A recent chicken repeat 1 retrotransposition confirms the Coscoroba-Cape Barren goose clade

Characterization of the Complete Mitogenome of the Ring-Necked Pheasant Phasianus colchicus (Galliformes: Phasianidae) and Systematic Implications for Phasianinae Phylogenetics

BACKGROUND

Phasianidae mitogenomes exhibit significant structural variations critical for understanding evolution and subspecies divergence. However, annotations of these features in some pheasant species remain limited. This study aimed to enhance understanding of Phasianidae mitogenomes and their evolutionary patterns.

METHODS

A comparative analysis of complete mitogenomes from Phasianus colchicus, Phasianus versicolor, and 22 other accipitrids was conducted, examining codon usage, rRNA structures, selective pressures, phylogenetics, and structural variations.

RESULTS

The mitogenome of P. colchicus is 16,696 bp, comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, with a base composition of A: 30.61%, T: 25.26%, C: 30.85%, and G: 13.28%. Phylogenetic analysis revealed P. colchicus and P. versicolor are closely related, with the following relationship: ((Phasianus + Chrysolophus) + (Crossoptilon + Lophura)). Divergence timing aligns with the Tibetan Plateau uplift during the Tertiary Pliocene. Ka/Ks analysis suggests the CO I, CO II, CO III, ND1, ND4L, and ND6 genes in Phasianus underwent strong selective pressure for plateau adaptation.

CONCLUSIONS

The study confirms Phasianus monophyly and its close relationship with Chrysolophus. Adaptation-related selective pressures on the CO I, CO II, CO III, ND1, ND4L, and ND6 genes highlight its role in plateau environments, offering valuable insights into pheasant phylogeny.

Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity

Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.

De-novo emergence of SINE retroposons during the early evolution of passerine birds

BACKGROUND

Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes.

RESULTS

Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching.

CONCLUSIONS

We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

Low diversity, activity, and density of transposable elements in five avian genomes

In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.

Tandem duplications in the C-terminal domain of the mesotocin receptor exclusively identified among East Eurasian thrushes

Mesotocin is a neurohypophyseal hormone found in some non-mammalian vertebrates, including birds, reptiles, and amphibians. In this study, we identified and characterized 18-amino acid duplications in the C-terminal domain of the mesotocin receptor (MTR), specifically found in Turdus thrushes (Aves: Passeriforms: Turdidae). These duplicated elements are located in the distal part of the C-terminal tails of MTR and consist of amino acids that are highly conserved among major vertebrates. Intraspecific polymorphisms in a variable number of tandem duplications are commonly found in East Eurasian Turdus, but not in any other genus of Turdidae. Moreover, the genus Turdus can be further classified into 2 groups according to the presence or absence of a 3-amino acid deletion just adjacent to the putative palmitoylation site in the cytoplasmic C-terminal tail. The phylogeny presented here strongly supports the conspecific group of 4 East Eurasian thrushes (Turdus pallidus, T. chrysolaus, T. obscurus, and T. celaenops). Our findings, therefore, provide a new synapomorphy that can be used for phylogenetic assumptions and shed a light on the history of diversification within Eurasian Turdus clades.

CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes)

Chicken repeat 1 (CR1) elements, a class of retroposons belonging to non-long-terminal repeats, have been recognized as powerful tools for phylogenetic studies. Here we examine the phylogenetic relationships of 11 Phasianidae species based on CR1 retroposons. Together with 19 loci reported previously, a total of 99 CR1 loci were identified from chicken genome and turkey BAC clone sequences. 75 insertion events were used to address the branching order of 11 species in Phasianidae. The topology of our tree suggests that: 1) Gallus gallus possessed a basal phylogenetic position within Phasianidae and was related to Bambusicola thoracica (BSP=100%); 2) After the split of G. gallus and B. thoracica, Arborophila rufipectus diverged from Phasianidae (BSP=100%). Nine unambiguous insertion events supported a phylogenetic position of A. rufipectus different to previous mitochondrial data suggesting a hybrid origin or an ancient introgression of A. rufipectus; and 3) 22 CR1 insertion events strongly supported the eight phasianids under investigation sharing a common ancestor. Our study has revisited the phylogenetic position of G. gallus and A. rufipectus and provided a new insight into the phylogeny of Phasianidae birds. It showed that a CR1-based methodology has a great potential to be informative within Phasianidae in resolving relationships of closely related species whose radiation and speciation have occurred very recently.

