reviews discoveries in molecular biology, evolutionary genetics, and human genetic engineering, and discusses the relevance of these findings to issues of concern traditionally reserved for mythology, theology and religious faith. The text explains how the "genetic gods" figure in our development - not just our metabolism and physiology, but even our emotional disposition, personality, ethical leanings and even religiosity. Yet genes are physical rather than metaphysical entities. Having arisen via an amoral evolutionary process - natural selection - genes have no consciousness, no sentient code of conduct, no reflective concern about the consequences of their actions. It is Avise's contention that late-1990s genetic knowledge can inform attempts to answer typically religious questions - about origins, fate and meaning.
TL;DR: The taxonomic status and evolutionary history of the flattened musk turtle (S. depressus) were investigated in this article, where the authors employed sequence data from mitochondrial DNA to address the phylogenetic distinctiveness and phylogeographic position of S. minor relative to all other musk and mud turtles in North America.
Abstract: 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 discov- ered 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 distribu- tion 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 gener- ated 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 . Ge- netic 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 ratio- nale for the taxonomic recognition of S. depressus and, hence, for special efforts to protect this federally threatened species.
TL;DR: Results underscore a distinction between the composite genealogical information in a population pedigree and the subsets of that information registered in allelic lineage pathways.
Abstract: In sexual species, autosomal alleles are transmitted through multigeneration organismal pedigrees via pathways of descent involving both genders. Here, models assess the sampling properties of these gender-described transmission pathways. An isolation-by-distance model of mating was used to construct a series of computer population pedigrees by systematically varying neighborhood size and the timing of isolation events in sundered populations. For each known pedigree, a matrix of true coancestry coefficients between all individuals in the final generation was calculated and compared (using cophenetic correlations) to mean pairwise times to common ancestry as estimated by sampling varying numbers of gender-defined lineage routes available to individual alleles through that pedigree. When few lineage routes were sampled, agreement between the estimated and the true pedigree was poor and showed a large variance. Agreement improved as more lineage routes were incorporated and asymptotically approached plateau levels predictably relatable to the magnitude of population structure. Results underscore a distinction between the composite genealogical information in a population pedigree and the subsets of that information registered in allelic lineage pathways.
TL;DR: The majority of adults in the population apparently failed to produce any surviving offspring, and even those that did usually did so in only 1 of the 4 years, which is unexpected, given the rapid and successful range extension of this species throughout the southeastern United States in this century.
Abstract: We used microsatellite DNA markers to identify the putative parents of 69 litters of nine-banded armadillos (Dasypus novemcinctus) over 4 years. Male and female parents did not differ in any measure of body size in comparisons with nonparents. However, males observed paired with a female were significantly larger than unpaired males, although paired females were the same size as unpaired females. Females categorized as possibly lactating were significantly larger than females that were either definitely lactating or definitely not lactating. There was no evidence of assortative mating: body-size measurements of mothers were not significantly correlated with those of fathers. Nine- banded armadillos give birth to litters of genetically identical quadruplets. Mothers (but not fathers) of female litters were significantly larger than mothers of male litters, and maternal (but not paternal) body size was positively correlated with the number of surviving young within years, but not cumulatively. There were no differences in dates of birth between male and female litters, nor were there any significant relationships between birth date and maternal body size. Body size of either parent was not correlated with the body sizes of their offspring. Cumulative and yearly reproductive success did not differ between reproductively successful males and females. Average reproductive success (which included apparently unsuccessful individuals) also did not differ between males and females. The majority of adults in the population apparently failed to produce any surviving offspring, and even those that did usually did so in only 1 of the 4 years. This low reproductive success is unexpected, given the rapid and successful range extension of this species throughout the southeastern United States in this century. Resume : Nous avons utilise des marqueurs d'ADN microsatellites pour identifier les parents putatifs de 69 portees de Tatous a neuf bandes (Dasypus novemcinctus) au cours d'une periode de 4 ans. Les parents mâles et femelles ne differaient par aucune mesure de leur corps des individus non parents. Par ailleurs, les mâles paires a une femelle etaient significativement plus gros que les mâles non paires, alors que les femelles pairees ou non pairees etaient de la meme taille. Les femelles classifiees comme possiblement nourricieres etaient plus grosses que les femelles