The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae)

The phylogenetic placement of the monotypic crab plover Dromasardeola (Aves, Charadriiformes) remains controversial. Phylogenetic analysis of anatomical and behavioral traits using phenetic and cladistic methods of tree inference have resulted in conflicting tree topologies, suggesting a close association of Dromas to members of different suborders and lineages within Charadriiformes. Here, we revisited the issue by applying Bayesian and parsimony methods of tree inference to 2,012 anatomical and 5,183 molecular characters to a set of 22 shorebird genera (including Turnix). Our results suggest that Bayesian analysis of anatomical characters does not resolve the phylogenetic relationship of shorebirds with strong statistical support. In contrast, Bayesian and parsimony tree inference from molecular data provided much stronger support for the phylogenetic relationships within shorebirds, and support a sister relationship of Dromas to Glareolidae (pratincoles and coursers), in agreement with previously published DNA-DNA hybridization studies.     

RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds

The Charadriiformes is a large and diverse order of shorebirds currently classified into 19 families, including morphologically aberrant forms that are of uncertain phylogenetic placement within non-passerine birds in general. Recent attempts using morphological characters have failed to recover a well-supported phylogeny depicting higher level relationships within Charadriiformes and the limits to the order, primarily because of inconsistency and homoplasy in these data. Moreover, these trees are incongruent with the relationships presented in the DNA hybridization tapestry of, including the location of the root and the branching order of major clades within the shorebirds. To help clarify this systematic confusion we therefore sequenced the large RAG-1 nuclear exon (2850 bp) from 36 species representing 17 families of shorebirds for which DNA was available. Trees built with maximum parsimony, maximum likelihood or Bayesian methods are topologically identical and fully resolved, with high support at basal nodes. This further attests to the phylogenetic utility of the RAG-1 sequences at higher taxonomic levels within birds. The RAG-1 tree is topologically similar to the DNA hybridization tree in depicting three major subordinal clades of shorebirds, the Charadrii (thick-knees, sheathbills, plovers, oystercatchers, and allies), Scolopaci (sandpipers and jacanas) and the Lari (coursers, pratincoles, gulls, terns, skimmers, and skuas). However, the basal split in the RAG-1 tree is between Charadrii and (Scolopaci+Lari), whereas in the DNA hybridization tree Scolopaci is the sister group to the (Charadrii+Lari). Thus in both of these DNA-based trees the Alcidae (auks, murres, and allies) are not basal among shorebirds as hypothesized in morphological trees, but instead are placed as a tip clade within Lari. The enigmatic buttonquails (Turnicidae), variously hypothesized as being allied to either the Galliformes, Gruiformes, or Charadriiformes, are shown to be a basal lineage in the more conventional Lari clade. Divergence times estimated with rate-smoothing methods and minimum time constraints imposed at nodes with key fossils suggest that Charadriiformes originated in Gondwanaland.     

A supertree approach to shorebird phylogeny

Background

Order Charadriiformes (shorebirds) is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species. Here we use the matrix representation with parsimony method to produce the first fully inclusive supertree of Charadriiformes. We also provide preliminary estimates of ages for all nodes in the tree.

Results

Three main lineages are revealed: i) the plovers and allies; ii) the gulls and allies; and iii) the sandpipers and allies. The relative position of these clades is unresolved in the strict consensus tree but a 50% majority-rule consensus tree indicates that the sandpiper clade is sister group to the gulls and allies whilst the plover group is placed at the base of the tree. The overall topology is highly consistent with recent molecular hypotheses of shorebird phylogeny.

Conclusion

The supertree hypothesis presented herein is (to our knowledge) the only complete phylogenetic hypothesis of all extant shorebirds. Despite concerns over the robustness of supertrees (see Discussion), we believe that it provides a valuable framework for testing numerous evolutionary hypotheses relating to the diversity of behaviour, ecology and life-history of the Charadriiformes.