Evolution of serum albumin intron-1 is shaped by a 5' truncated non-long terminal repeat retrotransposon in western Palearctic water frogs (Neobatrachia)

A 5' truncated non-LTR CR1-like retrotransposon, named RanaCR1, was identified in the serum albumin intron-1 (SAI-1) of at least seven species of western Palearctic water frogs (WPWF). Based on sequence similarity of the carboxy-terminal region (CTR) of ORF2 and/or the highly conserved 3' untranslated region (3' UTR), RanaCR1-like elements occur also in the genome of Xenopus tropicalis and Rana temporaria. Unlike other CR1 elements, RanaCR1 contains a CA microsatellite in its 3' UTR. The low nucleotide diversity of the 3' UTR compared to the CTR and to SAI-1 suggests that this region still plays a role in WPWF, either as a structure-stabilizing element, or within a species-specific transcriptional network. Length variation of water frog SAI-1 sequences is caused by deletions that extend in some cases beyond the 5' or 3' ends of RanaCR1, probably a result of selection for structural and functional stability of the primary transcript. The impact of RanaCR1 on SAI-1 evolution is also indicated by the significant negative correlation between the length of both SAI-1 and RanaCR1 and the percentage GC content of RanaCR1. Both SAI-1 and RanaCR1 sequences support the sister group relationship of R. perezi and R. saharica, which are placed in the phylogenetic tree at a basal position, the sister clade to other water frog taxa. It also supports the monophyly of the R. lessonae group; of Anatolian water frogs (R. cf. bedriagae), which are not conspecific with R. bedriagae, and of the European ridibunda group. Within the ridibunda clade, Greek frogs are clearly separated, supporting the hypothesis that Balkan water frogs represent a distinct species. Frogs from Atyrau (Kazakhstan), the type locality of R. ridibunda, were heterozygous for a ridibunda and a cf. bedriagae specific allele.

Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats

Chicken Repeat 1 (CR1) repeats are the most abundant family of repeats in the chicken genome, with more than 200,000 copies accounting for approximately 80% of the chicken interspersed repeats. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to the 22 CR1 subfamilies as previously reported in Repbase. We performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the chicken genome. We identified and validated 57 chicken CR1 subfamilies and further analyzed the correlation between these subfamilies and their regional GC contents. We also discovered one novel lineage-specific CR1 subfamilies in turkeys when compared with chickens. We built an evolutionary tree of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

Recent CR1 non-LTR retrotransposon activity in coscoroba reveals an insertion site preference

Background

Chicken repeat 1 (CR1) is a taxonomically widespread non-LTR retrotransposon. Insertion site bias, or lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site.

Results

Elucidation of the exact octomer repeat sequence (TTCTGTGA) allowed for the identification of younger insertion events. The number of octomer repeats associated with a CR1 element increases after insertion with CR1s having one octomer being youngest. These young CR1s are flanked by regions of low GC content (38%). Furthermore, a bias for specific bases within the first four positions at the site of insertion was revealed.

Conclusion

This study focused on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events. Our data suggest that CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, preferentially inserting into regions of lower GC content. Furthermore, there appears to be a base preference (TTCT) for the insertion site. The results of this study increase the current level of understanding regarding the elusive CR1 non-LTR retrotransposon.

Testing whether macroevolution follows microevolution: are colour differences among swans (Cygnus) attributable to variation at the MCIR locus?

Background

The MC1R (melanocortin-1 receptor) locus underlies intraspecific variation in melanin-based dark plumage coloration in several unrelated birds with plumage polymorphisms. There is far less evidence for functional variants of MC1R being involved in interspecific variation, in which spurious genotype-phenotype associations arising through population history are a far greater problem than in intraspecific studies. We investigated the relationship between MC1R variation and plumage coloration in swans (Cygnus), which show extreme variation in melanic plumage phenotypes among species (white to black).

