Complete genome sequence of a subgenotype XXI.1.1 pigeon paramyxovirus type 1 virus (PPMV­1) isolated from Iran in 2018 and phylogenetic analysis of a possible novel, but unassigned, PPMV-1 group isolated in 2014.

Newcastle disease (ND) is one of the most serious infectious and contagious viral diseases in avian species. Recently, several ND outbreaks in pigeon caused by pigeon paramyxovirus serotype-1 (PPMV-1) have been reported from Iran, but unfortunately, phylogenetic studies have been mostly conducted on partial sequence of NDV fusion (F) gene. In addition, a complete genome data of Iranian PPMV-1 strains are not available. In the present study, a PPMV-1, named Avian avulavirus 1/pigeon/Iran/UT-EGV/2018, isolated from an infected pigeon, was subjected to whole-genome sequencing. The isolate showed an MDT of 74 h, thus categorizing it as mesogenic. The phylogenetic analysis based on the F gene sequence revealed the isolate belongs to XXI.1.1 subgenotype (min 0.9 % and max 3 %). To our knowledge, our study is the first study to publish the complete genome of a PPMV-1 from Iran. According to BLAST results, the whole genome of UT-EGV had high homology with some Russian, Egyptian and Ukrainian strains (the highest was 96.55 %). Additionally, we conducted a phylogenetic analysis on five PPMV-1 that we isolated in 2014 to find that they may belong to a completely unreported subgenotype (6 % distance when compared as a group). The information obtained from this study can be useful in preventive measures, including constructing an effective vaccine against PPMV-1 in Iran.

A Comprehensive Cytogenetic Analysis of Several Members of the Family Columbidae (Aves, Columbiformes).

The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68-86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) probes for chromosomes GGA11-28 for Columbina passerina, Columbina talpacoti, Patagioenas cayennensis, Geotrygon violacea and Geotrygon montana. Streptopelia decaocto was only investigated with paints because BACs for GGA10-28 had been previously analyzed. We also performed phylogenetic analyses in order to trace the evolutionary history of this family in light of chromosomal changes using our wcp data with chicken probes and from Zenaida auriculata, Columbina picui, Columba livia and Leptotila verreauxi, previously published. G-banding was performed on all these species. Comparative chromosome paint and G-banding results suggested that at least one interchromosomal and many intrachromosomal rearrangements had occurred in the diversification of Columbidae species. On the other hand, a high degree of conservation of microchromosome organization was observed in these species. Our cladistic analysis, considering all the chromosome rearrangements detected, provided strong support for L. verreauxi and P. cayennensis, G. montana and G. violacea, C. passerina and C. talpacoti having sister taxa relationships, as well as for all Columbidae species analyzed herein. Additionally, the chromosome characters were mapped in a consensus phylogenetic topology previously proposed, revealing a pericentric inversion in the chromosome homologous to GGA4 in a chromosomal signature unique to small New World ground doves.

Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds.

Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.

Identification and comparative profiling of gonadal microRNAs in the adult pigeon (Columba livia).

1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.

Detection of novel adenovirus in sick pigeons.

This study reports a novel adenovirus that was found circulating in pigeons in China. Nucleotide homology analysis of the hexon gene showed a nucleotide similarity of 79.0 and 70.9% with PiAd-2 variant A and PiAd-1, respectively. Phylogenetic analysis suggested that the identified virus, together with PiAd-2 variant, constitutes a monophyletic group (proposed as Pigeon Aviadenovirus B) in the genus Aviadenovirus. The present study contributes to the understanding of the epidemiology, ecology, and taxonomy of adenoviruses in pigeons.

Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds.

Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated the present-day distribution and diversity of Goura crowned pigeons (Columbidae), a group of large forest-dwelling pigeons comprising four recognized species that are all endemic to New Guinea. We used a comprehensive geographical and taxonomic sampling based mostly on historical museum samples, and shallow shotgun sequencing, to generate complete mitogenomes, nuclear ribosomal clusters and independent nuclear conserved DNA elements. We used these datasets independently to reconstruct molecular phylogenies. Divergence time estimates were obtained using mitochondrial data only. All analyses revealed similar genetic divisions within the genus Goura and recovered as monophyletic groups the four species currently recognized, providing support for recent taxonomic changes based on differences in plumage characters. These four species are grouped into two pairs of strongly supported sister species, which were previously not recognized as close relatives: Goura sclaterii with Goura cristata, and Goura victoria with Goura scheepmakeri. While the geographical origin of the Goura lineage remains elusive, the crown age of 5.73 Ma is consistent with present-day species diversity being the result of a recent diversification within New Guinea. Although the orogeny of New Guinea's central cordillera must have played a role in driving diversification in Goura, cross-barrier dispersal seems more likely than vicariance to explain the speciation events having led to the four current species. Our results also have important conservation implications. Future assessments of the conservation status of Goura species should consider threat levels following the taxonomic revision proposed by del Hoyo and Collar (HBW and BirdLife International illustrated checklist of the birds of the world 1: non-passerines, 2014), which we show to be fully supported by genomic data. In particular, distinguishing G. sclaterii from G. scheepmakeri seems to be particularly relevant.

Guia de manejo e controle de pombas-domésticas (columba livia) em áreas urbanas / Guide of management and control of pombas-domes (columba livia) in urban areas

Estudo das doenças transmitidas pelas pombas-domésticas (columba livia) em contato com a população humana.

Phylogeny and biogeography of the imperial pigeons (Aves: Columbidae) in the Pacific Ocean.

We reconstruct the phylogeny of imperial pigeons (genus Ducula) using mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. The divergence time analysis suggests that the basal divergences within Ducula occurred more recently than in the fruit doves (genus Ptilinopus), a group that is also well diversified in Oceania. The imperial pigeons colonized the Melanesian region several times independently, and the diversification within this region led to several species in sympatry, in particular in the Bismarck archipelago. Central Polynesia was also colonized several times, first by a lineage during the Miocene that led to the large D. latrans, sister to the New Caledonian endemic D. goliath, then more recently by the widespread D. pacifica, during the Pleistocene. The phylogenetic pattern obtained with the extant Ducula species showed that the Eastern Polynesian endemics do not form a monophyletic group, with the Pacific Imperial Pigeon D. pacifica sister species with good support to the Polynesian Imperial Pigeon D. aurorae. However, the impact of recent anthropic extinctions has been important for the imperial pigeons, more than for the smaller fruit doves, suggesting that several Ducula lineages might be missing today.

Comparative cophylogenetics of Australian phabine pigeons and doves (Aves: Columbidae) and their feather lice (Insecta: Phthiraptera).

Host-parasite coevolutionary histories can differ among multiple groups of parasites associated with the same group of hosts. For example, parasitic wing and body lice (Insecta: Phthiraptera) of New World pigeons and doves (Aves: Columbidae) differ in their cophylogenetic patterns, with body lice exhibiting higher phylogenetic congruence with their hosts than wing lice. In this study, we focus on the wing and body lice of Australian phabine pigeons and doves to determine whether the patterns in New World pigeons and doves are consistent with those of pigeons and doves from other regions. Using molecular sequence data for most phabine species and their lice, we estimated phylogenetic trees for all three groups (pigeons and doves, wing lice and body lice), and compared the phabine (host) tree with both parasite trees using multiple cophylogenetic methods. We found a pattern opposite to that found for New World pigeons and doves, with Australian wing lice showing congruence with their hosts, and body lice exhibiting a lack of congruence. There are no documented records of hippoboscid flies associated with Australian phabines, thus these lice may lack the opportunity to disperse among host species by attaching to hippoboscid flies (phoresis), which could explain these patterns. However, additional sampling for flies is needed to confirm this hypothesis. Large differences in body size among phabine pigeons and doves may also help to explain the congruence of the wing lice with their hosts. It may be more difficult for wing lice than body lice to switch among hosts that vary more dramatically in size. The results from this study highlight how host-parasite coevolutionary histories can vary by region, and how local factors can shape the relationship.

Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation.

BACKGROUND: Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context. RESULTS: We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves. CONCLUSIONS: Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.

Cophylogenetic analysis of New World ground-doves (Aves: Columbidae) and their parasitic wing lice (Insecta: Phthiraptera: Columbicola).

