complete mitochondrial genome sequences and the

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Nov 25, 2009 - Además, Grus canadensis se resuelve como el taxón hermano del grupo de especies ...... the Royal Society of London, Series B 266:305–309.
The Auk 127(2):440−452, 2010  The American Ornithologists’ Union, 2010. Printed in USA.

Complete Mitochondrial Genome Sequences and the Phylogeny of Cranes (Gruiformes: Gruidae) C arey K r ajewski,1 J ustin T. S ipiorski, 2

and

Fr ank E. A nderson

Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, USA

Abstract.—We estimated phylogenetic relationships among all 15 extant species of cranes in the gruiform family Gruidae from complete sequences of their mitochondrial genomes. The gene order of crane mitochondrial genomes corresponds to that of the chicken and present few structural novelties compared with previously described birds. Sequences of the control region, particularly domains I and III, are highly divergent among species and include tandem repeats, duplications, and numerous indels. Phylogenetic analyses confirmed the well-established, reciprocal monophyly of clades Balearicinae (crowned cranes) and Gruinae (anatomically derived cranes), as well as previously identified lineages within Gruinae: Leucogeranus and the species groups Anthropoides, Canadensis, Antigone, and Americana. As in previous molecular phylogenies, Leucogeranus is resolved as sister to all other gruines. In addition, the Sandhill Crane (Grus canadensis) is resolved as sister to the Antigone species group, resulting in a Pacific Rim clade that has not previously been suggested. Only relationships among the Anthropoides, Americana, and Pacific Rim groups remain unresolved in our analyses. The crane fossil record provides reasonable calibration points for the most recent common ancestor of Gruinae (Middle Miocene) and the minimum age of Grus americana (Late Pliocene). Bayesian estimates of divergence dates from mitochondrial DNA sequences suggest that balearicines and gruines separated in the late Oligocene and that radiations of living species within these clades took place in the Neogene. Received 25 June 2009, accepted 25 November 2009. Key words: complete mitochondrial genomes, cranes, divergence times, Gruidae, phylogeny.

Secuencias Completas del Genoma Mitocondrial y la Filogenia de las Grullas (Gruiformes: Gruidae) Resumen.—Estimamos las relaciones filogenéticas entre las 15 especies vivientes de la familia Gruidae a partir de las secuencias completas de sus genomas mitocondriales. El orden de los genes del genoma mitocondrial de estas aves corresponde al de la gallina y presenta pocas novedades estructurales comparado con el de aves descritas previamente. Las secuencias de la región de control, particularmente los dominios I y III, son altamente divergentes entre las especies e incluyen repeticiones en tándem, duplicaciones y numerosas inserciones/deleciones. Los análisis filogenéticos confirmaron la monofilia recíproca bien establecida de los clados Balearicinae y Gruinae, así como de los linajes previamente identificados dentro de Gruinae: Leucogeranus y los grupos de especies Anthropoides, Canadensis, Antigone y Americana. Como en filogenias moleculares previas, Leucogeranus se resuelve como el taxón hermano del resto de los Gruinae. Además, Grus canadensis se resuelve como el taxón hermano del grupo de especies Antigone, lo que revela la existencia de un clado del borde del Pacífico que no había sido sugerido previamente. En nuestros análisis, sólo permanecen sin resolverse las relaciones entre los grupos Anthropoides, Americana y del borde del Pacífico. El registro fósil de las grullas brinda puntos de calibración razonables para el ancestro común más reciente de Gruinae (Mioceno Medio) y la edad mínima de Grus americana (Plioceno Tardío). Los estimados bayesianos de las fechas de divergencia calculados a partir de secuencias de ADN mitocondrial sugieren que Balearicinae y Gruinae se separaron a finales del Oligoceno y que las radiaciones de las especies vivientes dentro de estos clados ocurrieron en el Neógeno. The 15 extant species of cranes (Table 1) constitute the family Gruidae within the traditional avian order Gruiformes (Monroe and Sibley 1993). Cranes are large, strong-flying birds that occur in wetlands and grasslands on all continents except South America and Antarctica (Johnsgard 1983). Many migrate seasonally, with breeding and wintering grounds separated by thousands of miles (e.g., Whooping Crane [Grus americana]), but others are 1 2

nonmigratory (e.g., crowned cranes [Balearica spp.]). Habitat degradation has resulted in severe conservation problems for most cranes, with 11 species recognized as being at risk of extinction (Meine and Archibald 1996, IUCN 2007). Crane taxonomy dates from Linnaeus, but virtually all modern authors have placed living cranes in their own, exclusive family (Gruidae), the monophyly of which has repeatedly been

E-mail: [email protected] Present address: Department of Biology, University of Wisconsin—Stevens Point, Stevens Point, Wisconsin 54481, USA.

The Auk, Vol. 127, Number 2, pages 440−452. ISSN 0004-8038, electronic ISSN 1938-4254.  2010 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.2009.09045

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Table 1.  Current classification of cranes, breeding areas, and exemplar individuals for the present study. Taxon Gruidae   Balearicinae    Balearica     B. pavonina (Grey Crowned Crane)     B. regulorum (Black Crowned Crane) Gruinae   Anthropoides    A. virgo (Demoiselle Crane)    A. paradisea (Blue Crane)   Bugeranus    B. carunculatus (Wattled Crane)   Leucogeranus    L. leucogeranus (Siberian Crane)   Grus   Species Group Canadensis    G. canadensis (Sandhill Crane)   Species Group Antigone    G. antigone (Sarus Crane)    G. rubicunda (Brolga Crane)    G. vipio (White-naped Crane)   Species Group Americana    G. grus (Eurasian Crane)    G. monachus (Hooded Crane)    G. americana (Whooping Crane)    G. nigricollis (Black-necked Crane)    G. japonensis (Red-crowned Crane)

Main breeding area

Exemplar individual a

Subsaharan Africa Eastern and South Africa

ICF 1-9 ICF 2-18

Central Asia South Africa

ICF 3-12 ICF 4-7

South Africa

ICF 5-7

Siberia

ICF 6-6

North America

ICF 7-31

India to Australia Australia Manchuria

ICF 8-28 ICF 9-8 ICF 10-2

Northern Asia Northern Asia North America Tibet Manchuria

ICF 11-16 ICF 12-21 FWS 830004 ICF 14-2 ICF 15-38

a  ICF = International Crane Foundation (Baraboo, Wisconsin); FWS = U.S. Fish and Wildlife Service, Patuxent Wildlife Research Center (Laurel, Maryland).

corroborated by morphological and molecular analyses (Livezey 1998, Fain et al. 2007). Although Gruiformes is probably polyphyletic, cranes are part of a robustly supported, core gruiform clade with limpkins (Aramidae), trumpeters (Psophiidae), sungrebes (Heliornithidae), and rails (Rallidae) (Fain and Houde 2004, Fain et al. 2007, Hackett et al. 2008). Within Gruidae, taxonomists since Peters (1934) and Brodkorb (1967) have recognized two subfamilies (Table 1). Balearicinae includes two species of crowned cranes (Balearica) distinguished by their lack of the derived sternotracheal morphology found in Gruinae. In gruines, distal ends of the furculae are fused to the sternum and the trachea exhibits some degree of coiling posterior to the neck, often within an excavated and sculptured carina. Plumage and other external characteristics are the primary basis for recognition of genera within Gruinae: Anthropoides are gracile cranes with fully feathered heads and short bills; the monotypic Bugeranus is a large bird with conspicuous feathered lappets on the throat; members of Grus and Leucogeranus lack lappets but have bare, red-pigmented patches of skin on their heads. Modern attempts to establish a phylogeny of cranes began with Archibald’s (1976) study of unison calls, the complex, stereotyped patterns of vocalization and display performed by mated pairs. Subsequent phylogenetic investigations were done from a variety of perspectives, including morphometrics (Wood 1979), allozymes (Ingold et al. 1987, Dessauer et al. 1992), DNA hybridization (Krajewski 1989), mitochondrial gene sequences (Krajewski

