Saturday, 12 August 2017

Creationism In Crisis. A Notion With No Practical Use

Scientists Map Sex Chromosome Evolution in Fungi | Duke Today

Chemical profile of ants adapts quickly to selection pressure

I won't call creationism a theory in crisis because that would be giving it a scientific standing far about what it deserves. It's a notion; a guess with no supporting evidence; an idea with no practical application other than making a few deeply ignorant people feel important enough.

A point I've made several time recently, but which I'll repeat again for those who may have missed it, science, especially biological, geological, archaeological and cosmological science, daily and routinely refutes creationism without the slightest effort or intent simply by reporting the facts.

This is illustrated by two papers published today which show that evolution is the very foundation of modern biology and the theory which makes sense of almost everything we can observe. The first concerns an explanation for how sex determinism in a species of pathological fungus came about. It was published today in PLoS Biology
by a research team from Duke University Medical Center, Durham, North Carolina, USA: It comes complete with a neat animation summarising the process:

A schematic figure from the paper illustrates how recombination occurred at the centromere and then genes migrated and fused to leave Cryptococcus with just two sexes, when before it had many.

Credit: Sheng Sun, Duke University
This is an uncorrected proof

Abstract
Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million infections globally annually. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species, as well as its possible link with the origin and evolution of pathogenesis. In this study, we sequenced, assembled, and annotated the genomes of 2 C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the 2 C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Bioinformatic and chromatin immunoprecipitation sequencing (ChIP-seq) analyses revealed that, similar to those of the pathogenic Cryptococcus species, C. amylolentus has regional centromeres (CENs) that are enriched with species-specific transposable and repetitive DNA elements. Additionally, we found that while neither the P/R nor the HD locus is physically closely linked to its centromere in C. amylolentus, and the regions between the MAT loci and their respective centromeres show overall synteny between the 2 genomes, both MAT loci exhibit genetic linkage to their respective centromere during meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the MAT-CEN intervening regions. Furthermore, genomic comparisons between C. amylolentus and related pathogenic Cryptococcus species provide evidence that multiple chromosomal rearrangements mediated by intercentromeric recombination have occurred during descent of the 2 lineages from their common ancestor. Taken together, our findings support a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by similar repetitive centromeric DNA elements shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and further chromosomal rearrangements then resulted in the 2 MAT loci becoming physically linked and eventually fusing to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species.

Author summary
This manuscript explores the evolution of the genomic regions encoding the mating type loci of basidiomycetous fungi. Typically, the mating system is tetrapolar, meaning that it is composed of 2 unlinked mating type (MAT) loci (P/R and HD) that are located on different chromosomes. However, species with bipolar mating systems, in which the P/R and HD loci are located on the same chromosome, have also been identified. Tetrapolar and bipolar species are often closely related, suggesting the transition between these 2 mating systems might occur frequently. For example, the species within the human fungal pathogenic Cryptococcus species complex have bipolar mating systems, with 1 large MAT locus that appears to be a fusion product of the P/R and HD loci. On the other hand, the species that is the closest outgroup to these pathogenic species, Cryptococcus amylolentus, appears to have a classic tetrapolar mating system. Interestingly, the 2 MAT loci of C. amylolentus exhibit centromeric linkage during meiosis, and as a consequence, their resulting meiotic segregation pattern differs from other regions of the genome. Additionally, both pathogenic and non-pathogenic species are found to have large regional centromeres enriched with transposable and repetitive elements. Our genome comparison analyses indicated that these regional centromeres underwent ectopic recombination during the evolution of these 2 lineages. Based on these observations, we propose a model for the transition from the tetrapolar mating system in non-pathogenic C. amylolentus to the bipolar mating system in its related pathogenic species that is initiated by intercentromeric ectopic recombination, followed by chromosomal rearrangements. These events moved the 2 MAT loci closer to each other and eventually fused them to form a single MAT locus. This model is also consistent with recent findings on the organization of MAT loci in other basidiomycetous species.



The Duke press release explains:

Scientists have been studying the evolution of sex chromosomes for more than a century. In the 1960’s, Japanese-American geneticist and evolutionary biologist Susumu Ohno proposed a theory in which the genes determining sex first arose at various spots scattered across the entire genome, but over time were “captured” on the sex chromosomes. In humans, those chromosomes go by the familiar X and Y; in birds, they are known as Z and W; in moss, they are called U and V.

Regardless of the name or species, Heitman contends that some universal principles could govern the evolution of all sex chromosomes. He and an international team of researchers focused on the last common ancestor of the human pathogen Cryptococcus neoformans and its nearest sibling species, a non-pathogen called Cryptococcus amylolentus.

In C. amylolentus, dozens of genes at two different locations on the chromosomes control what’s called a tetrapolar, or four-part, mating system. At one location or locus known as P/R, genes encode pheromones and pheromone receptors that help the fungus recognize compatible mating types. At the other locus, called HD, genes govern the development of sexual structures and reproductive spores.

The researchers sequenced the entire genome of C. amylolentus, mapping the location of all the genes as well as the centromeres on each of the organism’s 14 chromosomes.

