Polyploidy and the Genome (Research Article)

Polyploidy and the Genome (Research Article)

Building on the last article’s discussion of heredity and the genome, we need to take some time and discuss polyploidy. Polyploidy is probably a foreign word to many of you but it is a fairly straightforward word to understand. The prefix “poly” means many or multiple. The word “ploid” comes from Greek and roughly translates as “fold”[1]. Thus, the word “polyploid” means many folds.

In practice, polyploidy is used in reference to having extra chromosomes in the genome.  This increase in chromosome number can be genome-wide or limited to just one chromosome.  For example, in humans, Downs Syndrome is caused by a condition called trisomy-21, which involves a child having three chromosome twenty-ones instead of two which is what diploid humans usually have.  Normal humans have 46 chromosomes. Downs Syndrome individuals have an extra chromosome. If it is a single chromosome increase, it is generally called trisomy instead of polyploidy. Polyploidy is generally reserved an extra copy of every chromosome in the genome. While Downs Syndrome is clearly deleterious not all polyploidy is as easy to classify.

Animal Polyploidy

 It has been known for years the polyploidy is relatively uncommon in animals, though this has been challenged in recent years[2]. The reasons for this have been hotly debated. Orr proposed that polyploidy is harder to maintain in animals because the extra Y chromosome in males tended to break down easily[3].  Others have pointed out that, even if a polyploid animal were to arise, it would almost certainly be reproductively isolated and the likelihood of a polyploid individual of the opposite gender arising in the same population is incredibly low. Still others have postulated that because animals reproduce sexually, polyploidy is not favored. However, a final answer to why the rarity exists is still elusive[4].

However rare, polyploidy does arise in animal genomes.  One mechanism for polyploidy is hybridization.  Using a loach (a type of fish) species, researchers were able to induce polyploidy in the lab by simple hybridization[5]. However, in this instance, the resultant polyploid offspring were unable to reproduce sexually.  The females laid diploid eggs that were clones of themselves.  The resultant offspring were bred with adults from both species. When sperm cells actually fertilized the eggs, the results were triploid individuals. When sperm simply triggered the female to spawn but did not actually fertilize the egg, the result was a clone of the female.   While the researchers did not attempt it, it would be interesting to know if the male and female triploid fry could breed and produce stable offspring. This matters because it affects whether a new species can be produced or not. It would also have been interesting to know how well the triploid results would survive in the presence of the wild type.  There is potential for further research in this area.

Another study demonstrated that new species of freshwater snails had arisen due to polyploidy[6]. Polyploid species have also been observed in other fish, such as barbs[7] and, lungfish, perch, and salmon[8]. Parthenogenic animals are the most frequently observed polyploid creatures, but other animals, as we have seen, are not immune to polyploidy[9]. Other polyploid animals include insects, mollusks, amphibians, reptiles, and mammals[10].

Polyploidy is important because it produces reproductive isolation, almost by default.  Reproductive isolation is a key part of the definition of the biospecies.  Speciation by means of polyploidy has been known in plants for a very long time. Mayr considered it “…one of the important mechanisms of speciation in the plant kingdom.[11]” Coyne and Orr concur, writing “…polyploid speciation is instantaneous, sympatric, and may often involve population bottlenecks.[12]” The population bottlenecks Coyne and Orr mention occur because of the small population sizes available when they arise.  This means generally a low amount of genetic variability in these species. Perhaps this is the reason that polyploid species go extinct more quickly than their diploid counterparts[13].

With all these polyploid animals that we know exist in the world, it is logical to ask whether polyploidy is a blessing or a curse. Does polyploidy confer an advantage to animals or is it disadvantageous? Most of the literature on this topic points out that animal polyploids, particularly in vertebrates, typically die in the womb[14].  In a few prokaryotes, there is some postulated advantage, but in general, polyploidy in animals has been considered negative[15]. However, this consensus is beginning to fade.  As noted previously in this article, polyploid animals are beginning to be noticed and recognized, even in mammals[16][17]. This leads to a very obvious observation. Polyploidy cannot be as deleterious in animals as has been believed. This does not mean that polyploidy is not deleterious, however. Instead, polyploidy might be considered a minor nuisance rather than a fatality, if it is even deleterious. I will not delve much deeper into animal polyploidy here, as it is likely new information will be brought to light in the next few years that will change our understanding of animal polyploidy.