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and Fetzner 1994, Krajewski et al. 1999), morphocladistics (Livezey 1998), and combined mitochondrial-nuclear DNA sequences (Fain 2001). All these studies confirmed the monophyly of crane subfamilies, and most identified five well-supported clades within Gruinae (Fig. 1), which Krajewski (1989) referred to as species groups. One of these (species group Leucogeranus) consisted only of the Siberian Crane. Livezey (1998) transferred the Siberian Crane from Grus to the monotypic Leucogeranus, a recommendation that we endorse and further validate herein. Molecular data place Anthropoides as sister to Bugeranus, and Krajewski (1989) referred to this clade as the Anthropoides group. In contrast to molecular results, behavioral (Archibald 1976) and morphometric (Wood 1979) studies linked Leucogeranus with Bugeranus, which is consistent with poorly developed tracheal coiling in these birds. Morphocladistic analyses (Livezey 1998) found the Anthropoides group to be paraphyletic, with Anthropoides sister to all other gruines. DNA data have consistently placed Leucogeranus as sister to other gruines, but the degree of confidence in this result from any individual study has been only moderate. Archibald (1976) and Krajewski (1989) recognized three species groups among the remaining Grus: Canadensis (the North American Sandhill Crane [G. canadensis]), Antigone (three Australasian species), and Americana (five Eurasian–North American species). Beyond conflicting results over the placement of Leucogeranus and the Anthropoides group, no study to date has resolved (or even suggested) relationships among the gruine clades. Even within groups, the only

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of living gruines took place in the late Miocene or early Pliocene. If correct, this scenario suggests that the living cranes are a much more recent radiation than is frequently supposed on the basis of the family’s long fossil history. Here, we estimate crane phylogeny and divergence times from complete sequences of the mitochondrial DNA (mtDNA) molecule obtained from representatives of each living species. Beginning with Desjardins and Morais’s (1990) publication of the chicken (Gallus gallus domesticus) mitochondrial genome, numerous authors have presented complete avian mtDNA sequences. Many of these focused on the structure and organization of avian mtDNA molecules (Härlid et al. 1997; Mindell et al. 1998a, b; Slack et al. 2003), and others emphasized phylogenetic and divergencetime problems at ordinal or family levels (Härlid et al. 1998, Härlid and Arnasson 1999, Mindell et al. 1999, Cooper et al. 2001, Haddrath and Baker 2001, Braun and Kimball 2002, Paton et al. 2002, Harrison et al. 2004, Slack et al. 2006, Morgan-Richards et al. 2008). Few publications have used complete mtDNA sequences to address intrafamilial problems for birds (but see Nishibori et al. 2001), and none has employed complete species sampling of reasonably diverse groups. Because previous estimates of crane phylogeny produced broadly congruent (if incompletely resolved) results, increasing the sample size of characters to obtain a more precise estimate of the crane mtDNA gene tree is a crucial step toward recovering the species phylogeny. M ethods

Fig. 1.  A phylogeny of cranes based on previously published analyses (Archibald 1976, Krajewski 1989, Krajewski and Fetzner 1994, Krajewski et al. 1996, Livezey 1998, Fain 2001, Fain et al. 2007). Polytomies indicated nodes that have not been consistently resolved. Clade names are those used in the text. Genus abbreviations: A. = Anthropoides, Ba. = Balearica, Bu. = Bugeranus, G. = Grus, L. = Leucogeranus.

well-supported relationships have been the pairing of Hooded Crane (G. monachus) and Black-necked Crane (G. nigricollis) and the placement of Red-crowned Crane (G. japonensis) as sister to the other Americana species. In short, the subfamily and speciesgroup clades identified in Table 1 and Figure 1 are a fair reflection of the current state of knowledge regarding crane phylogeny. The fossil record of cranes is relatively rich (Table 2) but has not yet shed much light on phylogenetic relationships or divergence times. Although extinct genera from the Eocene through the Pliocene have been assigned to Balearicinae, the phylogenetic placement of these fragmentary fossils is dubious at best. It is possible that some of these putative balearicines represent plesiomorphic stem-lineages in relation to a crown group defined by the living species. Gruine remains date from the Late Miocene, with two Eurasian specimens assigned to Grus. Krajewski (1990) and Krajewski and Fetzner (1994) assumed an early Miocene divergence of crane subfamilies and speculated that the diversification

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Taxon sampling.—We obtained a complete mtDNA sequence from one individual of each recognized crane species. Blood samples for DNA extraction were obtained from captive birds at the International Crane Foundation (ICF) in Baraboo, Wisconsin. The individuals sampled (Table 1) are identical to those used by Krajewski and Fetzner (1994) for cytochrome-b analyses. The most recent taxonomic review of extant cranes (Meine and Archibald 1996) identified no uncertainties regarding species boundaries within Gruidae, a view supported by all available data on intraspecific genetic variation. Several studies have shown that mtDNA haplotype divergences within individual crane species are much smaller than those between species (Rhymer et al. 2001, Glenn et al. 2002, Petersen et al. 2003), and others have demonstrated that intraspecific haplotypes coalesce at much shallower depths than interspecific ones (Wood and Krajewski 1996, Hasegawa et al. 1999). If, as these studies suggest, crane species are genetically isolated and reciprocally monophyletic for mtDNA haplotypes, then a singleexemplar approach should provide a robust estimate of phylogeny while simultaneously avoiding the computational burden of analyzing a multiple-exemplar data set. The monophyly of extant gruids has been resolved by analyses of both morphological (Livezey 1998) and molecular (Fain et al. 2007) data and has never been a point of serious contention in systematic ornithology. The reciprocal monophyly of Balearicinae and Gruinae is supported by these same studies and others that draw on a variety of character types (Archibald 1976, Wood 1979, Ingold et al. 1987, Krajewski 1989, Krajewski and Fetzner 1994). These well-established nodes on the crane tree allow us to use the two balearicine species (B. pavonina and B. regulorum) as outgroups to the more diverse Gruinae.

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Table 2.  The fossil record of cranes. Localities are given in parentheses. Authorities in footnotes summarize recent opinions on taxonomy and stratigraphic ages. Fossils listed for modern species are first occurrences. Epoch

Subdivision a

Pleistocene

Age range (mya)

Gruinae

1.8–0.01

Pliocene

Late

3.6–1.8

Miocene

Early Late

5.3–3.6 11.2–5.3

Middle Early

16.4–11.2 23.8–16.4

Late

33.7–23.8 37.0–33.7

Middle

49.0–37.0

Oligocene Eocene

Balearicinae

Probalearica mongolica (Central Asia) e Pliogrus pentelici (Europe) e Probalearica moldavica (Europe) e Balearica exigua (North America) d Palaeogrus mainburgensis (Europe) e Probalearica cratagensis (North America) b Balearica rummeli (Europe) e Palaeogrus excelsa (Europe) e

Bugeranus carunculatus (Africa) b Anthropoides virgo (Eurasia) b Leucogeranus leucogeranus (Central Asia) b Grus antigone (Europe) b G. canadensis (North America) b G. grus (Eurasia) b G. rubicunda (Australia) c G. primigenia (Europe) d G. melitensis (Malta) e G. cubensis (Cuba) d G. bohatshevi (Central Asia) d G. latipes (Bermuda) d G. americana (North America) f G. nannodes (North America) b Camusia quintanai (Europe) d G. conferta (North America) d G. afghana (Central Asia) e G. miocenicus (Europe) e