     

Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleocene

Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies. We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 genera plus 8 outgroup taxa, and, together with sequences from 5 other pigeon genera retrieved from GenBank, recovered a strong phylogenetic hypothesis for the Columbiformes. Three major clades were recovered with the combined data set, comprising the basally branching New World pigeons and allies (clade A) that are sister to Neotropical ground doves (clade B), and the Afro-Eurasian and Australasian taxa (clade C). None of these clades supports the monophyly of current families and subfamilies. The extinct, flightless dodo and solitaires (Raphidae) were embedded within pigeons and doves (Columbidae) in clade C, and monophyly of the subfamily Columbinae was refuted because the remaining subfamilies were nested within it. Divergence times estimated using a Bayesian framework suggest that Columbiformes diverged from outgroups such as Apodiformes and Caprimulgiformes in the Cretaceous before the mass extinction that marks the end of this period. Bayesian and maximum likelihood inferences of ancestral areas, accounting for phylogenetic uncertainty and divergence times, respectively, favor an ancient origin of Columbiformes in the Neotropical portion of what was then Gondwana. The radiation of modern genera of Columbiformes started in the Early Eocene to the Middle Miocene, as previously estimated for other avian groups such as ratites, tinamous, galliform birds, penguins, shorebirds, parrots, passerine birds, and toucans. Multiple dispersals of more derived Columbiformes between Australasian and Afro-Eurasian regions are required to explain current distributions.     

Evolutionary history of woodpeckers and allies (Aves: Picidae): placing key taxa on the phylogenetic tree

We analyzed 2995 base pairs of nucleotide sequence data (nuclear beta-fibrinogen intron 7 and mitochondrial cytochrome b and ND2 genes), using parsimony and model-based approaches to infer phylogenetic relationships of the woodpeckers and allies, yielding novel hypotheses for several critical gaps in the knowledge of picid phylogeny. We tested the monophyly of sub-families within the Picidae, and sampled from widely distributed and diverse genera (Celeus, Colaptes, Dryocopus, Melanerpes, Picoides, Picumnus, Sasia, Piculus, and Picus). Relationships of three poorly known Southeast Asian genera (Dinopium, Reinwardtipicus, and Blythipicus) were also examined, revealing unexpected sister relationships. All phylogenetic approaches recovered largely congruent topologies, supporting a monophyletic Picinae and paraphyletic Picumninae, with the monotypic piculet, Nesoctites micromegas, as sister to the Picinae. We report paraphyly for Celeus and Piculus, whereas the broadly distributed genera Picumnus and Dryocopus were supported as monophyletic. Our phylogenetic results indicate a complex geographic history for the Picidae, with multiple disjunct sister lineages distributed between the New World and Asia. The relationships and geographic distribution of basal picid lineages indicates an Old World origin of the Picidae; however, the geographic origin of the Picinae remains equivocal, as the sister relationship between the Caribbean N. micromegas and the true woodpeckers presents the possibility of a New World origin for the Picinae.     

Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.     

Molecular phylogenetics, vocalizations, and species limits in Celeus woodpeckers (Aves: Picidae)

Species limits and the evolutionary mechanisms that have shaped diversification of woodpeckers and allies (Picidae) remain obscure, as inter and intraspecific phylogenetic relationships have yet to be comprehensively resolved for most genera. Herein, we analyzed 5020 base pairs of nucleotide sequence data from the mitochondrial and nuclear genomes to reconstruct the evolutionary history of Celeus woodpeckers. Broad geographic sampling was employed to assess species limits in phenotypically variable lineages and provide a first look at the evolution of song and plumage traits in this poorly known Neotropical genus. Our results strongly support the monophyly of Celeus and reveal several novel relationships across a shallow phylogenetic topology. We confirm the close sister relationship between Celeus spectabilis and the enigmatic Celeus obrieni, both of which form a clade with Celeus flavus. The Mesoamerican Celeus castaneus was placed as sister to a Celeus undatus-grammicus lineage, with the species status of the latter drawn into question given the lack of substantial genetic, morphological, and vocal variation in these taxa. We recovered paraphyly in Celeus elegans; however, this result appears to be the consequence of mitochondrial introgression from Celeus lugubris considering the monophyly of elegans at the ?-FIBI7 locus. A second instance of paraphyly was observed in Celeus flavescens with deep genetic splits and substantial phenotypic variation indicating the presence of two distinct species in this broadly distributed lineage. As such, we advocate elevation of Celeus flavescens ochraceus to species status. Our analysis of Celeus vocalizations and plumage characters demonstrates a pattern of lability consistent with a relatively recent origin of the genus and potentially rapid speciation history.     

