| 1. |
- Faria, R., et al.
(författare)
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Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
- 2019
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 28:6, s. 1375-1393
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Tidskriftsartikel (refereegranskat)abstract
- Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.
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| 2. |
- Bacon, Christine D., et al.
(författare)
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Genomic and niche divergence in an Amazonian palm species complex
- 2021
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Ingår i: Botanical Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 197:4, s. 498-512
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Tidskriftsartikel (refereegranskat)abstract
- Environmental heterogeneity across the landscape can cause lineage divergence and speciation. The Geonoina macrostachys (Arecaceae) species complex has been proposed as a candidate case of ecological speciation in Amazonia due to evidence of habitat partitioning and pre-zygotic reproductive barriers between co-occurring morphotypes at a local scale. In this study, we provide a continent-wide perspective of the divergence patterns in a macrostachys by integrating data from morphological traits, target sequence capture, climate, soil and reproductive biology. A morphometric analysis revealed four morphogroups, defined by traits related to leaf shape. A coalescence-based phylogenetic analysis did not recover the morphogroups as monophyletic, indicating independent evolution of leaf shape across geographical space. We demonstrate scale-dependent habitat differentiation for two of the morphogroups, in which segregation driven mostly by climate was complete at the regional scale but incomplete at the continental scale. Contrary to previous evidence of reproductive isolation in the form of different pollinators and flowering times between sympatric G. macrostachys forms in Peru and Ecuador, these were not found in Colombia, suggesting reproductive barriers have evolved multiple times across its geographical range. Taken together, our findings suggest that ecological divergence and local adaptation is driving diversification in G. macrostachys, and that hyperdiverse regions such as Amazonia are probable arenas for ecological divergence in sympatry.
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| 3. |
- Gan, H. M., et al.
(författare)
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Genomic evidence of neo-sex chromosomes in the eastern yellow robin
- 2019
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Ingår i: Gigascience. - : Oxford University Press (OUP). - 2047-217X. ; 8:9
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Tidskriftsartikel (refereegranskat)abstract
- Background: Understanding sex-biased natural selection can be enhanced by access to well-annotated chromosomes including ones inherited in sex-specific fashion. The eastern yellow robin (EYR) is an endemic Australian songbird inferred to have experienced climate-driven sex-biased selection and is a prominent model for studying mitochondrial-nuclear interactions in the wild. However, the lack of an EYR reference genome containing both sex chromosomes (in birds, a female bearing Z and W chromosomes) limits efforts to understand the mechanisms of these processes. Here, we assemble the genome for a female EYR and use low-depth (10x) genome resequencing data from 19 individuals of known sex to identify chromosome fragments with sex-specific inheritance. Findings: MaSuRCA hybrid assembly using Nanopore and Illumina reads generated a 1.22-Gb EYR genome in 20,702 scaffolds (94.2% BUSCO completeness). Scaffolds were tested for W-linked (female-only) inheritance using a k-mer approach, and for Z-linked inheritance using median read-depth test in male and female reads (read-depths must indicate haploid female and diploid male representation). This resulted in 2,372 W-linked scaffolds (total length: 97,872,282 bp, N50: 81,931 bp) and 586 Z-linked scaffolds (total length: 121,817,358 bp, N50: 551,641 bp). Anchoring of the sex-linked EYR scaffolds to the reference genome of a female zebra finch revealed 2 categories of sex-linked genomic regions. First, 653 W-linked scaffolds (25.7 Mb) were anchored to the W sex chromosome and 215 Z-linked scaffolds (74.4 Mb) to the Z. Second, 1,138 W-linked scaffolds (70.9 Mb) and 179 Z-linked scaffolds (51.0 Mb) were anchored to a large section (coordinates similar to 5 to similar to 60 Mb) of zebra finch chromosome 1A. The first similar to 5 Mb and last similar to 14 Mb of the reference chromosome 1A had only autosomally behaving EYR scaffolds mapping to them. Conclusions: We report a female (W chromosome-containing) EYR genome and provide genomic evidence for a neo-sex (neo-W and neo-Z) chromosome system in the EYR, involving most of a large chromosome (1A) previously only reported to be autosomal in passerines.
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| 4. |
- Krzeminska, U., et al.
