The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

December 6th, 2019
Marchant, D. B., E. B. Sessa, P. G. Wolf, K. Heo, W. B. Barbazuk, P. S. Soltis, and D. E. Soltis. 2019. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly. Scientific Reports 9. [View on publisher’s site]

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Predicting the Impact of Describing New Species on Phylogenetic Patterns

November 13th, 2019
Blackburn, D. C., G. Giribet, D. E. Soltis, and E. L. Stanley. 2019. Predicting the Impact of Describing New Species on Phylogenetic Patterns. Integr Org Biol, doi: 10.1093/iob/obz028.

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Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

November 13th, 2019
Godden, G. T., T. J. Kinser, P. S. Soltis, and D. E. Soltis. 2019. Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints. Genome Biol Evol, doi: 10.1093/gbe/evz239.

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Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)

November 13th, 2019
Carpenter, E. J., N. Matasci, S. Ayyampalayam, S. Wu, J. Sun, J. Yu, F. R. Jimenez Vieira, C. Bowler, R. G. Dorrell, M. A. Gitzendanner, L. Li, W. Du, K. K. Ullrich, N. J. Wickett, T. J. Barkmann, M. S. Barker, J. H. Leebens-Mack, and G. K.-S. Wong. 2019. Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). Gigascience 8. [View on Publisher’s site]

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One thousand plant transcriptomes and the phylogenomics of green plants

November 13th, 2019

Leebens-Mack, J. H., M. S. Barker, E. J. Carpenter, M. K. Deyholos, M. A. Gitzendanner, and One Thousand Plant Transcriptomes Initiative. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature, doi:

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Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

November 13th, 2019
Jantzen, J. R., W. M. Whitten, K. M. Neubig, L. C. Majure, D. E. Soltis, and P. S. Soltis. 2019. Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics. Ecology and Evolution 9:9479–9499. [View on Publisher’s site]

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Natural selection and repeated patterns of molecular evolution following allopatric divergence

November 13th, 2019
Dong, Y., S. Chen, S. Cheng, W. Zhou, Q. Ma, Z. Chen, C.-X. Fu, X. Liu, Y. Zhao, P. S. Soltis, G. K.-S. Wong, D. E. Soltis, and Q.-Y. Xiang. 2019. Natural selection and repeated patterns of molecular evolution following allopatric divergence. eLife 8. [View on Publisher’s site]

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Phylogenetic relationships of Coreanomecon (Papaveraceae: Chelidonioideae) inferred from seed morphology and nrITS sequence data

November 13th, 2019
Ghimire, B., Y. Suh, D. E. Soltis, and K. Heo. 2019. Phylogenetic relationships of Coreanomecon (Papaveraceae: Chelidonioideae) inferred from seed morphology and nrITS sequence data. Nordic Journal of Botany 37. [View on Publisher’s site]

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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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