Palaeogrus hordwelliensis (Europe) e Geranopsis hastingsiae (Europe) e Eobalearica turgarinovi (Central Asia) e Palaeogrus princeps (Europe) e

a

 Epoch and subdivision boundaries based on the Geological Society of America (1999).  Brodkorb 1967. c  Rich and Van Tets 1984. d  Seguí 2002. e  Gölich 2003. f  Feduccia 1967. b

Data collection.—Krajewski and Fetzner (1994) reported details of DNA extraction and purification, as well as protocols for polymerase chain reaction (PCR) amplification and sequencing of cytochrome-b genes (cyt b). Similar information on amplification and sequencing of the crane NADH dehydrogenase subunit 6 gene (ND6) was given by Wood and Krajewski (1996), and the ND6 sequences of all cranes were reported by Krajewski et al. (1999). Crane control region (CR) sequences were obtained by Fain (2001). Sequences of all other loci were obtained during the course of the present study. The locations and sequences of all PCR primers employed are listed in the Appendix. The PCR amplifications were performed in 50–100 μL volumes containing 1.5 mM MgCl2, 200 μM dNTPs, 5 μM primers, 1.5 U Taq polymerase, and 10–100 ng template DNA. Thermal profiles for PCR included the following steps: initial denaturation at 94°C for 5 min; 35 cycles of denaturation (94°C for 1 min), annealing (50–62°C for 1 min), and extension (72°C for 1 min); final extension at 72°C for 20 min. Annealing temperatures were optimized for each primer pair. Most amplicons were 500–1,000 base pairs (bp). The PCR products were visualized on 1.5% agarose gels and purified with QIAquick gel-extraction kits (Qiagen, Valencia, California). Concentrations of purified products were

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measured with a Hoefer fluorometer. Cycle sequencing employed Big Dye chemistry (Applied Biosystems, Foster City, California) followed by electrophoresis in ABI 373 or 377 automated sequencers. For most regions, sequence was obtained from both strands of each amplicon; overlapping amplicons provided ≥2× coverage for ∼25% of the mtDNA molecule. Individual sequencing reads for each amplicon were initially aligned with each other and with published mtDNA sequences from various birds; any reads that showed characteristics of contaminants or nuclear pseudogenes were rejected. Because cranes are genetically similar, multispecies sequence-alignment was performed manually for all loci except CR, for which Fain (2001) used CLUSTALX, version 1.8 (Thompson et al. 1997), with default settings and a guide tree (Fig. 1) to align indel-rich regions. Sequence characterization.—Protein-coding genes were conceptually translated with the vertebrate mitochondrial genetic code, and no instances of frameshifts or premature stops were found, except those consistent with previous reports for avian mtDNA. Ribosomal RNA sequences (12S and 16S) were folded into stems and loops according to the gruiform secondary structure models used by Fain et al. (2007). The 22 transfer RNAs (tRNAs) were also folded into secondary structures based on those derived

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for chicken by Desjardins and Morais (1990). Conserved regions and boundaries of domains I–III in the CR were identified by Fain (2001) following Baker and Marshall (1997). Nucleotide compositions of the entire mtDNA sequence, individual loci, and intralocus partitions were obtained using MEGA, version 2.1 (Kumar et al. 2001). Complete sequences and individual loci were tested for compositional homogeneity of variable sites using the chi-square test implemented in PAUP*, version 4b10 (Swofford 2001). Phylogenetic analysis.—Because of alignment problems, numerous gaps, and potential saturation associated with high divergence between subfamilies, the CR locus was excluded from phylogenetic analyses. Trees for every other individual locus and all loci combined were obtained using maximum-parsimony (MP), maximum-likelihood (ML), and Bayesian (MB) criteria. Levels of support for nodes on MP and ML trees were estimated by bootstrap resampling of sites (Felsenstein 1985). All sites with one or more gaps were deleted prior to analysis. An appropriate substitution model for each locus and multilocus combination was inferred using MODELTEST, version 3.06 (Posada and Crandall 1998) or DT-MODSEL (Minin et al. 2003) for ML analyses, and MRDT-MODSEL for Bayesian analyses. MRDT-MODSEL is a modification of DT-MODSEL developed by F.E.A. that compares 24 DNA substitution models available in MRBAYES (Perl script available upon request). For each data set or partition, models were evaluated with the second-order Akaike’s information criterion (AICc) using all sites or only variable sites as estimates of sample size (Posada and Buckley 2004). When model-selection methods favored different models, we chose the model with fewer parameters. MP analyses treated informative sites as unweighted, unordered characters. Heuristic searches were conducted with PAUP* using 100 random-addition sequences of taxa, tree bisection– reconnection (TBR) branch swapping, and 100 bootstrap replicates. ML analyses were performed with PAUP* using an initial neighbor-joining tree for TBR branch swapping; 100 bootstrap replicates were performed with GARLI (Zwickl 2006) using default settings, two runs per pseudoreplicate, and starting substitution model parameter values estimated on the ML topology. All MB analyses were performed with MRBAYES, version 3.1.2 (Ronquist and Huelsenbeck 2003), and consisted of four independent runs with different random starting trees, each consisting of four Markov-chain Monte Carlo chains (one cold and three heated). Single-locus MB analyses were terminated when the value of a topological convergence diagnostic (the average standard deviation of tree partition frequencies across runs) dropped below 0.005. Multilocus analyses were terminated when the chain length reached 40 million generations. TRACER (Rambaut and Drummond 2007) and AWTY (Wilgenbusch et al. 2004) were used to visually inspect trends in parameter estimates and tree output and to select appropriate burn-in lengths for the 40-milliongeneration multilocus analyses. In all cases, the first 25% of trees from each run was discarded as burn-in and the remaining trees were pooled among runs to produce a 50% majority-rule consensus tree. Estimated Bayesian posterior probabilities (BPPs) of clades on inferred trees were interpreted as measures of support. Trees from individual protein-coding, rRNA, and a concatenation of tRNA loci were examined for congruence by identifying conflicting nodes with 75% bootstrap or 0.90 BPP support.

