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| 2. |
- Alström, Per, Professor, et al.
(författare)
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Systematics of the avian family Alaudidae using multilocus and genomic data
- 2023
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Ingår i: Avian Research. - : Elsevier BV. - 2053-7166. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single species extending their ranges to North and northernmost South America and Australia. A decade-old molecular phylogeny, comprising ∼80% of the species, revealed multiple cases of parallel evolution and large variation in rates of morphological evolution, which had misled taxonomists into creating many non-monophyletic genera. Here, we reconstruct the phylogeny of the larks, using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species (in total 133 taxa; not all loci available for all species). We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling (in total 51 samples of 44 taxa across 40 species). Our results confirm the previous findings of rampant morphological convergence and divergence, and reveal new cases of paraphyletic genera. We propose a new subfamily classification, and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae. Our study supports recently proposed species splits as well as some recent lumps, while also questioning some of the latter. This comprehensive phylogeny will form an important basis for future studies, such as comparative studies of lark natural history, ecology, evolution and conservation.
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| 3. |
- Reeve, Andrew Hart, et al.
(författare)
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Population genomics of the island thrush elucidates one of earth's great archipelagic radiations.
- 2023
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Ingår i: Evolution letters. - 2056-3744. ; 7:1, s. 24-36
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Tidskriftsartikel (refereegranskat)abstract
- Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range and is arguably the world's most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted a comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea, and New Guinea to Polynesia. The island thrush's success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.
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| 4. |
- Alström, Per, et al.
(författare)
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Multiple species within the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex revealed through an integrative taxonomic approach
- 2020
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Ingår i: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 162:3, s. 936-967
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Tidskriftsartikel (refereegranskat)abstract
- We re-evaluated the taxonomy of the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age-related, geographical and taxon-specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non-sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan's Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography.
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| 5. |
- Irestedt, Martin, 1968-, et al.
(författare)
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A crowd-sourced genomic project to assess hybrid content in a rare avian vagrant (Azure Tit Cyanistes cyanus (Pallas, 1770))
- 2023
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Ingår i: Avian Research. - : Elsevier. - 2053-7166. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus (Pallas, 1770) and European Blue Tit Cyanistes caeruleus (Linnaeus, 1758), by re-sequencing the genomes of museum specimens of non-hybrids and presumed hybrids with varying plumages. The project was funded by crowdsourcing and initiated when two presumed Azure Tits, observed by hundreds of Swedish birdwatchers, were rejected as hybrids based on minor plumage deviations assumed to indicate hybrid contents from the European Blue Tit. The results confirm that hybrids with intermediate plumages, so called Pleske’s Tits, are first generation hybrids (F1 hybrids). Individuals, whose plumages are similar to Azure Tits, but assessed as hybrids based on minor plumage deviations, are all backcrosses but vary in their degree of hybrid content. However, some individuals morphologically recognized as pure Azure Tits expressed similar degrees of hybrid content. The results indicate that: (1) hybrid content may be widespread in Azure Tits in the western part of its habitat distribution; (2) plumage deviation in backcrosses is not linearly correlated with the genetic degree of hybrid origin; and (3) all Azure Tits observed in Europe outside its natural distribution may have some degree of hybrid origin. We therefore suggest that it is very difficult to phenotypically single out hybrids beyond first generation backcrosses. We argue that decreased sequencing costs and improved analytical tools open the doors for museomic crowd-sourced projects that may not address outstanding biological questions but have a major interest for lay citizens such as birdwatchers.
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| 6. |
- Irestedt, Martin, 1968-
(författare)
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Molecular systematics of the antbird-ovenbird complex (Aves: Furnariida)
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns the phylogenetic relationships among suboscine birds with special emphasis on the antbird-ovenbird complex (Aves: Furnariida). The principal aim is to produce a framework for future systematic and comparative studies of suboscines by generating robust phylogenetic hypotheses from DNA-sequence data. Several gene regions, mostly from the nuclear genome, are used in order to get genetically independent estimates of phylogenetic relationships. The study is pioneering in the extensive use of nuclear DNA sequences to resolve passerine relationships.The phylogenetic hypotheses are overall well supported by high nodal support values, and there is an overall good phylogenetic agreement between the different gene regions used. Several existing hypotheses about deeper relationships among New World suboscines based on morphology and DNA-DNA hybridisations are corroborated. In addition, novel hypotheses of relationships within the antbird-ovenbird complex are generated, e.g., a non-monophyletic origin of the ground antbirds, a basal position of the genus Sclerurus in relation to woodcreepers and core-ovenbirds, and a basal position of the genera Terenura, Myrmornis, Pygiptila and Thamnistes in relation to other typical antbirds. Based on the results the current knowledge of systematic relationships among suboscines in general, and within the antbird-ovenbird complex in particular, are summarised and discussed. The thesis also includes discussions of recent methodological developments in avian molecular systematics, the use of morphological characters in phylogenetic reconstruction, and the problem of phylogenetic incongruence between data sets.
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| 7. |
- Irestedt, Martin, 1968-, et al.
(författare)
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No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)
- 2019
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Ingår i: DIVERSITY-BASEL. - : MDPI. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.
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| 8. |
- Jonsson, Knud Andreas, et al.
(författare)
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Unrecognised (species) diversity in New Guinean passerine birds
- 2019
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Ingår i: Emu (Print). - : TAYLOR & FRANCIS AUSTRALASIA. - 0158-4197 .- 1448-5540. ; 119:3, SI, s. 233-241
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Tidskriftsartikel (refereegranskat)abstract
- Species represent an important unit for the study of diversity, but may not always be delimited consistently across regions and clades. Many of these taxonomic inconsistencies are due to the variable views of taxonomists. In recent years, however, new methodologies have attempted to circumvent this problem by assigning more objective criteria for the delimitation of species, drawing on a wide range of data such as DNA, morphology, vocalisation and ecology. Here, we apply a genetic screening approach in which we sequence the mitochondrial gene ND2 for all recognised subspecies of 16 species in eight genera (a mix of lowland and montane species) from the geologically complex tropical island of New Guinea. We show that populations within some species are genetically highly divergent despite little morphological differentiation, but we also find an example in which populations from five morphologically distinct species are genetically very similar. Overall, our data show higher levels of genetic differentiation than expected, but also highlight the difficulty of predicting which groups contain unrecognised diversity. These results are interesting in their own right, but also have implications for further analyses that focus on increasing our understanding of how diversity builds up over time.
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| 9. |
- Le Pepke, Michael, et al.
(författare)
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Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)
- 2019
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Ingår i: Journal of Biogeography. - : WILEY. - 0305-0270 .- 1365-2699. ; 46:6, s. 1214-1225
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Tidskriftsartikel (refereegranskat)abstract
- Aim The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of ‘supertramps’, ‘great speciators’ and relictualization. Location The Indo-Pacific, Australia, Asia and Africa. Taxon Corvoid passerine birds. Methods We constructed a new time-calibrated molecular phylogeny of the core Campephagidae (cuckooshrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non-independence. Results The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo-Pacific, Australia, Southeast Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated (’supertramps’) or show strong differentiation of local populations (’great speciators’), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in ‘great speciators’ with intermediate levels of dispersal abilities (as per hand-wing index). Main conclusions Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of ‘supertramps’, ‘great speciators’ and relictual palaeoendemics within the temporal stages of the taxon cycle.
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| 10. |
- Prost, Stefan, et al.
(författare)
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Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
- 2019
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Ingår i: GigaScience. - : OXFORD UNIV PRESS. - 2047-217X. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.
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