A multi-gene phylogeny of aquiline eagles (Aves: Accipitriformes) reveals extensive paraphyly at the genus level.
TL;DR: Parsimony reconstruction of the evolution of plumage pattern within Aquilini suggests that transverse barring of parts of the body plumage was lost in the Palearctic Aquila-Hieraaetus clade, pale underparts in adult plumages evolved three times independently, and dimorphic adult plumage is a derived character of the small-bodied HieraaetusClade.
Abstract: The phylogeny of the tribe Aquilini (eagles with fully feathered tarsi) was investigated using 4.2 kb of DNA sequence of one mitochondrial (cyt b) and three nuclear loci (RAG-1 coding region, LDH intron 3, and adenylate-kinase intron 5). Phylogenetic signal was highly congruent and complementary between mtDNA and nuclear genes. In addition to single-nucleotide variation, shared deletions in nuclear introns supported one basal and two peripheral clades within the Aquilini. Monophyly of the Aquilini relative to other birds of prey was confirmed. However, all polytypic genera within the tribe, Spizaetus, Aquila, Hieraaetus, turned out to be non-monophyletic. Old World Spizaetus and Stephanoaetus together appear to be the sister group of the rest of the Aquilini. Spizastur melanoleucus and Oroaetus isidori are nested among the New World Spizaetus species and should be merged with that genus. The Old World 'Spizaetus' species should be assigned to the genus Nisaetus (Hodgson, 1836). The sister species of the two spotted eagles (Aquila clanga and Aquila pomarina) is the African Long-crested Eagle (Lophaetus occipitalis). Hieraaetus fasciatus/spilogaster are closest to Aquila verreauxii and should be merged with that genus. Wahlberg's Eagle H. wahlbergi, formerly placed in Aquila, is part of a clade including three small Hieraaetus species (pennatus, ayresii, and morphnoides). The Martial Eagle (Polemaetus bellicosus) is the sister species of the Aquila/Hieraaetus/Lophaetus clade. Basal relationships within this clade remained unresolved. Parsimony reconstruction of the evolution of plumage pattern within Aquilini suggests that: (1) transverse barring of parts of the body plumage was lost in the Palearctic Aquila-Hieraaetus clade, (2) pale underparts in adult plumage evolved three times independently, and (3) dimorphic adult plumage is a derived character of the small-bodied Hieraaetus clade.
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TL;DR: A global map of zoogeographic regions is generated by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals, and it is shown that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere.
Abstract: Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
1,014 citations
TL;DR: A phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes, confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the NeornIthes.
Abstract: In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.
506 citations
Cites background from "A multi-gene phylogeny of aquiline ..."
...…in only limited capacitiy or secondary focus, e.g. as outgroups for the Falconidae (Griffiths, 1994, 1999; Haring et al., 2001; Griffiths et al., 2004), or in treatments of other phylogenetic issues within the Accipitridae (Seibold & Helbig, 1996; Helbig et al., 2005; Lerner & Mindell, 2005)....
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TL;DR: Monophyly of sea eagles and booted eagles was supported, however, harpy eagles (Harpiinae), snake eagles, and Old World vultures were found to be non-monophyletic, presenting an example of convergent evolution for specialized limb morphology enabling predation on cavity nesting species.
Abstract: We assessed phylogenetic relationships for birds of prey in the family Accipitridae using molecular sequence from two mitochondrial genes (1047 bases ND2 and 1041 bases cyt-b) and one nuclear intron (1074 bases b-fibrinogen intron 7). We sampled representatives of all 14 Accipitridae subfamilies, focusing on four subfamilies of eagles (booted eagles, sea eagles, harpy eagles, and snake eagles) and two subfamilies of Old World vultures (Gypaetinae and Aegypiinae) with nearly all known species represented. Multiple well-supported relationships among accipitrids identified with DNA differ from those traditionally recognized based on morphology or life history traits. Monophyly of sea eagles (Haliaeetinae) and booted eagles (Aquilinae) was supported; however, harpy eagles (Harpiinae), snake eagles (Circaetinae), and Old World vultures were found to be non-monophyletic. The Gymnogene (Polyboroides typus) and the Crane Hawk (Geranospiza caerulescens) were not found to be close relatives, presenting an example of convergent evolution for specialized limb morphology enabling predation on cavity nesting species. Investigation of named subspecies within Hieraaetus fasciatus and H. morphnoides revealed significant genetic differentiation or non-monophyly supporting recognition of H. spilogaster and H. weiskei as distinctive species. 2005 Elsevier Inc. All rights reserved.
