| 51. |
- Bacon, Christine D., et al.
(författare)
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Endemic palm species shed light on habitat shifts and the assembly of the Cerrado and Restinga floras
- 2017
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 110, s. 127-133
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Tidskriftsartikel (refereegranskat)abstract
- Species expansions into new habitats are often associated with physiological adaptations, for instance when rain forest lineages colonize dry habitats. Although such shifts have been documented for the Brazilian savanna (Cerrado), little is known about the biogeographic origin of species occupying an extreme South American habitat type, the coastal dunes (Restinga). We examined the formation of this poorly known, endangered habitat by reconstructing the evolutionary history of two endemic species. Due to the proposed recency and uniqueness of this habitat, we hypothesized that Restinga species of the palm genus Allagoptera to be recently evolved and to present derived morphological characters. To detect habit shifts in absolute time, we used one plastid and nine nuclear genes to reconstruct the phylogenetic and biogeographic history of Allagoptera. We used light microscopy and stable isotope analysis to explore whether morphological adaptations occurred concomitantly with habitat shifts. Phylogenetic relationships were well supported and we found ancestral lineages of Allagoptera to be widely distributed throughout habitats that are currently occupied by extant species. Over the last ca. 7 Ma Allagoptera has shifted its preference to increasingly dry habitats. Coincident with the colonization of the Cerrado and Restinga, morphological adaptations also evolved, including subterranean stems that are fire-resistant and long underground stem and root systems that facilitate water access. We did not find differences in metabolic pathway or modifications to pollen morphology when compared to other palm lineages. Assuming that the evolutionary history of Allagoptera is indicative of the habitat in which it occurs, our results infer a recent origin for Cerrado species. Although little is known about the formation of the Restinga habitat, our results also suggest a longer history than currently proposed; with an origin of Restinga habitats dating back to the Late Pliocene. (C) 2017 Elsevier Inc. All rights reserved.
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| 52. |
- Bacon, Christine D., et al.
(författare)
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Phylogenetics of Iriarteeae (Arecaceae), cross-Andean disjunctions and convergence of clustered infructescence morphology in Wettinia
- 2016
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Ingår i: Botanical Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074. ; 182:2, s. 272-286
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Tidskriftsartikel (refereegranskat)abstract
- The Neotropical palm tribe Iriarteeae is ubiquitous in several lowland and montane biomes across northern South America, but the phylogenetic relationships among genera and species remain unresolved. A well resolved phylogenetic tree is key to exploring morphological evolution in the tribe, including striking features such as the complex and unique inflorescence structures in Wettinia. We generated data from five plastid (ndhA, petD-rpoA, psbK-trnS and trnG) and six nuclear (AG1, CISPs 4 and 5, PRK, RPB2 and WRKY21) molecular loci to infer the phylogeny. We explored the evolutionary patterns of trait evolution using the D statistic and stochastic character mapping. All genera were inferred as monophyletic and their relationships were recovered with strong to moderate support. Based on these results we synonymize the two species of Iriartella under I. setigera and resurrect Socratea montana from S. rostrata. Interspecific relationships were mostly consistent with current morphological classification. One exception concerns trait evolution in Wettinia, in which the clustered infructescence was found to have evolved at least four times. Phylogenetic signal for this trait was weak and randomly distributed across the tree, probably representing convergence. Our results provide a robust phylogenetic framework for Iriarteeae, largely corroborating current morphological classification and laying the groundwork for macroevolutionary studies in the tribe.
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| 53. |
- Bacon, Christine D., et al.
(författare)
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The seasonally dry tropical forest species Cavanillesia chicamochae has a middle Quaternary origin
- 2022
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Ingår i: Biotropica. - : Wiley. - 0006-3606 .- 1744-7429. ; 54:1, s. 91-99
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Tidskriftsartikel (refereegranskat)abstract
- We use DNA sequence data to understand the evolutionary history of the genus Cavanillesia (Malvaceae), with particular emphasis on C. chicamochae, an emblematic succulent-trunked tree endemic to seasonally dry tropical forests (SDTFs) of the Chicamocha Canyon of Colombia, South America. Based on field sampling of multiple individuals from different populations, we inferred a phylogeny calibrated into absolute time using robust macrofossil information. We show strong support for a monophyletic Cavanillesia chicamochae, with a mean stem age of 1.46 Ma. Two different mechanisms could explain its origin, either a late uplift age of the eastern cordillera or increased dryness of the Chicamocha Canyon during the Middle Pleistocene Transition. We also find marked genetic differentiation of its populations within the Chicamocha Canyon, likely driven by a combination of climate change and local landscape processes. Our results suggest that within northern inter-Andean SDTFs, as has been demonstrated in the central Andes, dispersal limitation leads to species and even population monophyly within individual valleys. The genetic differentiation of populations of C. chicamochae, together with the presence of other endemic and threatened species in the Chicamocha Canyon, calls for urgent management to conserve the unique biodiversity in the region. Abstract in Spanish is available with online material.
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| 54. |
- Bacon, David J., et al.
