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- Zuntini, Alexandre R., et al.
(författare)
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Phylogenomics and the rise of the angiosperms
- 2024
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Ingår i: NATURE. - 0028-0836 .- 1476-4687. ; 629, s. 843-850
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Tidskriftsartikel (refereegranskat)abstract
- Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods(1,2). A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome(3,4). Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins(5-7). However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes(8). This 15-fold increase in genus-level sampling relative to comparable nuclear studies(9) provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
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2. |
- Biggs, Reinette, et al.
(författare)
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Toward Principles for Enhancing the Resilience of Ecosystem Services
- 2012. - 37
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Ingår i: Annual Review Environment and Resources. - : Annual Reviews. - 1543-5938 .- 1545-2050. ; 37, s. 421-448
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Forskningsöversikt (refereegranskat)abstract
- Enhancing the resilience of ecosystem services (ES) that underpin human well-being is critical for meeting current and future societal needs, and requires specific governance and management policies. Using the literature, we identify seven generic policy-relevant principles for enhancing the resilience of desired ES in the face of disturbance and ongoing change in social-ecological systems (SES). These principles are (P1) maintain diversity and redundancy, (P2) manage connectivity, (P3) manage slow variables and feedbacks, (P4) foster an understanding of SES as complex adaptive systems (CAS), (P5) encourage learning and experimentation, (P6) broaden participation, and (P7) promote polycentric governance systems. We briefly define each principle, review how and when it enhances the resilience of ES, and conclude with major research gaps. In practice, the principles often co-occur and are highly interdependent. Key future needs are to better understand these interdependencies and to operationalize and apply the principles in different policy and management contexts.
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3. |
- Morris, John A, et al.
(författare)
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An atlas of genetic influences on osteoporosis in humans and mice.
- 2019
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 51, s. 258-266
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Tidskriftsartikel (refereegranskat)abstract
- Osteoporosis is a common aging-related disease diagnosed primarily using bone mineral density (BMD). We assessed genetic determinants of BMD as estimated by heel quantitative ultrasound in 426,824 individuals, identifying 518 genome-wide significant loci (301 novel), explaining 20% of its variance. We identified 13 bone fracture loci, all associated with estimated BMD (eBMD), in ~1.2 million individuals. We then identified target genes enriched for genes known to influence bone density and strength (maximum odds ratio (OR)=58, P=1 × 10-75) from cell-specific features, including chromatin conformation and accessible chromatin sites. We next performed rapid-throughput skeletal phenotyping of 126 knockout mice with disruptions in predicted target genes and found an increased abnormal skeletal phenotype frequency compared to 526 unselected lines (P<0.0001). In-depth analysis of one gene, DAAM2, showed a disproportionate decrease in bone strength relative to mineralization. This genetic atlas provides evidence linking associated SNPs to causal genes, offers new insight into osteoporosis pathophysiology, and highlights opportunities for drug development.
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4. |
- Cowan-Turner, Daniel, et al.
(författare)
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Sequencing complex plants on a budget: The development of Kalanchoë blossfeldiana as a C3, CAM comparative tool
- 2024
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Ingår i: Plants, People, Planet. - : WILEY. - 2572-2611.
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Tidskriftsartikel (refereegranskat)abstract
- Despite the increasing number of well-studied plant species with well-annotated genomes across plant life, there are few densely sampled genera with more than a couple of genome sequences representing the diversity of whole genera. Here, we develop an economic approach to full-genome sequencing that could be used to sequence many species within a genus. We made use of the Nanopore rapid sequencing kit to assist in plant genome assembly, dramatically reducing the cost. Here we applied this method to cost-effectively develop genomic resources for Kalancho & euml; blossfeldiana, a commercially important ornamental, in which Crassulacean Acid Metabolism (CAM), a water-conserving mode of photosynthesis can be induced. We present a physiological and biochemical characterisation of Kalanchoe blossfeldiana with its nuclear and chloroplastic genome and a comparative C3, CAM dusk transcriptome. We apply this approach to a complex tetraploid genome, making use of a relative species for chromosomal scaffolding to reduce assembly ploidy, we provide a resource for future gene expression studies. We highlight its limitations, e.g. the need for deeper sequencing to accurately resolve genome structure and haplotypes without using a relative species for scaffolding. T he study demonstrates the merits of K. blossfeldiana as a comparative system for studying C3 and CAM within a plant and has identified substantial changes in the dusk transcriptome between young C3 and mature CAM K. blossfeldiana leaves in response to age-induced CAM, and shows that in the absence of abiotic stress, CAM induction still involves the engagement of drought and abscisic acid (ABA) response pathways.
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