Polemoniaceae phylogeny and classification: implications of sequence data from the chloroplast gene ndhF

The chloroplast gene ndhF was used to study phylogenetic relationships of the Polemoniaceae at two levels: among members of the Ericales and among genera of the family. Sequence data for interfamilial analyses consisted of 2266 bp for 14 members of the Ericales, including four species of the Polemoniaceae, plus three outgroup taxa. The Polemoniaceae were found to be related to Diospyros, Fouquieria, the Primulales, Rhododendron, and Impatiens, but relationships among taxa were generally not well supported. The precise position of the Polemoniaceae within the Ericales remains obscure. Data for intrafamilial analyses consisted of 1031 bp for 27 species of the Polemoniaceae, including at least one species from most genera of the family, plus five outgroup taxa. A single most parsimonious tree was identified. The analyses suggested that subfamily Cobaeoideae, excluding Loeselia, is monophyletic and that Huthia is sister to Cantua. Acanthogilia was sister to the remainder of subfamily Cobaeoideae. Subfamily Polemonioideae plus Loeselia formed four subclades that were strongly supported as monophyletic and represent the major lineages of the subfamily.     

Phylogeny and co-speciation in feather mites of the subfamily Avenzoariinae (Analgoidea: Avenzoariidae)

A cladistic analysis of phylogenetic relationships is carried out for the feather mite subfamily Avenzoariinae. The analysis is made at two different taxonomic levels, for 19 genera of the all family Avenzoariidae and for taxa of species rank for the Avenzoaria and Bychovskiata generic groups. A subsequent comparative analysis of phylogenetic hypotheseis for the subfamily Avenzoariinae and recently accepted phylogenetic hypotheses of the shorebirds Charadriiformes indicates co-speciation of feather mites with their hosts. As a result of the comparative analysis it is suggested, that the subfamily Avenzoariinae originated from an ancestor of the order Charadriiformes and co-speciated with this host order. The expected pattern of parallel evolution is disturbed by different evolutionary events, such as host shifts, extinction of mites and differential evolutionary rates of mite lineages in different phyletic branches of feather parasites.     

Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes

Several different groups of birds have been proposed as being the oldest or earliest diverging extant lineage within the avian phylogenetic tree, particularly ratites (Struthioniformes), waterfowl (Anseriformes), and shorebirds (Charadriiformes). Difficulty in resolving this issue stems from several factors, including the relatively rapid radiation of primary (ordinal) bird lineages and the lack of characters from an extant outgroup for birds that is closely related to them by measure of time. To help resolve this question, we have sequenced entire mitochondrial genomes for five birds (a rhea, a duck, a falcon, and two perching birds), one crocodilian, and one turtle. Maximum parsimony and maximum likelihood analyses of these new sequences together with published sequences (18 taxa total) yield the same optimal tree topology, in which a perching bird (Passeriformes) is sister to all the other bird taxa. A basal position for waterfowl among the bird study taxa is rejected by maximum likelihood analyses. However, neither the conventional view, in which ratites (including rhea) are basal to other birds, nor tree topologies with falcon or chicken basal among birds could be rejected in the same manner. In likelihood analyses of a subset of seven birds, alligator, and turtle (9 taxa total), we find that increasing the number of parameters in the model shifts the optimal topology from one with a perching bird basal among birds to the conventional view with ratites diverging basally; moreover, likelihood scores for the two trees are not significantly different. Thus, although our largest set of taxa and characters supports a tree with perching birds diverging basally among birds, the position of this earliest divergence among birds appears unstable. Our analyses indicate a sister relationship between a waterfowl/chicken clade and ratites, relative to perching birds and falcon. We find support for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis (birds and mammals as sister taxa) and the placement of turtles as basal within the phylogenetic tree for amniote animals.     

