More Tangled Branches that Confound Darwinian Trees

Darwin’s branching “tree of life” diagram made for a nice, simple, easy-to-understand, convenient myth. It has sent scientists on a wild tree chase ever since.

Mitochondria

Redefining the origin of the cellular powerhouse (Science Daily). Mitochondria produce most of the energy for the cell. That’s where the ATP synthase rotary engines work to generate ATP at the end of a chain of complex molecular machines. You may have heard the evolutionists’ favorite story for the origin of mitochondria, the ‘endosymbiont’ theory. This claims that mitochondria are evolutionary remnants of a microbe that ingested another microbe that knew how to run the powerhouse, and the two lived happily ever after. What you may not have heard is that there is a “fierce debate” that has raged between evolutionists about the details of this account.

Evidence from the past few decades strongly supports that mitochondria evolved via endosymbiosis, a process in which a free-living bacterium is taken up by a host cell. Yet, both the identity of the mitochondrial ancestor, as well as the nature of the endosymbiosis, are subject of fierce debates.

The Darwinists at the University of Uppsala decided to enter the debate and see if they could understand the reasons for it.

“We believe that there are two main reasons for the lack of consensus on the identity of the mitochondrial ancestor,” says Thijs Ettema, researcher at the Department of Cell and Molecular Biology at Uppsala University who led the team conducting the study. “First, it is possible that present-day relatives simply have not been found yet — if they even still exist. Second, the reconstruction of the evolutionary history of the mitochondria is extremely challenging, and can easily lead to very different and hence conflicting results.“

Their divination efforts may only increase tensions, because their proposed common ancestor is not even a member of the most popular candidate group, the Alphaproteobacteria. Where did the ancestor go? It seems to have disappeared into the misty realms of the unobservable past. Ratcheting up the perhapsimaybecouldness index, they speculate freely:

Unexpectedly, their analyses supported a new position of mitochondria, which were now placed outside of the Alphaproteobacteria.

These results indicate that mitochondria are not the closest relatives to any of the currently recognized alphaproteobacterial groups, including the Rickettsiales. Rather, the mitochondria evolved from an ancestor which later gave rise to all currently recognized Alphaproteobacteria.

“We suspect that the popular Rickettsiales-related ancestry of mitochondria is the result of a methodological artefact.” explains Martijn. “Mitochondria and Rickettsiales have evolved under very similar conditions, which could have resulted in very similar but independent modes of evolution and sequence patterns. This in turn may have complicated previous efforts to determine the evolutionary origin of mitochondria.”

The study failed to identify any present-day relatives of the mitochondrial ancestor.

Disappointed, the researchers hope the ancestor will be found some day in Tomorrowland.

Spiders

Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life (Current Biology). In this paper, seven Darwinians tried really hard to get spiders to fit into a Darwinian tree. They claim success:

Photo by David Coppedge.

Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators. However, despite considerable effort, their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the “ancient orb-web hypothesis”) and suggest that orb webs evolved multiple times since the late Triassic–Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade—the most diverse araneomorph spider lineage—shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.

If you read past the confident claims, you notice that up till now this family tree has been “poorly understood” and can only be reconciled with tricks of the tree-building trade, including novel placements, convergent evolution [Darwin Flubber] and storytelling (“the spider evolutionary chronicle”). Surely orb-web building is one of the most complex phenomena in zoology, requiring both incredible expertise in materials science and in behavior. Can anyone really accept their claim that “orb webs evolved multiple times” without comparing it to belief in miracles?

Yeast

Genome evolution across 1,011 Saccharomyces cerevisiae isolates (Nature). This paper talks about another huge tree-building effort, but it’s just for one species: the common yeast Saccharomyces cerevisiae. Yeast has been an important organism for people groups, involved as it is in the making of bread and beer. The 21 authors looked for differences in over a thousand members of this one-celled eukaryote and found some interesting things:

Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single ‘out-of-China’ origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter-individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome-wide association are copy-number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms.

Sanford’s book examines the impact of mutations that are invisible to selection.

What they found is a surprising lack of evolution. The biggest differences were single-nucleotide polymorphisms (SNPs), which are neutral mutations. As John Sanford explained in his book Genetic Entropy, the accumulation of neutral or nearly-neutral mutations puts a mutational load on any genome, scrambling the original information and degrading it. Undoubtedly lineages went extinct that degraded too much, or did not survive in the first place. The other major change observed in the study was copy-number changes, including aneuploidy (chromosome duplications), which do not create new information.

Nothing in the study claimed yeast made evolutionary progress in any way. There were no innovations or cases of positive selection mentioned. Evidence of “purifying selection” was mentioned, but that results from repair mechanisms in the cell that try to get rid of bad mutations—an example of intelligent design.

While it’s helpful to perform genetic studies such as this to tease out effects of mutations and domestication, no Darwinian evolution was observed. No mutations were selected for a fitter kind of yeast. In the end, the “tree of life” for all 1,011 isolates were still yeast. Not only that, they were still one species of yeast: Saccharomyces cerevisiae. Where in any of these examples do we see the Origin of Species by Natural Selection?

See also yesterday’s entry for three other examples of tree-building exercises by Darwinians. The results in both these entries would do nothing to convince an impartial observer to believe that bacteria evolved into humans.