Monophyly and phylogeny of cuckoos (Aves, Cuculidae) inferred from osteological characters

A reanalysis of 32 characters from the literature previously deemed diagnostic of the Cuculidae revealed only five to be synapomorphic. I subsequently examined skeletons from 54 avian families and identified nine additional synapomorphies that supported cuckoo monophyly. My cladistic analysis of 33 cuculid genera using 135 skeletal characters differs markedly from currently accepted taxonomies. The most striking deviation is the placement of both New and Old World parasitic cuckoos in the Cuculinae, supporting the evolution of brood parasitism in a single event rather than three times as previously proposed. Unlike earlier classifications, the Cuculinae also includes the facultative parasites Coccyzus. This, suggests that the ancestral Coccyzus was an obligate parasite, and is consistent with the many behavioral adaptations to parasitism exhibited by this genus. Other changes include the placement of three subfamilies, comprising non-parasitic, terrestrial cuckoos of Old World (Centropodinae and Carpococcystinae) and New World (Neomorphinae) distribution, in basal positions on the tree. Nineteen characters support a sister relationship between the Hoatzin ( Opisthocamus hoatzin Müller) and turacos (Musophagidae), and not cuckoos. Three synapomorphies of the os carpi ulnare were found to unite the Cuculidae, turacos, and the Hoatzin, suggesting that these three diverse taxa may constitute a monophyletic group.     

Skull and mandible formation in the cuckoo (Aves, Cuculidae): contributions to the nomenclature in avian osteology and systematics

The study of the contributions of different bones to the formation of the skeleton in birds is necessary: (1) to establish homologies in comparative anatomy; (2) to delimit each bone structure correctly, mainly in relation to the skull and mandible where the bones are fused to each other in adults; and (3) to standardize nomenclature in avian osteology. In this paper at least one young specimen belonging to each sub-family of Cuculidae was examined in order to identify each bone in terms of boundaries and contributions to skull and mandible formation. These cuckoos specimens were also compared with adults and young of turacos and hoatzin. The results show little variation of skull and jaw among the young cuckoos studied compared with the variations among adult specimens. However, it provides new suggestions for the boundaries and nomenclature of certain osseous structures in the skull and mandible of birds, specifically fissura zona flexoria craniofacialis, prominetia frontoparietalis, crista temporalis transversa, processus squamosalis, fossa laterosphenoidalis, tuberculum laterosphenoidale and processus retroangularis. This study also provides more reliable homologies for use in cladistic analysis and above all it contributes to the phylogenetic position of Cuculidae within Neognathae, specifically the skull formation suggest that turacos and hoatzin are more similar to each other than either is to the cuckoos.     

A molecular phylogeny of the New World orioles (Icterus): the importance of dense taxon sampling.

We sequenced 2005 bp of the mitochondrial ND2 and cytochrome b genes from the 25 recognized species of New World orioles (Icterus). Our data confirmed the monophyly of Icterus and produced a well-resolved phylogeny showing three main clades of orioles. We also sequenced multiple subspecies for most polytypic taxa. Our findings demonstrated the importance of dense taxon sampling below the species level in two ways. First, we found evidence that two species are polyphyletic, I. galbula (Northern oriole) and I. dominicensis (Black-cowled oriole). Choosing different subspecies from either of these taxa would lead to different species-level phylogenies. Second, adding subspecies even to monophyletic groups produced a bootstrap tree with significantly more support. Of the two genes that we used, ND2 provided more resolution than did cytochrome b. ND2 evolved up to 40% faster than cytochrome b, yet shows a higher saturation threshold. Our findings suggest that ND2 may be superior to cytochrome b for resolving species-level phylogenies in passerine birds.     

Phylogeny of the cuckoo genus Coccyzus (Aves: Cuculidae): A test of monophyly

Coccyzus comprises nine species of New World cuckoos (Aves: Cuculidae) that breed from southern Canada to central South America. The phylogeny of this genus was reconstructed using 2490 base pairs of the mitochondrial genes cytochrome oxidase II and III, and cytochrome b. Maximum likelihood, maximum parsimony, and Bayesian inference approaches produced similar topologies in which Coccyzus, as currently classified, is polyphyletic. Topological‐constraint analyses demonstrated that trees resulting from this study were significantly better than those derived from conventional classifications. Furthermore, results support paraphyly of Piaya, another genus of New World cuckoos. These conclusions reflect some early classifications of these genera and support the resurrection of Micrococcyx to house the ash‐coloured (Coccyzus cinereus) and dwarf (C. pumilus) cuckoos, and Coccycua for the little cuckoo (Piaya minuta).     

