Molecular Ecology And Evolution: The Organismal Side: Selected Writings From The Avise Laboratory Selected Writings from the Avise Laboratory

This volume is a reprinted collection of 69 “classics” from the Avise laboratory, chosen to illustrate a trademark brand of research that harnesses molecular markers to scientific studies of natural history and evolution in the wild. Spanning the early 1970s through the late 2000s, these articles trace how the author and his colleagues have used molecular genetics techniques to address multifarious conceptual topics in genetics, ecology, and evolution, in a fascinating menagerie of creatures with oft-peculiar lifestyles. The organisms described in this volume range from blind cavefish to male-pregnant pipefishes and sea spiders, from clonal armadillos to natal-homing marine turtles, from hermaphroditic sea snails to hybridizing monkeys and tree frogs, from clonal marine sponges to pseudohermaphroditic mollusks to introgressing oysters, and from endangered pocket gophers, terrapins, and sparrows to unisexual (all-female) fish species to “living-fossil” horseshoe crabs, and even to a strange little fish that routinely mates with itself. The conceptual and molecular topics addressed in this volume are also universal, ranging from punctuated equilibrium to coalescent theory to the need for greater standardization in taxonomy, from cytonuclear disequilibrium statistics to the ideas of speciation duration and sympatric speciation, from historical population demography to phylogenetic reconstructions of males' sexual ornaments, from the population genetic consequences of inbreeding to Pleistocene effects on phylogeography, and from the molecular underpinnings of null alleles to the notion of clustered mutations that arise in groups to compelling empirical evidence for the unanticipated processes of gene conversion and concerted evolution in animal mitochondrial DNA. Overall, this collection includes many of the best, most influential, sometimes controversial, occasionally provocative, always intriguing, or otherwise entertaining publications to have emerged from the Avise laboratory over the last four decades. Thus, this book conveys, through the eyes of one of the field's longstanding pioneers, what “the organismal side” of molecular ecology and evolution really means. Contents......Page 6 Introduction: What is "The Organismal Side" of Molecular Ecology and Evolution?......Page 12 Part 1 Genetic Variation, Population Structure, and Phylogeography......Page 22 EVOLUTIONARY GENETICS OF CAVE-DWELLING FISHES OF THE GENUS ASTYANAX......Page 30 BIOCHEMICAL POLYMORPHISM AND SYSTEMATICS IN THE GENUS PEROMYSCUS. V. INSULAR AND MAINLAND SPECIES OF THE SUBGENUS HAPLOMYLOMYS......Page 49 Mitochondria1 DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher, Geomys pinetis*......Page 62 Mitochondria1 DNA differentiation in North Atlantic eels: Population genetic consequences of an unusual life history pattern......Page 67 GENETIC VARIATION AND GEOGRAPHIC DIFFERENTIATION IN MITOCHONDRIAL DNA OF THE HORSESHOE CRAB, LIMULUS POLYPHEMUS......Page 72 Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA......Page 87 A Genetic Test of the Natal Homing Versus Social Facilitation Models for Green Turtle Migration......Page 92 Balancing Selection at Allozyme Loci in Oysters: Implications from Nuclear RFLPs......Page 97 Phylogeography of colonially nesting seabirds, with special reference to global matrilineal patterns in the sooty tern (Sterna fuscata)......Page 100 Part 2 Clonality, Unisexuality, and Hermaphroditism......Page 110 Histocompatibility bioassays of population structure in marine sponges......Page 116 Mode of Inheritance and Variation of Mitochondria1 DNA in Hybridogenetic Fishes of the Genus Poeciliopsis'......Page 123 An ancient clonal lineage in the (Atheriniformes: Poeciliidae) fish genus Poeciliopsis......Page 135 Molecular documentation of polyembryony and the