Phylogenetics is the New Genetics (for Most of Biodiversity)

Smith, Stacey; Pennell, Matthew W.; Dunn, Casey W.; Edwards, Scott V.

doi:10.1016/j.tree.2020.01.005

Cited by 87 publications

(92 citation statements)

References 66 publications

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“…Unfortunately, we understand little of the functional significance of plastid gene content outside of model organisms. We highlight the need for characterization of plastid genome evolution, further examination its relationship to life history traits, and the continued promise of comparative phylogenomic approaches [39] for shedding light on this enigmatic pattern.…”

Section: Discussionmentioning

confidence: 99%

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

et al. 2020

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Background: Plastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of pseudogenization and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context. Results: We find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the ndh complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional. Conclusions: Saniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, perhaps related to its extreme habitat specialization, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

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Section: Discussionmentioning

confidence: 99%

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

et al. 2020

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“…The above‐mentioned studies linking phenotypic to genotypic variation are restricted to a limited number of model systems that can be propagated and crossed in great numbers (Smith et al ., 2020). The vast majority of biological systems and plant–pollinator interactions is not part of this group, however.…”

Section: A Critical Review Of the Pollination‐syndrome Literature Fromentioning

confidence: 99%

“…Earlier this year, the extension of comparative methods to genotype‐to‐phenotype mapping approaches through the development of new software tools has been proposed (Smith et al ., 2020). This extension holds tremendous and exciting potential for pollination syndromes to more deeply investigate the questions and patterns outlined above in nonmodel organisms (Smith et al ., 2020).…”

Section: A Critical Review Of the Pollination‐syndrome Literature Fromentioning

confidence: 99%

Pollination syndromes in the 21^stcentury: where do we stand and where may we go?

2020

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Pollination syndromes, recurring suites of floral traits appearing in connection with specific functional pollinator groups, have served for decades to organise floral diversity under a functional-ecological perspective. Some potential caveats, such as oversimplification of complex plant-animal interactions or lack of empirical observations, have been identified and discussed in recent years. Which of these caveats do indeed cause problems, which have been solved and where do future possibilities lie? I address these questions in a review of the pollination-syndrome literature of 2010 to 2019. I show that the majority of studies was based on detailed empirical pollinator observations and could reliably predict pollinators based on a few floral traits such as colour, shape or reward. Some traits (i.e. colour) were less reliable in predicting pollinators than others (i.e. reward, corolla width), however. I stress that future studies should consider floral traits beyond those traditionally recorded to expand our understanding of mechanisms of floral evolution. I discuss statistical methods suitable for objectively analysing the interplay of system-specific evolutionary constraints, pollinator-mediated selection and adaptive trade-offs at microecological and macroecological scales. I exemplify my arguments on an empirical dataset of floral traits of a neotropical plant radiation in the family Melastomataceae.

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“…POInT, which we recently extended to allow the analysis of WGTs (Schoonmaker et al 2020), probabilistically infers the orthologous regions surviving from ancient duplications/triplications; it can be used to test for biases in fractionation without ad hoc assumptions. Moreover, POInT's models operate on complete genomes along a phylogeny (Dunn et al 2018;Smith et al 2020), helping to mask rearrangements in single genomes and giving larger synteny blocks (Emery et al 2018).…”

Section: Introductionmentioning

confidence: 99%

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

Hao

Mabry

Edger

et al. 2020

Preprint

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The members of the tribe Brassiceae share an ancient whole genome triplication (WGT), and plants in this tribe display extraordinarily high within-species morphological diversity. One proposed model for the formation of these hexaploid Brassiceae is that they result from a “two-step” pair of hybridizations. However, direct evidence supporting this model of formation has been lacking; meanwhile, the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. After adding this new genome to three others that are also descended from the ancient hexaploidy, we traced the history of gene loss after the WGT using a phylogenomic pipeline called POInT (the Polyploidy Orthology Inference Tool). This approach allowed us to confirm the two-step model of hexaploidy formation and to assign statistical confidence to our parental “subgenome” assignments for >90,000 individual genes. We show that each subgenome has a statistically distinguishable rate of homeolog losses. Moreover, our modeling allowed us to infer that there was a significant temporal gap between the two allopolyploidizations, with about one third of the total shared gene losses between the four analyzed Brassiceae species in the first two subgenomes prior to the arrival of the third subgenome. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a “mix and match” model of allopolyploidy, where subgenome origin drives homeolog loss propensities but where genes from different subgenomes function together without difficulty.

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Phylogenetics is the New Genetics (for Most of Biodiversity)

Cited by 87 publications

References 66 publications

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

Pollination syndromes in the 21^stcentury: where do we stand and where may we go?

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

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Phylogenetics is the New Genetics (for Most of Biodiversity)

Cited by 87 publications

References 66 publications

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

Pollination syndromes in the 21stcentury: where do we stand and where may we go?

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

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Product

Resources

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Pollination syndromes in the 21^stcentury: where do we stand and where may we go?