Hosts-parasite interactions are plentiful and diverse, and understanding the patterns of these interactions can provide great insight into the evolutionary history of the organisms involved. Estimating the phylogenetic relationships of a group of parasites and comparing them to that of their hosts can indicate how factors such as host or parasite life history, biogeography, or climate affect evolutionary patterns. In this study we compare the phylogeny generated for a clade of parasitic chewing lice (Insecta: Phthiraptera) within the genus Columbicola to that of their hosts, the small New World ground-doves (Aves: Columbidae). We sampled lice from the majority of host species, including samples from multiple geographic locations. From these samples we sequenced mitochondrial and nuclear loci for the lice, and used these data to estimate phylogenetic trees and population networks. After estimating the appropriate number of operational taxonomic units (OTUs) for the lice, we used cophylogenetic analyses to compare the louse phylogeny to an existing host phylogeny. Our phylogenetic analysis recovered significant structure within the louse clade, including evidence for potentially cryptic species. All cophylogenetic analyses indicated an overall congruence between the host and parasite trees. However, we only recovered a single cospeciation event. This finding suggests that certain branches in the trees are driving the signal of congruence. In particular, lice with the highest levels of congruence are associated with high Andean species of ground-doves that are well separated altitudinally from other related taxa. Other host-parasite associations are not as congruent, and these often involved widespread louse taxa. These widespread lice did, however, have significant phylogeographic structure, and their phylogenetic relationships are perhaps best explained by biogeographic patterns. Overall these results indicate that both host phylogeny and biogeography can be simultaneously important in influencing the patterns of diversification of parasites.

The type species of the genus Geotrygon Gosse, 1847 (Aves: Columbidae).

The generic name Geotrygon was introduced by Gosse (1847: 316) for some doves from the island of Jamaica and has been subsequently used for the so-called quail-doves of Middle and South America (Baptista et al. 1997; Gibbs et al. 2001; Dickinson 2003; Dickinson & Remsen 2013). Johnson & Weckstein (2011) and Banks et al. (2013) indicated that this genus is polyphyletic. The application of a generic name is determined by its type species (Art. 42.3 of the International Code of Zoological Nomenclature; ICZN 1999; hereafter the Code). A literature search showed that different nominal species have been proposed as the type species of Geotrygon, and the situation thus requires clarification.

Complete mitochondrial genome of the Spotted dove (Streptopelia chinensis).

The Spotted dove (Streptopelia chinensis) is a member of the bird family Columbidae. In this study, we report the complete mitochondrial genome of this species. The mitochondrial genome of Spotted dove is a circular molecule of 16,966 bp in size and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition is 30.1% for A, 32.1% for C, 13.9% for G, and 23.9% for T. These data will be useful for the phylogenetic and population diversity analyses of birds, especially Columbidae species.

Determination of the complete mitogenome of Spotted Dove, Spilopelia chinensis (Columbiformes: Columbidae).

The Spotted Dove Spilopelia chinensis (Columbiformes: Columbidae) is widely distributed in Southeast Asia. In the present study, we investigated the complete mitochondrial genome of S. chinensis and the mitogenome is 16,964 bp in length, consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region, with the base composition of A 31.1%, G 13.9%, T 23.9%, and C 32.1%. A single extra base "C" at position 174 is inserted in gene Nd3, similar to some other birds and turtles. The phylogenetic relationships using partitioned Bayesian inference based on the 12 concatenated PCGs indicated that ((((Spilopelia, Columba) Ectopistes) (Geotrygon (Leptotila, Zenaida))) Hemiphaga). While, more complete mitogenome sequences should be determined to confirm the phylogenetic status of Spilopelia within family Columbidae.

Analysis of Pigeon (Columba) Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp) were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred.

BACKGROUND: The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors' remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some similarities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. Today only one of the original two specimens survives and nothing is known about the origin of the taxon. Due to its potential close relationship, the Spotted Green Pigeon may hold clues to the historical migration, isolation and morphological evolution of the Dodo and its kindred. RESULTS: We use ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. A novel extraction method with the ability to retain and purify heavily fragmented DNA is used to investigate two feathers from the sole surviving specimen. Maximum Likelihood phylogenetic analyses reveal that the Spotted Green Pigeon is a unique lineage and together with the Nicobar Pigeon, is basal to the Dodo and Rodrigues Solitaire. CONCLUSIONS: The distance observed for the Spotted Green Pigeon and Nicobar Pigeon is larger than that observed within other Pigeon species, indicating that the Spotted Green pigeon is a unique taxon, thereby also indicating it is a genuine addition to the list of extinct species. The phylogenetic placement of the Spotted Green Pigeon indicates that the ancestors of both Caloenas and therefore Raphinae displayed and shared the following traits: ability of flight, semi-terrestrial habits and an affinity towards islands. This set of traits supports the stepping stone hypothesis, which states that the Raphinae got to their respective localities by island hopping from India or Southeast Asia.