Plant Polyploidy

 While animal polyploidy is just beginning to be understood, plant polyploidy has been well known and well documented for decades.  Some estimates state that upwards of seventy percent of the plant species are polyploid or of polyploid origin[18]. While these numbers are undoubtedly high, since they are based on a universal common ancestor for plants, there is no doubt that plant polyploidy is a common occurrence. Even throwing out common ancestry, one study estimated that somewhere between twenty-five and thirty percent of flowering plants are polyploid[19].  This number is likely to change however as molecular data improves and more information is gained about polyploid plants and how they arise[20]. As a side note, while they are not plants, polyploidy also appears to be quite common in fungi[21].

Polyploidy in plants is a common mechanism of speciation.  Yet Mayr regarded polyploidy as a problem rather than a simple, straightforward speciation event.  “Polyploids pose a difficult taxonomic problem. An autopolyploid may be virtually indistinguishable, at the time of origin, from the parental diploid.  Such a form is often referred to as a “polyploid race”…Yet such a “race” is reproductively isolated from the parental species and is, biologically speaking, a good species.[22]” This would seem to imply that polyploid speciation is instantaneous, an idea Coyne and Orr concurred with in their 2004 book.

Plant polyploidy appears in just about every major plant group but is most prominent in angiosperms. In some cases, researchers have suggested that a given angiosperm has undergone multiple rounds of polyploidy before reaching its current state[23]. Other authors have postulated that every single flowering plant has undergone at least one polyploid generation in the past[24]. While this is unprovable, it is still a remarkable testament to how common polyploidy is among plants.

Plant polyploids are postulated to be at least situationally more evolutionarily fit to survive than their diploid cousins[25].  This fitness varies from being able to adapt more easily, to being able to survive mutations more easily. This is believed to enable the polyploids to gain new habitats. However, there is no consensus on this purported increase in fitness. One recent study found little evidence for such a claim[26]. The increase or decrease of plant polyploid fitness remains controversial for the moment.

That said, polyploidy in plants and even animals is far more beneficial than the duplication of a single chromosome. As mentioned earlier in this chapter, having a duplication of a single chromosome is almost universally bad.  There are multiple trisomy disorders in humans alone, all of which are negative[27]. A whole genome duplication (WGD) as polyploidy is known in the literature has been postulated to be at least partially positive. Why the difference? Numerous reasons have been postulated.  One explanation is that the extra chromosomes provide a sort of malleability to the genome, enabling it to survive the duplication. Others have postulated that by duplicating the whole genome, balance is maintained, preventing damage.  The two explanations are not mutually exclusive[28].  In fact, they could work together quite well.  However, neither hypothesis has been demonstrated as yet.

While trisomy is undoubtedly negative, some aspects of polyploidy have been studied and have been deemed beneficial to the plant.  One studied concluded that polyploidy played a role in the ability of plants to become invasive, though the link was not strong and the exact role not firmly established[29]. Another group of authors examined a connection between the level of polyploidy and parasite resistance and found limited evidence that polyploidy was beneficial to immune responses in plants[30]. Because polyploid plants tend to self-fertilize more often than their diploid progenitors, it has been speculated that they have a slight reproductive advantage and enable them to establish populations more easily. This, while theorized, has not been completely confirmed as yet[31].

As we have seen, even the postulated benefits from polyploidy are either ambiguous or disputed. Thus calling polyploidy beneficial across the board seems a bit tentative at this point, but then, so is calling it negative. Our understanding of polyploidy continues to grow, however, and in the next fifty years, I suspect that we will be able to reach a much better conclusion on that subject than we can at present.

Polyploid Speciation

 Polyploid speciation occurs regularly in the wild. It is aided by the fact polyploidy does not usually require geographical isolation to become reproductively isolated. Instead, often simply becoming polyploid is enough to reproductively isolate the offspring. However, this is not always the case, as some researchers studying the mustard family discovered in 2008[32]. Thus, based on Mayr’s biospecies, that particular example did not produce a new species.

Polyploid species can arise in two ways. The first is a process called autopolyploidy.  Autopolyploidy involves a mistake in gamete formation in both parents. Instead of splitting the chromosomes and putting them in separate gametes, the chromosomes remain together and end up creating diploid gametes instead of haploid gametes. When these diploid gametes combine and develop into an offspring, the offspring will be tetraploid.  Tetraploid offspring will then produce diploid gametes, resulting in a new, tetraploid species.

The second mechanism, which is slightly more complicated, is allopolyploidy. Allopolyploidy is a much more difficult path to a new species. The offspring produced are sterile in most cases, particularly when chromosome numbers in the original were odd.  However, if an allopolyploid offspring produce gametes that are diploid, rather than haploid, they can breed with each other and produce a tetraploid species.  Alternatively, they can produce a diploid gamete and breed with one of the parent species to produce a triploid, usually sterile, offspring.  However, it is possible to take this triploid hybrid and cross it back to one of the parents and occasionally produce viable offspring, which would then create a new species with a chromosome number equal to the sum of chromosomes in the original parents[33].

