Search Results (14)

Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data. Phylogenomic studies of Neoaves, a large clade of birds (>9000 species) that first diversified near the Cretaceous–Paleogene boundary, have yielded an array of robustly supported, contradictory relationships among deep lineages. Here, we reanalyzed a large RI matrix for birds using recently proposed quartet-based coalescent methods that enable inference of large species trees including branch lengths in coalescent units, clade-support, statistical tests for gene flow, and combined analysis with DNA-sequence-based gene trees. Genome-scale coalescent analyses revealed extremely short branches at the base of Neoaves, meager branch support, and limited congruence with previous work at the most challenging nodes. Despite widespread topological conflicts with DNA-sequence-based trees, combined analyses of RIs with thousands of gene trees show emergent support for multiple higher-level clades (Columbea, Passerea, Columbimorphae, Otidimorphae, Phaethoquornithes). RIs express asymmetrical support for deep relationships within the subclade Afroaves that hints at ancient gene flow involving the owl lineage (Strigiformes). Because DNA-sequence data are challenged by gene tree-reconstruction error, analysis of RIs represents one approach for improving gene tree-based methods when divergences are deep, internodes are short, terminal branches are long, and introgressive hybridization further confounds species–tree inference. Full article

Avian sex chromosomes evolved after the divergence of birds and crocodilians from their common ancestor, so they are younger than the better-studied chromosomes of mammals. It has long been recognized that there may have been several stages to the evolution of avian sex chromosomes. For example, the CHD1 undergoes recombination in paleognaths but not neognaths. Genome assemblies have suggested that there may be variation in the timing of barriers to recombination among Neognathae, but there remains little understanding of the extent of this variability. Here, we look at partial sequences of ATP5F1A, which is on the avian Z and W chromosomes. It is known that recombination of this gene has independently ceased in Galliformes, Anseriformes, and at least five neoavian orders, but whether there are other independent cessations of recombination among Neoaves is not understood. We analyzed a combination of data extracted from published chromosomal-level genomes with data collected using PCR and cloning to identify Z and W copies in 22 orders. Our results suggest that there may be at least 19 independent cessations of recombination within Neognathae, and 3 clades that may still be undergoing recombination (or have only recently ceased recombination). Analyses of ATP5F1A protein sequences revealed an increased amino acid substitution rate for W chromosome gametologs, suggesting relaxed purifying selection on the W chromosome. Supporting this hypothesis, we found that the increased substitution rate was particularly pronounced for buried residues, which are expected to be more strongly constrained by purifying selection. This highlights the dynamic nature of avian sex chromosomes, and that this level of variation among clades means they should be a good system to understand sex chromosome evolution. Full article

Despite many decades of studies, our knowledge of skeletal development in birds is limited in many aspects. One of them is the development of the vertebral column. For many years it was widely believed that the column ossifies anteroposteriorly. However, later studies indicated that such a pattern is not universal in birds and in many groups the ossification starts in the thoracic rather than cervical region. Recent analyses suggest that two loci, located in the cervical and thoracic vertebrae, were ancestrally present in birds. However, the data on skeletal development are very scarce in the Neoaves, a clade that includes approximately 95% of extant species. We review the available information about the vertebral column development in birds and describe the ossification pattern in three neoavians, the domestic pigeon (Columba livia domestica), the great crested grebe (Podiceps cristatus) and the red-necked grebe (Podiceps grisegena). In P. cristatus, the vertebral column starts ossifying in the thoracic region. The second locus is present in the cervical vertebrae. In the pigeon, the cervical vertebrae ossify before the thoracics, but both the thoracic and cervical loci are present. Our ancestral state reconstructions confirm that both these loci were ancestrally present in birds, but the thoracic locus was later lost in psittacopasserans and at least some galloanserans. Full article