micro-spatial dispersion of clonal sibships in the nine-banded armadillo, Dasypus novemcinctus......Page 140 Genetic sex determination, gender identification and pseudohermaphroditism in the knobbed whelk, Busycon carica (Molluscs: Melongenidae)......Page 147 A mixed-mating strategy in a hermaphroditic vertebrate......Page 153 Extensive outcrossing and androdioecy in a vertebrate species that otherwise reproduces as a self-fertilizing hermaphrodite......Page 157 Long-term retention of self-fertilization in a fish clade......Page 162 Part 3 Genetic Parentage, Kinship, and Mating Behaviors......Page 166 EVALUATING KINSHIP OF NEWLY SETTLED JUVENILES WITHIN SOCIAL GROUPS OF THE CORAL REEF FISH ANTHIAS SQUAMIPINNIS......Page 172 A MICROSATELLITE ASSESSMENT OF SNEAKED FERTILIZATIONS AND EGG THIEVERY IN THE FIFTEENSPINE STICKLEBACK......Page 181 The Bateman gradient and the cause of sexual selection in a sex-role-reversed pipefish......Page 192 How cuckoldry can decrease the opportunity for sexual selection: Data and theory from a genetic parentage analysis of the sand goby, Pomatoschistus minutus......Page 196 Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipefish......Page 202 Genetic markers substantiate long-term storage and utilization of sperm by female painted turtles......Page 207 Genetic documentation of filial cannibalism in nature......Page 214 Genetic parentage assessment in the crayfish Orconectesplacidus, a high-fecundity invertebrate with extendedmaternal brood care......Page 217 Polygynandry and sexual size dimorphism in the sea spiderAmmothea hilgendorfi (Pycnogonida: Ammotheidaef, a marine arthropod with brood-carrying males......Page 225 Part 4 Hybridization and Introgression Phenomena......Page 238 Allelic expression and genetic distance in hybrid macaque monkeys......Page 244 CHARACTERIZATION OF MITOCHONDRIAL DNA VARIABILITY IN A HYBRID SWARM BETWEEN SUBSPECIES OF BLUEGILL SUNFISH (LEPOMIS MACROCHIRUS)......Page 252 Directional introgression of mitochondrial DNA in a hybrid population of tree frogs: The influence of mating behavior......Page 263 THE EVOLUTIONARY GENETIC STATUS OF ICELANDIC EELS......Page 268 POECILIA MEXICANA IS THE RECENT FEMALE PARENT OF THE UNISEXUAL FISH P. FORMOSA......Page 277 Cytonuclear genetics of experimental fish hybrid zones inside Biosphere 2......Page 281 Hybridization Among the Ancient Mariners: Characterization of Marine Turtle Hybrids With Molecular Genetic Assays......Page 285 MOLECULAR GENETIC ANALYSIS OF A STEPPED MULTILOCUS CLINE IN THE AMERICAN OYSTER (CRASSOSTREA VIRGINICA)......Page 292 Cytonuclear lntrogressive Swamping and Species Turnover of Bass After an Introduction......Page 303 Part 5 Genetic Diagnoses of Endangered Species......Page 310 GENETIC DETERMINATION OF THE STATUS OF AN ENDANGERED SPECIES OF POCKET GOPHER IN GEORGIA......Page 316 Molecular Genetic Relationships of the Extinct Dusky Seaside Sparrow......Page 323 Evolutionary distinctiveness of the endangered Kemp's ridley sea turtle......Page 326 Molecular and Population Genetic Aspects of Mitochondrial DNA Variability in the Diamondback Terrapin, Malaclemys terrapin......Page 329 APPLICATION OF GENEALOGICAL-CONCORDANCE PRINCIPLES TO THE TAXONOMY AND EVOLUTIONARY HISTORY OF THE SHARP-TAILED SPARROW (AMMODRAMUS CAUDACUTUS) SHARP-TAILED SPARROW (AMMODRAMUS CAUDACUTUS)......Page 337 GLOBAL PHYLOGEOGRAPHY OF THE LOGGERHEAD TURTLE (CARETTA CARETTA) AS ONDICATED BY MITOCHONDRIAL DNA HAPLOTYPES......Page 350 Phylogenetic Distinctiveness of a Threatened Aquatic Turtle (Sternotherus depressus)......Page 359 Part 6 Phylogeny and Macroevolutionary Patterns......Page 366 Is evolution gradual or rectangular? Evidence from living fishes......Page 372 Evolutionary genetics of birds......Page 377 An odyssey of the green sea turtle: Ascension Island revisited......Page 386 A molecular phylogeny for marine turtles: Trait mapping, rate assessment, and conservation relevance......Page 390 A Comparative