Eight independent nuclear genes support monophyly of the plovers: The role of mutational variance in gene trees

Molecular phylogenies of Charadriiformes based on mtDNA genes and one to three nuclear loci do not support the traditional placement of Pluvialis in the plovers (Charadriidae), assigning it instead to oystercatchers, stilts, and avocets (Haematopodidae and Recurvirostridae). To investigate this hypothesis of plover paraphyly, the relationships among Pluvialis and closely related families were revisited by sequencing two individuals of all taxa except Peltohyas for eight independent single copy nuclear protein-coding loci selected for their informativeness at this phylogenetic depth. The species tree estimated jointly with the gene trees in the coalescent programme (*)BEAST strongly supported plover monophyly, as did Bayesian analysis of the concatenated matrix. The data sets that supported plover paraphyly in Baker et al. (2007) and Fain and Houde (2007) reflect two to four independent gene histories, and thus discordance with the plover monophyly species tree might have arisen by chance through stochastic mutational variance. For the plovers we conclude there is no conclusive evidence of coalescent variance from ancient incomplete lineage sorting across the interior branch leading to Pluvialis in the species tree. Rather, earlier studies seem have been misled by faster evolving mtDNA genes with high mutational variance, and a few nuclear genes that had low resolving power at the Pluvialis sister group level. These findings are of general relevance in avian phylogenetics, as they show that careful attention needs to be paid to the number and the phylogenetic informativeness of genes required to obtain accurate estimates of the species tree, especially where there is mutational heterogeneity in gene trees.     

Phylogeny of giant clams (Cardiidae: Tridacninae) based on partial mitochondrial 16S rDNA gene sequences.

We have performed the first DNA molecular phylogenetic analysis of giant clams. An approximately 462-nucleotide fragment of the mitochondrial large ribosomal subunit (16S) was sequenced for all eight species of giant clams and two species of an outgroup taxon, the edible cockle Cerastoderma. The data were analyzed using a maximum parsimony approach and a single most parsimonious tree was found. The resulting phylogenetic hypothesis indicates that the genera Hippopus and Tridacna are monophyletic sister taxa. Tridacna (Chametrachea) is the sister taxon to (T. tevoroa (T. derasa + T. gigas)), with these latter three taxa all being placed in a single subgenus, Tridacna (Tridacna). The number of recognized giant clam species has increased by one-third over the last two decades with the discovery of two rare new species having restricted geographic ranges: H. porcellanus (Palau and the Sulu Archipelago) and T. tevoroa (Tonga and Fiji). These two species lack a known fossil record but exhibit greater genetic distances from sister taxa than do extant giant clam species pairs which are recognizable in Neogene strata, e.g., T. gigas/T. derasa and T. maxima/T. squamosa. We propose that the two new species represent ancient relict lineages of Miocene origin.     

Rare and enigmatic genera (Dunnia, Schizocolea, Colletoecema), sisters to species-rich clades: phylogeny and aspects of conservation biology in the coffee family

Despite extensive efforts, parts of the phylogeny of the angiosperm family Rubiaceae has not been resolved and consequently, character evolution, ancestral areas and divergence times of major radiations are difficult to estimate. Here, phylogenetic analyses of 149 taxa and five plastid gene regions show that three enigmatic genera are sisters to considerably species rich clades. The rare and endangered species Dunnia, endemic to southern Guangdong, China, is sister to a large clade in the Spermacoceae alliance; the rarely collected Schizocolea from western tropical Africa is sister to the Psychotrieae alliance; and Colletoecema from central tropical Africa is sister to remaining Rubioideae. The morphology of these taxa has been considered "puzzling". In combination with further morphological studies, our results may help understanding the apparently confusing traits of these plants. Phylogenetic, morphological, and geographical isolation of Dunnia, Schizocolea and Colletocema may indicate high genetic diversity. They are lone representatives of unique lineages and if extinct, the loss would not only mean loss of genetic diversity of a single species but of an entire lineage.     

