Mitochondrial-dna variation and evolutionary relationships in the amakihi complex
TL;DR: Genetic distances and the pattern of relationships among amakihi taxa indicate that species status for H. v. chloris and H. stejnegeri may be warranted, and the relationships within the chloris-stejnegersi-parvus clade generally are consistent with the previously proposed model of double invasion.
Abstract: AssRAcT.-An analysis of restriction-site variation in mitochondrial DNA was conducted to examine relationships among five taxa in one group of honeycreepers-the amakihi complex (genus Hemignathus). We analyzed 35 ingroup and 3 outgroup samples. Tree topologies, based on both distance and parsimony methods, grouped taxa into two distinct lineages: the virens-wilsoni lineage; and the chloris-stejnegeri-parvus group. Inter-island sequence divergence (average d,X = 0.0368) is considerably higher than intra-island variation (mean d, = 0.0035), and is higher than average for avian species. Variability (measured as both nucleotide diversity and maximum divergence between haplotypes) differs among island populations. Molecular evolutionary rates were calibrated on the basis of maximum island age estimates; sequence divergence in this lineage is approximately 2% per million years. The relationships within the chloris-stejnegeri-parvus clade generally are consistent with the previously proposed model of double invasion. Genetic distances and the pattern of relationships among amakihi taxa indicate that species status for H. v. chloris and H. v. stejnegeri may be warranted. Received 15
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TL;DR: An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms, but a survey of mtDNA‐haplotype diversity in 34 species of birds indicates that coalescence is generally very recent, which suggests that coalescent times are typically much shorter than internodal branch lengths of the species Tree, and that sorting of mt DNA lineages is not likely to confound the species trees.
Abstract: An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree. In contrast, a set of nuclear genes can be selected from distinct chromosomes, such that each gene tree provides an independent estimate of the species tree. Another aspect of the gene-tree versus species-tree problem, however, favors the use of mtDNA for inferring species trees. For a three-species segment of a phylogeny, the branching order of a gene tree will correspond to that of the species tree if coalescence of the alleles or haplotypes occurred in the internode between the first and second bifurcation. From neutral theory, it is apparent that the probability of coalescence increases as effective population size decreases. Because the mitochondrial genome is maternally inherited and effectively haploid, its effective population size is one-fourth that of a nuclear-autosomal gene. Thus, the mitochondrial-haplotype tree has a substantially higher probability of accurately tracking a short internode than does a nuclear-autosomal-gene tree. When an internode is sufficiently long that the probability that the mitochondrial-haplotype tree will be congruent with the species tree is 0.95, the probability that a nuclear-autosomalgene tree will be congruent is only 0.62. If each of k independently sampled nuclear-gene trees has a probability of congruence with the species tree of 0.62, then a sample of 16 such trees would be required to be as confident of the inference based on the mitochondrial-haplotype tree. A survey of mtDNA-haplotype diversity in 34 species of birds indicates that coalescence is generally very recent, which suggests that coalescence times are typically much shorter than internodal branch lengths of the species tree, and that sorting of mtDNA lineages is not likely to confound the species tree. Hybridization resulting in transfer of mtDNA haplotypes among branches could also result in a haplotype tree that is incongruent with the species tree; if undetected, this could confound the species tree. However, hybridization is usually easy to detect and should be incorporated in the historical narrative of the group, because reticulation, as well as cladistic events, contributed to the evolution of the group.
1,248 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: K–Ar estimates of the date of an island’s formation provide a maximum age for the taxa inhabiting the island and can be used to calibrate rates of molecular change under the following assumptions: (i) K–Ar dates are accurate; (ii) tree topologies show that derivation of taxa parallels the timing of island formation;
Abstract: The Hawaiian Islands form as the Pacific Plate moves over a ‘hot spot’ in the earth’s mantle where magma extrudes through the crust to build huge shield volcanos. The islands subside and erode as the plate carries them to the north-west, eventually to become coral atolls and seamounts. Thus islands are ordered linearly by age, with the oldest islands in the north-west (e.g. Kauai at 5.1 Ma) and the youngest in the south-east (e.g. Hawaii at 0.43 Ma). K‐Ar estimates of the date of an island’s formation provide a maximum age for the taxa inhabiting the island. These ages can be used to calibrate rates of molecular change under the following assumptions: (i) K‐Ar dates are accurate; (ii) tree topologies show that derivation of taxa parallels the timing of island formation; (iii) populations do not colonize long after island emergence; (iv) the coalescent point for sister taxa does not greatly predate the formation of the colonized younger island; (v) saturation effects and (vi) among-lineage rate variation are minimal or correctable; and (vii) unbiased standard errors of distances and regressions can be estimated from multiple pairwise comparisons. We use the approach to obtain overall corrected rate calibrations for: (i) part of the mitochondrial cytochrome b gene in Hawaiian drepanidines (0.016 sequence divergence/Myr); (ii) the Yp1 gene in Hawaiian Drosophila (0.019/Myr Kambysellis et al. 1995); and (iii) parts of the mitochondrial 12S and 16S rRNA and tRNA val in Laupala crickets (0.024‐0.102/Myr, Shaw 1996). We discuss the reliability of the estimates given the assumptions (i‐vii) above and contrast the results with previous calibrations of Adh in Hawaiian Drosophila and chloroplast DNA in lobeliods.
460 citations
Cites background or methods from "Mitochondrial-dna variation and evo..."