The complete mitochondrial genome of the Feral Rock Pigeon (Columba livia breed feral).

Abstract In the present work, we report the complete mitochondrial genome sequence of feral rock pigeon for the first time. The total length of the mitogenome was 17,239 bp with the base composition of 30.3% for A, 24.0% for T, 31.9% for C, and 13.8% for G and an A-T (54.3 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of feral rock pigeon would serve as an important data set of the germplasm resources for further study.

Molecular classification of Pakistani collared dove through DNA barcoding.

Pakistan is bestowed by a diversified array of wild bird species including collared doves of which the taxonomy has been least studied and reported. DNA barcoding is a geno-taxonomic tool that has been used for characterization of bird species using mitochondrial cytochrome c oxidase I gene (COI). This study aimed to identify taxonomic order of Pakistani collared dove using DNA barcoding. Purposely herein, we present a phylogenetic analysis of Pakistani collared dove based on 650 base pairs of COI gene sequences. Analysis of phylogenetic tree revealed that Pakistani collared dove shared a common clade with Eurasian collared dove (Streptopelia decaocto) and African collared dove (Streptopelia roseogrisea) which indicated a super-species group in Streptopelia genus. This is the first report of molecular classification of Pakistani collared dove using DNA barcoding.

COI barcodes and phylogeny of doves (Columbidae family).

Cytochrome oxidase subunit I (COI) gene has been recognized as an authentic tool for species identification. Besides its potential barcoding capacity, COI sequences have also been used for inferring the phylogeny. Phylogenetic relationships among genera of Columbidae (pigeons and doves family) have not been fully resolved because of scarce sampling of taxa and limited availability of sequence data. In this study, we have evaluated the efficiency of COI barcodes for species identification and phylogenetic analysis of various doves. We sequenced the 693 bp region of COI gene of three species of doves including Oena capensis, Streptopelia decaocto, and Streptopelia senegalensis. After retrieving the relevant sequences from the GenBank, the entire data-set of 85 sequences represented 25 dove species from 11 different genera of the family Columbidae. The COI sequences of four species including Chalcophaps indica (two specimens), Columbina inca (five specimens), Geopelia striata (three specimens), and Macropygia phasianella (three specimens) were identical. The mean intraspecific base differences ranged from 0 to 37 while the P-distances ranged between 0 and 0.058. For most of the species, the P-distances were ≤ 0.008. Phylogenetic analysis differentiated the taxa into three major clusters. One of the clusters grouped five genera including Claravis, Columbina, Gallicolumba, Geopelia, and Geotrygon. The remaining two clusters grouped three genera each including Chalcophaps, Oena, and Turtur in one cluster and Macropygia, Streptopelia, and Zenaida in another cluster. Further sub-clustering clearly separated all the genera into individual clusters except two discrepancies for the genera Streptopelia and Turtur. Species-level cladistics clearly separated all the species into distinctive clades. In conclusion, COI barcoding is a powerful tool for species identification with added information on phylogenetic inference. The finding of this study will help to understand the complex phylogeny of the family Columbidae.

Genomic diversity and evolution of the head crest in the rock pigeon.

The geographic origins of breeds and the genetic basis of variation within the widely distributed and phenotypically diverse domestic rock pigeon (Columba livia) remain largely unknown. We generated a rock pigeon reference genome and additional genome sequences representing domestic and feral populations. We found evidence for the origins of major breed groups in the Middle East and contributions from a racing breed to North American feral populations. We identified the gene EphB2 as a strong candidate for the derived head crest phenotype shared by numerous breeds, an important trait in mate selection in many avian species. We also found evidence that this trait evolved just once and spread throughout the species, and that the crest originates early in development by the localized molecular reversal of feather bud polarity.