Variation in Coding (NADH Dehydrogenase Subunits 2, 3, and 6) and Noncoding Intergenic Spacer Regions of the Mitochondrial Genome in Octocorallia (Cnidaria: Anthozoa)

Low rates of evolution in cnidarian mitochondrial genes such as COI and 16S rDNA have hindered molecular systematic studies in this important invertebrate group. We sequenced fragments of 3 mitochondrial protein-coding genes (NADH dehydrogenase subunits ND2, ND3 and ND6) as well as the COI-COII intergenic spacer, the longest noncoding region found in the octocoral mitochondrial genome, to determine if any of these regions contain levels of variation sufficient for reconstruction of phylogenetic relationships among genera of the anthozoan subclass Octocorallia. Within and between the soft coral families Alcyoniidae and Xeniidae, sequence divergence in the genes ND2 (539 bp), ND3 (102 bp), and ND6 (444 bp) ranged from 0.5% to 12%, with the greatest pairwise distances between the 2 families. The COI-COII intergenic spacer varied in length from 106 to 122 bp, and pairwise sequence divergence values ranged from 0% to 20.4%. Phylogenetic trees constructed using each region separately were poorly resolved. Better phylogenetic resolution was obtained in a combined analysis using all 3 protein-coding regions (1085 bp total). Although relationships among some pairs of species and genera were well supported in the combined analysis, the base of the alcyoniid family tree remained an unresolved polytomy. We conclude that variation in the NADH subunit coding regions is adequate to resolve phylogenetic relationships among families and some genera of Octocorallia, but insufficient for most species - or population-level studies. Although the COI-COII intergenic spacer exhibits greater variability than the protein-coding regions and may contain useful species-specific markers, its short length limits its phylogenetic utility.     

Biomechanical features of the bill and and jaw apparatus of cuckoos,turacos and the hoatzin in relation to food acquisition and processing

A morphofunctional analysis of the feeding apparatus was conducted from an evolutionary perspective on the hoatzin (Opisthocomidae), some cuckoos (Cuculidae) and some turacos (Musophagidae). These goups share a common ancestral adaptation of the bill apparatus linked to starting food processing at base of the bill. The morphofunctional analyses give results different from what is known for the Galliformes and allow the construction of the hypothesis of two trophic adaptive pathways. One followed by the Cuculidae would have led to the consumption of a large range of arthropods, including toxic species; the other, followed by the Musophagidae and Opisthocomidae, would have led to the consumption of plant parts.     

Evolution of mitochondrial and ribosomal gene sequences in anophelinae (Diptera: Culicidae): implications for phylogeny reconstruction

In this study, two mitochondrial genes, cyt b and ND5, and the D2 expansion segment of the 28S nuclear ribosomal gene were used to reconstruct a phylogeny of the mosquito subfamily Anophelinae. The ingroup consisted of all three genera of Anophelinae and five of six subgenera of Anopheles. Six genera of Culicinae were used as the outgroup. Extreme conservation at the protein level coupled with rapid saturation of synonymous positions probably accounted for the lack of meaningful phylogenetic signal in the cyt b gene. In contrast, abundant variation at all codon positions of the ND5 gene allowed recovery of the basal and most of the recent relationships. Phylogenetic analysis of D2 produced results consistent with those of ND5. Combined analysis indicated well-supported monophyletic Anophelinae (with Chagasia basal), Anopheles + Bironella, and subgeneric clades within the genus Anopheles. Moreover, subgenera Nyssorhynchus and Kerteszia were supported as a monophyletic lineage. The Kishino-Hasegawa test could not reject the monophyly of Anopheles, whereas the recently proposed hypothesis of close affinity of Bironella to the subgenus Anopheles was rejected by the analyses of ND5 and combined data sets. The lack of resolution of Bironella and Anopheles clades, or basal relationships among subgeneric clades within Anopheles, suggests their rapid diversification. Recovery of relationships consistent with morphology and previous molecular studies provides evidence of substantial phylogenetic signal in D2 and ND5 genes at levels of divergence from closely related species to subfamily in mosquitoes.     

