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- Hart Reeve, Andrew, et al.
(författare)
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The formation of the Indo-Pacific montane avifauna
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The processes generating the earth’s montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species’ ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region’s montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
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| 2. |
- Kennedy, Jonathan D., et al.
(författare)
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Diversification and community assembly of the world’s largest tropical island
- 2022
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 31:6, s. 1078-1089
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Tidskriftsartikel (refereegranskat)abstract
- AimThe species diversity and endemism of tropical biotas are major contributors to global biodiversity, but the factors underlying the formation of these systems remain poorly understood.LocationThe world's largest tropical island, New Guinea.Time periodMiocene to present.Major taxa studiedPasserine birds.MethodsWe first generated a species-level phylogeny of all native breeding passerine birds to analyse spatial and elevational patterns of species richness, species age and phylogenetic diversity. Second, we used an existing dataset on bill morphology to analyse spatial and elevational patterns of functional diversity.ResultsThe youngest New Guinean species are principally distributed in the lowlands and outlying mountain ranges, with the lowlands also maintaining the majority of non-endemic species. In contrast, many species occurring in the central mountain range are phylogenetically distinct, range-restricted, endemic lineages. Centres of accumulation for the oldest species are in montane forest, with these taxa having evolved unique bill forms in comparison to the remaining New Guinean species. For the morphological generalists, attaining a highland distribution does not necessarily represent the end to dispersal and diversification, because a number of new species have formed in the outlying mountain ranges, following recent colonization from the central range.Main conclusionsWe conclude that a general model of tropical montane diversification is that lineages commonly colonize the lowlands, shifting their ranges upslope through time to become range-restricted montane forest endemics, attaining novel functional adaptations to these environments.
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| 4. |
- Peona, Valentina, et al.
(författare)
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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
- 2020
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 21:1, s. 263-286
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Tidskriftsartikel (refereegranskat)abstract
- Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.
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| 5. |
- Peona, Valentina, 1990-, et al.
(författare)
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The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities
- 2021
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : Royal Society. - 0962-8436 .- 1471-2970. ; 376:1833
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Tidskriftsartikel (refereegranskat)abstract
- It is a broadly observed pattern that the non-recombining regions of sex- limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in Drosophila males. Furthermore, Haldane’s rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane’s rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
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| 6. |
- 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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