211 citations
Cites methods from "A multi-gene phylogeny of aquiline ..."
...Author s note After this article was accepted for publication a treatment of a subset of booted eagles (Aquilinae) using H.R.L. Lerner, D.P. Mindell / Molecular Phylogenetics and Evolution 37 (2005) 327–346 345 cyt-b and additional nuclear sequences was published by Helbig et al. (2005)....
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TL;DR: It is shown that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology.
Abstract: Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from ‘universal’ gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous non-genic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.
132 citations
Cites background from "A multi-gene phylogeny of aquiline ..."
...While it is worth bearing in mind the idea that different loci may provide resolution on different parts of the tree (e.g. Pennington 1996; Ree et al. 2004; Helbig et al. 2005), this has not been convincingly demonstrated and balanced contributions of character data from a set of highly variable individual loci is likely to be more informative....
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...…is worth bearing in mind the idea that different loci may provide resolution on different parts of the tree (e.g. Pennington 1996; Ree et al. 2004; Helbig et al. 2005), this has not been convincingly demonstrated and balanced contributions of character data from a set of highly variable…...
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...A similarly wide span of variation has been found for LCNG loci used in phylogenetic analyses of animal species where most LCNG sequences are less variable than mtDNA loci (e.g. Helbig et al. 2005; Peters et al. 2005)....
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TL;DR: This is a first attempt at a supertree of both extinct and extant birds, not intended to be utilised in an overhaul of avian systematics or as a basis for taxonomic re-classification but provides a strong basis on which to base further studies on macroevolution, conservation, biodiversity, comparative biology and character evolution.
Abstract: Our knowledge of the avian tree of life remains uncertain, particularly at deeper levels due to the rapid diversification early in their evolutionary history. They are the most abundant land vertebrate on the planet and have been of great historical interest to systematists. Birds are also economically and ecologically important and as a result are intensively studied, yet despite their importance and interest to humans around 13% of taxa currently on the endangered species list perhaps as a result of human activity. Despite all this no comprehensive phylogeny that includes both extinct and extant species currently exists. Here we present a species-level supertree, constructed using the Matrix Representation with Parsimony method, of Aves containing approximately two thirds of all species from nearly 1000 source phylogenies with a broad taxonomic coverage. The source data for the tree were collected and processed according to a strict protocol to ensure robust and accurate data handling. The resulting tree topology is largely consistent with molecular hypotheses of avian phylogeny. We identify areas that are in broad agreement with current views on avian systematics and also those that require further work. We also highlight the need for leaf-based support measures to enable the identification of rogue taxa in supertrees. This is a first attempt at a supertree of both extinct and extant birds, it is not intended to be utilised in an overhaul of avian systematics or as a basis for taxonomic re-classification but provides a strong basis on which to base further studies on macroevolution, conservation, biodiversity, comparative biology and character evolution, in particular the inclusion of fossils will allow the study of bird evolution and diversification throughout deep time.
84 citations
References
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TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
Abstract: Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
20,627 citations
"A multi-gene phylogeny of aquiline ..." refers methods in this paper
...This was analysed with MrBayes, applying different models to mitochondrial, nuclear coding and non-coding partitions ....
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...Trees were constructed from singlelocus or concatenated sequence matrices using four methods: (1) neighbor-joining (NJ) with Kimura 2- parameter distance (MEGA 2.0; Kumar et al., 2001); (2) maximum likelihood using the quartet puzzling (QP) algorithm (TREE-PUZZLE 5.2; Schmidt et al., 2004) with the HKY85 model (Hasegawa et al., 1985); (3) maximum likelihood (ML) using heuristic searches performed with PAUP*; (4) Bayesian analysis (program MrBayes, Huelsenbeck and Ronquist, 2001; http:// morphbank.ebc.uu.se/mrbayes/) using the General Time Reversible (GTR) substitution model with T-distributed rate variation....
