Double Your Pleasure: What Exactly Can You Get from Polyploidy?
Polyploidy, also known as Whole Genome Duplication (WGD), means having multiple copies of your chromosomes in your genome. For unknown reasons, many flowering plants are polyploid, but polyploidy is rare in animals, although animal hybrids are common. This much is uncontroversial.
The reasons for these observations are not fully understood, nor are the implications. We know that extra copies of chromosomes can occur accidentally during cell division and persist in some plant genomes, although their impacts on speciation are questionable (see Casey Luskin's explanation from ENV).
Darwinists get excited whenever natural selection gets more DNA to play with. Whether it occurs by well-known processes of gene duplication, hybridization or polyploidy, the thinking is that Darwin's tinkerer can keep the old genes working and play with the new genes, inventing new functions ("neofunctionalization"). How much more so when a whole copy of the genome becomes available! Some flowering plants have as many as ten copies of their genomes. Wow! Natural selection must be like a kid in a candy store. We say "wow" because Douglas E. Soltis did in a news item at Science Daily:
As Soltis explains, "If two plants with 12 chromosomes hybridized, you would expect the offspring to have 12 chromosomes, right? What if the offspring had 24 chromosomes? That is genome doubling -- every chromosome, every gene duplicated -- wow, 2X the genetic material to work with instantaneously!" (Emphasis added.)
Soltis is the lead author in an open-access paper in the American Journal of Botany, "The Polyploidy Revolution Then... and Now" focusing on the pioneering work of George Ledyard Stebbins (1906-2000). Stebbins represents the "Then" side of the title. The "Now" side is represented by two of the authors, Doug Soltis and Pamela Soltis, who have the second highest number of papers on polyploidy in the references. Their fellow Floridian Clayton J. Visger is the third author.
These evolutionists are all very enthusiastic about the potential for polyploidy to help with the speciation problem in evolutionary theory:
Polyploidy, or whole genome duplication (WGD), is now recognized as a major evolutionary force not only in plants, but also in all eukaryotes (e.g., Mable, 2003 ; Gregory and Mable, 2005). WGD generally results in instant speciation, increasing biodiversity and providing new genetic material for evolution (e.g., Levin, 1983 , 2002). Illustrating the broad impact of polyploidy, ancient WGD events have been documented in vertebrates (e.g., Ca�estro, 2012 ; Braasch and Postlethwait, 2012), fungi ( Kellis et al., 2004 ), and ciliates ( Aury et al., 2006 ); both recent and ancient events occur extensively in plants, particularly in lineages such as the angiosperms. In fact, researchers have long recognized that polyploidy is an inseparable part of angiosperm biology.
With "instant speciation" so readily available, there must be a lot of evidence for "endless forms most beautiful" arising by polyploidy. Let's do a word search to find them:
- "innovation" -- 0 hits
- "novel" or "novelty" -- 10 hits, discussed below
- "information" in terms of genetic information -- 0 hits
- "new species" -- 1 hit, only as a hypothetical
- "speciation" -- 5 hits, discussed below
- "creat-" stem -- 1 hit, only as a hypothetical
- "gain" as in gain of function -- 0 hits
- "adapt-" as in adaptation -- 4 hits, hypothetical or negative
- "positive-" stem, as in positive selection -- 0 hits
- "select" as in natural selection -- 4 hits, either negative or stabilizing selection
Our initial word search leaves us disappointed. In spite of over 60 hits on "evolution" or its derivatives in this paper, authored by 3 evolutionists obviously excited about the possibilities for speciation by polyploidy, we can't find any clear evidence for something new. In fact, the hero of the paper, Ledyard Stebbins, saw polyploidy as a drag on evolution:
Stebbins viewed polyploid species as genetically depauperate with limited evolutionary potential. A new polyploidy species was envisioned as forming via a single polyploidization event and would therefore exhibit a high degree of genetic uniformity across individuals. Following this model of formation, an allopolyploid would exhibit no homologous, or segregating, variation, only homeologous (nonsegregating) variation. Furthermore, if a mutation were to arise in the polyploid, its effect would be masked by either the presence of a homeologous locus (in an allotetraploid) or multiple alleles (in an autopolyploid). Although not impossible, the fixation of a new mutation is much slower in a polyploid than in its diploid parents. Stebbins (1971 , p. 127) correctly noted that "...the large amount of gene duplication dilutes the effects of new mutations... polyploids have great difficulty evolving truly new adaptive gene complexes" and that "...chromosome doubling will most often have a retarding effect on evolutionary change via mutation, genetic recombination, and selection." Furthermore, this buffering effect of multiple genomes may extend to the origins of morphological variation in a polyploid (Stebbins, 1950 , 1971 [pp. 147-148]): "Very often, even in complexes on which the basis of phytogeographical evidence must be regarded as hundreds of thousands or even millions of years old, the range of morphological variability encompassed by all of the tetraploids is less than the total range of that found among the diploids..."