They found that the genomes had undergone quite a bit of rearrangement since the two species shared a common ancestor, at least 50 million years ago. For example, chromosome 1 of C. neoformans contained pieces of four different chromosomes from C. amylolentus, providing evidence of multiple translocations, some within the centromere.

[...]

In this study, the researchers showed that in Cryptococcus amylolentus, the ancestral state, the P/R locus resided on chromosome 10 and the HD locus on chromosome 11. But in Cryptococcus neoformans, the evolved state, those loci ended up in one place. According to their model, multiple translocations deposited the two sex determinants on the same chromosome, with a centromere in between. Subsequent rearrangements put P/R and HD next to each other. The result was an organism with a bipolar mating system, much like the male and female sexes that embody most species.

“In any kind of model like this, you are thinking about what could have been the organization in the last common ancestor, which is now extinct so you can’t know definitively,” said Heitman. “But in each of these lineages, there are multiple evolutionary events that have occurred, and you can use genomics to turn back the hands of time and deduce the trajectory.”


So there we have the entire explanation in terms of evolution and the study was predicated on the two species sharing a common ancestor. The current situation makes no sense otherwise but is perfectly understandable as the product of an evolutionary process. What doesn't make sense is that a designer, intelligent or not, would use two widely different systems for sex determination in two related species unless it keeps inventing solutions to the same problem then forgetting them and starting over.

Nest of Crematogaster scutellaris in a cork oak in southern France.

Photo credit: Florian Menzel, JGU
The second paper deal with the ability of ants to quickly adapt to environmental change. The question for creationists is obvious, and unanswerable - why would an intelligent designer design ants for one environment, then change the environment so it had to redesign the ants. Or perhaps that should be, how can that possibly be described as intelligent or even good design?

Sadly, the paper by evolutionary biologist Dr. Florian Menzel of the University of Würzburg, Germany together with colleagues from the Smithsonian Institute, Washing DC, USA, is behind a paywall and I haven't been able yet to obtain permission to reprint the abstract, but a University of Würzburg press release gives the details (auto-translated from German into English):


Crematogaster levior, a South American ant species that lives in symbiosis with other ant species in the same nest.

Photo credit: Florian Menzel, JGU
The body of ants and other insects is covered by a thin, waxy layer, which protects them from drying out, and which, especially in the case of social insects, serve the exchange of information, for example to distinguish enemies from nesting companions. Because of its dual function, this skin layer is not only essential for life, it is also so unique that it can serve as a unique identification and identification feature for an insect species like a fingerprint. Even closely related species can be distinguished by this layer. This is due to their composition of cuticular hydrocarbons, which form a specific chemical profile. Biologists of the Johannes Gutenberg-University Mainz (JGU) have now determined.

Kuticular hydrocarbons can consist of over 100 different substances, so they are extremely diverse. They are found on the cuticle of almost all insects and prevent water loss and dehydration so that the animals can survive even in a dry environment. CHCs, abbreviated by English Cuticular Hydrocarbons, are also the most important communication channel for social insects: they provide information about the affiliation of an animal to the colony, its caste and its task in the colony as well as in the case of queens about reproductive status The functioning of an insect colony is irreplaceable. In many solitary insects they serve as sexuallock [sexual pheromones].

"The evolution of such complex features, which fulfill quite different functions, is still bound up with many puzzles", explains the evolutionary biologist Dr. Florian Menzel. The scientist is particularly interested in whether CHC profiles remain relatively stable during the course of evolution, such as morphological features such as size or body shape, or whether they can change more rapidly and flexibly as a result of evolutionary change than other characteristics.

Related ant species with different CHC profiles

For the study Menzel and his co-operation partners from the Smithsonian Institution in Washington and the University of Würzburg investigated ants of the genus Crematogaster, with about 1000 species one of the most species of genotypes at all. These tipping elements can tilt their rear body upwards and in this way release poison or defenses into the environment and also into the surrounding air. The scientists selected 43 species of ants from the genus Crematogaster from five continents and examined them for their kinship and their chemical profile. "We wanted to know whether species that are juxtaposed in the family tree also have similar hydrocarbon profiles", says Menzel.

In fact, the evolutionary biologists found no agreement, however: species can differ strongly in the CHC profile. The profiles can therefore change more quickly in the course of evolution than morphological features or behaviors. "The ants obviously have a large genetic arsenal that they can adapt to change their CHC profile", explains Menzel. He assumes that the ants have the possibility to bring the chemical signals to a new level in an evolutionary short time if, for example, they require altered environmental conditions.

The important point from the point of view of this blog post is that once again, evolution provides the only logical way to understand these results. It makes absolutely no sense at all to ascribe it to intelligent design. What intelligent designer would design ants to function in a given environment than have to redesign them because it has change their environment?

Every paper on almost anything to do with biology has the Theory of Evolution as its fundamental basis. No piece of scientific research ever concludes that it was magic done by a magic entity. Simply reporting on the facts as discovered refutes creationism incidentally and without intent. This doesn't look to me like a theory in crisis as the Dishonesty Institute and other fundamentalist Christian extremist front organisations would have their dupes believe. It look very much to any objective observer as though the crisis is with the notion of creationism.

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