Regardless of the mechanism, speciation by means of polyploidy does occur and creates a new species within a couple of generations. Evolutionists regularly acknowledge this. “Polyploidy provides a rapid route for species evolution and adaptation.[34]” However, just because polyploids can speciate rapidly, does not mean that polyploid species will create new species faster than their diploid cousins[35].   This holds true, in absence of another whole genome duplication event which would start the speciation process all over again.

It turns out that speciation in quite a few plants is based in part, at least, on polyploidy. In cord grass of genus Spartina for example, hybridization between species and polyploidy produced numerous varieties, including some tetraploid species. However, in this genus, hybridization is believed to have been the primary mover in speciation[36]. In ivies, however, polyploidy played a major role in speciation. In genus Hedera there are “…six diploid, two tetraploid, three hexaploidy, and one octoploid species.[37]” Obviously polyploidy has a major influence in forming new species in this genus. Yarrows are another group where polyploidy played a major role in forming the existing species and doing so rapidly[38].  Other groups that have at least some rapid polyploid speciation include the sunflowers, ferns, and mustards, among others. A full list would be extensive. The important point is that polyploid speciation occurs regularly in plants and does so quickly, in some cases one to two generations[39].

Plants are not the only life forms that undergo polyploid speciation.  Some treefrogs undergo it as well.  The American native Gray Treefrog has been postulated for two decades to have originated by means of autopolyploidy[40]. Yeasts also undergo speciation by polyploidy, though calling yeasts “species” is stretching the limits of the biospecies[41]. Coyne and Orr point out that “Evolutionists now appreciate that no single species concept can encompass sexual taxa, asexual taxa, and taxa having mixed modes of reproduction.[42]” As pointed out in chapter 2, the biospecies does not work well for microbes.

Polyploid speciation, as mentioned above, proceeds very rapidly.  Rapid speciation presents solid evidence for Biblical creation, and the baramin, which predictably makes evolutionists angry.  Some of them have attempted to explain away the rapid rate, using punctuated equilibrium proposed by Gould and Eldredge. “The tempo of speciation in the fossil record unquestionably agrees with that predicted by the theory of punctuated equilibrium.[43]” In other words, species appear rapidly. However, arguing over speciation rates is missing the point because as we demonstrated in article three, defining a species is completely arbitrary.  The species is not a unit of nature, so really, evolutionists even attempting to argue the impossibility of creation based on the extant number of species is absurd. There is no hard number of species because the species is not real in nature, it is only real in the minds of scientists.

Polyploidy in the Beginning?

Since plant genomes demonstrate a certain amount of plasticity and tolerate polyploidy very well, it is reasonable to ask if at least some plants were created polyploid.  Based on the high rates of polyploidy in plants, this is a legitimate question.  Since we do not observe the original state of creation, this is not something that we can observe in the present. To make a determination on this, we need something we can observe in the present.

If polyploidy were created in an original baramin, we would expect that a sizeable majority of the baramin would exist in a polyploid state today. Further, we would expect multiple levels of ploidy in the baramin.  The reason we would expect this comes from genetics. If a kind was created tetraploid, it would produce diploid gametes. However, what we observe is polyploid levels change due to mistakes in the formation of gametes. If, in the post-fall world, a tetraploid kind had a malfunction in gamete formation and produced a triploid and a haploid gamete, the resultant offspring would be hexaploidy and diploid. Whether those offspring could survive or not is debatable, but even if one could, a new polyploid level is created and likely a new species.  These predictions can be tested by simply examining known created baramins and seeing how they compare.

This is where we run into problems. Not many created baramins have been delineated as noted previously, due to lack of research. However, some plant baramins have been delineated. Dr. Todd Charles Wood has published numerous plant baraminology studies. While I do not subscribe to Dr. Wood’s preference for statistics over hybridization and genomic studies to determine the baramins in living creatures, he is one of the few doing baraminology work and covering plants. In one of his books, he presented twenty-two baraminology studies for plants[44]. While not all of them were conclusive, there were some that we can use to determine polyploidy in the original created kinds.

