| 1. |
- Anderson, Bruce, et al.
(författare)
-
Opposing effects of plant traits on diversification
- 2023
-
Ingår i: iScience. - : Cell Press. - 2589-0042. ; 26:4
-
Tidskriftsartikel (refereegranskat)abstract
- Species diversity can vary dramatically across lineages due to differences in speciation and extinction rates. Here, we explore the effects of several plant traits on diversification, finding that most traits have opposing effects on diversification. For example, outcrossing may increase the efficacy of selection and adaptation but also decrease mate availability, two processes with contrasting effects on lineage persistence. Such opposing trait effects can manifest as differences in diversification rates that depend on ecological context, spatiotemporal scale, and associations with other traits. The complexity of pathways linking traits to diversification suggests that the mechanistic underpinnings behind their correlations may be difficult to interpret with any certainty, and context dependence means that the effects of specific traits on diversification are likely to differ across multiple lineages and timescales. This calls for taxonomically and context-controlled approaches to studies that correlate traits and diversification.
|
|
| 2. |
- Antonelli, Alexandre, 1978, et al.
(författare)
-
SUPERSMART: ecology and evolution in the era of big data
- 2014
-
Ingår i: PeerJ PrePrints. - : PeerJ. - 2167-9843.
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Rapidly growing biological data volumes – including molecular sequences, species traits, geographic occurrences, specimen collections, and fossil records – hold an unprecedented, yet largely unexplored potential to reveal how ecological and evolutionary processes generate and maintain biodiversity. Most biodiversity studies integrating ecological data and evolutionary history use an idiosyncratic step-by-step approach for the reconstruction of time-calibrated phylogenies in light of ecological and evolutionary scenarios. Here we introduce a conceptual framework, termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of biodiversity research. This framework reconstructs dated phylogenies based on the assembly of molecular datasets and collects pertinent data on ecology, distribution, and fossils of the focal clade. The data handled for each step are continuously updated as databases accumulate new records. We exemplify the practice of our method by presenting comprehensive phylogenetic and dating analyses for the orders Primates and the Gentianales. We believe that this emerging framework will provide an invaluable tool for a wide range of hypothesis-driven research questions in ecology and evolution.
|
|
| 3. |
- Antonelli, Alexandre, 1978, et al.
(författare)
-
Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
- 2017
-
Ingår i: Systematic biology. - : Oxford University Press (OUP). - 1076-836X .- 1063-5157. ; 66:2, s. 152-166
-
Tidskriftsartikel (refereegranskat)abstract
- Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a "Dated Tree of Life" where all node ages are directly comparable. [Bayesian phylogenetics; data mining; divide-and-conquer methods; GenBank; multilocus multispecies coalescent; next-generation sequencing; palms; primates; tree calibration.].
|
|
| 4. |
- Chartier, Marion, et al.
(författare)
-
How (much) do flowers vary? Unbalanced disparity among flower functional modules and a mosaic pattern of morphospace occupation in the order Ericales
- 2017
-
Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 284:1852
-
Tidskriftsartikel (refereegranskat)abstract
- The staggering diversity of angiosperms and their flowers has fascinated scientists for centuries. However, the quantitative distribution of floral morphological diversity (disparity) among lineages and the relative contribution of functional modules (perianth, androecium and gynoecium) to total floral disparity have rarely been addressed. Focusing on a major angiosperm order (Ericales), we compiled a dataset of 37 floral traits scored for 381 extant species and nine fossils. We conducted morphospace analyses to explore phylogenetic, temporal and functional patterns of disparity. We found that the floral morphospace is organized as a continuous cloud in which most clades occupy distinct regions in a mosaic pattern, that disparity increases with clade size rather than age, and that fossils fall in a narrow portion of the space. Surprisingly, our study also revealed that among functional modules, it is the androecium that contributes most to total floral disparity in Ericales. We discuss our findings in the light of clade history, selective regimes as well as developmental and functional constraints acting on the evolution of the flower and thereby demonstrate that quantitative analyses such as the ones used here are a powerful tool to gain novel insights into the evolution and diversity of flowers.
|
|
| 5. |
- Falster, Daniel, et al.
(författare)
-
AusTraits, a curated plant trait database for the Australian flora
- 2021
-
Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
|
|
| 6. |
- Helmstetter, Andrew J., et al.
(författare)
-
Trait‐dependent diversification in angiosperms : Patterns, models and data
- 2023
-
Ingår i: Ecology Letters. - : John Wiley & Sons. - 1461-023X .- 1461-0248. ; 26:4, s. 640-657
-
Tidskriftsartikel (refereegranskat)abstract
- Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.
|
|
| 7. |
- Sauquet, Herve, et al.
(författare)
-
Contrasted patterns of hyperdiversification in Mediterranean hotspots
- 2009
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 106:1, s. 221-225
-
Tidskriftsartikel (refereegranskat)abstract
- Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates.
|
|
| 8. |
- Sauquet, Herve, et al.
(författare)
-
Using fossils and molecular data to reveal the origins of the Cape proteas (subfamily Proteoideae)
- 2009
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 51:1, s. 31-43
-
Tidskriftsartikel (refereegranskat)abstract
- The angiosperm family Proteaceae is a distinct component of the Cape Floristic Region biodiversity hot-spot with 330 endemic species. Phylogenetic analyses of subfamily Proteoideae using sequence data from one nuclear and six plastid loci show that most of this diversity is contained in two distinct Cape floral clades. Molecular dating analyses, using Bayesian and penalized likelihood methods and four phylogenetically supported fossil age constraints. reveal contrasting histories for these two clades. The genus Protea belongs to a lineage that may have been in Africa since the Late Cretaceous but began to diversify in the Cape only 5-18 Myr ago. In contrast, the Leucadendrinae clade presumably arrived in the region no earlier than 46 Myr ago by long-distance dispersal from an Australian ancestor and the extant members of this clade began to diversify in the Cape 22-39 Myr ago. These results join a growing number of case studies that challenge the commonly accepted view that most of the Cape flora radiated synchronously in the Late Miocene and Early Pliocene when a Mediterranean climate settled in the region. (C) 2008 Elsevier Inc. All rights reserved.
|
|
