Common house spider, Parasteatoda tepidariorum
For creationists still trying to get away with the absurd claim that mutations are always harmful and that no new information can arise in the genome because of the second law of thermodynamics, this is another of those bad news stories.
No! I'm not joking! They really do claim that! Creationists think nothing of claiming an observable thing can't happen, knowing that their willing dupes won't go and check. They'll no doubt continue to claim it even after this paper showing how the scorpions and arachnids have evidence of whole genome duplication in a common ancestor about 400 million years ago.
A similar things appears to have happened in an ancestor of the horseshoe crab, not once but twice. Similarly, there were two whole genome duplications in the early evolution of vertebrates.
In collaboration with scientists from the U.K., Europe, Japan and the United States, researchers at the Human Genome Sequencing Center at Baylor College of Medicine have discovered a whole genome duplication during the evolution of spiders and scorpions. The study appears in BMC Biology.
What makes this especially pleasing is that the lead author, Dr Alistair P. McGregor, is Professor of evolutionary developmental biology at Oxford Brookes University, my old alma mater, where I studies Applied Biology in the days when being able to analyse a species' genome was but a pipe dream. Even in those days, writing up the results of some lab work with the conclusion that "this is all to hard for me to understand so it must be magic", would have resulted in a swift ejection from the course. Mind you, if I had submitted that to an American diploma mill Bible college, with maybe a couple of random Bible quotes, with the appropriate fee, I'd probably have been awarded a 'doctorate' in 'Creation Science' or some such worthless piece of paper.
Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.
Results
We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication.
Conclusions
Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
Background
Gene duplication plays an important role in the evolutionary diversification of organisms [1, 2]. Unequal crossing-over commonly results in one or a few tandemly duplicated genes, but larger scale events, including whole genome duplications (WGDs) can also occur. Tandem duplication has been shown to underlie the evolution of many genes in both plants and animals, for example, of up to 32% of genes in the centipede Strigamia maritima [3, 4]. WGD is arguably the most sudden and massive change that a genome can experience in a single evolutionary event. The occurrence of WGDs across a wide variety of eukaryotic groups, including plants [5, 6], fungi [7, 8], ciliates [9], oomycetes [10], and animals [11,12,13,14,15,16,17], attests to the major impact that polyploidization events have had in reshaping the genomes of many different organisms.
Although most of the duplicated genes resulting from tandem duplication or WGD are subsequently lost, it is thought that these events provide new genetic material for some paralogous genes to undergo sub-functionalization or neo-functionalization and thus contribute to the rewiring of gene regulatory networks, morphological innovations and, ultimately, organismal diversification [2, 7, 18,19,20,21,22,23,24]. Comparisons of independent paleopolyploidization events across different eukaryotes, such as plants, yeast, and vertebrates [5, 8, 11, 13, 14, 24], have led to the development of models to elucidate genome-wide evolutionary patterns of differential gene loss and retention compared to smaller-scale events [2, 25]. However, the enormous differences between these disparate eukaryotic lineages in terms of genome structure, morphological and developmental organization, and ecology have impeded a critical assessment of the potential selective advantages and actual evolutionary consequences of WGDs. Thus, the extent to which WGDs may have contributed to taxonomic “explosions” and evolutionary novelties remains controversial, especially in the case of vertebrates [26,27,28]. For example, the two WGDs shared by all vertebrates have given rise to four clusters of Hox genes, providing new genetic material that may underlie the evolutionary success and innovations among these animals [24, 29, 30]. However, only three WGD events have been demonstrated in animals other than vertebrates, namely one in bdelloid rotifers and possibly two in horseshoe crabs [11, 14, 31], and these events are not associated with any bursts of diversification [32, 33]. It is clear, therefore, that documenting additional examples of WGD in metazoans would significantly increase our understanding of the genomic and morphological consequences of these events.