The authors are quick to update this quote with newer findings from the genomic revolution: "We now know, however, that polyploid species typically arise via multiple origins, and this mode of formation has genetic consequences that offset the limitations perceived by Stebbins," they say. They point to new findings that show polyploids are "highly dynamic -- experiencing numerous genetic changes spurred on following polyploidization, including genomic shock and chromosomal, epigenetic, and expression-level changes." But each of those could be harmful, not creative.
Casey Luskin showed the best example he found on TalkOrigins of speciation by polyploidy: a change in coloration in a species of snapdragon-like flowering plant. That's pretty weak. Everybody knows that angiosperms are tremendously varied in their presentations of leaves, flowers, stems, growth habits, sizes, and environments, from the weeds under our feet to towering trees, from cacti to water lilies. Aren't there any better examples of new species arising by polyploidy? If so, they are not found in this paper by champions of polyploidy as "instant speciation" loaded with "new genetic material for evolution."
A closer look at their use of "novel" or "novelty" reveals a pathetic scene. It starts with grandiose claims that turn Stebbins's discouragement on its head. Here's the beginning of a section called "The New Polyploidy Paradigm":
As early as the 1980s, new perspectives began emerging that countered many aspects of the Stebbinsian paradigm. Levin's (1983) classic paper emphasized the role of polyploidy -- particularly autopolyploidy -- in generating novelty at a range of organizational levels. In response to Stebbins's statement that chromosome doubling is not a help but a hindrance, Levin (1983, p. 1) stressed that "the idea that chromosome doubling per se hinders progressive evolution becomes less tenable as information on autopolyploids increases". This seminal paper was then followed by another paper challenging traditional views of autopolyploidy (e.g., Soltis and Rieseberg, 1986 ). Subsequent reviews compiled emerging data on topics ranging from multiple origins of polyploid species to the dynamic nature of polyploid genomes (e.g., Soltis and Soltis, 1993, 1999, 2000; Wendel, 2000; Levin, 2002). The current polyploidy paradigm benefits much from the contributions of Stebbins and others (e.g., Clausen et al., 1945 ; Wagner, 1970 ; Grant, 1981), but many earlier perceptions have been overturned: polyploidy is ubiquitous in green plants, with all angiosperms and all seed plants of ancient polyploid origin; polyploids are not "deadends", but instead ancient polyploidy events are often associated with major clades; genetic factors contribute to the success of polyploids -- for example, polyploids typically form more than once with important long-term genetic consequences, and polyploid genome evolution is highly dynamic, with major changes that begin to occur rapidly following polyploidization; and autopolyploidy is common and a major force in plant evolution.
It appears that much of this celebration depends on discerning ancient polyploidy events from looking at existing genomes. Here and there, they say that a difference here "seems to be" an ancient polyploidy event, or a trait there "might" have arisen after polyploidy. One author tosses this causal salad: "ultimate success of the crown group does not only involve the WGD and novel key traits, but largely subsequent evolutionary phenomena including later migration events, changing environmental conditions and/or differential extinction rates." The problem with appeals to multiple causation can be illustrated by the student's excuse, "Either the dog ate my homework, it fell down a manhole, or I thought it was due next week." The statement does not link any of these situations to actual innovation by WGD.
What we read when looking for "novelty" are speculations and excuses:
- Beyond genomic and genetic attributes of polyploids, epigenetic properties may also contribute to variation and novelty in polyploids....
- Few studies have empirically shown autopolyploids to occupy novel niche space following formation.
Beyond that is a lot of hype and hope: grandiose statements about what polyploidy has done or could do, and hope for better understanding with future research:
Following the report of Levin (1983) and others, perhaps the most important conclusion from such ongoing studies is that polyploidy could propel a population into a new adaptive sphere, given the myriad changes that accompany genome doubling and lead to novelty (e.g., Soltis et al., 2014).