Although an increasing number of studies are combining skeletal and neural morphology data in a phylogenetic context, most studies do not include extinct taxa due to the rarity of preserved endocasts. The early Eocene avifauna of the Fur Formation of Denmark presents an excellent opportunity for further study of extinct osteological and endocranial morphology as fossils are often exceptionally preserved in three dimensions. Here, we use X-ray computed tomography to present additional material of the previously described taxon Scandiavis mikkelseni and reassess its phylogenetic placement using a previously published dataset. The new specimen provides novel insights into the osteological morphology and brain anatomy of Scandiavis. The virtual endocast exhibits a morphology comparable to that of modern avian species. Endocranial evaluation shows that it was remarkably similar to that of certain extant Charadriiformes, yet also possessed a novel combination of traits. This may mean that traits previously proposed to be the result of shifts in ecology later in the evolutionary history of Charadriiformes may instead show a more complex distribution in stem Charadriiformes and/or Gruiformes depending on the interrelationships of these important clades. Evaluation of skeletal and endocranial character state changes within a previously published phylogeny confirms both S. mikkelseni and a putative extinct charadriiform, Nahmavis grandei, as charadriiform. Results bolster the likelihood that both taxa are critical fossils for divergence dating and highlight a biogeographic pattern similar to that of Gruiformes. Full article

Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred. Full article

The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge—data type effects—that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus. Full article

Sex chromosomes are unique genomic regions with sex-specific or sex-biased inherent patterns and are expected to be more frequently subject to sex-specific selection. Substantial knowledge on the evolutionary patterns of sex-linked genes have been gained from the studies on the male heterogametic systems (XY male, XX female), but the understanding of the role of sex-specific selection in the evolution of female-heterogametic sex chromosomes (ZW female, ZZ male) is limited. Here we collect the W-linked genes of 27 birds, covering the three major avian clades: Neoaves (songbirds), Galloanserae (chicken), and Palaeognathae (ratites and tinamous). We find that the avian W chromosomes exhibit very conserved gene content despite their independent evolution of recombination suppression. The retained W-linked genes have higher dosage-sensitive and higher expression level than the lost genes, suggesting the role of purifying selection in their retention. Moreover, they are not enriched in ancestrally female-biased genes, and have not acquired new ovary-biased expression patterns after becoming W-linked. They are broadly expressed across female tissues, and the expression profile of the W-linked genes in females is not deviated from that of the homologous Z-linked genes. Together, our new analyses suggest that female-specific positive selection on the avian W chromosomes is limited, and the gene content of the W chromosomes is mainly shaped by purifying selection. Full article

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction. Full article

Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up. Full article

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well. Full article

The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves. Full article

Pellornis mikkelseni is an early gruiform from the latest Paleocene-earliest Eocene Fur Formation of Denmark. At approximately 54 million years old, it is among the earliest clear records of the Gruiformes. The holotype specimen, and only material thus far recognised, was originally considered to comprise a partial postcranial skeleton. However, additional mechanical preparation of the nodule containing the holotype revealed that the skeleton is nearly complete and includes a well-preserved skull. In addition to extracting new information from the holotype, we identify and describe two additional specimens of P. mikkelseni which reveal further morphological details of the skeleton. Together, these specimens show that P. mikkelseni possessed a schizorhinal skull and shared many features with the well-known Paleogene Messelornithidae (“Messel rails”). To reassess the phylogenetic position of P. mikkelseni, we modified an existing morphological dataset by adding 20 characters, four extant gruiform taxa, six extinct gruiform taxa, and novel scorings based on the holotype and referred specimens. Phylogenetic analyses recover a clade containing P. mikkelseni, Messelornis, Songzia and crown Ralloidea, supporting P. mikkelseni as a crown gruiform. The phylogenetic position of P. mikkelseni illustrates that some recent divergence time analyses have underestimated the age of crown Gruiformes. Our results suggest a Paleocene origin for this important clade, bolstering evidence for a rapid early radiation of Neoaves following the end-Cretaceous mass extinction. Full article

Vav proteins play roles as guanosine nucleotide exchange factors for Rho GTPases and signaling adaptors downstream of protein tyrosine kinases. The recent sequencing of the genomes of many species has revealed that this protein family originated in choanozoans, a group of unicellular organisms from which animal metazoans are believed to have originated from. Since then, the Vav family underwent expansions and reductions in its members during the evolutionary transitions that originated the agnates, chondrichthyes, some teleost fish, and some neoaves. Exotic members of the family harboring atypical structural domains can be also found in some invertebrate species. In this review, we will provide a phylogenetic perspective of the evolution of the Vav family. We will also pay attention to the structure, signaling properties, regulatory layers, and functions of Vav proteins in both invertebrate and vertebrate species. Full article

In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus, which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds. Full article