Despite how widely evolution is taught across academia and considered to be strongly supported by science, there is an apparent conflict that exists and lurks deep in the shadows behind phylogenetic inference in support of common descent. Despite the widely held claim that evolution has been strongly supported by the utilization of phylogenetic or phylogenomic (i.e. data derived from genome rather than individual genes) data, in reality the utilization of comparitive anatomy / genetic sequencing establish true evolutionary history has been conflicting, though not necessarily mentioned to the students of academia.
There are two types of methods used to infer evolutionary relationships: 1) morphological & 2) molecular.
Phylogenetic relationships derived from morphological data is mostly what is known as comparative anatomy. Comparative anatomy involves the utilization of anatomical structures and doing a compare and contrast analysis. If two or more different taxon groups share anatomical features that underlie common morphological, for example the case of forelimbs, the radius, the ulna, etc. they are considered homologous. Homology is not necessarily dependent on whether two or more separate anatomical features look similar, but rather is defined on the basis of individual anatomical interdependent parts, that is the radius, the ulna, etc.
The essential idea is, if two or more different taxon share homologous features, those features must have been derived from a common ancestor. Similarly, in the case of molecular homology, that is the finding of nucleotide or amino acid sequence similarity between two different group species, it is also derived from common descent. However, the logic of constructing phylogenetic relationships based on homologous anatomical structures or genetics is actually something not necessarily consistent with the scientific literature.
The Incomplete Lineage Sorting: A Problem for Evolution
In Rokas 2005 paper, “Animal Evolution and the Molecular Signature of Radiations Compressed in Time”
Here researchers sought to determine the evolutionary history of the animal phyla by analyzing about 50 genes across 17 taxa. At the same time, he hoped that a single dominant phylogenetic tree would emerge. Rokas and his team reported that
“a 50-gene data matrix does not resolve relationships among most metazoan phyla………..Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved”
Their conclusion was unambiguous: instead of them establishing true evolutionary history, they constructed inconsistent molecular phylogenies that contradicted evolutionary history. What was the cause of such incongruent phylogeny? The answer to that was a mysterious rapid ancient event known as incomplete lineage sorting. It is where the species have diverged extremely rapidly as opposed to speciating slowly. Due to the rapid divergence, like the Cambrian Explosion, genetic markers in genes from species has become rather elusive and quite difficult. Thus, generating numerous conflicting evolutionary relationships from genetics. Scientists like Rokas realized just how difficult it is to get high-resolution relationships when the divergence between them is extremely short, like during the ‘Cambrian explosion’, as is being researched in the paper.
Both Rokas and Carroll tried to explain the many contradictory molecular trees by proposing that the animal phyla might have evolved too quickly for the genes to record some signal of phylogenetic relationships into the respective genomes. In their view, if the evolutionary process responsible for anatomical novelty works quickly enough, there would not be sufficient time for differences to accumulate in key molecular markers, in particular those used to infer evolutionary relationships in different animal phyla.
Therefore, when groups of organisms branch rapidly and then evolve separately for long periods of time, this can overwhelm the true historical signal, leading to the inability to determine true evolutionary history. So unfortunately for evolutionists the argument of using all genetics to determine true evolutionary history doesn’t work either since the rapid divergence of species has corrupted the genetic markers that scientists use to establish a high resolution evolutionary history signal.
Not even the highly respected scientific findings of “evolution” has been found to be conclusive when it comes to establishing evolutionary relationships.
In the peer-reviewed paper, “Insect Phylogenomics: results, problems and the impact of matrix composition”
Researchers in this paper tried to establish evolutionary history of insect lineages using phylogenomic (i.e. genome data) & matrix data. As the abstract reads:
In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense).
Yet, despite evolutionary expectations of establishing such phylogeny, reality has flipped that expectation upside down as they have found problems in their data as quoted below:
Even though molecular studies on the insect phylogeny are legion [1–9], a consensus on the relationships between the insect orders is not yet in sight. The difficulties in reaching a robust phylogenetic tree are most probably due to an ‘ancient rapid radiation’ phenomenon [10–12]: most of the modern lower neopteran orders appeared in a geologically relatively short time span in the Early Mesozoic [13], followed by a long period of intra-ordinal diversification. Thus, only traces of phylogenetic signal are left in the data. Molecular analyses based on ribosomal RNA (rRNA) genes, complete mitochondrial (mt) genomes, and few housekeeping protein-coding genes, are not only plagued by this loss of phylogenetic signal, but also hampered by lineage-specific substitution rates and base compositional biases potentially misleading tree inference. For example, genes of flies (Diptera) show highly accelerated substitution rates, whereas genes of roaches (Blattodea) evolve comparatively slowly [3,10,13].
Corruption of ribosomal RNA, mitochondrial genomes, and protein-coding genes blurred out by non-sensical noise/misleading phylogeny? What happened to the so-called claim that evolution has been strongly supported with mountains of evidence containing no problems whatsoever? Sounds more like evolution has many holes in its theory given the numerous conflicts that exist in the scientific literature.
Even though researchers have acknowledged this problem, they tried to use reasonable approaches by trying to eliminate signal from noise and more prestigous approaches:
Our approach provides the first phylogenomic support for the monophyletic origin of several lineages of Polyneoptera, and for a sistergroup relationship between webspinners and stick insects (i.e. Eukinolabia). Furthermore, our analyses suggest a sistergroup relationship between true bugs and cicadas, leaf hoppers, and their allies. Since our analyses did not include several polyneopteran orders and thrips, as well as only one family of plant hoppers and leaf hoppers, respectively, they must be seen as preliminary and as a first step towards a phylogenomic approach to the reconstruction of inter-ordinal relationships.
but despite their best to establish true evolutionary history, they have found conflicts that still exist in their phylogenomic analysis,
Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.
So it seems that rather these evolutionists establishing a single phylogenomic tree, they have rather generated numerous conflicted groupings where one group of insect is said to be related to this certain insect group while ironically the other says no it is that other group. Due to the ambiguity found in evolutionary relationships, the evolutionists in the paper have failed to justify true evolutionary relationships given the numerous conflicts that exist. Thus, giving the researchers the expression of hope that better methods will and once for all prove evolution to be true.
Yet, that has all yet to be proven true.
angeldiaz. 