| 1. |
- Alström, Per, et al.
(författare)
-
Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae.
- 2011
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 58:3, s. 513-26
-
Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of most of the species in the avian passerine family Locustellidae is inferred using a Bayesian species tree approach (Bayesian Estimation of Species Trees, BEST), as well as a traditional Bayesian gene tree method (MrBayes), based on a dataset comprising one mitochondrial and four nuclear loci. The trees inferred by the different methods agree fairly well in topology, although in a few cases there are marked differences. Some of these discrepancies might be due to convergence problems for BEST (despite up to 1×10(9) iterations). The phylogeny strongly disagrees with the current taxonomy at the generic level, and we propose a revised classification that recognizes four instead of seven genera. These results emphasize the well known but still often neglected problem of basing classifications on non-cladistic evaluations of morphological characters. An analysis of an extended mitochondrial dataset with multiple individuals from most species, including many subspecies, suggest that several taxa presently treated as subspecies or as monotypic species as well as a few taxa recognized as separate species are in need of further taxonomic work.
|
|
| 2. |
- Christidis, Les, et al.
(författare)
-
The suboscine passerines
- 2020
-
Ingår i: <em>The Largest Avian Radiation</em>. - Barcelona : Lynx Edicions. - 9788416728336 ; , s. 65-65
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
| 3. |
- Ericson, Per G P, 1956-, et al.
(författare)
-
A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens.
- 2002
-
Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 269:1488, s. 235-41
-
Tidskriftsartikel (refereegranskat)abstract
- Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for passerine birds, while accumulating molecular data suggest that most extant avian orders originated in the mid-Late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and here we demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We propose that (i) the acanthisittids were isolated when New Zealand separated from Gondwana (ca. 82-85 Myr ago), (ii) suboscines, in turn, were derived from an ancestral lineage that inhabited western Gondwana, and (iii) the ancestors of the oscines (songbirds) were subsequently isolated by the separation of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.
|
|
| 4. |
- Ericson, Per G P, et al.
(författare)
-
Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics
- 2020
-
Ingår i: Systematic Biology. - 1063-5157 .- 1076-836X. ; 69:5, s. 820-829
-
Tidskriftsartikel (refereegranskat)abstract
- The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits.
|
|
| 5. |
- Ericson, Per G P, 1956-, et al.
(författare)
-
Systematic affinities of the lyrebirds (Passeriformes : Menura), with a novel classification of the major groups of passerine birds.
- 2002
-
Ingår i: Molecular Phylogenetics and Evolution. - 1055-7903 .- 1095-9513. ; 25:1, s. 53-62
-
Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyrebirds unambiguously belong to the oscine radiation, and that they are the sister taxon to all other oscines. The results do not support the suggestion based on DNA-DNA hybridization data (Sibley and Ahlquist, 1990) that the treecreepers and bowerbirds are part of the lyrebird clade. Nevertheless, treecreepers and bowerbirds are sister taxa to all other oscines (except the lyrebirds) and may constitute a monophyletic group, although bootstrap support values for this clade are low. A major disagreement between the present analysis and that based on DNA-DNA hybridization data is that the Corvida (sensu Sibley and Ahlquist, 1990) and Passerida are not reciprocally monophyletic, as we find the latter group be nested within the Corvida. Also, the superfamilies Meliphagoidea and Corvoidea sensu, are not recovered as monophyletic in the present study. Within the oscine radiation, all taxa belonging to the earliest splits are confined to the Australo-Papuan region. This suggests strongly that the origins and early radiation of the oscines occurred in the southern supercontinent Gondwana. A new classification of the major groups of passerines is presented following from the results presented in the present study, as well as those published recently on analyses of sequence data from the nuclear c-myc and RAG-1 genes (Ericson et al., 2002; Irestedt et al., 2001).
|
|
| 6. |
- Feng, Shaohong, et al.
(författare)
-
Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
|
|
| 7. |
- Fjeldså, Jon, et al.
