Next‐generation lineage discovery: A case study of tuberous <i>Claytonia</i> L.

Stoughton, Thomas R.; Kriebel, Ricardo; O’Quinn, Robin

doi:10.1002/ajb2.1061

Cited by 23 publications

(37 citation statements)

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“…Support for branches of interest deteriorated further in Smith et al's [12] Montiaceae phylogeny, although this analysis covered all of Caryophyllales and was not optimized for finer scale phylogeny. Phylogenetic uncertainty may be mitigated by whole genome sequencing approaches (e.g., [4,27]), though in some cases in favor of reticulate rather than cladistic evolution (e.g., [27]). Reticulate evolution of genes implicates reticulate evolution of phenotypic traits, also.…”

Section: Characteristics Of Phca Methods Applied In Montiaceae Analysismentioning

confidence: 99%

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Perspectives from Montiaceae (Portulacineae) Evolution. II. Ecological Evolution, Phylogenetic Comparative Analysis, and the Principle of Evolutionary Idiosyncraticity

Hershkovitz¹

2018

Preprint

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The present paper reviews evidence for ecological evolution of Montiaceae. Montiaceae (Portulacineae) comprise a family of ca. 275 species and ca. 25 subspecific taxa of flowering plants distributed mainly in extreme western America, with additional endemism elsewhere, including other continents and islands. They have diversified repeatedly across steep ecological gradients. Based on narrative analysis, I argue that phylogenetic transitions from annual to perennial life history have been more frequent than suggested by computational phylogenetic reconstructions. I suggest that a reported phylogenetic correlation between the evolution of life history and temperature niche is coincidental and not causal. I demonstrate how statistical phylogenetic comparative analysis (PhCA) missed evidence for marked moisture niche diversification among Montiaceae. I discount PhCA evidence for the relation between Montiaceae genome duplication and ecological diversification. Based on the present analysis of Montiaceae evolution, I criticize the premise of the prevalent statistical approach to PhCA, which tests Darwinian deterministic hypotheses against stochastic evolutionary null models. I discuss theoretical/empirical evidence that evolution is neither stochastic, nor Darwinistically-determined, but idiosyncratic. Idiosyncraticity describes the outcome of a stochastically perturbed nonlinear chaos-like process. The Principle of Evolutionary Idiosyncraticity (PEI) is based on the evolutionary theory of Natural Drift, which maintains that determinism in evolution is a property of the organism and not, as maintained by the theory of Natural Selection, its traits or its milieu. This determinism is characteristic of chaotic functions, which are absolutely determinate, generate self-similarity, but remain absolutely unpredictable. PEI explains precisely observations that evolution proceeds not linearly, but chaotically, producing both quasi-linear fractal-like patterns and non-linear jumps. PEI has ramifications for all areas of macroevolutionary research. In particular, it demonstrates both the fallacy and futility of the statistical PhCA approach that interprets evolutionary causes in terms of evolutionary correlations. However, statistical methods of PhCA can be applied heuristically and fruitfully to reveal idiosyncraticity and discover evolutionary novelty. This, in turn, is demonstrated by the emergence of statistical anomalies in evolutionary analyses of Montiaceae.

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Section: Characteristics Of Phca Methods Applied In Montiaceae Analysismentioning

confidence: 99%

“…Tap-rooted caudiciformy in Claytonia is derived at least once and possibly twice from epicotyledonous tuberous forms [27,65]. One rhizomatous perennial species, C. washingtoniana, may have evolved from an annual, but might be a hybrid with rhizomatous C. sibirica [65].…”

Section: Montioideae-montieae-montiinaementioning

confidence: 99%

Perspectives from Montiaceae (Portulacineae) Evolution. II. Ecological Evolution, Phylogenetic Comparative Analysis, and the Principle of Evolutionary Idiosyncraticity

Hershkovitz¹

2018

Preprint

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“…Geophytic taxa are found throughout the plant tree of life and have a widespread geographic distribution, but are particularly diverse in Mediterranean ecosystems (Rundel, ; Hoffmann et al., ; Parsons and Hopper, ; Procheş et al., ). Although our overall knowledge of geophytes is slowly improving—in particular, the evolution of different underground traits (Patterson and Givnish, ; Wilson, ; Sosa et al., ; Stoughton et al., ) and the ecological factors controlling their distribution (Evans et al., ; Cuéllar‐Martínez and Sosa, ; Sosa and Loera, )—the economic and evolutionary importance of these taxa warrant increased scientific attention. To date, most studies pertaining to geophyte evolution have focused on a handful of taxonomic groups (Patterson and Givnish, ; Perret et al., ; Wilson, ; Oberlander et al., ; Evans et al., ; Sosa et al., ) or geographic regions (Pate and Dixon, ; Rundel, ; Hoffmann et al., ; Parsons, ; Parsons and Hopper, ; Cuéllar‐Martínez and Sosa, ; Sosa and Loera, ).…”