Conflicting molecular phylogenies of European long-eared bats (Plecotus) can be explained by cryptic diversity

Conflicting phylogenetic signals of two data sets that analyse different portions of the same molecule are unexpected and require an explanation. In the present paper we test whether (i) differential evolution of two mitochondrial genes or (ii) cryptic diversity can better explain conflicting results of two recently published molecular phylogenies on the same set of species of long-eared bats (genus Plecotus). We sequenced 1714bp of three mitochondrial regions (16S, ND1, and D-loop) of 35 Plecotus populations from 10 European countries. A likelihood ratio test revealed congruent phylogenetic signals of the three data partitions. Our phylogenetic analyses demonstrated that the existence of a previously undetected Plecotus lineage caused the incongruities of previous studies. This lineage is differentiated on the species level and lives in sympatry with its sister lineage, Plecotus auritus, in Switzerland and Northern Italy. A molecular clock indicates that all European Plecotus species are of mid or late Pliocene origin. Plecotus indet. was previously described as an intergrade between P. auritus and Plecotus austriacus since it shares morphological characters with both. It is currently known from elevations above 800 m a.s.l. in the Alps, the Dinarian Alps and the Pindos mountains in Greece. Since we could demonstrate that incongruities of two molecular analyses simply arose from the mis-identification of one lineage, we conclude that molecular phylogenetic analyses do not free systematists from a thorough inclusion of morphological and ecological data.     

Chemical defence in avian brood parasites: production and function of repulsive secretions in common cuckoo chicks

The use of active chemical defence against predators is relatively rare in birds. Among others, it has been reported for some members of family Cuculidae whose chicks, when threatened, expel dark foul‐smelling liquid from their cloaca. Apart from the brood parasitic great spotted cuckoo Clamator glandarius, however, this phenomenon has not yet been systematically studied in any other cuckoo species. Here we investigated the repellent behaviour in the evicting brood parasite, the common cuckoo Cuculus canorus, parasitizing the great reed warbler Acrocephalus arundinaceus. We explored whether production of secretions varies with chick age or size, and tested its presumed repellent function against various types of predators. We found that the production of secretions commenced at the age of approximately eight days, then gradually increased and decreased again shortly before fledging. Furthermore, we experimentally confirmed a more intensive repellent effect of the secretions on mammal predators than on avian predators, such as raptors and owls. The secretions have, however, no effect on corvid predators, probably because these scavengers often consume malodorous food. Further experimental studies together with phylogenetic comparative analyses are needed to elucidate the origin and function of this intriguing phenomenon both in parasitic and non‐parasitic cuckoos.     

Egg Rejection and Brain Size among Potential Hosts of the Common Cuckoo

Interspecific brood parasitism by the common cuckoo (Cuculus canorus) lowers host fitness, and has selected for discrimination and rejection of parasitic eggs in their commonly parasitized hosts. Cognitive demands needed to discriminate and reject cuckoo eggs may have led to augmentation of relative brain size among passerine hosts parasitized by cuckoos. This hypothesis predicts for across species positive relationships of brain size with rejection rate, host suitability and parasitism level. Here we test these predictions while controlling for phylogenetic, ecological and developmental factors known to affect brain size and egg rejection in a comparative study using the cuckoo and their hosts in Europe as a model system. Contrary to expected the rate of rejection of non‐mimetic cuckoo eggs covaried negatively with relative brain size across bird species. Either suitability as cuckoo host, which reflects long‐time duration of exposure to cuckoo parasitism, and level of parasitism, did not relate to brain size. Our results do not support the hypothesis that cuckoo parasitism was a main direct force affecting brain size variation across passerine hosts.     

Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrinogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximately 3750 bp) and combined mt and nuclear data (nine genes; approximately 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manul within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7.     

Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.     

Local origin and diversification among Lampornis hummingbirds: a Mesoamerican taxon

The huge biodiversity found in Mesoamerica is often explained by its geographic situation as a natural bridge between two large biogeographic regions. Often overlooked, however, are the high levels of speciation and diversification in the area. Here we assess the phylogenetic relationships within a Mesoamerican group of hummingbirds (Lampornis). We sequenced both mtDNA (1,143 bp of cyt b and 727 bp of ND5) and nuclear genes (505 bp of AK-5 intron and 567 bp of c-mos) for each of the seven recognised species and outgroups. We find two or three clades of similar age within this genus: L. clemenciae and L. amethystinus (singly or as each other's sister taxa) and a Central American clade. This Central-American clade presents a clear bipartition between northern (L. viridipallens and L. sybillae) and southern Mesoamerica, which is shared with many other Mesoamerican organisms. Our analyses suggest that L. hemileucus does not belong in the genus Lampornis. While we refrain to apply a time-scale to our data because of the lack of an appropriate calibration, our results indicate that the genus Lampornis predates the uprising of the Panama land-bridge, and that diversification among the isthmian species (L. castaneoventris and L. calolaema) is a very recent event. Our results strongly suggest a local Mesoamerican origin for this genus.     

The mitochondrial genome of the spinyhead croaker Collichthys lucida: genome organization and phylogenetic consideration

The complete mitochondrial genome of the spiny head croaker Collichthys lucida was determined in the present study. The mitochondrial DNA was 16,442 base pairs in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major non-coding control region, with the content and order of genes being similar to those in typical teleosts. Most of the genes of C. lucida were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pairs of genes overlapped: ATPase 8 and 6 and ND4L and ND4 by ten and seven nucleotides, respectively. The control region was unusually short at only 768bp, and absence of typical conserved blocks (CSB-D, CSB-E, and CSB-F). Phylogenetic analyses indicated that C. lucida was located in the cluster of fish species from the family Sciaenidae, supporting the traditional taxonomic classification of fish, and in the cluster of Serranidae, the divergence time in Plectropomus leopardus is longer than that among its coordinal species. On the other hand, phylogenetic analyses do not support the monophyletic of family Centracanthidae and genera Larimichthys and Collichthys, which is against the morphological results.     

Diet specialization and brood parasitism in cuckoo species

1. Brood parasitism is a breeding strategy adopted by many species of cuckoos across the world. This breeding strategy influences the evolution of life histories of brood parasite species.
2. In this study, we tested whether the degree on diet specialization is related to the breeding strategy in cuckoo species, by comparing brood parasite and nonparasite species. We measured the gradient of diet specialization of cuckoos, by calculating the Gini coefficient, an index of inequality, on the multiple traits describing the diet of species. The Gini coefficient is a measure of statistical dispersion on a scale between 0 and 1, reflecting a gradient from low to high specialization, respectively. First, we tested the strength of the phylogenetic signal of diet specialization index among cuckoo species worldwide. Then, we ran phylogenetic generalized least square (PGLS) models to compare diet specialization, distribution range, and body mass of parasitic and nonparasitic cuckoo species, considering the phylogenetic signal of data.
3. After adjusting for the phylogenetic signal of the data and considering both, species distribution range and species body mass, brood parasitic cuckoos were characterized by higher diet specialization than nonbrood parasitic species. Brood parasitic species were also characterized by a larger breeding distribution range than nonparasitic species.
4. The findings of this study provide an additional understanding of the cuckoos’ ecology, relating diet and breeding strategies, information that could be important in conservation ecology.

     

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.     

Breeding biology of Coquerel’s Coua ( Coua coquereli ) in Western Madagascar

The breeding biology of the endemic Coquerel’s Coua (Coua coquereli), a non-parasitic cuckoo species for which few ecological data are available, was studied in the dry deciduous forest of western Madagascar. Nestling C. coquereli remain in the nest for only a short time after hatching. At approximately 9 days old and still unable to fly, they were observed to leave the nest and then remained on the ground where they were fed by both parents. This behaviour is probably a strategy used to reduce nestling predation.     

Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes

Nucleotide sequences of the mitochondrial protein coding cytochrome b (cyt b; 650 bp) and small-subunit 12S ribosomal RNA (approximately 350 bp) genes were used in analyses of phylogenetic relationships among extant phrynosomatid sand lizards, including an examination of competing hypotheses regarding the evolution of "earlessness." Sequences were obtained from all currently recognized species of sand lizards as well as representatives of the first and second outgroups and analyzed using both parsimony and likelihood methods. The cyt b data offer strong support for relationships that correspond with relatively recent divergences and moderate to low support for relationships reflecting more ancient divergences within the clade. These data support monophyly of the "earless" taxa, the placement of Uma as the sister taxon to the other sand lizards, and monophyly of all four taxa traditionally ranked as genera. All well-supported relationships in the 12S phylogeny are completely congruent with well-supported relationships in the cyt b phylogeny; however, the 12S data alone provide very little support for deeper divergences. Phylogenetic relationships within species are concordant with geography and suggest patterns of phylogeographic differentiation, including the conclusion that at least one currently recognized species (Holbrookia maculata) actually consists of more than one species. By independently optimizing likelihood model parameters for various subsets of the data, we found that nucleotide substitution processes vary widely between genes and among the structural and functional regions or classes of sites within each gene. Therefore, we compared competing phylogenetic hypotheses, using parameter estimates specific to those subsets, analyzing the subsets separately and in various combinations. The hypothesis supported by the cyt b data was favored over rival hypotheses in all but one of the five comparisons made with the entire data set, including the set of partitions that best explained the data, although we were unable to confidently reject (P < 0.05) alternative hypotheses. Our results highlight the importance of optimizing models and parameter estimates for different genes or parts thereof--a strategy that takes advantages of the strengths of both combining and partitioning data.     

Cuckoos versus reed warblers: Adaptations and counteradaptations

At study sites in Cambridgeshire, England, the percentage of reed warbler, Acrocephalus scirpaceus, nests parasitized by cuckoos, Cuculus canorus, in 2 years was 22·5% and 9·1%. The warblers rejected cuckoo eggs at 19% of parasitized nests. Parasitized clutches suffered less predation than unparasitized clutches, suggesting that the cuckoo itself was the major predator, plundering nests too advanced for parasitism so that the hosts would re-lay. The cuckoos laid a mimetic egg, parasitized nests in the afternoons during the host laying period, usually removed one host egg, laid a remarkably small egg and laid very quickly. Nests were experimentally parasitized with model eggs to study the significance of this procedure. Experiments showed that host discrimination selects for: (1) egg mimicry by cuckoos (poorer matching model eggs were more likely to be rejected); (2) parasitism during the laying period (mimetic eggs put in nests before host laying began were rejected); (3) afternoon laying (mimetic eggs were less likely to be accepted in the early morning than in the afternoon, when hosts were more often absent from the nest); (4) a small egg (large eggs, typical of non-parasitic cuckoos, were more likely to be rejected); (5) rapid laying (a stuffed cuckoo on the nest stimulated increased rejection of model eggs), and (6) sets a limit to host egg removal by cuckoos (if more than one or two are removed desertion may occur). Mimicry may also be selected for because it reduced the chance that second cuckoos can discriminate the first cuckoo's egg from the host's clutch. Predation did not select for mimicry; nests with a non-mimetic egg did not suffer greater predation than those with a mimetic egg. Host rejection of model eggs did not depend on: (1) stage of parasitism once host egg laying had begun (nevertheless cuckoos were more likely to lay early in the host laying period probably to increase the chance the cuckoo chick hatched); (2) removal of a host egg (however, this reduced the incidence of unhatched eggs so cuckoos may remove a host egg so as not to exceed the host incubation limit). There were two costs of rejection, an ‘ejection’ cost (own eggs ejected as well as the cuckoo egg) and, with mimetic eggs, a ‘recognition’ cost (own eggs ejected instead of the cuckoo egg). Reed warblers did not discriminate against unlike chicks (another species) and did not favour either a cuckoo chick or their own chicks when these were placed in two nests side by side. Possible reasons why the hosts discriminate against unlike eggs but not unlike chicks are discussed.