Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges.

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.

Methanogenesis on Early Stages of Life: Ancient but Not Primordial.

Of the six known autotrophic pathways, the Wood-Ljungdahl pathway (WL) is the only one present in both the acetate producing Bacteria (homoacetogens) and the methane producing Archaea (hydrogenotrophic methanogens), and it has been suggested that WL is one of the oldest metabolic pathways. However, only the so-called carbonyl branch is shared by Archaea and Bacteria, while the methyl branch is different, both in the number of reactions and enzymes, which are not homologous among them. In this work we show that some parts of the methyl branch of archaeal Wood-Ljungdahl pathway (MBWL) are present in bacteria as well as in non-methanogen archaea, although the tangled evolutionary history of MBWL cannot be traced back to the Last Common Ancestor. We have also analyzed the different variants of methanogenesis (hydrogenotrophic, acetoclastic and methylotrophic pathways), and concluded that each of these pathways, and every different enzyme or subunit (in the case of multimeric enzymes), has their own intricate evolutionary history. Our study supports the scenario of hydrogenotrophic methanogenesis being older than the other variants, albeit not old enough to be present in the last archaeal common ancestor.

Phylogenomic Testing of Root Hypotheses.

The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch-the root branch-of the true species tree and should therefore be a much easier task than the full resolution of the species tree. Discarding the reliance on a hypothesized species tree and its rooting leads us to reevaluate what phylogenetic signal is directly relevant to LCA inference and to recast the task as that of sampling the total evidence from all gene families at the genomic scope. Here, we reformulate LCA and root inference in the framework of statistical hypothesis testing and outline an analytical procedure to formally test competing a priori LCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species. Applying our methods to two demonstrative data sets, we show that our inference of the opisthokonta LCA is well in agreement with the common knowledge. Inference of the proteobacteria LCA shows that it is most closely related to modern Epsilonproteobacteria, raising the possibility that it may have been characterized by a chemolithoautotrophic and anaerobic life style. Our inference is based on data comprising between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching LCA inference within a statistical framework renders the phylogenomic inference powerful and robust.

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa.

Vavilovia formosa is a relict leguminous plant growing in hard-to-reach habitats in the rocky highlands of the Caucasus and Middle East, and it is considered as the putative closest living relative of the last common ancestor (LCA) of the Fabeae tribe. Symbionts of Vavilovia belonging to Rhizobium leguminosarum bv. viciae compose a discrete group that differs from the other strains, especially in the nucleotide sequences of the symbiotically specialised (sym) genes. Comparison of the genomes of Vavilovia strains with the reference group composed of R. leguminosarum bv. viciae strains isolated from Pisum and Vicia demonstrated that the vavilovia strains have a set of genomic features, probably indicating the important stages of microevolution of the symbiotic system. Specifically, symbionts of Vavilovia (considered as an ancestral group) demonstrated a scattered arrangement of sym genes (>90 kb cluster on pSym), with the location of nodT gene outside of the other nod operons, the presence of nodX and fixW, and the absence of chromosomal fixNOPQ copies. In contrast, the reference (derived) group harboured sym genes as a compact cluster (<60 kb) on a single pSym, lacking nodX and fixW, with nodT between nodN and nodO, and possessing chromosomal fixNOPQ copies. The TOM strain, obtained from nodules of the primitive "Afghan" peas, occupied an intermediate position because it has the chromosomal fixNOPQ copy, while the other features, the most important of which is presence of nodX and fixW, were similar to the Vavilovia strains. We suggest that genome evolution from the ancestral to the derived R. leguminosarum bv. viciae groups follows the "gain-and-loss of sym genes" and the "compaction of sym cluster" strategies, which are common for the macro-evolutionary and micro-evolutionary processes. The revealed genomic features are in concordance with a relict status of the vavilovia strains, indicating that V. formosa coexists with ancestral microsymbionts, which are presumably close to the LCA of R. leguminosarum bv. viciae.

Lower Ilium Evolution in Apes and Hominins.

Elucidating the pelvic morphology of the Pan-Homo last common ancestor (LCA) is crucial for understanding ape and human evolution. The pelvis of Ardipithecus ramidus has been the basis of controversial interpretations of the LCA pelvis. In particular, it was proposed that the lower ilium became elongate independently in the orangutan and chimpanzee clades, making these taxa poor analogues for the pelvis of the LCA. This study examines the variation in relative lower ilium height between and within living and fossil hominoid species (and other anthropoids), and models its evolution using available fossil hominoids as calibration points. We find nuanced differences in relative lower ilium height among living hominoids, particularly in regards to gorillas, which do not have elongate lower ilia (because they are likely to represent the plesiomorphic hominoid condition for this trait). We also show that differences in relative lower ilium height among hominoid taxa are not readily explained by differences in size between species. Our maximum likelihood ancestral state reconstructions support inferences that chimpanzees (Pan troglodytes in particular) and orangutans evolved their elongate lower ilia independently. We also find that the predicted lower ilium height of the Pan-Homo LCA is shorter than all great apes except gorillas. This study adds to a growing body of evidence that finds different regions of the body show different evolutionary histories in different hominoids, and underscores that the unique combinations of morphologies of each modern and fossil hominoid species should be considered when reconstructing the mosaic nature of the Pan-Homo LCA. Anat Rec, 300:828-844, 2017. © 2017 Wiley Periodicals, Inc.

A phylogenetic approach to the early evolution of autotrophy: the case of the reverse TCA and the reductive acetyl-CoA pathways.

In recent decades, a number of hypotheses on the autotrophic origin of life have been presented. These proposals invoke the emergence of reaction networks leading from CO or CO2 to the organic molecules required for life. It has also been suggested that the last (universal) common ancestor (LCA or LUCA) of all extant cell lineages was a chemolitho-autotrophic thermophilic anaerobe. The antiquity of some carbon fixation pathways, the phylogenetic basal distribution of some autotrophic organisms, and the catalytic properties of iron-sulfur minerals have been advanced in support of these ideas. Here we critically examine the phylogenetic distribution and evolution of enzymes that are essential for two of the most ancient autotrophic means of metabolism: the reductive tricarboxylic acid (rTCA) cycle and the reductive acetyl-CoA pathway. Phylogenetic analysis of citryl-CoA synthetase and of citryl-CoA lyase, key enzymatic components of the rTCA cycle, and of CO dehydrogenase/acetyl-CoA synthase, a key enzyme in the reductive acetyl-CoA pathway, revealed that all three enzymes have undergone major lateral transfer events and therefore cannot be used as proof of the LCA's metabolic abilities nor as evidence of an autotrophic origin of life.