Summary of Genetic Distances in the Vertebrates from the Mitochondrial Cytochrome b Gene......Page 394 Pleistocene phylogeographic effects on avian populations and the speciation process......Page 404 Speciation durations and Pleistocene effects on vertebrate phylogeography......Page 411 PHYLOGENETIC PERSPECTIVES IN THE EVOLUTION OF PARENTAL CARE IN RAY-FINNED FISHES......Page 417 COMPARATIVE PHYLOGENETIC ANALYSIS OF MALE ALTERNATIVE REPRODUCTIVE TACTICS IN RAY-FINNED FISHES......Page 426 Part 7 Population-Genetic, Speciational, and Evolutionary Theory......Page 432 Definition and Properties of Disequilibrium Statistics for Associations Between Nuclear and Cytoplasmic Genotypes......Page 440 Current versus Historical Population Sizes in Vertebrate Species with High Gene Flow: A Comparison Based on Mitochondrial DNA Lineages and Inbreeding Theory for Neutral Mutations ......Page 454 ESTIMATION OF SINGLE GENERATION MIGRATION DISTANCES FROM GEOGRAPHIC VARIATION IN ANIMAL MITOCHONDRIAL DNA......Page 468 Phylogenetics and the origin of species......Page 478 Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome......Page 486 Proposal for a standardized temporal scheme of biological classification for extant species......Page 490 A genetic analogue of 'mark-recapture' methods for estimating population size: an approach based on molecular parentage assessments......Page 496 Sympatric speciation as a consequence of male pregnancy in seahorses......Page 504 Microsatellite null alleles in parentage analysis......Page 510 Sex chromosomes and male ornaments: a comparative evaluation in ray-finned fishes......Page 516 Time to Standardize Taxonomies......Page 520 Hemiplasy: A New Term in the Lexicon of Phylogenetics......Page 524 Part 8 Molecular-Level Features and Processes......Page 530 Critical experimental test of the possibility of "paternal leakage" of mitochondrial DNA......Page 534 Size polymorphism and heteroplasmy in the mitochondrial DNA of lower vertebrates......Page 537 Phylogenetic assessment of length variation at a microsatellite locus......Page 541 The Molecular Basis of a Microsatellite Null Allele From the White Sands Pupfish......Page 546 Clustered Microsatellite Mutations in the Pipefish Syngnathus WhZe......Page 550 Rapid cancerted evolution in animal mitochondrial DNA......Page 557 Appendix. Complete list of publications by Avise and colleagues from 1972-2010.......Page 562 Pt. 1. Genetic variation, population structure, and phylogeography. 1. Evolutionary genetics of cave-dwelling fishes of the genus Astyanax / Avise, J.C. and R.K. Selander. 2. Biochemical polymorphism and systematics in the genus Peromyscus / Avise, J.C. [und weitere]. 3. Mitochondrial DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher, Geomys pinetis / Avise, J.C. [und weitere]. 4. Mitochondrial DNA differentiation in North Atlantic eels : population genetic consequences of an unusual life history pattern / Avise, J.C. [und weitere]. 5. Genetic variation and geographic differentiation in mitochondrial DNA of the horseshoe crab, Limulus polyphemus / Saunders, N.C., L.G. Kessler, and J.C. Avise. 6. Phylogeographic population structure of red-winged blackbirds assessed by mitochondrial DNA / Ball, R.M. [und weitere]. 7. A genetic test of natal homing versus social facilitation models for green turtle migration / Meylan, A.B., B.W. Bowen, and J.C. Avise. 8. Balancing selection at allozyme loci in oysters : implications from nuclear RFLPs / Karl, S.A. and J.C. Avise. 9. Phylogeography of colonially nesting seabirds, with special reference to global matrilineal patterns in the sooty tern (Sterna fuscata) / Avise, J.C. [und weitere] -- pt. 2. Clonality, unisexuality, and hermaphroditism. 10. Histocompatibility bioassays of population structure in marine sponges : clonal structure in Verongia longissima and Iotrochota birotulata / Neigel, J.E. and J.C. Avise. 