One of the baramins delineated by Wood was the birthworts, family Aristolochiaceae. Polyploidy studies have been done on this particular family. One particular genus, which contains the majority of the species, has a vast variety of chromosome numbers, including some hexaploids[45].  However, in this instance, it seems unlikely that polyploidy was the original state of the created kind, as only one genus in the family is heavily ploidized, and an evolutionary phylogenetic study indicates only a few polyploidy events in the past[46]. While the article is heavily weighed down with evolutionary dogma and I generally am suspicious of cladistics in general, they make a valid point because the ploidy is contained in one genus. This baramin was likely created diploid.

The madder family has been extensively studied in secular literature and with good reason. It is the fourth largest family of flowering plants and is found throughout the world. However, the most likely reason why this family has been extensively studied is probably sitting on your kitchen counter.  The madder family contains coffee.  Since coffee is a staple of American life, this family has been subjected to a lot more studies than the average plant family.  In the context of polyploidy, the family exhibits a vast array of chromosome numbers, which have likely been derived through polyploidy[47]. They come in tetraploid, and diploid variants and, according to evolutionary phylogeny, multiple lineages have resulted in polyploidy[48]. Based on this information, it is possible that the madder family was created polyploid in the original. However, this cannot be determined definitively.

The conifer family Cupressaceae was also studied. This family contains the junipers, redwoods, and several other conifer variants. Polyploidy in conifers, in general, is very rare[49].  While polyploidy can be induced in this family for decorative purposes[50], most of the family is not polyploid, with the notable exception of the coast redwood which is hexaploid[51]. Given the low incidence of polyploidy in this family, it is very unlikely that it was polyploid in the beginning.

One final example is the family Alstroemeriaceae, a flowering plant family most known for the Peruvian Lilies. Chromosome number variation in this family is quite small, varying only by four[52]. No polyploids are known from at least one genus[53]. Being that this is a small family, to begin with, this kind was likely created diploid.

Based on this admittedly small sample, we can see that polyploidy was not the created form in the majority of thus far delineated baramins.  The madder family is the only one of the four that could potentially have been created polyploid.  This matters because of the heterozygosity.

The madder family is quite large, while the other three families are quite small for plant baramins.  This leads to the obvious assumption that the madder family is more diverse in form than the other three. The madder family does display great diversity, containing trees, shrubs, and herbs. To diversify to this point from one originally created kind, a massive amount of genetic information would have been required. Adding extra two copies of the genome doubles the potential alleles in the genome. Assuming normal Mendelian genetics are in play, a pair of diploid creatures that are heterozygous for a given trait can create four different combinations and thus potentially four different phenotypes.  However, if those same two individuals are heterozygous tetraploids, instead of four possible alleles, there are eight. This means each parent passes four alleles to their offspring, leading to sixteen separate combinations of alleles, meaning sixteen potential phenotypes[54].  Doing this for several generations could easily produce herbs, shrubs, and trees based on one created kind. While it is not as simple as this due to rates of recombination and linkage between alleles, it gives a general idea of how much variation could be produced by a tetraploid original kind. Since a change in ploidy level almost always results in an instant speciation event, having this increased amount of information built into the created kind would have resulted in a vast variety of species as ploidy levels changed. Traits would have split and changed ploidy level, resulting in an incredible number of phenotypes and species, some separated by ploidy level, some separated by conventional variation.

Polyploidy and Baramins

 How does polyploidy relate to the created kinds? Why does polyploidy matter in the broad scheme of things, particularly related to the baramin? It matters for a number of reasons, particularly if it was built into some of the original kinds.

Polyploidy seems to be a net neutral. It appears in most living forms, from plants to animals, to even fungi and microbes.  There are some postulated benefits to polyploidy as well as some negatives. Both are somewhat unclear at this point as most of the research into polyploidy has been based on delineating species and evolutionary fitness, rather than phenotypic success.  Determining whether polyploidy is deleterious or not is an area where further research is needed.

Even if it is determined for a given organism that polyploidy is harmful, that explanation may not apply to every kind. As we have seen in the madder kind above, polyploidy may have been the original created kind and diploid speciation occurred post-fall. I will emphasize that this claim is not made dogmatically. There is inferred evidence that polyploidy could have been the created state in some of the created kinds.  However, until there is stronger evidence, it cannot be held to fervently.  That said, given the possibility that polyploidy could have been part of some of the original baramins, it is unwise to make sweeping statements about the relative goodness of polyploidy.  This is particularly true in light of God calling His creation “very good”[55].  If polyploidy is universally deleterious and it was created in the original baramin, then the creation was not “very good” and God is a liar, something no Christian should claim.  Thus before making any sweeping claims about polyploidy, we should await further research.