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Data were partitioned in several ways for MB analyses. In one treatment, a single substitution model was applied to the entire alignment (i.e., no partitioning). Data were also partitioned by locus, by codon positions pooled across loci, or by both locus and codon position. Partioning by codon position across loci entailed separate models for each of the following: first positions pooled across all protein-coding genes, second positions pooled across all protein-coding genes, third positions pooled across all protein-coding genes, 12S rRNA, 16S rRNA, pooled tRNAs, and pooled spacer regions between genes (seven partitions). Partitioning by both locus and codon position entailed separate substitution models for each codon position in each protein-coding gene except for second positions (which, because of low levels of variation, were pooled across protein-coding genes), 12S rRNA, 16S rRNA, pooled tRNAs, and pooled spacer regions. In all partitioned analyses, topology and branch lengths were linked across partitions, but other model parameters were unlinked. A rate multiplier was used for analyses involving two or more partitions (the rate multiplier associates substitution rates for different partitions with a Dirichlet prior to allow different rates across partitions). The four partitioning schemes described above were compared using the AICc and the Bayesian information criterion (BIC). The AICc and BIC are preferable to Bayes factors (Nylander et al. 2004) for selecting an appropriate partitioning scheme because they include penalties for overparameterization, whereas Bayes factors do not (McGuire et al. 2007). The harmonic mean of likelihood values from the stationary (post-burn-in) phase of each analysis was calculated using the “sump” command in MRBAYES and used as an estimate of model likelihood. AICc and BIC values for each partitioning scheme were calculated using the equations listed in McGuire et al. (2007) and Posada and Buckley (2004) and citations therein. To provide a perspective on nodal support independent of bootstrap and BPP values, we employed tree-comparison tests to the set of all trees consistent with the framework phylogeny in Figure 1. These 945 trees were produced in PAUP* with the “generatetrees” command, using the framework phylogeny as a constraint. Likelihoods of the data under various partitioning schemes were calculated for all 945 trees in PAUP*. Likelihoods were summed across data partitions for each tree and sorted in Microsoft EXCEL for evaluation. Furthermore, the 945 trees were evaluated using the Shimodaira-Hasegawa (SH) test (Shimodaira and Hasegawa 1999) and approximately unbiased (AU; Shimodaira 2002) tests under the best-fitting unpartitioned model (GTR+I+Γ). Because of computational limitations, it was impossible to evaluate all 945 trees using the AU test. Therefore, the trees were first subjected to the more conservative SH test (Shimodaira 2002) using a single (unpartitioned) substitution model to produce a confidence set of trees. We then evaluated trees in the SH set using the AU test as implemented in CONSEL, version 0.1 (Shimodaira and Hasegawa 2001). These tests allowed the identification of a confidence set of trees that could not be statistically rejected as candidates for the ML tree. We summarized the results as the strict consensus of each confidence set. Estimation of divergence dates.—The fossil record of cranes (Table 2) permits an estimate of the minimum time elapsed since the most recent common ancestor (tMRCA) of gruines. The oldest

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fossil gruines (Grus afghana and G. miocenicus) are from Late Miocene deposits, presumably no older than 12 Ma, though Gölich (2003) assigned G. miocenicus to the Middle Miocene. Moreover, Pliocene skeletal fragments of G. americana come from deposits dated to ∼3.5 Ma (Feduccia 1967). Using 12 Ma as a minimum calibration for the gruine t MRCA and 3.5 Ma as a minimum age for G. americana, we obtained divergence-time estimates from complete crane mtDNA data with BEAST, version 1.4.7 (Drummond and Rambaut 2007). In these analyses, we used a lognormal prior with mean = 0 and zero-offsets of 12 and 3.5 for the tMRCA of Gruinae and the minimum age of G. americana, respectively. We performed parallel analyses with standard deviations of 0.5, 1.0, and 1.5 on the priors for both calibration points. The lognormal priors are appropriate for our calibration data in that the fossils place hard upper bounds, but no lower bounds, on the ancestors. The range of standard deviations we examined allowed for diminishing probabilities of the gruine tMRCA reaching back to the Oligocene. We performed a set of unpartitioned analyses and a set of analyses with the data partitioned to match the best partitioning scheme as estimated using AICc and BIC. The following settings were employed in the unpartitioned analyses: GTR+I+Γ; model (selected by all methods described above as most appropriate for the unpartitioned mtDNA alignment), variable mean substitution rates, relaxed clock with an uncorrelated lognormal distribution of rates, Yule speciation process for the prior on the distribution of node heights, 20 million generations sampled every 10,000 generations, 400 burn-in trees (20% of sample), and default settings for all other options. Other than constraining Gruinae and the Americana group to be monophyletic, we allowed BEAST to estimate topology and model parameters along with divergence times. The settings used for the partitioned BEAST analysis were as follows: data partitioned by codon position (for a total of seven data partitions, as described above, with the same substitution models for each partition as in MRBAYES analyses by codon position); variable mean substitution rates; relaxed clock model with an uncorrelated lognormal distribution of rates; Yule speciation process for the prior on the distribution of node heights; 50 million generations; 5 million burn-in trees (10% of sample); and default settings for all other options. For the partitioned BEAST analyses, no topological constraints were employed, but a starting tree was used. The starting tree was based on the Bayesian majority-rule consensus tree and branch lengths from the 40-million-generation MRBAYES analysis, with the branch lengths scaled so that the Americana group and Gruinae were 3.5 and 12 million years old, respectively. A starting tree with scaled branch lengths was employed simply to avoid a “tree likelihood is zero” error that can arise when a random starting tree does not conform to multiple calibration bounds. For the partitioned analyses, two runs of BEAST were performed for each value of the standard deviation, the results of which were examined for convergence (which was obtained in every case) and combined for a divergence-tree estimate based on 50 million generations (9,000 trees). R esults Characteristics of the crane mitochondrial genome.—MtDNA sequences from the 15 crane species have been deposited in GenBank (accession numbers FJ769841–FJ769855). In most respects,

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Table 3.  Alignment summary for crane mtDNA loci. Alignment position Locus tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNA Ala tRNA Asn tRNACys tRNATyr COI tRNASer(UCN) tRNA Asp COII tRNALys ATPase8 ATPase6 COIII tRNAGly ND3 tRNA Arg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 cytb tRNAThr tRNAPro ND6 tRNAGlu CR

Punctuation codons

Strand

From

To

Length

H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H H H L L L H

1 75 1,057 1,131 2,758 2,838 3,802 3,883 3,957 4,026 5,065 5,137 5,208 5,286 5,352 5,424 6,966 7,043 7,114 7,799 7,870 8,034 8,717 9,501 9,570 9,924 9,995 10,285 11,671 11,742 11,807 11,878 13,703 14,850 14,942 15,019 15,545 15,615

74 1,056 1,130 2,757 2,832 3,801a 3,874 3,957b 4,025 5,066 5,135 5,205 5,280 5,352 5,422 6,974 7,039 7,111 7,797 7,868 8,043 8,717 9,500 9,569 9,921 9,993 10,291 11,652 11,740 11,806 11,877 13,692 14,845 14,919 15,011 15,540 15,614 16,939

74 982 74 1,627 75 964 73 71 70 1,040 71 69 79 67 71 1,551 74 69 684 70 174 684 784 69 352 70 297 1,368 70 65 71 1,815 1,143 70 70 522 70 1,325

Start

Stop

ATG

TAA

ATY

TAG

GTG

AGG

ATG

TAA

ATG ATG ATG

TAA TAA T-

ATY

TAR

ATG ATG

TAA AGA

ATG ATG

TAA TAA

ATG

TAR

a

1-base insert before stop codon in ND1. 4-base insert before last base of tRNAGln in L. leucogeranus.

b

crane mitochondrial genomes are similar to those reported in other birds. The alignment length with gap sites is 16,939 positions (16,377 without gap sites); individual sequences range from 16,541 (A. virgo) to 16,802 (B. regulorum) bases. Much of this variation is attributable to indels in CR, which account for 416 of the 562 total gap sites (74%), and most of these occur in the highly variable domains I (220) and III (187). There are tandem repeats at the 3′ end of domain III in both Balearica sequences: CAATCAAA is repeated 17 times in B. regulorum and 15 times in B. pavonina. In gruines other than A. virgo and G. antigone, domain I contains an imperfect (2×) tandem repeat of a 23mer. Gene order in crane mtDNA (Table 3) matches that in chicken mtDNA (Desjardins and Morais 1990) rather than the rearranged pattern noted by Mindell et al. (1998b) in several other

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Table 4.  Support values (BPP × 100, except as noted) for nodes of the mtDNA tree from Bayesian analyses of individual loci and multilocus combinations. Node numbers refer to Figure 2. “X” indicates a conflicting node (i.e., one that appears on the mtDNA tree but not on the single-locus tree); an asterisk indicates a conflicting node with ≥0.90 BPP; “u” indicates an unresolved node (75% bootstrap (not shown) or >0.90 BPP (Table 4). Most loci in most analyses support sister-pairing of G. antigone and G. rubicunda, but Bayesian analysis of cyt b linked G. rubicunda and G. vipio (0.98 BPP). Krajewski and Wood (1995) also reported this result for cyt b. Parsimony analysis of ND6 placed