11. Mode of inheritance and variation of mitochondrial DNA in hybridogenetic fishes of the genus Poeciliopsis / Avise, J.C. and R.C. Vrijenhoek. 12. An ancient clonal lineage in the fish genus Poeciliopsis (Atheriniformes : Poeciliidae / Quattro, J.M., J.C. Avise, and R.C. Vrijenhoek. 13. Molecular documentation of polyembryony and the micro-spatial dispersion of clonal sibships in the nine-banded armadillo, Dasypus novemcinctus / Prodohl, P.A. [und weitere]. 14. Genetic sex determination, gender identification, and pseudohermaphroditism in the knobbed whelk, Busycon carica (Mollusca : Melongenidae) / Avise, J.C., A.J. Power, and D. Walker. 15. A mixed-mating strategy in a hermaphroditic vertebrate / Mackiewicz, M. [und weitere]. 16. Extensive outcrossing and androdioecy in a vertebrate species that otherwise reproduces as a self-fertilizing hermaphrodite / Mackiewicz, M. [und weitere]. 17. Long-term retention of self-fertilization in a fish clade / Tatarenkov, A. [und weitere] -- pt. 3. Genetic parentage, kinship, and mating behaviors. 18. Evaluating kinship of newly settled juveniles within social groups of the coral reef fish Anthias squamipinnis / Avise, J.C. and D.Y. Shapiro. 19. A microsatellite assessment of sneaked fertilizations and egg thievery in the fifteenspine stickleback / Jones, A.G., S. Ostlund-Nilsson and J.C. Avise. 20. The Bateman gradient and the cause of sexual selection in a sex-role-reversed pipefish / Jones, A.G. [und weitere]. 21. How cuckoldry can decrease the opportunity for sexual selection : data and theory from a genetic parentage analysis of the sand goby, Pomatoschistus minutus / Jones, A.G. [und weitere]. 22. Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipefish / Jones, A.G., D. Walker, and J.C. Avise. 23. Genetic markers substantiate long-term storage and utilization of sperm by female painted turtles / Pearse, D.E., F.J. Janzen, and J.C. Avise. 24. Genetic documentation of filial cannibalism in nature / DeWoody, J.A. [und weitere]. 25. Genetic parentage assessment in the crayfish Orconectes placidus, a high-fecundity invertebrate with extended maternal brood care / Walker, D., B.A. Porter, and J.C. Avise. 26. Polygynandry and sexual size dimorphism in the sea spider Ammothea hilgendorfi (Pycnogonida :Ammotheidae), a marine arthropod with brood-carrying males / Barreto, F.S. and J.C. Avise -- pt. 4. Hybridization and introgression phenomena. 27. Allelic expression and genetic distance in hybrid macaque monkeys / Avise, J.C. and S.W. Duvall. 28. Characterization of mitochondrial DNA variability in a hybrid swarm between subspecies of bluegill sunfish (Lepomis macrochirus) / Avise, J.C. [und weitere]. 29. Directional introgression of mitochondrial DNA in a hybrid population of treefrogs : the influence of mating behavior / Lamb, T. and J.C. Avise. 30. The evolutionary genetic status of Icelandic eels / Avise, J.C. [und weitere]. 31. Poecilia mexicana is the recent female parent of the unisexual fish P. formosa / Avise, J.C. [und weitere]. 32. Cytonuclear genetics of experimental fish hybrid zones inside Biosphere 2 / Scribner, K.T. and J.C. Avise. 33. Hybridization among the ancient mariners : characterization of marine turtle hybrids with molecular genetic assays / Karl, S.A., B.W. Bowen, and J.C. Avise. 34. Molecular genetic analysis of a stepped multilocus cline in the American oyster (Crassostrea virginica) / Hare, M.P. and J.C. Avise. 35. Cytonuclear introgressive swamping and species turnover of bass after an introduction / Avise, J.C. [und weitere] -- pt. 5. Genetic diagnoses of endangered species. 36. Genetic determination of the status of an endangered species of pocket gopher in Georgia / Laerm, J. [und weitere]. 37. Molecular genetic relationships of the extinct Dusky Seaside Sparrow / Avise, J.C. and W.S. Nelson. 38. Evolutionary distinctiveness of the endangered Kemp's ridley sea turtle / Bowen, B.W., A.B. Meylan, and J.C. Avise. 39. Molecular and population genetic aspects of mitochondrial DNA variability in the diamondback terrapin, Malaclemys terrapin / Lamb, T. and J.C. Avise. 