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confidence: 99%

The monocotyledonous underground: global climatic and phylogenetic patterns of geophyte diversity

Howard

Folk

Beaulieu

et al. 2019

American J of Botany

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Premise Geophytes—plants that typically possess a bulb, corm, tuber, and/or rhizome—have long captured the attention of hobbyists and researchers. However, despite the economic and evolutionary importance of these traits, the potential drivers of their morphological diversity remain unknown. Using a comprehensive phylogeny of monocots, we test for correlations between climate and geophyte growth form to better understand why we observe such a diversity of underground traits in geophytes. Understanding the evolutionary factors promoting independent origins of these potentially adaptive organs will lend insights into how plants adapt to environmental hardships. Methods Using a comprehensive phylogeny incorporated with global occurrence and climate data for the monocots, we investigated whether climatic patterns could explain differences between geophytes and non‐geophytes, as well as differences among bulbous, cormous, tuberous, rhizomatous, and non‐geophytic taxa. We used phylogenetically‐informed ANOVAs, MANOVAs, and PCAs to test differences in climatic variables between the different growth forms. Results Geophytes inhabit cooler, drier, and more thermally variable climates compared to non‐geophytes. Although some underground traits (i.e., bulb, corm, and tuber) appear to inhabit particular niches, a result supported by strong phylogenetic signal, our data has limited evidence for an overall role of climate in the evolution of these traits. However, temperature may be a driving force in rhizome evolution, as well as the evolution of taxa which we considered here as non‐geophytic (e.g., trees, epiphytes, etc.). Conclusions While precipitation patterns have played a role in the evolution of geophytism, our results suggest that temperature should be more strongly considered as a contributing factor promoting the evolution of belowground bud placement, specifically in rhizomatous and non‐geophytic taxa. Bulbous, cormous, and tuberous taxa need closer examination of other mechanisms, such as anatomical constraints or genetic controls, in order to begin to understand the causes behind the evolution of their underground morphology.

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“…16 species plus 12 additional subspecific taxa; tuberous to tap-rooted caudiciform perennials. Whole-genome DNA sequence sampling and analysis has revealed evidence of ancient hybridization and/or genetic lineage sorting among several species (Stoughton 2017b Ca. 18 perennial species plus six additional subspecific taxa of western North America, concentrated in California (Hershkovitz and Hogan 2002;Wilson et al 2005).…”

Section: A1b1 Claytoniasect Claytoniamentioning

confidence: 99%

Synopsis of a New Taxonomic Synthesis of Montiaceae (Portulacineae) Based on Rational Metadata Analysis, with Critical New Insights on Historically Poorly Understood Taxa and a Reevaluation of Historical Biogeography

Hershkovitz¹

2018

Preprint

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Montiaceae (Portulacineae) comprise a clade of at least 270 species primarily of western America and Australia. This work uses existing phylogenetic metadata to elaborate a new cladistic taxonomic synthesis, and clarifies morphological circumscriptions of several poorly known species. A total of 21 taxa are validated, seven new and 14 necessary nomenclatural recombinations). Hypotheses of Montiaceae historical biogeography and phenotypic evolution are evaluated in light of recent metadata.

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Next‐generation lineage discovery: A case study of tuberous Claytonia L.

Cited by 23 publications

References 54 publications

Perspectives from Montiaceae (Portulacineae) Evolution. II. Ecological Evolution, Phylogenetic Comparative Analysis, and the Principle of Evolutionary Idiosyncraticity

Perspectives from Montiaceae (Portulacineae) Evolution. II. Ecological Evolution, Phylogenetic Comparative Analysis, and the Principle of Evolutionary Idiosyncraticity

The monocotyledonous underground: global climatic and phylogenetic patterns of geophyte diversity

Synopsis of a New Taxonomic Synthesis of Montiaceae (Portulacineae) Based on Rational Metadata Analysis, with Critical New Insights on Historically Poorly Understood Taxa and a Reevaluation of Historical Biogeography

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