(författare)
-
An updated classification of passerine birds
- 2020
-
Ingår i: <em>The Largest Avian Radiation</em>. - Barcelona : Lynx Edicions. - 9788416728336 ; , s. 45-63
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
| 8. |
- Fjeldså, Jon, et al.
(författare)
-
Introduction
- 2020
-
Ingår i: <em>The Largest Avian Radiation</em>. - Barcelona : Lynx Edicions. - 9788416728336 ; , s. 11-13
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
| 9. |
- Fjeldså, Jon, et al.
(författare)
-
The Largest Avian Radiation: The Evolution of Perching Birds, or the Order of Passeriformes
- 2020
-
Bok (övrigt vetenskapligt/konstnärligt)abstract
- This book reveals the remarkable new history of how passerines diversified and dispersed across the entire world. It also presents and explains the new classification, which reflects the phylogenetic history. The new insights reveal that many of the old evolutionary lineages comprise only a few species that remained in their area of origin or underwent limited dispersal. Only a small number of groups underwent significant proliferation of new species and just five (of 145) passerine families are represented on all continents but Antarctica. Even so, the global variation in species richness generally correlates well with the variation in productivity across different environments. We see how a seemingly constant overall rate of evolution of new species is possible because of rapid proliferation in new ecological niches, including archipelagos, and an extraordinary accumulation of endemic species in certain tropical mountain ranges. In addition to describing the revised evolutionary history of passerine birds, the authors try to identify adaptational changes, including shifts in life history strategies, that underlie major evolutionary expansions.
|
|
| 10. |
- Irestedt, Martin, et al.
(författare)
-
An unexpectedly long history of sexual selection in birds-of-paradise.
- 2009
-
Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9, s. 235-
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The birds-of-paradise (Paradisaeidae) form one of the most prominent avian examples of sexual selection and show a complex biogeographical distribution. The family has accordingly been used as a case-study in several significant evolutionary and biogeographical syntheses. As a robust phylogeny of the birds-of-paradise has been lacking, these hypotheses have been tentative and difficult to assess. Here we present a well supported species phylogeny with divergence time estimates of the birds-of-paradise. We use this to assess if the rates of the evolution of sexually selected traits and speciation have been excessively high within the birds-of-paradise, as well as to re-interpret biogeographical patterns in the group.RESULTS: The phylogenetic results confirm some traditionally recognized relationships but also suggest novel ones. Furthermore, we find that species pairs are geographically more closely linked than previously assumed. The divergence time estimates suggest that speciation within the birds-of-paradise mainly took place during the Miocene and the Pliocene, and that several polygynous and morphologically homogeneous genera are several million years old. Diversification rates further suggest that the speciation rate within birds-of-paradise is comparable to that of the enitre core Corvoidea.CONCLUSION: The estimated ages of morphologically homogeneous and polygynous genera within the birds-of-paradise suggest that there is no need to postulate a particularly rapid evolution of sexually selected morphological traits. The calculated divergence rates further suggest that the speciation rate in birds-of-paradise has not been excessively high. Thus the idea that sexual selection could generate high speciation rates and rapid changes in sexual ornamentations is not supported by our birds-of-paradise data. Potentially, hybridization and long generation times in polygynous male birds-of-paradise have constrained morphological diversification and speciation, but external ecological factors on New Guinea may also have allowed the birds-of-paradise to develop and maintain magnificent male plumages. We further propose that the restricted but geographically complex distributions of birds-of-paradise species may be a consequence of the promiscuous breeding system.
|
|
| 11. |
|
|
| 12. |
- Irestedt, Martin, et al.