(författare)
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Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens)
- 2018
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 120:4, s. 296-309
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Tidskriftsartikel (refereegranskat)abstract
- The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (similar to 630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.
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| 5. |
- Morales, Hernán E., 1985, et al.
(författare)
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Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates
- 2018
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Ingår i: Nature Ecology & Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2:8, s. 1258-1267
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Tidskriftsartikel (refereegranskat)abstract
- Metabolic processes in eukaryotic cells depend on interactions between mitochondrial and nuclear gene products (mitonuclear interactions). These interactions could have a direct role in population divergence. Here, we study mitonuclear co-evolution in a widespread bird that experienced population divergence followed by bidirectional mitochondrial introgression into different nuclear backgrounds. Using >60,000 single nucleotide polymorphisms, we quantify patterns of nuclear genetic differentiation between populations that occupy areas with different climates and harbour deeply divergent mitochondrial lineages despite ongoing nuclear gene flow. We find that strong genetic differentiation and sequence divergence in a region of similar to 15.4 mega-bases on chromosome 1A mirror the geographic pattern of mitochondrial DNA divergence. This result is seen in two different transects representing populations with different nuclear backgrounds. The chromosome 1A region is enriched for genes performing mitochondrial functions (N-mt genes). Molecular signatures of selective sweeps in this region alongside those in the mitochondrial genome suggest a history of adaptive mitonuclear co-introgression. Moreover, evidence for large linkage disequilibrium blocks in this genomic region suggests that low recombination could facilitate functional interactions between co-evolved nuclear alleles. Our results are consistent with mitonuclear co-evolution as an important mechanism for population divergence and local adaptation.
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| 6. |
- Morales, Hernán E., 1985, et al.
(författare)
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Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast
- 2019
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:12
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Tidskriftsartikel (refereegranskat)abstract
- The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.
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| 7. |
- Morales, Hernán E., 1985, et al.
(författare)
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Perpendicular axes of differentiation generated by mitochondrial introgression
- 2017
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 26:12, s. 3241-3255
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Tidskriftsartikel (refereegranskat)abstract
- Differential introgression of mitochondrial vs. nuclear DNA generates discordant patterns of geographic variation and can promote population divergence and speciation. We examined a potential case of mitochondrial introgression leading to two perpendicular axes of differentiation. The Eastern Yellow Robin Eopsaltria australis, a widespread Australian bird, shows a deep mitochondrial split that is perpendicular to north–south nuclear DNA and plumage colour differentiation. We propose a scenario to explain this pattern: (i) first, both nuclear and mitochondrial genomes differentiated in concert during north–south population divergence; (ii) later, their histories disconnected after two mitochondrial introgression events resulting in a deep mitochondrial split perpendicular to the nuclear DNA structure. We explored this scenario by coalescent modelling of ten mitochondrial genes and 400 nuclear DNA loci. Initial mitochondrial and nuclear genome divergences were estimated to have occurred in the early Pleistocene, consistent with the proposed scenario. Subsequent climatic transitions may have driven later mitochondrial introgression. We consider neutral introgression unlikely and instead propose that the evidence is more consistent with adaptive mitochondrial introgression and selection against incompatible mitochondrial-nuclear combinations. This likely generated an axis of coastal-inland mitochondrial differentiation in the face of nuclear gene flow, perpendicular to the initial north–south axis of differentiation (reflected in genomewide nuclear DNA and colour variation).
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| 8. |
- Sunnucks, Paul, et al.
(författare)
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Integrative approaches for studying mitochondrial and nuclear genome co-evolution in oxidative phosphorylation
- 2017
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ~80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes. In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it. We advocate that recent interdisciplinary advances assist in the consolidation of links between genotype and phenotype. For example, advances in genomics allow us to unravel signatures of selection in mitochondrial and nuclear OXPHOS genes at population-relevant scales, while newly published complete atomic-resolution structures of the OXPHOS machinery enable more robust predictions of how these genes interact epistatically and co-evolutionarily. We use three case studies to show how integrative approaches have improved the understanding of mitonuclear interactions in OXPHOS, namely those driving high-altitude adaptation in bar-headed geese, allopatric population divergence in Tigriopus californicus copepods, and the genome architecture of nuclear genes coding for mitochondrial functions in the eastern yellow robin.
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