Intriguingly, there is increasing evidence for extensive gene duplication among chelicerates other than horseshoe crabs, particularly in spiders and scorpions [34,35,36,37,38,39,40,41,42,43,44], indicating that large-scale gene duplications occurred during the evolution of these arachnids. However, although the genomes of some arachnids have been sequenced, including the tick Ixodes scapularis [45, 46], the mite Tetranychus urticae [47], the Chinese scorpion Mesobuthus martensii [48], and three spiders (the velvet spider Stegodyphus mimosarum [49], the Brazilian whiteknee tarantula Acanthoscurria geniculata [49], and the golden orb-weaver Nephila clavipes [50]), a systematic analysis of genome evolution among these diverse animals has yet to be performed (Fig. 1) [51].
As a step towards this goal, we herein report the sequencing and analysis of the genomes of the common house spider Parasteatoda tepidariorum (C. L. Koch, 1841; formerly Achaearanea tepidariorum) [52] and the bark scorpion Centruroides sculpturatus (Wood, 1863) (Fig. 1), together with comparative genomic analyses of other available chelicerate genomes. We found that the genome of P. tepidariorum contains many paralogous genes, including two Hox gene clusters, which is also the case in other spiders and in scorpions (this work; [36]). These similar patterns of gene duplication between spiders and scorpions are consistent with recent molecular phylogenies, which support a much closer phylogenetic relationship of spiders and scorpions than previously thought, in a clade known collectively as Arachnopulmonata [53] (Fig. 1). We also document extensive divergence in the timing and location of expression of each pair of Hox gene paralogs, suggesting there may be far reaching functional consequences. Furthermore, an analysis of synteny among paralogs across the P. tepidariorum genome is consistent with a WGD. Comparison with other chelicerates suggests that this WGD took place in the common ancestor of the Arachnopulmonata and is probably independent of the WGDs in the horseshoe crab lineage.Fig. 1The relationships of Parasteatoda tepidariorum to select arthropods. Representatives of spiders (Araneae) with sequenced genomes (P. tepidariorum, Stegodyphus mimosarum, and Acanthoscurria geniculata) are shown with respect to other chelicerates with sequenced genomes including scorpions (Centruroides sculpturatus and Mesobuthus martensii), a tick (Ixodes scapularis), a mite (Tetranychus urticae), and a horseshoe crab (Limulus polyphemus) as well as representatives of Myriapoda (Strigamia maritima), Crustacea (Daphnia pulex), and Insecta (Drosophila melanogaster). Topology is based on Sharma et al. [53]
Schwager, E.E., Sharma, P.P., Clarke, T. et al.
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 15, 62 (2017). https://doi.org/10.1186/s12915-017-0399-x
Copyright: © 2017 The authors.
Published by Springer Nature BioMed Central Ltd. Open .
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
While most of the new genetic material generated by whole genome duplication is subsequently lost, some of the new gene copies can evolve new functions and may contribute to the diversification of shape, size, physiology and behavior of animals. Comparing the whole genome duplication in spiders and scorpions with the independent events in vertebrates reveals a striking similarity. In both cases, duplicated clusters of Hox genes have been retained. These are very important genes that regulate development of body structures in all animals, and therefore can cause evolutionary changes in animal body plans.
Dr. Alistair McGregor, Lead author.
Professor of evolutionary developmental biology
Oxford Brookes University.
Professor of evolutionary developmental biology
Oxford Brookes University.
There is also scope for exaptation of these genes for a new purpose. In the case of whole gene duplication, it's like having the entire genome to experiment with without harming the individual. Only if a mutation created something harmful would this be detrimental, and then it would be rapidly removed from the species gene pool. On the other hand, if something beneficial arose, it would spread throughout the gene pool.
Whole genome duplication is thus a major driver of evolutionary radiation and diversification. It is a mutation which not only need not be harmful but which, if it doesn't create new information as opposed to duplicated information, it created the opportunity for new information to arise by harmless mutation in the duplicated genes.
Once again, and I seem to be saying this for almost every science paper these days, a piece of research refutes creationism quite incidentally and without any intention on the part of the authors. Creationism is now so detached from reality that almost the slightest whiff of a verifiable fact refutes it.
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