...This ‘lineage sorting’ source of error is usually small relative to the distances between differentiated taxa (e.g. Bishop & Hunt 1988; Tarr & Fleischer 1993; Moore 1995)....
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...Only for the two amakihi comparisons could we correct for potential divergence of ancestral alleles prior to population separation (see Assumption 4; Wilson et al. 1985; Nei 1987; Bishop & Hunt 1988; Tarr & Fleischer 1993)....
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...…within-island variation in the ancestral population today is similar to variation at the time of offspring population formation, the betweenpopulation distance can be at least partly corrected by subtracting the mean within-island variation (Wilson et al. 1985; Nei 1987; Tarr & Fleischer 1993)....
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...It is preferable in these cases to use internal or ‘local’ molecular rate calibrations (Hillis et al. 1996), and the geological history of the Hawaiian Islands offers unique opportunities for making such calibrations (e.g. Bishop & Hunt 1988; Tarr & Fleischer 1993; Givnish et al. 1995)....
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...Biochemical and molecular © 1998 Blackwell Science Ltd, Molecular Ecology, 7, 533–545 data suggest that they did not radiate prior to the formation of the current main islands (Johnson et al. 1989; Tarr & Fleischer 1993, 1995; Fleischer et al. unpublished; see below)....
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TL;DR: A broad range of cases in which molecular techniques have been used to provide insight into conservation efforts is presented, rather than showcasing exhaustive details from a few well-known examples.
Abstract: Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective pop- ulation size, population-specific markers, etc. PCR (polymerase chain reaction) amplifi- cation of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.
343 citations
Smithsonian Institution1, National Museum of Natural History2, University of Minnesota3, University of California, Berkeley4, Florida Museum of Natural History5, Cornell University6, Michigan State University7, Houston Museum of Natural Science8, University of Toronto9, Field Museum of Natural History10, University of Alaska Fairbanks11
TL;DR: The Auk, Vol.
Abstract: The Auk, Vol. 128, Number 3, pages 600−613. ISSN 0004-8038, electronic ISSN 1938-4254. 2011 by The American Ornithologists’ Union. All rights reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Rights and Permissions website, http://www.ucpressjournals. com/reprintInfo.asp. DOI: 10.1525/auk.2011.128.3.600 R. TeRRy ChesseR,1,12,13 RiChaRd C. Banks,1 F. keiTh BaRkeR,2 CaRla CiCeRo,3 Jon l. dunn,4 andRew w. kRaTTeR,5 iRBy J. loveTTe,6 Pamela C. Rasmussen,7 J. v. Remsen, JR.,8 James d. Rising,9 douglas F. sToTz,10 and kevin winkeR11
261 citations
References
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TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
57,055 citations
Book•
01 Feb 1987
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Abstract: Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.
15,840 citations
TL;DR: This poster presents a probabilistic procedure to characterize the response of the immune system to E.coli bacteria and shows clear patterns in response to the presence of E. coli.
Abstract: 1Department of Genetics, University of Georgia, Athens, Georgia 30602; 2NMFS/ CZES, Genetics, 2725 Montlake Boulevard East, Seattle, Washington 98112; 3Savannah River Ecology Laboratory, Drawer E, Aiken, South Carolina 29801; ~Department of Microbiology and Immunology, School of Medicine, University of California, Los Angeles, California 90024; -SSchool f Veterinary Medicine, Virginia Tech University, Blacksburg, Virginia 24046
3,366 citations
TL;DR: In this article, a comparative study of mtDNA and nuclear DNA variability is presented, with emphasis on mtDNA's uniparental and apparently haploid mode of inheritance, which makes mtDNA a superb tool for building trees and time scales relating molecular lineages at and below the species level.
Abstract: This essay reviews comparative studies of animal mitochondrial DNA (mtDNA), with emphasis on findings made and ideas developed at Berkeley. It argues that such studies are bringing together two previous paths of progress in evolutionary biology. One path is that of those who worked far above the species level and were concerned with genealogical trees, time scales and the accumulation of new mutations on surviving molecular lineages. The other path is that of those who worked at and below the species level and were concerned mainly with population structure, migration and the frequencies of alleles that existed in an ancestral population. This fusion of paths is made possible by the high rate at which mutations accumulate on mtDNA lineages and by this molecule's uniparental and apparently haploid mode of inheritance. These properties make mtDNA a superb tool for building trees and time scales relating molecular lineages at and below the species level. In addition, owing to its mode of inheritance, mtDNA is more sensitive to bottlenecks in population size and to population subdivision than are nuclear genes. Joint comparative studies of both mtDNA and nuclear DNA variability give us valuable insights into how effective population size has varied through time. Such studies also give insight into the conditions under which mtDNA from one species can colonize another species.
1,208 citations
Book•
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01 Sep 1983
TL;DR: Part I. An evolutionary tree: The origin of the Galapagos fauna, the origin of subspecies, and an evolutionary tree of species: The persistence of species.
Abstract: Part I. Description: 1. Galapagos scene 2. Classification 3. Ecology 4. Female plumage 5. Male plumage and sexual selection 6. Beak differences and food 7. Size differences between island forms 8. Size differences between species 9. Individual variation 10. Hybridisation 11. An evolutionary tree Part II. Interpretation: 12. The origin of the Galapagos fauna 13. The origin of subspecies 14. The origin of species 15. The persistence of species 16. Adaptive radiation Summary Acknowledgements Tables of measurements References Indexes.
823 citations