40. Application of genealogical-concordance principles to the taxonomy and evolutionary history of the sharp-tailed sparrow (Ammodramus caudacutus) / Rising, J.D. and J.C. Avise. 41. Global phylogeography of the loggerhead turtle (Caretta caretta) as indicated by mitochondrial DNA haplotypes / Bowen, B.W. [und weitere]. 42. Phylogenetic distinctiveness of a threatened aquatic turtle (Sternotherus depressus) / Walker, D., G. Orti, and J.C. Avise -- pt. 6. Phylogeny and macroevolutionary patterns. 43. Is evolution gradual or rectangular? Evidence from living fishes / Avise, J.C. 44. Evolutionary genetics of birds. III. Comparative molecular evolution in New World warblers (Parulidae) and rodents (Cricetinae) / Avise, J.C., J.C. Patton, and C.F. Aquadro. 45. An odyssey of the green sea turtle : Ascension Island revisited / Bowen, B.W., A.B. Meylan, and J.C. Avise. 46. A molecular phylogeny for marine turtles : trait mapping, rate assessment, and conservation relevance / Bowen, B.W., W.S. Nelson, and J.C. Avise. 47. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene / Johns, G.C. and J.C. Avise. 48. Pleistocene phylogeographic effects on avian populations and the speciation process / Avise, J.C. and D. Walker. 49. Speciation durations and Pleistocene effects on vertebrate phylogeography / Avise, J.C., D. Walker, and G.C. Johns. 50. Phylogenetic perspectives in the evolution of parental care in ray-finned fishes / Mank, J. E, D.E.L. Promislow, and J.C. Avise. 51. Comparative phylogenetic analysis of male alternative reproductive tactics in ray-finned fishes / Mank, J.E. and J.C. Avise -- pt. 7. Population-genetic, speciational, and evolutionary theory. 52. Definition and properties of disequilibrium statistics for associations between nuclear and cytoplasmic genotypes / Asmussen, M.A., J. Arnold, and J.C. Avise. 53. Current versus historical population sizes in vertebrate species with high gene flow : a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations / Avise, J.C., R.M. Ball, Jr., and J. Arnold. 54. Estimation of single generation migration distances from geographic variation in animal mitochondrial DNA / Neigel, J.E., R.M Ball., Jr., and J.C. Avise. 55. Phylogenetics and the origin of species / Avise, J.C. and K. Wollenberg. 56. Species realities and numbers in sexual vertebrates : perspectives from an asexually transmitted genome / Avise, J.C. and D. Walker. 57. Proposal for a standardized temporal scheme of biological classification for extant species / Avise, J.C. and G.C. Johns. 58. A genetic analogue of 'mark-recapture' methods for estimating population size : an approach based on molecular parentage assessment / Pearse, D.E. [und weitere]. 59. Sympatric speciation as a consequence of male pregnancy in seahorses / Jones, A.G. [und weitere]. 60. Microsatellite null alleles in parentage analysis / Dakin, E.E. and J.C. Avise. 61. Sex chromosomes and male ornaments : a comparative evaluation in ray-finned fishes / Mank, J.E. [und weitere]. 62. Time to standardize taxonomies / Avise, J.C. and D. Mitchel. 63. Hemiplasy : a new term in the lexicon of phylogenetics / Avise, J.C. and T.J. Robinson -- pt. 8. Molecular-level features and processes. 64. Critical experimental test of the possibility of "paternal leakage" of mitochondrial DNA / Lansman, R.A., J.C. Avise, and M.D. Huettel. 65. Size polymorphism and heteroplasmy in the mitochondrial DNA of lower vertebrates / Bermingham, E., T. Lamb, and J.C. Avise. 66. Phylogenetic assessment of length variation at a microsatellite locus / Orti, G., D.E. Pearse, and J.C. Avise. 67. The molecular basis of a microsatellite null allele from the White Sands pupfish / Jones, A.G. [und weitere]. 68. Clustered microsatellite mutations in the pipefish Syngnathus typhle / Jones, A.G. [und weitere]. 69. Rapid concerted evolution in animal mitochondrial DNA / Tatarenkov, A. and J.C. Avise