(författare)
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Cosmology with Phase 1 of the Square Kilometre Array Red Book 2018 : Technical specifications and performance forecasts
- 2020
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Ingår i: Publications Astronomical Society of Australia. - : Cambridge University Press (CUP). - 1323-3580 .- 1448-6083. ; 37
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Tidskriftsartikel (refereegranskat)abstract
- We present a detailed overview of the cosmological surveys that we aim to carry out with Phase 1 of the Square Kilometre Array (SKA1) and the science that they will enable. We highlight three main surveys: a medium-deep continuum weak lensing and low-redshift spectroscopic HI galaxy survey over 5 000 deg2; a wide and deep continuum galaxy and HI intensity mapping (IM) survey over 20 000 deg2 from z = 0.35 to 3; and a deep, high-redshift HI IM survey over 100 deg2 from z = 3 to 6. Taken together, these surveys will achieve an array of important scientific goals: measuring the equation of state of dark energy out to z = 3 with percent-level precision measurements of the cosmic expansion rate; constraining possible deviations from General Relativity on cosmological scales by measuring the growth rate of structure through multiple independent methods; mapping the structure of the Universe on the largest accessible scales, thus constraining fundamental properties such as isotropy, homogeneity, and non-Gaussianity; and measuring the HI density and bias out to z = 6. These surveys will also provide highly complementary clustering and weak lensing measurements that have independent systematic uncertainties to those of optical and near-infrared (NIR) surveys like Euclid, LSST, and WFIRST leading to a multitude of synergies that can improve constraints significantly beyond what optical or radio surveys can achieve on their own. This document, the 2018 Red Book, provides reference technical specifications, cosmological parameter forecasts, and an overview of relevant systematic effects for the three key surveys and will be regularly updated by the Cosmology Science Working Group in the run up to start of operations and the Key Science Programme of SKA1.
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| 55. |
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| 56. |
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| 57. |
- Barrett, C. F., et al.
(författare)
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Ancient Polyploidy and Genome Evolution in Palms
- 2019
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 11:5, s. 1501-1511
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Tidskriftsartikel (refereegranskat)abstract
- Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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| 58. |
- Barrett, C. F., et al.
(författare)
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Phylogenomics, biogeography and evolution in the American genus Brahea (Arecaceae)
- 2019
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Ingår i: Botanical Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 190:3, s. 242-259
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Tidskriftsartikel (refereegranskat)abstract
- Slow rates of molecular evolution at low taxonomic levels hamper studies of relationships among species and subsequent biogeographic and evolutionary analyses. An example is the genus Brahea, which is among the most poorly understood lineages of American palms and is characterized by a wide variety of growth forms and intermediate morphological features. We generated c. 400 kb of genome-scale data from all three genomes for the 11 currently described Brahea spp. to infer phylogenetic relationships, reconstruct ancestral growth form, estimate ancestral geographical ranges and test for niche differences among closely related species with geographical overlap. Relationships receive strong support and conform to previous subgeneric assignments, except for placement of the dwarf species B. moorei in Brahea subgenus Erythea. Our robust phylogenetic hypothesis reveals trends in growth form, including an overall increase in height in the B. armata clade and independent evolution of dwarf forms from taller ancestors in the B. pimo and B. dulcis clades. Ancestral range estimation reveals roles of dispersal (e.g. B. edulis on Guadalupe Island) and putative divergence within geographical regions in some cases (e.g. in the B. armata clade) but is equivocal in others (e.g. in the B. pimo clade). We find evidence of niche non-equivalency among species in the B. armata clade in north-western Mexico and some evidence of niche non-equivalency between B. berlandieri and B. dulcis, the former of which is synonymized under B. dulcis. Our findings have implications for the complex biogeographic history in Central America and Mexico, suggesting that divergence within regions and dispersal are the predominant processes of species diversification. Future studies should include population-level sampling across the genus, along with morphological and ecological information, to assess distinctness among species and, particularly, levels of gene flow, in an integrative fashion.
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| 59. |
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| 60. |
- Bernal, R., et al.
(författare)
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- Could coastal plants in western Amazonia be relicts of past marine incursions?
- 2019
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 46:8, s. 1749-1759
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Tidskriftsartikel (refereegranskat)abstract
- - The rainforests of Amazonia comprise some of the most biologically diverse ecosystems on Earth. Despite this high biodiversity, little is known about how landscape changes that took place in deep history have affected the assembly of its species, and whether the impact of such changes on biodiversity can still be observed. Here, we present a hypothesis to explain our observation that plants typical of Neotropical coastal habitats also occur in western Amazonia, in some cases thousands of kilometres away from the coast. Evidence on their current distribution, dispersal biology and divergence times estimated from molecular phylogenies suggest that these plants may be the legacy of the large marine-influenced embayment that dominated the area for millions of years in the Neogene. We hypothesize that coastal plants dispersed along the shores of this embayment and persisted as inland relicts after the marine incursion(s) retreated, probably with the aid of changes in soil conditions caused by the deposition of marine sediments. This dispersal corridor may also have facilitated the colonization of coastal environments by Amazonian lineages. These scenarios could imply an unexpected coastal source that has contributed to Amazonia's high floristic diversity and led to disjunct distributions across the Neotropics. We highlight the need for future studies and additional evidence to validate and shed further light on this potentially important pattern. © 2019 John Wiley & Sons Ltd
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