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G. americana as sister to (G. monachus, G. nigricollis) with 79% bootstrap support, rather than the more common (G. grus, [G. monachus, G. nigricollis]) arrangement. Multilocus mtDNA tree searches.—Comparisons of AICc and BIC values across the four partitioning schemes for the 40-milliongeneration runs supported codon-position partitioning as the best-fitting scheme (Table 5). All analyses of complete mtDNA sequences returned the optimal tree shown in Figure 2. On this tree, Leucogeranus is sister to all other gruines. The Grus species groups are recovered and relationships within them are fully resolved and strongly supported. Grus monachus and G. nigricollis are sisters, with G. grus, G. americana, and G. japonensis as successively earlier branches within the Americana group. Grus antigone and G. rubicunda are sisters apart from G. vipio in the Antigone group. Bugeranus is sister to a monophyletic Anthropoides. The Canadensis and Antigone groups are resolved as sisters. Only the relationships of the Anthropoides, Americana, and Antigone+Canadensis clades are not resolved. Exhaustive evaluation of plausible trees.—The SH tests on the 945 plausible trees returned a preliminary confidence set of 136 trees, to which we applied the AU test. A strict consensus of the AU set showed considerably less structure than results from tree searches. Indeed, the AU consensus tree was no more resolved than the original plausible tree (Fig. 1), which indicates that the SH-AU approach was the most conservative of the procedures we employed for assessing phylogenetic support.

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Table 5.  Akaike’s information criterion (AICc) and Bayesian information criterion (BIC) values for the 40-million-generation partitioned multilocus mtDNA analyses. AICc values were calculated using all characters and with variable characters only; only the results based on all characters are shown. The number of parameters for each partitioning scheme is the sum of parameters for each substitution model across all data partitions plus rate multiplier parameters (the number of rate multiplier parameters is equal to the number of data partitions). The partitioning scheme with the lowest AICc or BIC value was chosen as the best scheme (indicated by an asterisk). Abbreviations: N = no partitioning, L = partitioned by locus, C = partitioned by codon position pooled across loci, and LC = partitioned by both locus and codon position. Partitioning scheme N C L LC

Number of parameters

Number of partitions

lnL

AICc

BIC

12 72 138 215

1 7 17 31

−49,363.40 −46,465.93 −49,034.44 −46,431.67

98,750.84 93,076.54* 98,347.39 93,299.44

98,842.53 93,626.26* 99,399.82 94,936.91

Divergence time estimates.—All parameter estimates in BEAST analyses converged well before 20 million generations, with effective samples sizes (ESSs) in the range 390–8,102. Results of partitioned and unpartitioned analyses were very similar, so we report only the partitioned results here. BEAST returned estimates of 31–37 Ma for the separation of gruines and balearicines (Table 6 and Fig. 3). Divergences among gruine species groups were dated at 10–14 Ma, and first divergences within species groups at 4.5–10 Ma. Only the divergence between

G. monachus and G. nigricollis was later than the Pliocene. Varying the standard deviation of lognormal priors on the calibration points produced little effect on the confidence intervals of estimated dates. Interestingly, the unpartitioned Bayesian estimate of mean substitution rate for crane mtDNA sequences was 0.0035 substitutions site−1 Ma−1, or 0.7% divergence Ma−1. This corresponds to the low end of the range (0.7–1.7% Ma−1) of divergence rates for crane cyt b obtained by Krajewski and King (1996).

Fig. 2.  Crane phylogeny based on complete mtDNA (without the control region). Branch lengths are derived from Bayesian analyses of combined mtDNA sequences partitioned by codon position. All nodes have Bayesian posterior probability (BPP) values of 1.00, except node 11 (BPP = 0.94, shown in italics). Support values from other analyses are given in Table 4.

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Table 6.  Estimated dates (in millions of years) of branch points on the crane mtDNA tree (without gap and control region sites), derived from BEAST analyses partitioned by codon position. Node numbers refer to Figure 3. All analyses assumed lognormal prior distributions (mean = 0) for the most recent common ancestors of Gruinae (zero offset = 12) and Grus americana (zero offset = 3.5). Results are shown for three different values of the standard deviation of this distribution. Each analysis represents the combined results of two 50-million-generation runs, with results logged every 10,000 generations (5,000 × 2 = 10,000 trees) and a burn-in of 10% (500 × 2 = 1,000 trees). Divergence values are rounded to two significant digits. The 95% highest posterior density (HPD) interval of node height is shown below each nodal age. Standard deviation

Node 1

2

3

4

5

6

7

8

9

10

11

12

13

14

0.5

3.5 2.8–4.1

1.3 1.2–1.7

2.8 2.5–3.4

3.7 3.7–4.4

7.6 7.3–9.4

4.5 4.0–5.5

8.5 7.9–10

3.8 3.5–4.8

4.7 4.4–5.9

10 10–13

11 11–13

11 11–14

13 12–15

31 30–40

1.0

2.6 2.7–4.2

1.4 1.1–1.7

2.7 2.4–3.4

3.6 3.5–4.4

7.7 7.0–9.6

4.3 3.8–5.7

7.8 7.6–10

3.8 3.3–4.9

4.5 4.2–6.0

11 9.5–13

11 10–14

11 11–14

12 12–16

31 29–41

1.5

3.7 2.6–4.1

1.4 1.1–1.7

2.8 2.4–3.3

3.9 3.5–4.3

9.0 6.9–9.6

4.7 3.7–5.5

10 7.4–10

4.9 3.3–4.9

5.7 4.1–6.0

12 9.3–13

13 10–14

13 10–14

14 12–15

37 28–40

D iscussion Crane phylogeny.—Our results show that branches at the base of Gruinae (i.e., those among species groups) are short and may remain difficult to resolve with confidence, even using long DNA

sequences. Nevertheless, the mtDNA tree (Figs. 2 and 3) is the strongest hypothesis yet put forward for crane relationships. Along with the approximate divergence dates obtained from BEAST, it provides a framework for interpreting crane cladogenesis. Popular natural-history literature (e.g., Hughes 2008) has long

Fig. 3.  Time-calibrated tree obtained using BEAST based on complete mtDNA sequences without control region and gap sites, partitioned by codon position. The analysis assumed lognormal prior distributions (mean = 0, standard deviation = 1.0) and fossil calibration points for the most recent common ancestor of Gruinae (12 Ma) and the minimum age of Grus americana (3.5 Ma). Tick marks on the time axis represent 5-Ma intervals. Calibration points are indicated by circles. Node numbers refer to Table 7. Bars on nodes are 95% confidence intervals on node heights.