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...…model (Hasegawa et al., 1985); (3) maximum likelihood (ML) using heuristic searches performed with PAUP*; (4) Bayesian analysis (program MrBayes, Huelsenbeck and Ronquist, 2001; http:// morphbank.ebc.uu.se/mrbayes/) using the General Time Reversible (GTR) substitution model with T-distributed…...
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TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
Abstract: Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.
20,105 citations
"A multi-gene phylogeny of aquiline ..." refers methods in this paper
...For ML heuristic searches with PAUP*, models of sequence evolution and rate heterogeneity parameters were evaluated using methodologies described in Model- Test version 3.06 (Posada and Crandall, 1998)....
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TL;DR: A rapid, safe and inexpensive method was developed to simplify the deprotein-ization procedure that yielded quantities comparable to those obtained from phenol-chloroform extractions, rendering the entire process of RFLP analysis free of toxic materials.
Abstract: One of the obstacles encountered when extracting DNA from a large number of samples is the cumbersome method of deprotein-izing cell digests with the hazardous organic solvents phenol and isochloroform. Several other non-toxic extraction procedures have been published, but require either extensive dialysis (1) or the use of filters (2). A rapid, safe and inexpensive method was developed to simplify the deprotein-ization procedure. This method involves salting out of the cellular proteins by dehydration and precipitation with a saturated NaCl solution. Buffy coats of nucleated cells obtained from anticoagulated blood (ACD or EDTA) were resuspended in 15 ml polypropylene centrifugation tubes with 3 ml of nuclei lysis buffer (10 mM Tris-HCl t 400 mM NaCl and 2 mM Na 2 EDTA, pH 8.2). The cell lysates were digested overnight at 37°C with 0.2 ml of 10Z SDS and 0.5 ml of a protease K solution (1 mg protease K in 1Z SDS and 2 mM Na2EDTA). After digestion was complete, 1 ml of saturated NaCl (approximately 6M) was added to each tube and shaken vigorously for 15 seconds, followed by centrifugation at 2500 rpm for 15 minutes. The precipitated protein pellet was left at the bottom of the tube and the supernatant containing the DNA was transferred to another 15 ml polypropylene tube. Exactly 2 volumes of room temperature absolute ethanol was added and the tubes inverted several times until the DNA precipitated. The precipitated DNA strands were removed with a plastic spatula or pipette and transferred to a 1.5 ml microcentrifuge tube containing 100-200 pi TE buffer (10 mM Tris-HCl, 0.2 mM Na 2 EDTA, pH 7.5). The DNA was allowed to dissolve 2 hours at 37°C before quantitating. The DNA obtained from this simple technique yielded quantities comparable to those obtained from phenol-chloroform extractions. The 260/280 ratios were consistently 1.8-2.0, demonstrating good deproteinization. Restrictions were performed using a number of different enzymes requiring high, medium or low salt concentrations, all resulting in complete restriction. This procedure has been used in our laboratory on several thousand blood samples for parentage, population and forensic studies. This technique is used with our non-isotopic hybridization procedures (3) rendering the entire process of RFLP analysis free of toxic materials.
19,905 citations
01 Jan 2002
16,957 citations
TL;DR: A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed, and this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago, was ancestral to man and evolved after the human-ape splitting.
Abstract: A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized least-squares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3 +/- 11.7, 13.3 +/- 1.5, 10.9 +/- 1.2, 3.7 +/- 0.6, and 2.7 +/- 0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the pipedal creature Australopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a proto-chimpanzee after the former had developed bipedalism.
8,124 citations
"A multi-gene phylogeny of aquiline ..." refers methods in this paper
...…Kumar et al., 2001); (2) maximum likelihood using the quartet puzzling (QP) algorithm (TREE-PUZZLE 5.2; Schmidt et al., 2004) with the HKY85 model (Hasegawa et al., 1985); (3) maximum likelihood (ML) using heuristic searches performed with PAUP*; (4) Bayesian analysis (program MrBayes,…...
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