Phylogenetic relationships and historical biogeography of neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences

Previous hypotheses of phylogenetic relationships among Neotropical parrots were based on limited taxon sampling and lacked support for most internal nodes. In this study we increased the number of taxa (29 species belonging to 25 of the 30 genera) and gene sequences (6388 base pairs of RAG-1, cyt b, NADH2, ATPase 6, ATPase 8, COIII, 12S rDNA, and 16S rDNA) to obtain a stronger molecular phylogenetic hypothesis for this group of birds. Analyses of the combined gene sequences using maximum likelihood and Bayesian methods resulted in a well-supported phylogeny and indicated that amazons and allies are a sister clade to macaws, conures, and relatives, and these two clades are in turn a sister group to parrotlets. Key morphological and behavioral characters used in previous classifications were mapped on the molecular tree and were phylogenetically uninformative. We estimated divergence times of taxa using the molecular tree and Bayesian and penalized likelihood methods that allow for rate variation in DNA substitutions among sites and taxa. Our estimates suggest that the Neotropical parrots shared a common ancestor with Australian parrots 59 Mya (million of years ago; 95% credibility interval (CrI) 66, 51 Mya), well before Australia separated from Antarctica and South America, implying that ancestral parrots were widespread in Gondwanaland. Thus, the divergence of Australian and Neotropical parrots could be attributed to vicariance. The three major clades of Neotropical parrots originated about 50 Mya (95% CrI 57, 41 Mya), coinciding with periods of higher sea level when both Antarctica and South America were fragmented with transcontinental seaways, and likely isolated the ancestors of modern Neotropical parrots in different regions in these continents. The correspondence between major paleoenvironmental changes in South America and the diversification of genera in the clade of amazons and allies between 46 and 16 Mya suggests they diversified exclusively in South America. Conversely, ancestors of parrotlets and of macaws, conures, and allies may have been isolated in Antarctica and/or the southern cone of South America, and only dispersed out of these southern regions when climate cooled and Antarctica became ice-encrusted about 35 Mya. The subsequent radiation of macaws and their allies in South America beginning about 28 Mya (95% CrI 22, 35 Mya) coincides with the uplift of the Andes and the subsequent formation of dry, open grassland habitats that would have facilitated ecological speciation via niche expansion from forested habitats.     

Incomplete Lineage Sorting Is Common in Extant Gibbon Genera

We sequenced reduced representation libraries by means of Illumina technology to generate over 1.5 Mb of orthologous sequence from a representative of each of the four extant gibbon genera (Nomascus, Hylobates, Symphalangus, and Hoolock). We used these data to assess the evolutionary relationships between the genera by evaluating the likelihoods of all possible bifurcating trees involving the four taxa. Our analyses provide weak support for a tree with Nomascus and Hylobates as sister taxa and with Hoolock and Symphalangus as sister taxa, though bootstrap resampling suggests that other phylogenetic scenarios are also possible. This uncertainty is due to short internal branch lengths and extensive incomplete lineage sorting across taxa. The true phylogenetic relationships among gibbon genera will likely require a more extensive whole-genome sequence analysis.     

Evolutionary heritage shapes tree distributions along an Amazon‐to‐Andes elevation gradient

Understanding how evolutionary constraints shape the elevational distributions of tree lineages provides valuable insight into the future of tropical montane forests under global change. With narrow elevational ranges, high taxonomic turnover, frequent habitat specialization, and exceptional levels of endemism, tropical montane forests and trees are predicted to be highly sensitive to environmental change. Using plot census data from a gradient traversing > 3,000 m in elevation on the Amazonian flank of the Peruvian Andes, we employ phylogenetic approaches to assess the influence of evolutionary heritage on distribution trends of trees at the genus‐level. We find that closely related lineages tend to occur at similar mean elevations, with sister genera pairs occurring a mean 254 m in elevation closer to each other than the mean elevational difference between non‐sister genera pairs. We also demonstrate phylogenetic clustering both above and below 1,750 m a.s.l, corresponding roughly to the cloud‐base ecotone. Belying these general trends, some lineages occur across many different elevations. However, these highly plastic lineages are not phylogenetically clustered. Overall, our findings suggest that tropical montane forests are home to unique tree lineage diversity, constrained by their evolutionary heritage and vulnerable to substantial losses under environmental changes, such as rising temperatures or an upward shift of the cloud‐base.