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portrayed cranes as a collection of ancient lineages, perhaps little changed from their gruiform ancestors of the Mesozoic. We demonstrate here that living cranes are the product of relatively recent radiations coincident with Neogene global cooling and the spread of temperate grasslands (see, e.g., Ségalen et al. 2006). If the Balearica lineage diverged from Gruinae 31–37 mya, the Eocene genera Paleogrus, Eobalearica, and Geranopsis, as well as their Neogene representatives, may be part of a monophyletic Balearicinae or may represent gruid stem-lineages that predate the Balearica–Gruinae split. Given their stratigraphic levels (Miocene–Pliocene), the three species of Probalearica could be part of a clade with Balearica and constitute a restricted Balearicinae. The anatomical similarity between Probalearica cratagensis and Balearica (along with the putative limpkin Amaurornis from the Miocene) was noted by Feduccia and Voorhies (1992). The Early Pliocene Pliogrus has been considered both a balearicine (Gölich 2003) and a gruine (e.g., Seguí 2002), and both possibilities are consistent with our results. Even accepting the Early Miocene Balearica rummeli as a crane (it was originally described as an owl; Göhlich 2003), both modern gruid lineages diversified in the Miocene. After the Miocene, balearicines declined in diversity and geographic extent while gruines experienced the reverse trend (Table 2 and Fig. 3). Although early gruine fossils are confined to North America and Eurasia, the modern subfamily has a nearly cosmopolitan distribution. Arguably, the reversal of fortunes between crane subfamilies was a result of global cooling that began during the Miocene, allowing the more cold-tolerant gruines to occupy temperate latitudes and restricting balearicines to warm, wet grasslands in Africa (Hughes 2008). The phylogeny we present (Figs. 2 and 3) addresses several outstanding questions about gruine relationships. Leucogeranus appears to have separated from other gruines in the Late Miocene, followed quickly by diversification of the other species groups, as first suggested by Krajewski (1989) on the basis of DNA hybridization. Our tree unites the Canadensis and Antigone groups as sisters, a novel but geographically coherent result representing a “Pacific Rim” clade distributed from Australia through southeast Asia, northeast Asia, and across the Bering Straits into North America. Clearly, isolation of the Sandhill Crane (G. canadensis) lineage at 10–12 mya, either in North America or eastern Asia (the Sandhill breeding range includes northeastern Siberia), considerably predates diversification within the more southerly Antigone group (3.8–5.7 mya). A similar branching tempo applies to the other two species groups. In Anthropoides, Bugeranus was isolated some 7.8–10 mya, followed by separation of the Anthropoides species 4.3–4.7 mya. In Americana, the Red-crowned Crane (G. japonensis) originated 7.6–9.0 mya, but cladogenesis in its sister lineage did not begin until 3.6–3.9 mya. Species-level relationships dating to the Plio-Pleistocene are well resolved by mtDNA. Within the Americana group, the widespread Eurasian Crane (G. grus) is sister to a G. monachus– G. nigricollis clade from east-central Asia, the North American Whooping Crane (G. americana) occupying a branch between these and G. japonensis. Within Antigone, the Australasian Sarus (G. antigone) and Australian Brolga (G. rubicunda) are sisters apart from the east-Asian White-naped Crane (G. vipio). Although Krajewski and Wood (1995) found Brolga and White-naped cranes to be sisters on the basis of cyt b sequences, combined cyt b + ND6

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data (Krajewski et al. 1999) restored the more traditional pairing of Brolga and Sarus recovered here. Classification.—Crane classification had been reasonably stable throughout the 20th century until Krajewski (1989) suggested that Grus as constituted by Peters (1934) was not monophyletic, because of the early separation of the Siberian Crane (then “Grus” leucogeranus) from other gruines. Krajewski’s remedy was to transfer the species of Bugeranus and Anthropoides to Grus, leaving the latter as the only extant genus within Gruinae. Krajewski and Fetzner (1994) failed to resolve the Siberian Crane as a basal gruine with cyt b sequences and lamented that Krajewski’s (1989) lumping expedient may have been premature. Unfortunately, that classification has since been adopted in some prominent tabulations of avian diversity (e.g., Monroe and Sibley 1993, IUCN 2007). Although our mtDNA results confirm Krajewski’s (1989) phylogeny, we endorse Livezey’s (1998) proposal to recognize the Siberian Crane as a monotypic genus (Leucogeranus) and retain Peters’s (1934) other gruine genera (Anthropoides, Bugeranus, and Grus; Table 1). This scheme captures what is well supported by numerous phylogenetic analyses while otherwise maintaining nomenclatural stability. In particular, the position of the Anthropoides genera in relation to Grus (node 11 in Fig. 2) is not highly resolved by mtDNA sequences. A fully satisfactory phylogenetic classification will also require confirmation of the novel mtDNA alliance of the Canadensis and Antigone groups. Acknowledgments We thank G. W. Archibald, C. Mirande, and the staff of the International Crane Foundation, as well as the late J. A. W. Kirsch, for facilitating collection of crane blood samples. Much of the preliminary laboratory work for this study was performed by M. G. Fain. We also thank G. R. Moyer, A. Córdoba, J. Rommel, and N. Gluckleder for assistance in the lab. M. S. Springer provided instructive insights on BEAST analyses. M. Westerman and several anonymous reviewers provided helpful comments on the manuscript. Financial support was provided by National Science Foundation (NSF) grant DEB-0108656 and Research Experiences for Undergraduates supplements to C.K. and P. Houde, and NSF grant DEB-0235794 to F.E.A. Literature Cited Archibald, G. W. 1976. Crane taxonomy as revealed by the unison call. Pages 225–251 in Proceedings of the International Crane Workshop (J. C. Lewis, Ed.). Oklahoma State University Publishing and Printing Department, Stillwater. Baker, A. J., and H. D. Marshall. 1997. Mitochondrial control region sequences as tools for understanding evolution. Pages 51–82 in Avian Molecular Systematics (D. P. Mindell, Ed.). Academic Press, San Diego, California. Braun, E. L., and R. T. Kimball. 2002. Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling, and sequence length. Systematic Biology 51:614–625. Brodkorb, P. 1967. Catalogue of fossil birds: part 3 (Ralliformes, Ichthyornithiformes, Charadriiformes). Bulletin of the Florida State Museum, Biological Science 2:99–220.

4/7/10 5:09:29 PM

450

— K r ajewski, S ipiorski,

Cooper, A., C. Lalueza-Fox, S. Anderson, A. Rambaut, J. Austin, and R. Ward. 2001. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409:704–707. Desjardins, P., and R. Morais. 1990. Sequence and gene order of the chicken mitochondrial genome: A novel gene order in higher vertebrates. Journal of Molecular Biology 212:599–634. Dessauer, H. C., G. F. Gee, and J. S. Rogers. 1992. Allozyme evidence for crane systematics and polymorphisms within populations of Sandhill, Sarus, Siberian, and Whooping cranes. Molecular Phylogenetics and Evolution 1:279–288. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214. Fain, M. G. 2001. Phylogeny and evolution of cranes (Aves: Gruidae) inferred from DNA sequences of multiple genes. Ph.D. dissertation, Southern Illinois University, Carbondale. Fain, M. G., and P. Houde. 2004. Parallel radiations in the primary clades of birds. Evolution 58:2558–2573. Fain, M. G., C. Krajewski, and P. Houde. 2007. Phylogeny of “core Gruiformes” (Aves: Grues) and resolution of the LimpkinSungrebe problem. Molecular Phylogenetics and Evolution 43:515–529. Feduccia, A. 1967. Ciconia maltha and Grus americana from the Upper Pliocene of Idaho. Wilson Bulletin 79:316–318. Feduccia, A., and M. R. Voorhies. 1992. Crowned Cranes (Gruidae: Balearica) in the Miocene of Nebraska. Pages 239– 248 in Papers in Avian Paleontology Honoring Pierce Brodkorb (R. E. Campbell, Ed.). Los Angeles County Museum Science Series, Los Angeles, California. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783–791. Geological Society of America. 1999. Geological time scale. [Online.] Available at www.geosociety.org/science/timescale/ timescl-1999.pdf. Glenn, T. C., J. E. Thompson, B. M. Ballard, J. A. Roberson, and J. O. French. 2002. Mitochondrial DNA variation among wintering midcontinent Gulf Coast Sandhill Cranes. Journal of Wildlife Management 66:339–348. Gölich, U. B. 2003. A new crane (Aves: Gruidae) from the Miocene of Germany. Journal of Vertebrate Paleontology 23:387–393. Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, and others. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763–1768. Haddrath, O., and A. J. Baker. 2001. Complete mitochondrial DNA genome sequences of extinct birds: Ratite phylogenetics and the vicariance biogeography hypothesis. Proceedings of the Royal Society of London, Series B 268:939–945. Härlid, A., and U. Arnason. 1999. Analyses of mitochondrial DNA nest ratite birds within the Neognathae: Supporting a neotenous origin of ratite morphological characters. Proceedings of the Royal Society of London, Series B 266:305–309. Härlid, A., A. Janke, and U. Arnason. 1997. The mtDNA sequence of the ostrich and the divergence between paleognathouds and neognathus birds. Molecular Biology and Evolution 14:754–761. Härlid, A., A. Janke, and U. Arnason. 1998. The complete mitochondrial genome of Rhea americana and early avian divergences. Journal of Molecular Evolution 46:669–679.

