Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

May 20th, 2019
Folk, R. A., R. L. Stubbs, M. E. Mort, N. Cellinese, J. M. Allen, P. S. Soltis, D. E. Soltis, and R. P. Guralnick. 2019. Rates of niche and phenotype evolution lag behind diversification in a temperate radiation. PNAS 201817999. [View on publisher’s site]

Significance

Figure 1 from Folk et al 2019

Ancestral reconstruction across Saxifragales for PC1 of our dataset of 35 environmental variables; branches are colored in a rainbow scale from low ordinated values (red and yellow; hotter and to some extent wetter habitats, as well as the hottest arid habitats) to high ordinated values (green and blue; mostly colder and drier habitats). Black dots at nodes represent major ecological niche shifts (the upper 95th percentile of node–parent node differences). Red dots at nodes represent diversification shifts in the maximum credibility set. The inset density curves show tip rates for diversification (green), niche (orange), and phenotype (blue), all scaled from the minimum to the maximum reconstructed value. Around the edge are photographs of major representative habitats. Family codes are as follows: (a) Peridiscaceae, (b) Paeoniaceae, (c) Daphniphyllaceae, (d) Cercidiphyllaceae, (e) Altingiaceae, (f) Hamamelidaceae, (g) Iteaceae, (h) Grossulariaceae, (i) Saxifragaceae, (j) Cynomoriaceae, (k) Tetracarpaeaceae, (l) Aphanopetalaceae, (m) Penthoraceae, (n) Haloragaceae, and (o) Crassulaceae.

Alternative models of evolutionary processes suggest different associations between species diversification and trait evolution, but limited empirical evidence is available to test these models across large clades at global extents. Here we investigate the relative timing of species diversification and niche and phenotypic evolution across a global plant radiation (Saxifragales) with enormous phenotypic and habitat variation. We demonstrate strong temporal lags among rates, with increased diversification occurring first, followed by niche and phenotype. Accelerated diversification rates are coincident with mid-Miocene expansion of temperate biomes. Later increases in niche and phenotypic evolutionary rates argue against density-dependent diversification alone, indicating a major role for ecological opportunity. These results have broad implications for understanding diversification processes and the origin of present-day temperate biotas.

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Origin of angiosperms and the puzzle of the Jurassic gap

May 9th, 2019
Figure 1 from Li et al 2019Li, H.-T., T.-S. Yi, L.-M. Gao, P.-F. Ma, T. Zhang, J.-B. Yang, M. A. Gitzendanner, P. W. Fritsch, J. Cai, Y. Luo, H. Wang, M. van der Bank, S.-D. Zhang, Q.-F. Wang, J. Wang, Z.-R. Zhang, C.-N. Fu, J. Yang, P. M. Hollingsworth, M. W. Chase, D. E. Soltis, P. S. Soltis, and D.-Z. Li. 2019. Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants 1. [View on publisher’s site | Free PDF download]

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Darwin review: angiosperm phylogeny and evolutionary radiations

March 29th, 2019
Soltis Pamela S., Folk Ryan A., and Soltis Douglas E. 2019. Darwin review: angiosperm phylogeny and evolutionary radiations. Proceedings of the Royal Society B: Biological Sciences 286:20190099. [View on publisher’s site]

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Richie Hodel awarded Florida Museum Austin Award for Research

March 29th, 2019

Former lab member Richie Hodel was awarded the Florida Museum’s Austin Award for Research! Congrats Richie!

Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras

March 29th, 2019
Lorieul, T., K. D. Pearson, E. R. Ellwood, H. Goëau, J.-F. Molino, P. W. Sweeney, J. M. Yost, J. Sachs, E. Mata‐Montero, G. Nelson, P. S. Soltis, P. Bonnet, and A. Joly. 2019. Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras. Applications in Plant Sciences 7:e01233. [View on publisher’s site]

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Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass.

February 19th, 2019

A simplified example of how spike‐in standards can be used during read normalization to enable comparisons of expression level at different biological scales between a hypothetical diploid–polyploid pair with differing cell density. The large circles represent a unit of biomass and contain a number of cells (green squares). Beneath each circle is a depiction of how the read normalizations are calculated. Under a per transcriptome normalization, the ratio of target transcripts to the total transcriptome is compared. The per biomass normalization uses the ratio of the transcript of interest to the spike‐in transcripts. The per cell normalization also uses the ratio of the transcript of interest to spike‐in transcripts, but scales the spike‐in transcript abundance by cell density, represented here by multiplying the spike‐in abundance by the number of contributing cells. Whether the transcript of interest would be found as not differentially expressed (=) or upregulated (<) in the polyploid under each normalization is indicated (downregulated not included). DE: differential expression.

Visger, C. J., G. K.-S. Wong, Y. Zhang, P. S. Soltis, and D. E. Soltis. 2019. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. American Journal of Botany [View on publisher’s site]

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A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways.

February 13th, 2019
Zhao, D., J. P. Hamilton, W. W. Bhat, S. R. Johnson, G. T. Godden, T. J. Kinser, B. Boachon, N. Dudareva, D. E. Soltis, P. S. Soltis, B. Hamberger, and C. R. Buell. 2019. A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. Gigascience, doi: 10.1093/gigascience/giz005.

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Plastid phylogenomic insights into the evolution of Caryophyllales

February 12th, 2019
Graphical abstract of Gang et al 2019.Yao, G., J.-J. Jin, H.-T. Li, J.-B. Yang, V. Shiva Mandala, M. Croley, R. Mostow, N. A. Douglas, M. W. Chase, M. J. M. Christenhusz, D. E. Soltis, P. S. Soltis, S. A. Smith, S. F. Brockington, M. J. Moore, T.-S. Yi, and D.-Z. Li. 2019. Plastid phylogenomic insights into the evolution of Caryophyllales. Molecular Phylogenetics and Evolution, doi: 10.1016/j.ympev.2018.12.023.

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Nuclear genomes of two magnoliids

January 10th, 2019
Soltis, D. E., and P. S. Soltis. 2019. Nuclear genomes of two magnoliids. Nature Plants 5:6. [View on Publisher’s site]

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Biodiversity synthesis across the green branches of the tree of life.

January 10th, 2019
Figure 1 from paper

Global resources can be spatially, taxonomically or temporally subset to serve focused needs, as shown. The top rows in the inset show needed data resources, and the bottom row shows synthetic products, such as regional assessments of evolutionary diversity that inform about community processes and conservation priorities.

Allen, J. M., R. A. Folk, P. S. Soltis, D. E. Soltis, and R. P. Guralnick. 2019. Biodiversity synthesis across the green branches of the tree of life. Nature Plants 5:11. [View on Publisher’s site]

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