(författare)
-
Phylogeny, biogeography and taxonomic consequences in a bird-of-paradise species complex, Lophorina-Ptiloris (Aves: Paradisaeidae)
- 2017
-
Ingår i: Zoological Journal of the Linnean Society. - : OXFORD UNIV PRESS. - 0024-4082 .- 1096-3642. ; 181:2, s. 439-470
-
Tidskriftsartikel (refereegranskat)abstract
- Biogeographical history and taxonomic delimitation in the Australo-Papuan bird-of-paradise Lophorina-Ptiloris species complex is examined with a combination of DNA and morphological markers. The results suggest that the complex started to diverge in the mid-Pliocene, driven by initial isolation and adaptation to altitudinally different habitats. As in many other New Guinean avian taxa, phylogeographic structure is more varied in montane Lophorina than foothill Ptiloris. With the exception of populations of Lophorina in the eastern New Guinean cordillera, phylogenetic patterns from molecular data and morphological discontinuities are consistently concordant, as are molecular species delimitation tests with previous morphology-based circumscription of taxa in Ptiloris. In Lophorina, however, both molecular data and significant, re-discovered morphological traits identify several taxa as more deeply differentiated than hitherto thought. Accordingly, we use these data in an integrative taxonomic approach to re-delimit taxa in the entire clade, including the recognition of three species in the previously monospecific Lophorina. In Lophorina, the identity of several type specimens is reviewed, one new subspecies is described from the Vogelkop, and the identity of the species name superba Pennant is resolved by neotypification, with correction of its author.
|
|
| 13. |
- Jønsson, Knud A., et al.
(författare)
-
Biogeographical history of cuckoo‐shrikes (Aves: Passeriformes) : transoceanic colonization of Africa from Australo-Papua
- 2010
-
Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 37:9, s. 1767-1781
-
Tidskriftsartikel (refereegranskat)abstract
- Aim Cuckoo-shrikes and allies (Campephagidae) form a radiation of birds widely distributed in the Indo-Pacific and Africa. Recent studies on the group have been hampered by poor taxon sampling, causing inferences about systematics and biogeography to be rather speculative. With improved taxon sampling and analyses within an explicit spatiotemporal framework, we elucidate biogeographical patterns of dispersal and diversification within this diverse clade of passerine birds. Location Africa, Asia, Australo-Papua, the Pacific, the Philippines and Wallacea. Methods We use model-based phylogenetic methods (MrBayes and garli) to construct a phylogenetic hypothesis of the core Campephagidae (Campephagidae with the exclusion of Pericrocotus). The phylogeny is used to assess the biogeographical history of the group with a newly developed Bayesian approach to dispersal-vicariance analysis (Bayes-diva). We also made use of a partitioned beast analysis, with several calibration points taken from island ages, passerine mitochondrial substitution rates and secondary calibration points for passerine birds, to assess the timing of diversification and dispersal. Results We present a robust molecular phylogeny that includes all genera and 84% of the species within the core Campephagidae. Furthermore, we estimate divergence dates and ancestral area relationships. We demonstrate that Campephagidae originated in Australo-Papua with a single lineage (Pericrocotus) dispersing to Asia early. Later, there was further extensive transoceanic dispersal from Australo-Papua to Africa involving lineages within the core Campephagidae radiation. Main conclusions The phylogenetic relationships, along with the results of the ancestral area analysis and the timing of dispersal events, support a transoceanic dispersal scenario from Australo-Papua to Africa by the core Campephagidae. The sister group to core Campephagidae, Pericrocotus, dispersed to mainland Asia in the late Oligocene. Asia remained uncolonized by the core Campephagidae until the Pliocene. Transoceanic dispersal is by no means an unknown phenomenon, but our results represent a convincing case of colonization over a significant water gap of thousands of kilometres from Australo-Papua to Africa.
|
|
| 14. |
- Jønsson, Knud Andreas, et al.
(författare)
-
Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala).
- 2014
-
Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 281:1777, s. 20131727-
-
Tidskriftsartikel (refereegranskat)abstract
- Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles).
|
|
| 15. |
- Jønsson, Knud A, et al.
(författare)
-
Explosive avian radiations and multi-directional dispersal across Wallacea : evidence from the Campephagidae and other Crown Corvida (Aves).
