Rosa Rubicondior: Creationism in Crisis - Scientists Are Understanding More About How Plants Evolve and Diversify

Monday, 5 February 2024

Creationism in Crisis - Scientists Are Understanding More About How Plants Evolve and Diversify - No God-Magic Required

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression | Molecular Biology and Evolution | Oxford Academic

An effective way to refute the counter-factual claims of a wackaddodle cult like creationism is simply to reveal the facts and show how different they are to the cult beliefs. Sadly, this approach won't convince many creationists of course, especially those too arrogant to think their beliefs can be contradicted with mere facts, because part of being a creationist is to hold the self-idolatrous belief that your beliefs are inerrant, so trump anything science can produce, but one can but try.

In fact, researchers in biomedical sciences don't even try, they have more important things to do than try to convince fools who reject evidence before they see it and who are proud of the fact that nothing can make them change their minds. Scientists just discover the facts and add to the mountain of evidence that creationists have been conditioned to ignore or dismiss as lies or otherwise relegate to the realm of the unimportant.

For example, this week’s edition of Oxford University Press' journal Molecular Biology & Evolution has 10 different open access papers dealing with the minutia of evolution and not one of them shows any sign that the scientists are abandoning the Theory of Evolution as not fit for purpose and adopting instead, creationism's childish superstition complete with magic and unproven supernatural entities, as creationist cult leaders regularly tell their dupes.

None of these papers mention creationism or point out how the research findings refute it, of course, because they are written for people who understand the science, so don't need that to be pointed out to them. These are:

The last paper in particular deals with how plants evolve and radiate into distinct species, and even explains something that creationists claim to be impossible (although when pressed, they can never explain why) - macroevolution, i.e., the evolution of a new species.

Tell me all about the Penstemon genus, please. The genus Penstemon is a diverse group of flowering plants, commonly known as beardtongues, and is part of the family Plantaginaceae. These plants are native to North America, and they are particularly well-represented in the western United States. Penstemons are known for their tubular flowers, which often have a distinctive lip and are attractive to pollinators such as hummingbirds and bees. As of my last knowledge update in January 2022, there are over 270 recognized species within the Penstemon genus. However, taxonomy is subject to change, and new species may have been identified or classifications revised since then. Here are a few notable species within the Penstemon genus:

Penstemon digitalis - Also known as smooth white beardtongue, it has white tubular flowers and is native to eastern North America.

Penstemon spectabilis - This species, commonly known as showy penstemon, is native to the western United States and has vibrant pink to purple flowers.

Penstemon eatonii - Eaton's penstemon is found in various western states and is known for its bright red tubular flowers.

Penstemon barbatus - Scarlet bugler or beardlip penstemon, it has brilliant red flowers and is native to western North America.

Penstemon heterophyllus - Foothill penstemon, with blue to purple flowers, is native to California.

Penstemon palmeri - Palmer's penstemon, found in the southwestern United States, has showy spikes of lavender to pink flowers.

Subspecies and varieties within the Penstemon species can also exhibit variations in flower color, size, and growth habit. It's important to note that the taxonomy of plants, including the Penstemon genus, may be subject to updates and revisions as new research emerges. For the latest and most accurate information, consulting botanical databases, academic literature, or contacting botanical experts and institutions is recommended.

In this paper, the authors explain how evolutionary diversification and radiation into new environmental niches can be facilitated by hybridization, which can ingress new genes into the genome; by de novo mutation which cause a loss of genetic information (which is deemed to be impossible, by creationist dogma).

The team studies whole genome sequences of the Dasanthera subgenus of the Penstemon genus of humming-bird pollinated flowering plants and what they found was evidence of frequent hybridization events with ingression of beneficial alleles which can enhance the rate of evolution into new niches. They also found evidence of a change of pollinator from bees to hummingbirds was accompanied by a loss of the blue pigment which, together with a red pigment, had produced purple or violet flowers to give brighter magenta flowers, more attractive to humming birds. This had occurred twice by two different mechanisms in a case of convergent evolution. In one case, by a large deletion of about 500-pb of genetic information. This de novo mutation prevented the production of an enzyme essential for the production of the blue pigment, delphinin. In the second case and insertion of a 4-bp premature 'stop' codon by introgression from a related species with the same de novo mutation.

Details are provided in the abstract and introduction to their paper:

Abstract

Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie the parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.