Results

The two species with melanic plumage, C. atratus and C. melanocoryphus (black and black-necked swans respectively), both have amino acid changes at important functional sites in MC1R that are consistent with increased MC1R activity and melanism. Reconstruction of MC1R evolution over a newly generated independent molecular phylogeny of Cygnus and related genera shows that these putative melanizing mutations were independently derived in the two melanic lineages. However, interpretation is complicated by the fact that one of the outgroup genera, Coscoroba, also has a putative melanizing mutation at MC1R that has arisen independently but has nearly pure white plumage. Epistasis at other loci seems the most likely explanation for this discrepancy. Unexpectedly, the phylogeny shows that the genus Cygnus may not be monophyletic, with C. melanocoryphus placed as a sister group to true geese (Anser), but further data will be needed to confirm this.

Conclusion

Our study highlights the difficulty of extrapolating from intraspecific studies to understand the genetic basis of interspecific adaptive phenotypic evolution, even with a gene whose structure-function relationships are as well understood as MC1R as confounding variation make clear genotype/phenotype associations difficult at the macroevolutionary scale. However, the identification of substitutions in the black and black-necked swan that are known to be associated with melanic phenotypes, suggests Cygnus may be another example where there appears to be convergent evolution at MC1R. This study therefore provides a novel example where previously described intraspecific genotype/phenotype associations occur at the macroevolutionary level.

NUCLEAR LOCI AND COALESCENT METHODS SUPPORT ANCIENT HYBRIDIZATION AS CAUSE OF MITOCHONDRIAL PARAPHYLY BETWEEN GADWALL AND FALCATED DUCK (ANASSPP.)

Many species have mitochondrial DNA lineages that are phylogenetically intermixed with other species, but studies have rarely tested the cause of such paraphyly. In this study, we tested two hypotheses that could explain mitochondrial paraphyly of Holarctic gadwalls (Anas strepera) with respect to Asian falcated ducks (A. falcata). First, hybridization could have resulted in falcated duck mitochondrial DNA (mtDNA) introgressing into the gadwall gene pool. Second, gadwalls and falcated ducks could have diverged so recently that mtDNA lineages have not sorted to reciprocal monophyly. We used coalescent analyses of three independent loci to distinguish between these two hypotheses. Two lines of evidence support introgression. First, analyses of the three loci combined show that some introgression is necessary to explain current genetic diversity in gadwalls. Second, we generated alternative predictions regarding time since divergence estimated from mtDNA: falcated ducks and gadwalls would have diverged between 65,000 and 700,000 years before present (ybp) under the introgression hypothesis and between 11,000 and 76,000 ybp under the incomplete lineage sorting hypothesis. The two independent nuclear introns indicated that these species diverged between 210,000 and 5,200,000 ybp, which did not overlap the predicted time for incomplete lineage sorting. These analyses also suggested that ancient introgression ( approximately 14,000 ybp) has resulted in the widespread distribution and high frequency of falcated-like mtDNA (5.5% of haplotypes) in North America. This is the first study to use a rigorous quantitative framework to reject incomplete lineage sorting as the cause of mitochondrial paraphyly.

Specific chicken repeat 1 (CR1) retrotransposon insertion suggests phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae)

While the monophyly of the order Passeriformes as well as its suborders suboscines (Tyranni) and oscines (Passeri) is well established, both on morphological and molecular grounds, lower phylogenetic relationships have been a continuous matter of debate, especially within oscines. This is particularly true for the rockfowls (genus Picathartes), which phylogenetic classification has been an ongoing puzzle. Sequence-based molecular studies failed in deriving unambiguously resolved and supported hypotheses. We present here a novel approach: use of retrotransposon insertions as phylogenetic markers in passerine birds. Chicken repeat 1 (CR1) is the most important non-LTR retrotransposon in birds. We present two truncated CR1 loci in passerine birds, not only found in representatives of Corvinae (jays, crows and allies), but also in the West-African Picathartes species which provide new evidence for a closer relationship of these species to Corvidae than has previously been thought. Additionally, we show that not only the absence/presence pattern of a CR1 insertion, but also the CR1 sequences themselves contain phylogenetic information.