- 2008
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 47:1, s. 221-36
-
Tidskriftsartikel (refereegranskat)abstract
- The systematic relationships among avian families within Crown Corvida have been poorly studied so far and as such been of limited use for biogeographic interpretations. The group has its origin in Australia and is thought to have colonized Africa and the New World via Asia beginning some 35 Mya when terranes of Australian origin approached Asian landmasses. Recent detailed tectonic mapping of the origin of land masses in the region around Wallace's line have revealed a particularly complex movement of terranes over the last 20-30 Myr. Thus the biogeographic dispersal pattern of Crown Corvida is a particularly exciting case for linking vicariance and dispersal events with Earth history. Here we examine phylogenetic affinities among 72 taxa covering a broad range of genera in the basal radiations within Crown Corvida with an emphasis on Campephagidae and Pachycephalidae. Bayesian analyses of nuclear DNA sequence data identified the family Campephagidae as monophyletic but the large genus Coracina is not. Within the family Pachycephalidae the genera Pachycephala and Colluricincla are paraphyletic with respect to each other. The resulting phylogeny suggests that patterns of dispersal across Wallace's line are complex and began at least 25 Mya. We find evidence of explosive radiations and multi-directional dispersal within the last 10 Myr, and three independent long distance ocean dispersal events between Wallacea and Africa at 10-15 Mya. Furthermore, the study reveals that in the Campephagidae a complex series of dispersal events rather than vicariance is the most likely explanation for the current biogeographic pattern in the region.
|
|
| 16. |
- Norman, Janette A, et al.
(författare)
-
A multi-gene phylogeny reveals novel relationships for aberrant genera of Australo-Papuan core Corvoidea and polyphyly of the Pachycephalidae and Psophodidae (Aves : Passeriformes).
- 2009
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 52:2, s. 488-97
-
Tidskriftsartikel (refereegranskat)abstract
- The core Corvoidea is the largest and most diverse oscine assemblage within the Australo-Papuan region. Although central to an understanding of the evolutionary history and biogeography of the group the composition and intergeneric relationships of the Australo-Papuan radiation remain poorly understood. Here we analysed DNA sequence data from two nuclear gene regions and the mitochondrial cytochrome b gene, for 40 species of core Corvoidea to test the systematic affinities of key Australo-Papuan lineages. The families Pachycephalidae (whistlers, shrike-thrushes and allies) and Psophodidae (whipbirds, quail-thrush and allies) were both recovered as polyphyletic assemblages. The core pachycephaline assemblage comprised Pachycephala, Colluricincla, parts of Pitohui, and Falcunculus with the remaining genera resolving as four divergent lineages with no clearly defined affinities. Ptilorrhoa and Cinclosoma (Cinclosomatidae) formed a clade separate from Psophodes (Psophodidae) but neither clade showed clear affinities to any other taxa. Novel relationships were also identified for three aberrant New Guinean genera; ditypic Machaerirhynchus and monotypic Rhagologus were both nested within an assemblage that included the Artamidae and African malaconotoids (bush-shrikes and allies) while the enigmatic Ifrita was found to be part of an assemblage that included the Monarchidae and Paradisaeidae.
|
|
| 17. |
- Peona, Valentina, et al.
(författare)
-
The hidden structural variability in avian genomes
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Structural variants (SVs) are DNA mutations that can have relevant effects at the micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered especially in complex repetitive regions. In this study, we used a combination of long-read and linked-read genome assemblies to explore the occurrence of insertions and deletions across the chromosomes of 14 species birds-of-paradise and two species of estrildid finches. The species sampling encompasses all genera of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. Interestingly, we found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.
|
|
| 18. |
- Stervander, Martin, et al.
(författare)
-
An updated chronology of passerine birds
- 2020
-
Ingår i: <em>The Largest Avian Radiation</em>. - Barcelona : Lynx Edicions. ; , s. 387-396
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
| 19. |
- Xu, Luohao, et al.
(författare)
-
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds
- 2019
-
Ingår i: Nature Ecology & Evolution. - : NATURE PUBLISHING GROUP. - 2397-334X. ; 3:5, s. 834-844
-
Tidskriftsartikel (refereegranskat)abstract
- Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed ‘evolutionary strata’. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.
|
|