The information presented in this article points to polyploidy as a potential speciation mechanism. However, as mentioned in the preceding chapter, there is a hard limit to variation. Even if the aforementioned tetraploid plant was completely heterozygous and had eight separate alleles for the same trait, there is still a hard limit to the variation.  Even combining those alleles gives a finite number of combinations and could not produce phenotypes, for which there are no alleles. Only separate groups of individually created kinds could explain the vast variety we observe in the world today.  Polyploid speciation is not the answer for evolutionists.

 

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[42] Coyne and Orr, 2004.

[43] Niklas, 1997.

[44] Todd Charles Wood, Issues in creation: Animal and Plant Baramins  Eugene, OR: WIPF & Stock, 2008

[45] Regina Berjano, Fernando Roa, Salvador Talavera, and Marcel Guerra. “Cytotaxonomy of diploid and polyploid Aristolochia (Aristolochiaceae) species based on the distribution of CMA?DAPI bands and 5S and 45S rDNA sites.” Plant Systematics and Evolution Volume 280 (2009) Pages 219-227. http://personales.us.es/regina/uploads/publications/Berjano%20et%20al,%202009%20(2).pdf

[46] Tetsuo Ohi-Toma, Takashi Sugawara, Hiroko Murata, Stefan Wanke, Christoph Neinhuis, and Jin Murata. “Molecular Phylogeny of Aristolochia sensu lato (Aristolochiaceae) based on Sequences of rbcL, matK, and phyA Genes, with Special Reference to Differentiation of Chromosome Numbers.” Systematic Botany Volume 31, No. 3 (2006) Pages 481-492. https://www.researchgate.net/profile/Stefan_Wanke/publication/232273432_Molecular_Phylogeny_of_Aristolochia_sensu_lato_Aristolochiaceae_based_on_Sequences_of_rbcL_matK_and_phyA_Genes_with_Special_Reference_to_Differentiation_of_Chromosome_Numbers/links/0fcfd507fba70c03f9000000.pdf

[47] Lee Yoo Sung “Remarks on Chromosome Numbers in Rubiaceae.” Korean Journal of Plant Taxonomy Volume 9, Nos 1,2. (1979) Pages 57-66. https://www.e-kjpt.org/upload/pdf/0i800067.pdf

[48] Friedreich Ehrendorfer, Rosabelle Samuel, and Wilhelm Pinsker. “Enzyme analysis of genetic variation and relationships in diploid and polyploid taxa of Galium (Rubiaceae).” Plant Systematics and Evolution Volume 202 (1996) Pages 121-135. https://botany.natur.cuni.cz/fer/markers/papers/Enzyme%20analysis%20of%20genetic%20variation%20and%20relationships%20in%20diploid%20and%20polyploid%20taxa%20of%20Galium%20(Rubiaceae).pdf

[49] M. Raj Ahuja “Polyploidy in Gymnosperms: Revisited.” Silvae Genetica Volume 54 No. 1-6. (2005) Pages 59-69. https://content.sciendo.com/view/journals/sg/54/1-6/article-p59.xml

[50] Ryan N. Contreras. “A simple Chromosome Doubling Technique is Effective for Three Species of Cupressaceae.” HortScience Volume 47, No. 6 (2012) Pages 712-714. http://hortsci.ashspublications.org/content/47/6/712.full.pdf

[51] M. R. Ahuja and D.B. Neale. “Origins of Polyploidy in Coast Redwood (Sequoia sempervirens (D.Don) ENDL.) and the relationship of Coast Redwood to other Genera of Taxodiaceae.” Silvae Genetics Volume 51, No. 2-3 (2002). Pages 93-100. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.472.6484&rep=rep1&type=pdf

[52] Juliana Chacon Pinilla. “Biogeography and cytogenetic evolution of the Alstroemeriaceae/Colchicaceae inferred from multi-locus molecular phylogenies, fluorescent in situ hybridization data, and probabilistic models of geographic and chromosome number change.” (PhD diss., The Ludwig-Maximillian’s University of Munich, 2013.) https://edoc.ub.uni-muenchen.de/16533/1/Chacon_Pinilla_Juliana.pdf

[53] Juliana Chacon, Aretuza Sousa, Carlos M. Baeza and Susanne S. Renner. “Ribosomal DNA Distribution and a Genus-Wide Phylogeny Reveal Pattersn of Chromosomal Evolution in Alstroemeria (Alstroemeriaceae).” American Journal of Botany Volume 99, No. 9 (2012) Pages 1501-1512. https://onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.1200104

[54] To calculate this, I drew extensively on Dr. Nathaniel Jeanson’s work, Replacing Darwin

[55] Genesis 1:31

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