22_Krajewski_09-045.indd 450

and

A nderson — Auk, Vol. 127

Harrison, G. L., P. A. McLenachan, M. J. Phillips, K. E. Slack, A. Cooper, and D. Penny. 2004. Four new avian mitochondrial genomes help get to basic evolutionary questions in the late Cretaceous. Molecular Biology and Evolution 21:974–983. Hasegawa, O., S. Takada, M. C. Yoshida, and S. Abe. 1999. Variation of mitochondrial control region sequences in three crane species, the Red-Crowned Crane Grus japonesis, the Common Crane G. grus and the Hooded Crane G. monacha. Zoological Science 16:685–692. Hughes, J. M. 2008. Cranes: A Natural History of a Bird in Crisis. Firefly Books, Buffalo, New York. Ingold, J. L., S. I. Guttman, and D. O. Osborne. 1987. Biochemical systematics and evolution of the cranes (Aves: Gruidae). Pages 575–584 in Proceedings of the 1983 International Crane Workshop (G. W. Archibald and R. F. Pasquier, Eds.). International Crane Foundation, Baraboo, Wisconsin. IUCN. 2007. IUCN Red List of Threatened species. [Online.] Available at www.iucnredlist.org. Johnsgard, P. A. 1983. Cranes of the World. Indiana University Press, Bloomington. Krajewski, C. 1989. Phylogenetic relationships among cranes (Gruiformes: Gruidae) based on DNA hybridization. Auk 106: 603–618. Krajewski, C. 1990. Relative rates of single-copy DNA evolution in cranes. Molecular Biology and Evolution 7:65–73. Krajewski, C., M. G. Fain, L. Buckley, and D. G. King. 1999. Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes. Molecular Phylogenetics and Evolution 13:302–313. Krajewski, C., and J. W. Fetzner. 1994. Phylogeny of cranes (Gruiformes: Gruidae) based on cytochrome b DNA sequences. Auk 111:351–365. Krajewski, C., and D. G. King. 1996. Molecular divergence and phylogeny: Rates and patterns of cytochrome b evolution in cranes. Molecular Biology and Evolution 13:21–30. Krajewski, C., and T. C. Wood. 1995. Mitochondrial DNA relationships within the Sarus Crane species group (Gruiformes: Gruidae). Emu 95:99–105. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245. Livezey, B. C. 1998. A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters, with an emphasis on the rails (Rallidae). Philosophical Transactions of the Royal Society of London, Series B 353:2077–2151. McGuire, J. A., C. C. Witt, D. L. Altshuler, and J. V. Remsen, Jr. 2007. Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Systematic Biology 56:837–856. Meine, C. D., and G. W. Archibald, Eds. 1996. The Cranes: Status Survey and Conservation Action Plan. IUCN, Gland, Switzerland. Mindell, D. P., M. D. Sorenson, and D. E. Dimcheff. 1998a. An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Molecular Biology and Evolution 15: 1568–1571.

4/7/10 5:09:30 PM

A pril 2010

— C r ane P hylogeny

from

Mindell, D. P., M. D. Sorenson, and D. E. Dimcheff. 1998b. Multiple independent origins of mitochondrial gene order in birds. Proceedings of the National Academy of Sciences USA 95:10693–10697. Mindell, D. P., M. D. Sorenson, D. E. Dimcheff, M. Hasegawa, J. C. Ast, and T. Yuri. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Systematic Biology 48:138–152. Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performancebased selection of likelihood models for phylogeny estimation. Systematic Biology 52:674–683. Monroe, B. L., Jr., and C. G. Sibley. 1993. A World Checklist of Birds. Yale University Press, New Haven, Connecticut. Morgan-Richards, M., S. A. Trewick, A. Bartosch-Härlid, O. Kardailsky, M. J. Phillips, P. A. McLenachan, and D. Penny. 2008. Bird evolution: Testing the Metaves clade with six new mitochondrial genomes. BMC Evolutionary Biology 8:20. Nishibori, M., T. Hayashi, M. Tsudzuki, and H. Yasue. 2001. Complete sequence of the Japanese Quail (Coturnix japonica) mitochondrial genome and its relationship with related species. Animal Genetics 32:380–385. Nylander, J. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47–67. Paton, T., O. Haddrath, and A. J. Baker. 2002. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proceedings of the Royal Society of London, Series B 269:839–846. Peters, J. L. 1934. Check-list of Birds of the World, vol. 2. Cambridge University Press, Cambridge, United Kingdom. Petersen, J. L., R. Bischof, G. L. Krapu, and A. L. Szalanski. 2003. A phylogenetic analysis of the Sandhill Crane Grus canadensis. Biochemical Genetics 41:1–12. Posada, D., and T. R. Buckley. 2004. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53:793–808. Posada, D., and K. A. Crandall. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817–818. Rambaut, A., and A. J. Drummond. 2007. TRACER, version 1.4. [Online.] Available at beast.bio.ed.ac.uk/Tracer. Rhymer, J. M., M. G. Fain, J. E. Austin, D. H. Johnson, and C. Krajewski. 2001. Mitochondrialphylogeography, subspecific taxonomy, and conservation genetics of Sandhill Cranes (Grus canadensis; Aves: Gruidae). Conservation Genetics 2: 203–218. Rich, P., and G. Van Tets. 1984. What fossil birds contribute towards an understanding of origin and development of the Australian avifauna. Pages 421–446 in Vertebrate Zoogeography

22_Krajewski_09-045.indd 451

M itochondrial G enomes —

451

and Evolution in Australasia (M. Archer and G. Clayton, Eds.). Hesperian Press, Carlisle, Australia. Ronquist, F., and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574. Ségalen, L., M. Renard, J. A. Lee-Thorpe, L. Emmanuel, L. LeCallonnec, M. de Rafélis, B. Senut, M. Pickford, and J.-L. Melice. 2006. Neogene climate change and emergence of C4 grasses in the Namib, southwestern Africa, as reflected in ratitie 13 C and 18O. Earth and Planetary Science Letters 244:725–734. Seguí, B. 2002. A new genus of crane (Aves: Gruiformes) from the Late Tertiary of the Balearic Islands, Western Mediterranean. Ibis 144:411–422. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51:492–508. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16:114–116. Shimodaira, H., and M. Hasegawa. 2001. CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246–1247. Slack, K. E., A. Janke, D. Penny, and U. Arnason. 2003. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302:43–52. Slack, K. E., C. M. Jones, T. Ando, G. L. Harrison, R. E. Fordyce, U. Arnason, and D. Penny. 2006. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Molecular Biology and Evolution 23:1144–1155. Swofford, D. L. 2001. PAUP*: Phylogenetic Analysis Using Parsimony (*And Other Methods), version 4. Sinauer Associates, Sunderland, Massachusetts. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTALX Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24:4876–4882. Wilgenbusch, J. C., D. L. Warren, and D. L. Swofford. 2004. AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. [Online.] Available at ceb.csit.fsu.edu/awty. Wood, D. S. 1979. Phenetic relationships within the family Gruidae. Wilson Bulletin 91:384–399. Wood, T. C., and C. Krajewski. 1996. Mitochondrial DNA sequence variation among the subspecies of Sarus Crane (Grus antigone). Auk 113:655–663. Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, University of Texas, Austin. Associate Editor: J. Klicka

