Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis

The ratites have stimulated much debate as to how such large flightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of flight. Hypotheses regarding the relationships among taxa differ for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of five extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary and two tinamous from different genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and non-homogeneous maximum likelihood, the ratites are found to be monophlyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor-descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.     

Phylogeny and biogeography of ratite birds inferred from DNA sequences of the mitochondrial ribosomal genes

The origin of the flightless ratite birds of the southern continents has been debated for over a century. Whether dispersal or vicariance (continental breakup) best explains their origin depends largely on their phylogenetic relationships. No consensus has been reached on this issue despite many morphological and molecular studies. To address this question further we sequenced a 2.8-kb region of mitochondrial DNA containing the ribosomal genes in representative ratites and a tinamou. Phylogenetic analyses indicate that Struthio (Africa) is basal and Rhea (South America) clusters with living Australasian ratites. This phylogeny agrees with transferrin and DNA hybridization studies but not with sequence analyses of some protein-coding genes. These results also require reevaluation of the phylogenetic position of the extinct moas of New Zealand. We propose a new hypothesis for the origin of ratites that combines elements of dispersal and vicariance.      

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

On the origin and rarity of interspecific nest parasitism in birds

Interspecific nest parasitism is surprisingly rare in birds given the potential advantages for the parasite of exploiting the parental care of other species. One possibility is that chicks will not thrive with the parental care and food of heterospecifics. I simulated parasitism in nonparasitic congeners by switching eggs between nests of three species of titmice (great tit Parus major, blue tit Parus caeruleus, and coal tit Parus ater). The experiment showed that compatibility of parental care was not a constraint preventing parasitism. I also used the model system to compare fitness consequences of inter- and intraspecific nest parasitism, addressing the problem of which form is ancestral. Fledging success (body mass, survival) was higher when an egg was added to the nest of a smaller species than to the nest of a conspecific and also higher when the parasitic chick hatched early rather than late relative to host chicks. This suggests that interspecific nest parasitism may not require a stage of intraspecific nest parasitism before evolving but may start from a larger species directly exploiting the parental care of a smaller species or a species with shorter incubation period directly exploiting a species with longer incubation period.     

On the origin and evolution of major morphological characters

Although the mathematical principles underpinning population-level evolution are now well studied, the origin and evolution of morphological novelties has received far less attention. Here, a broad but general theory for how this sort of change takes place is outlined, relying on functional continuity, least-constrained components of morphology, redundancy and preadaptation. At least four distinct sorts of redundancy are identified: (i) redundancy arising through duplication (amplification); (ii) redundancy arising through regionalisation (parcellation); (iii) redundancy arising through functional convergence; and (iv) redundancy arising from shared function (functional degeneracy). Although organisms are here recognised to be functionally constrained ("burdened", in Riedl's terminology), these constraints can be overcome through the combination of the four principles given above. Contrary to its common treatment, functional constraint is neither an ever-increasing restriction on the scope of evolution, nor does it require drastic events to overcome or "break" it. Rather, it is an evolutionary quantity, subject to selection at some level. The rules that govern morphological evolution are the primary controls on what is allowed to happen in the evolution of the overall genotype-phenotype system, suggesting strong controls on the sorts of developmental changes that might be associated with macroevolution. This model, then, sees organism functionality as the primary control on evolvability, with exact genetic make-up being of secondary importance. It should prove possible to recast traditional notions of body-plan evolution into the formulations of complex system analysis, which in the future may prove a unifying discipline for fields as disparate as palaeontology and gene regulatory networks. In particular, understanding how morphology can evolve may provide the critical link between the ecological and morphological networks that are currently the intense focus of evolutionary investigations.     

Lessons from a complex biogeographical scenario: morphological characters match mitochondrial lineages within Iberian Coronella austriaca (Reptilia: Colubridae)

Molecular evidence suggests that climatic fluctuations in the peninsulas of southern European during the Miocene and Pleistocene resulted in considerable genetic differentiation of organisms, probably following a ‘refugia within refugia’ model. We examined morphometric and meristic characters in museum specimens from the three Iberian clades of the smooth snake Coronella austriaca, previously described by molecular markers. We found sexual and interclade differences in scale counts and head shape. Sexes were dimorphic in the number of ventral and subcaudal scales, although sexual disparities in scale counts differed among clades. Moreover, discriminant and canonical analyses showed higher interclade differences in males than in females. The results obtained in the present study match those from molecular markers and confirm the population structure identified within Iberian C. austriaca. The observed sex discrepancy in this pattern suggests that males and females are subjected to different selective pressures along their Iberian distribution. In light of the above, C. austriaca may offer a useful model system in which to explore phylogeographical patterns in southern Europe, as well as the conflicts between processes driving morphological sexual divergence. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 210–223.     

Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters

Of the basal clades of extant birds (Neornithes) the 'landfowl' or galliforms (Aves, Galliformes) are the most speciose. Cladistic analysis of more than 100 morphological characters coded at the generic level for most putative galliform genera confirms that the megapodes ('mound builders'; Megapodiidae) are the most basal clade within the order. They are followed successively by the curassows, guans and chachalacas (Cracidae), which comprise the sister-group to all other extant Galliformes (i.e. Phasianoidea). Within this large 'phasianoid' clade, analyses suggest that the guineafowl (Numididae) are the most basal taxon, although monophyly of this 'family' is not strictly supported on the basis of the morphological characters employed. An additional major clade within the phasianoid Galliformes is recovered by this analysis, comprising the traditional groupings of New World quails (Odontophoridae) and Old World quails ('Perdicini'), yet only monophyly of the former is supported unambiguously by morphological characters. Relationships within the remainder of the phasianoid taxa, including the grouse (Tetraonidae), turkeys (i.e. Meleagris / Agriocharus spp.) as well as other 'pavonine' galliforms (i.e. peafowl; Pavo , Afropavo , Rheinardia , Argusianus and Polyplectron spp.) remain largely unresolved on the basis of morphological characters, yet monophyly of the major subdivisions is supported here. Although there are a number of important differences, especially with regard to relationships within the nonquail phasianoids, the results of this morphological phylogenetic (cladistic) analysis are broadly congruent both with traditional classifications and existing molecular hypotheses of galliform phylogenetic relationships.     

On the evolutionary origin of mitochondrial DNA

Current theories of mitochondrial evolution assume that this organelle evolved either from endosymbiotic bacterial-like organisms which invaded other cells or by a gradual sequestering of functional cytoplasmic units within membranes. In either case there has been relatively little discussion of the origin of mitochondrial DNA. Because of the marked similarity in the size, physical properties, replication and sensitivity to acridine dyes and ethidium bromide of both bacterial plasmid and mitochondrial DNA, it is proposed that the plasmid of an ancestral bacterial-like organism evolved into the mitochondrial DNA of eukaryotes. This hypothesis is consistent with either theory of the whole organelle but is easier to explain if mitochondria evolved within a prokaryote by invagination of the plasma membrane.     

The origin of stomach oil in marine birds: Analyses of the stomach oil from six species of subantarctic procellariiform birds

The stomach oil produced by many marine birds of the order Procellariiformes is an important aspect of their breeding ecology. Fifty-seven samples of stomach oil from six species of subantarctic sea birds were examined by thin-layer and gas chromatography to determine the degree of variation in stomach oil composition between individuals of the same species. The wide variability detected, the typically marine composition of the component fatty acids and alcohols of the wax esters and triacyglycerols examined and the presence of pristane, squalene, and astaxanthin in the stomach oils all indicate that the bulk of the oil is derived directly from the food. This is in contrast to the nutritive fluids produced by secretion in several other groups of birds. Many of the stomach oils contain large amounts of wax ester and marine birds represent a significant link in the marine food web for the reconversion of zooplankton wax ester to triacylglycerol. No substantial offshore pollution by petroleum hydrocarbons was indicated by the samples; stomach oil samples from pelagic birds may be valuable in monitoring offshore pollution.     

Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin

The geographical distribution of single nucleotide polymorphism (SNP) in the mitochondrial genome of the human malaria parasite Plasmodium falciparum was investigated. We identified 88 SNPs in 516 isolates from seven parasite populations in Africa, Southeast Asia and Oceania. Analysis of the SNPs postulated a sub-Saharan African origin and recovered a strong negative correlation between within-population SNP diversity and geographic distance from the putative African origin over Southeast Asia and Oceania. These results are consistent with those previously obtained for nuclear genome-encoded housekeeping genes, indicating that the pattern of inheritance does not substantially affect the geographical distribution of SNPs.     

Evolution of the mitochondrial DNA cytochrome b gene in Tetraonidae birds

Mitochondrial fragments containing the cytochrome b gene (1020 bp in size) of four bird species belonging to four genera of the family Tetraonidae (Tetrao parvirostris, Bonasa umbellus, Lagopus lagopus scoticus, and Falcipennis falcipennis) were directly sequenced. Of the 1020 nucleotide positions, 186 were variable and uniformly distributed over the gene and only 46 were parsimony informative. Most substitutions were synonymous. Replacement substitutions were detected for 15 out of 340 amino acid sites; only four replacements were parsimony informative. The greatest codon bias was found for leucine and serine. The C-T transitions and the G-C transversions were, respectively, the most common (60.7%) and the most rare (5.9%). The mutation frequencies were high at the third codon position (85.2%) and relatively low at the first and the second position. At the third codon position of the species examined, the guanine content was the lowest (3.3%) and the cytosine content was the highest (44.5%). Based on the cytochrome b gene sequences, phylogenetic relationships in the order Galliformes are inferred.     