Introduction

Adaptive radiation—the proliferation of ecological roles and adaptations in different species within a lineage—is an important process considered to play a central role in the generation of biodiversity on Earth (Simpson 1953; Schluter 2000; Givnish 2015). This phenomenon, which often coincides with an increase in the rate of lineage diversification (and is thus termed a “rapid” or “explosive” adaptive radiation), encompasses a number of well-known and charismatic taxonomic groups, including Darwin's finches, Anolis lizards, and cichlid fishes. Sustained interest in adaptive radiations from evolutionary biologists has, over time, revealed several genomic features characteristic of rapidly radiating clades. Principal among these is an abundance of phylogenetic discordance that, in depicting species’ complicated evolutionary histories, may more closely resemble a web than a bifurcating tree. This discordance may be chiefly caused by incomplete lineage sorting (ILS), which is expected to be abundant—potentially overwhelmingly so—when speciation occurs rapidly (Pamilo and Nei 1988; Maddison 1997; Rosenberg 2002; Whitfield and Lockhart 2007). Rapid adaptive radiations are also commonly characterized by introgression between closely related species that have not had much time to develop barriers to reproduction. Given that introgressed genetic material may confer fitness effects and can be subject to strong selection, particularly in functionally important genomic regions (Moran et al. 2021), signatures of introgression are expected to be distributed heterogeneously across the genome (Harrison and Larson 2016; Martin and Jiggins 2017). Introgression may provide a source of genetic diversity in adaptive radiations (Edelman and Mallet 2021.1), and although its importance in this context has historically been somewhat controversial (Seehausen 2004), many recent efforts have highlighted the myriad ways in which introgression may effectively broaden the genomic substrate for adaptation through novel combinations of haplotypes (e.g. McGee et al. 2020; Ferreira et al. 2021.2; Ronco et al. 2021.3; De-Kayne et al. 2022; Suvorov et al. 2022.1; Cicconardi et al. 2023; Marcionetti and Salamin 2023.1).

In addition to widespread ILS and introgression, radiations also often feature patterns of repeated evolution, which may be either the result of the adaptive introgression of beneficial alleles or independent (convergent) adaptation in disparate lineages to similar ecological conditions.

While adaptive divergence progresses in adaptive radiations through complex interplays of standing genetic variation, introgression, and de novo mutation, it is standing or preexisting variation (often introduced through introgression) that is often implicated as the most important source of genetic variation underlying repeated or parallel evolution (Berner and Salzburger 2015.1; Haenel et al. 2019; Marques et al. 2019.1; Marques et al. 2022.2). Yet, it is clear that the repeated generation of similar phenotypes in ecologically similar habitats—a hallmark of adaptive radiation—is also driven by de novo mutation. For example, both processes appear to be important in the radiation of hares (genus Lepus), in which the repeated evolution of nonwhite winter coats has proceeded through both adaptive introgression (Jones et al. 2018; Giska et al. 2019.2) and independent loss-of-function (LOF) mutations at the Agouti pigmentation gene (Jones et al. 2020.1). Whether adaptation more often involves de novo versus standing variation informs whether trait evolution is constrained by mutation events or by the opportunity for hybridization between differentiated lineages (Marques et al. 2019.1). Empirical data from diverse lineages across the tree of life are needed to identify common genetic features of adaptive radiations.

The genus Penstemon is an adaptive radiation of North American angiosperms, which exhibits an astonishing array of phenotypic and ecological diversity across its nearly 300 described species. Many Penstemon species are interfertile and form hybrids in nature, fueling speculation that interspecific hybridization has played a major role in the diversification of the group (Straw 1955; Wolfe et al. 2006; Wessinger et al. 2016.1). Penstemon is also recent and rapid radiation, estimated to have originated 1.419 to 6.416 MYA (Wolfe et al. 2021), and this rapid speciation has been highlighted as a potential major source of genealogical discordance (due to ILS) in addition to discordance caused by interspecific hybridization (Wolfe et al. 2006; Wessinger et al. 2016.1). Within Penstemon, the subgenus Dasanthera (hereafter, “Dasanthera”) includes 9 ecologically diverse species and represents an adaptive radiation in microcosm. This group includes several species that hybridize in nature, making it an attractive system in which to study the importance of introgression and de novo mutation on adaptive divergence. A primary axis of variation in Dasanthera is floral pollination syndrome, wherein 2 hummingbird-adapted species (Penstemon newberryi and Penstemon rupicola) have evolved from the ancestral state of hymenopteran-adapted flowers (Datwyler and Wolfe 2004.1; Wilson et al. 2004.2; Kimball 2008). This mirrors a genus-wide trend involving the repeated evolution of specialist hummingbird-adapted flowers from more general hymenopteran-adapted progenitors (Wilson et al. 2007.1). The hummingbird-adapted species P. newberryi and P. rupicola each form hybrid zones with the hymenopteran-adapted, high-elevation Penstemon davidsonii; in each case, the hummingbird-adapted species occupies a lower elevation zone, and hybrids are formed and persist at intermediate elevations in the Cascades and Sierra Nevada Mountains where the parent species’ distributions overlap. Previous studies indicate that P. newberryi and P. rupicola are not sister species, suggesting parallel divergence in elevational tolerance and pollinator adaptation within Dasanthera (Stone and Wolfe 2021.5; Stone et al. 2023.2). An alternative scenario is that hummingbird pollination syndrome in Dasanthera could have a single evolutionary origin shared between species through introgression. Such a scenario has occurred in other plant groups; for example, the introgression of a MaMyb2 allele has led to repeated origins of red-flowered phenotypes in the Mimulus aurantiacus species complex (Stankowski and Streisfeld 2015.2; Short and Streisfeld 2023.3).