The same is true when looking at how they refer to "speciation." The notion seems to be, "We think we see an ancient polyploidy event in this genome, therefore its novel traits must be due to the polyploidy mechanism."
But correlation is not causation. If a plant is unique, and has duplicate chromosomes, it doesn't follow that the duplicate chromosomes caused the uniqueness. Many computer centers have extra copies of their backup tapes lying around. Those extra backup tapes don't build new rooms in the building or new factory robots. Where is evidence that innovative traits, like eyes or wings, come from copying already-existing genetic information?
Gene duplication may actually be a conservative process, allowing organisms to survive harsh conditions. Another article on Science Daily talks about work at Trinity College Dublin that showed evidence that "the products of gene duplication -- can survive across long evolutionary timescales, and allow organisms to tolerate otherwise lethal mutations." The copy might act like a mutational sponge, in other words. That could be viewed as a designed mechanism for genetic robustness. It's not the same as showing duplication to be an "evolutionary force" for innovation. That would be too hard to prove, the article admits: "understanding how duplication leads to biological innovation is difficult because evolution cannot be easily traced seeing as it occurs on timescales in the order of millions of years."
The Trinity College team believes that duplication can lead to innovation, but have not demonstrated it any more than the Florida team did. Like them, they merely assume that the extra DNA must have been the workshop for novel traits. Here, we see them making a flawed comparison to human civilization:
"Discovering the mechanism of innovation through gene duplication marks an exciting beginning for a new era of research in which evolution can be conducted in the laboratory and theories hitherto speculative tested," added Dr Fares.
"Our discovery also has implications for explaining the importance of redundancy in the human society as well. The role of increased redundancies in a fashioned job market in lenient economical conditions could lead, in crisis times, to the emergence of new companies, specialized workforces, and the optimization of individual capabilities, for example, although this requires a profound investigation."
But crisis times could just as easily lead to ghost towns. New companies with specialties and optimization don't just "emerge" from redundancies subjected to a crisis; that requires intelligent design.
Nowhere in any of these articles does anyone show actual novel traits caused by gene duplication. The evolutionists only think it could do so.
It seems they are hoping that polyploidy will rescue the mutation-selection process by throwing more DNA at it. But polyploidy itself can neither account for the original genetic information nor any novelty in the copies. The Florida team makes it clear in their conclusion that most of their belief is theoretical, with little tangible evidence to back it up:
Despite great progress in documenting the genomic and transcriptomic changes in polyploids relative to their diploid parents, we know little about the impact of WGD on the proteome (e.g., Albertin et al., 2006 , 2007; Gancel et al., 2006; Carpentier et al., 2011; Hu et al., 2011 , 2013; Kong et al., 2011; Koh et al., 2012; Ng et al., 2012). Given that the functional states of proteins in a proteome directly affect molecular and biochemical events in cells that determine phenotype, investigating how changes in gene expression profiles and AS events relate to protein-level changes is essential for understanding the molecular and evolutionary consequences of polyploidy, including molecular, biochemical, and physiological mechanisms that ultimately result in evolutionary change. Despite only a handful of proteomic studies of polyploids and their parents, some have revealed that the proteome of the polyploid does not always match the results predicted from the transcriptome alone; furthermore, novel proteins not found in either parent may be produced. These data point to the complexity of cellular-level plant processes, as well as the need for additional comparative analyses of the proteomes of polyploids and their diploid progenitor(s) (e.g., Gancel et al., 2006 ; Hu et al., 2011 , 2013; Kong et al., 2011; Koh et al., 2012; Ng et al., 2012).
The paper displays 6 single-spaced pages of references. It uses jargon like "subfunctionalization" and "neofunctionalization." Those are no substitute for evidence. If evidence for novelty were clear, they could have showcased some really good examples. Polyploidy may be reviving once again as "a lively topic of research and discussion," but it will take more than that for us to believe that new books arise from a copy machine.
We hope that this review will stimulate new research on unanswered questions raised by Stebbins, his predecessors and contemporaries, and those who have come since, and on new topics unimaginable even a decade ago.
Fine. Come back when your copy machine has spontaneously printed a new novel.