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A ppendix.  Primers for amplification of crane mtDNA. The locus in which each primer site occurs is given at left. Primer names are followed by their 5N-3N sequences. The alignment site corresponding to each primer’s 3N base is given in parentheses after its sequence. Locus tRNA

Phe

12S

tRNAVal 16S tRNALeu(UUR) tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNATyr CO1 tRNASer(UCN) tRNA Asp CO2 tRNALys ATPase 6 CO3 tRNAGly ND3 tRNA Arg ND4L ND4 tRNALeu(CUN) ND5

Cyt b

tRNAThr tRNAPro ND6

tRNAGlu CR

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Light strand primers

Heavy strand primers

L1239-AAAGCATGGCACTGAAGATG (40) 12S-Phe-AAAGCATGCACTGAAGATG (40) L1415-AGGAGCRGGYATCAGGC (194) L1091 AAACTGGGATTAGATACCCCACTAT (535) L2102-GAAGGCGGATTTAGCAGTAA (893) L2260-TAAGTGTACCGGAAGGTG (1046)

H1247-ATCTTCAGTGCCATGCTTTG (20)

L2825-GGTACAGCTCCTTTAAAAAG (1632) 12P-TRACCGTGCAAAGGTAGC (2098) L3920-AGTAATGARCCCAACTAAATT (2719) L3994-CAGAGGTTCAAATCCTCTCC (2826)

H1736-AGGCATAGTGGGGTATCTAATC (518) H1121-TAAGTATCGAGATTTAGGGC (541) H1827-ACCGCCAAGTCCTTAGAG (609) H1478-GAGGGTGACGGGCGGTATGT (937) H2291-CAGGTGTAAGCTGAATGCTTT (1078) H2894-TTGGTGGCTGCTTGAAGGCC (1681) H3408-AAGTTCCACAGGGTCTTCTC (2220) 12T-GCAATTACCGYYCTCTGCCA (2765) H3954-GCATTTACCGAGCTCTGCCA (2765) H5056-TACCTCTATGTTCACTTTATC (3834)

L5140 ACCTACACArAAGAGATCAA (3921) L5968 ACCCCMATACTAAATGCAAC (4753) L6003 CTCTCCCTRGCAGGYCTCCC (4789)

H5202-ACCATCATTTTCGGGGTATG (3987) H6074-AGYATRGTRATGATTGTAGCTGC (4879) H6330-CAGAAACTAAGAGAGTTTAAC (5115)

L6622-AAGGACTACAGCCTAACGCT (5382) L7465 TTCGGMTACATAGGAATAGT (6247) L7474 ATAGGAATAGTATGAGCCAT (6256) L8236 GTTTCAAGCCAACCGCATCA (7018) L8692-GGACAYCAATGATACTGAAC (7430) L9045-GCTATGCACCAGCACTAGCC (7828) L9045A-GCTATGTAAYCAGCGCTAGCC (7828) L9679-GCCCTAATCATAATCGAAAC (8473) L9681-GCATTAATTTTAATCGAAACCAC (8476) L10221 TTCCTAGGATTCTTCTGAGC (9015)

H6822-RATTATTACGAAGGCRTGRGCGGT (5601) H7536-TAKGCTCGGGTGTCTACGTC (6318) H8333-GTAATTGGTTTACTAACATC (7045) H8789-ATTGGGATRACAACGCGATG (7547) H9258-CATGGRCTTGTGAATTGGTC (8052) H9775-ATRGTTGGGAGTAGGGCAATTG (8569) H10235-TCTGGGGTGGGRACTAGGCT (9029) H10228-CCTAGYTCYGGGGTGGGGA (9036) H10123-TGRGCTCATGTTACGGTGAC (9159)

L10740-AMTMATTACAAYTGACTTCC (9533) L10769-AATCTGGTACAACCCCAGAG (9562) H10816-GTRGTTAGGATRATGCTTAG (9609) L11161-CTAACAAAGACAGYTGRTTTCG (9956) L11468-CAYGGCTCYGACCACCTACA (10038) L11991-ACAATYCTYCACCTACAYACA (10791) L12492-GCMAACACAAACTACGAACG (11291) L12301-AGGAGCAATCCGTTGGTCTTAGG (11842) L13322-CCACTCAGCCTAAAAATAGAC (12132) L13519-GGCTGAGAAGGAGTYGGCAT (12329) L13746-GCCACAGGAAAATCAGCCC (12556) L14770 ATAGGCCCAGAAGGCCTTGC (13580) L14851-TACCTGGGTTCCTTCGCCCT (13661) L14886 ATCATACTATCAACATAAACCA (13696) L14841 CCATCCAACATCTCAGCCATGATGAAA (13800) L14958 GAGACGTAAACTACGGCTGACTAATC (13942) L15087 TACTTAAACAAAGAAACCTGAAA (14046) L15136 ATAGCAACAGCATTTGTAGG (14094) L15418 GATAAAATCCCATTCCACCCCTA (14373) L15615 GTTCAATCCCAAACAAACTAGGA (14572) L16022-GGAGCCCTAGAAAACAAAAT (14832)

H11222-CTTARGGTGAAGGCTGAGTA (10266) H11488-GTRGGTAGGATGATTTTTAAC (10287) H12029-GTTRRTGAGTRTGGGGTGGGT (10828) H12513-TTGGACRCCTCGTGTTAGGA (11312) H13041-TTGGATTTGCACCAAGATGG (11849) H12766-GACATGATTCCTACTCCTTCTCA (12313) H14632-TCCTARTRTGGAKGAGAAGT (13442) H14847-ATRGTGAGGATRGAGAGGGC (13657)

H15024-AGTAGGCCRGTTAGGATTTG (13835) H14954-CCGTAATTTACGTCTCGGCA (13913) H15149-TGCAGCCCCTCAGAATGATATTTGTCCTCA (14108) H15498-GGAATAAGTTATCTGGGTCTC (14467) H15767-ATGAAGGGATGTTCTACTGGTTG (14726) H15915-AACTGCAGTCATCTCCGGTTTACAAGAC (14876)

L16152-ATCTCCAACTCCCAAAGCTG (14986) L16235 CGTACAAGCTCCAACACTAC (15072) L16303 CCCCCCACGAATAAAACAT (15138) L16598-CACCCACACCCTACAACAG (15434) L16707 GCATAAAATAAGTCATCAGA (15544) L83-TACATTACATYAATGTAGGA (15710) L514-CGTTCCTCGGTCAGGGCCAT (16158) L543-CTGGTTCCTATGTCAGGGCCAT (16158) L795-CATACATGGTATTCGTC (16352) L963-ACTTTTACACTTCCTCTAAC (16530)

H16208-AGCTTGTACGAGGGTTGT (15045) H16347-GGGGTGGTTACTGTGGATAG (15182) H16621-ATCCTTCACCGTACTATGGG (15457) H16744-TTACAACAGCGGCTTTG (15581) H514-ACATAGGAACCAGAGGCGCAA (16137) H778-ACGAATACCATGTATGC (16335)

4/7/10 5:09:30 PM