Location of the ureteral openings in the cloacas of tinamous, some ratite birds, and crocodilians: a primitive character

Cloacas of 67 avian species, of both sexes, from various habitats and differing dietary habits, were examined macro- and microscopically to investigate possible variation in the location of the ureteral openings. Differing from most birds studied, in adult male Rhea americana and several tinamous species the ureters were found to open into the coprodeum. In these species the urodeum receives only the vas deferens or oviduct. Similarly, in crocodiles Caiman crocodilus yacare, but not in lizards Tropidurus montanus and snakes Crotalus durissus terrificus, the ureters empty into the coprodeum. This similarity between ancient birds (ratites and tinamous) and crocodiles may indicate a primitive character linking reptiles and birds. This unusual position of the ureteral orifice can represent an adaptation to facilitate urine collection into the coprodeum and large intestine. Another possibility is that this variation in ureter position is a male reproductive strategy to avoid the mixture of urine and semen in the cloaca. There were no evident correlations between the location of the ureteral openings and the birds' habitat, diet, or histology of the coprodeal mucosa. The occurrence of a phallus in eight species of birds was detected, as well as a peculiar vascularization related to the coprodeal epithelium of anseriformes. Together, these data add to the scarce information about the morphophysiology of the avian cloaca, and also contribute to clarify avian phylogenetic linkages.     

Genetic variation of morphological characters within a single isolate of the endomycorrhizal fungus Glomus clarum (Glomaceae)

The nature of variation in morphological characters in spores of arbuscular endomycorrhizal fungi (Order Glomales, Class Zygomycetes) has received little attention, despite the importance of these characters in modern taxonomy of the order. We tested the hypothesis that genetic variation exists in spore size and color (presumably important taxonomic characters) within a single isolate of the glomalean fungus Glomus clarum. Phenotypic variation in size and color of spores was determined from a pot culture population (designated P). A 10% selection pressure was imposed on replicate pot cultures of the first progeny culture generation (G1) by selecting the smallest, largest, yellowest, and whitest spores from the P generation and inoculating Sorghum bicolor plants. The experiment was repeated for another generation (G2), but with a 5% selection pressure. In both the G1 and G2 generations, significant differences in spore size and color were observed among the various treatments, indicating substantial genetic variation in these characters. Despite efforts to keep the physical environment constant across generations, we observed variation in the overall means of spore size and color among the generations (regardless of treatment), indicating a strong nongenetic influence on character expression. This study provides empirical evidence that will help delimit species boundaries among isolates of Glomus clarum and similar morphospecies. It also demonstrates a promising method to help elucidate the nature of character diversity in obligately asexual fungi.     

Parent birds assess nest predation risk: influence of cavity condition and avian nest predator activity

Skutch hypothesized that nest predators visually assess parental activities to locate a prey nest, whereas parents modify fitness‐related traits to reduce the probability of nest predation. We examined how cavity condition and parental activity interact with avian nest predators to shape the nest success of two coexisting parid species, marsh tits Poecile palustris and oriental tits Parus minor, breeding in nest‐boxes during the incubation period. Nest‐boxes were manipulated to create a prolonged risk of nest predation (entrance diameter 2.6 cm control vs 5.5 cm treatment) soon after clutch completion. To measure changes in parental behavior, we also simultaneously simulated a pulsed risk of nest predation, using sound playbacks of a coexisting control bird and an avian nest predator. We found that the parent tits merely responded the pulsed risk, presumably due to an environment with high avian nest predator encounters, compared to the prolonged risk. Instead, both species spent more time on vigilance at the nest, only under prolonged risk conditions. The activity of corvids near the nest‐box was higher in the marsh tit than that in oriental tits. This activity was also higher in the treatment nest box than that in the control nest‐box. Nest predation during the incubation period was higher in marsh tits than in oriental tits, presumably due to higher and more plastic vigilance in oriental tits, compared to marsh tits. Our results highlight that the differences in cavity condition and parental activities at the nests of two coexisting non‐excavators may contribute to differential nest predation by attracting avian nest predators.     

Nucleotide sequence of a cloned fragment of rat mitochondrial DNA containing the replication origin

The nucleotide sequence was determined for the 717 bp HapII subfragment (HapEcoA5) of the EcoRI-A fragment of rat mitochondrial DNA, which contains the heavy-strand replication origin. Analysis of the heavy-strand initiation segments released from the D-loop molecules has revealed that some 5'-ends of these initiation segments are linked to ribonucleotide(s) and are heterogeneous. Sequence analysis of the 5'-end portion of the initiation segment indicated that one of the start points of the deoxyribonucleotide polymerization corresponds to the 425th bp on the HapEcoA5. Two-fold rotational symmetry and palindrome structures, and a G-cluster sequence around the start point have been discussed in connection with unidirectional replication.