Floral syndrome divergence in Dasanthera involves changes in floral morphology (hummingbird-pollinated: long, narrow flowers with exserted stamens and styles; hymenopteran-pollinated: short, wide flowers with inserted stamens and styles), and perhaps most strikingly, the evolution of bright magenta flowers in hummingbird-pollinated species from ancestral hymenopteran-pollinated blue-violet flowers. Whereas little is currently known about the underlying genetic mechanisms for floral morphological shifts, the evolution of red flowers tends to involve predictable changes to the genetic pathway for anthocyanin production. In other groups within Penstemon, shifts toward redder floral hues often involve the functional inactivation of the anthocyanin pathway enzyme flavonoid 3′,5′-hydroxylase (F3′5′H) (Wessinger and Rausher 2014; Wessinger and Rausher 2015.3). F3′5′H belongs to the functionally diverse superfamily of cytochrome P450-dependent monooxygenases. This enzyme catalyzes the hydroxylation of the B-ring of anthocyanins, leading to the production of blue-colored delphinidin-based pigments (Tanaka and Brugliera 2013). The degeneration of F3′5′h prohibits the production of delphinidin and has been shown in Penstemon to result in flowers that produce red pelargonidin-based anthocyanins; importantly, the evolution of red flowers in multiple Penstemon species appears to be the result of repeated de novo LOF mutations to the F3′5′h coding sequence (CDS) (Wessinger and Rausher 2014; Wessinger and Rausher 2015.3).

In this study, we used whole-genome resequencing data to trace the evolutionary history and source of genetic variation for hummingbird-pollinated flowers in Dasanthera and characterize genome-wide patterns of introgression. Signatures of introgression were uneven across the genome and were generally lower in gene-rich regions, suggesting that even in this very recent radiation, introgression often may be maladaptive. We found strong support for independent evolutionary origins of magenta floral pigments in the 2 hummingbird-pollinated species. These parallel shifts in floral pigment production are accompanied by distinct degenerative mutations to the F3′5′h CDS. While introgression is prevalent within Dasanthera, we found little evidence that the 2 hummingbird-pollinated species share a history of introgression; this suggests that despite the importance of introgression across Dasanthera generally, it is de novo mutation, and not adaptive introgression, that likely fuels parallel shifts to hummingbird pollination in this adaptive radiation.
Fig 1.
Sampling sites, species relationships, and anthocyanin pigmentation data for sampled Dasanthera taxa. Left: sampling localities for all ingroup samples included in this study. Right: 10-kb genomic window ASTRAL species tree, where tips are individual samples as shown on the map. Numbers on nodes indicate ASTRAL quartet support/gCFs/sCFs, respectively. All ASTRAL local posterior probabilities are 1. Circles at select nodes denote focal internal branches. Magenta and blue-violet squares indicate floral anthocyanidins produced by each sample; pigment extraction was unsuccessful for samples without squares. Inset shows a simplified cartoon version of the anthocyanin biosynthesis pathway where F3′5′H functions to convert the precursor of cyanidin (dihydroquercetin [DHQ]) into the precursor of delphinidin (dihydromyricetin [DHM]). Arrows indicate enzymatic reactions.

Benjamin W Stone, Carolyn A Wessinger,
Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression,
Molecular Biology and Evolution, 41(1) 2024, msae007, https://doi.org/10.1093/molbev/msae007

Copyright: © 2024 The authors.
Published by Oxford University Pres on behalf of Society for Molecular Biology and Evolution. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Of special note for creationists to ignore, on top of the complete dependence of the biologists on the TOE to explain the results, with no hint of abandoning it, and indeed the perfect fit of those results with the TOE, is the evidence of a beneficial loss of genetic information; beneficial in the context of pollination by humming birds which see different spectra to bees, enabling the transition from bee-pollination to bird-pollination in the genus.

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Rosa Rubicondior

Monday, 5 February 2024

Creationism in Crisis - Scientists Are Understanding More About How Plants Evolve and Diversify - No God-Magic Required

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