Joanna M. Wolfe

Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages

The study of ontogeny as an integral part of understanding the pattern of evolution dates back over 200 years, but only recently have ontogenetic data been explicitly incorporated into phylogenetic analyses. Pancrustaceans undergo radical ontogenetic changes. The spectacular upper Cambrian “Orsten” fauna preserves phosphatized fossil larvae, including putative crown‐group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages remains a source of debate, causing spurious placements in a traditional morphological analysis. We introduce a new coding method where each semaphoront (discrete larval or adult stage) is considered an operational taxonomic unit. This avoids a priori assumptions of heterochrony. Characters and their states are defined to identify changes in morphology throughout ontogeny. Phylogenetic analyses of semaphoronts produced possible relationships of each Orsten fossil to the crown‐group clade expected from morphology shared with extant larvae. Bredocaris is a member of the stem lineage of Thecostraca or (Thecostraca + Copepoda), and Yicaris and Rehbachiella are probably members of the stem lineage of Cephalocarida. These placements rely directly on comparisons between extant and fossil larval character states. The position of Phosphatocopina remains unresolved. This method may have broader applications to other phylogenetic problems which may rely on ontogenetically variable homology statements.

Horizontal gene transfer constrains the timing of methanogen evolution

Microbial methanogenesis may have been a major component of Earth’s carbon cycle during the Archaean eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the Sun’s lower luminosity at the time. Evaluation of potential solutions to the ‘faint young Sun’ hypothesis by determining the age of microbial methanogenesis has been limited by ambiguous geochemical evidence and the absence of a diagnostic fossil record. To overcome these challenges, we use a temporal constraint: a horizontal gene transfer event from within archaeal methanogens to the ancestor of Cyanobacteria, one of the few microbial clades with recognized crown-group fossils. Results of molecular clock analyses calibrated by this horizontal-gene-transfer-propagated constraint show methanogens diverging within Euryarchaeota no later than 3.51 billion years ago, with methanogenesis itself probably evolving earlier. This timing provides independent support for scenarios wherein microbial methane production was important in maintaining temperatures on the early Earth.Microbial methanogenesis during the Archaean eon may explain the high temperatures needed to support a liquid hydrosphere. Here, the authors find support for methanogenesis predating the Archaean by analysing horizontal gene transfer events between methanogenic Archaea and Cyanobacteria.

Evolutionary reduction of the first thoracic limb in butterflies

Abstract Members of the diverse butterfly families Nymphalidae (brush-footed butterflies) and Riodinidae (metalmarks) have reduced first thoracic limbs and only use two pairs of legs for walking. In order to address questions about the detailed morphology and evolutionary origins of these reduced limbs, the three thoracic limbs of 13 species of butterflies representing all six butterfly families were examined and measured, and ancestral limb sizes were reconstructed for males and females separately. Differences in limb size across butterflies involve changes in limb segment size rather than number of limb segments. Reduction of the first limb in both nymphalids and riodinids appears particularly extensive in the femur, but the evolution of these reduced limbs is suggested to be a convergent evolutionary event. Possible developmental differences as well as ecological factors driving the evolution of reduced limbs are discussed.

Reply to ‘Molecular clocks provide little information to date methanogenic Archaea’

To the Editor — In the accompanying Correspondence, Roger and Susko1 dispute our evidence for dating the evolution of microbial methanogenesis2. Here we contest these claims. Two major concerns are raised: (1) given uncertainties about the placement of the root within Archaea and the possibility of methanogenesis as an ancestral metabolism, the upper bound on the root is invalid; and (2) that the similarities between posterior and effective prior age distributions indicate that the sequence data do not significantly inform our results. The placement of the root of Archaea is a challenging phylogenetic problem, investigated by several studies using varied evolutionary models and datasets3–6. As Roger and Susko1 point out, models that include site-dependent substitution heterogeneity recover a root within Euryarchaeota3,6. Other substitution models and optimality criteria3, and an alternative rooting method reconciling large numbers of gene tree histories7, recover a monophyletic Euryarchaeota. This strong model dependence for the rooting of Archaea is likely to reflect the limited phylogenetic information within sequence alignments for resolving the placement of the bacterial outgroup. In fact, other recently published work dating methanogens, in the same journal and issue as our paper, also uses a tree with monophyletic Euryarchaeota (ref. 5, Supplementary Fig. 3). Therefore, the critique presented in this Correspondence seems better suited to a broader discussion of the state of the field, rather than a claim that our model choice and subsequent results are invalid in particular. Roger and Susko1 further claim that ancestral methanogenesis is evidenced by the presence of methanogen-specific genes within Verstraetearchaeota and Bathyarchaeota, clades that group within TACK based on 16S sequences8. Phylogenetic analyses of McrA/B proteins, however, support the acquisition of these proteins by horizontal gene transfer (HGT): homologues from Verstraetearchaeota group with Methanomassiliicoccales, and homologues from Bathyarchaeota group with Syntrophoarchaeum (ref. 4, Fig. 4; ref. 8, Supplementary Figs. 7 and 8; ref. 9). Furthermore, Mcr genes in Syntrophoarchaeum have been linked to anaerobic butane oxidation10, which may also be their function in Bathyarchaeota4. Scenarios wherein microbial methane production evolved in the archaeal ancestor are far less parsimonious9, requiring at least five to seven independent losses of this metabolism across many groups6, as opposed to only three losses with a monophyletic Euryarchaeota. Therefore, monophyletic Euryarchaeota containing the origin of methanogenesis remains a reasonable hypothesis, and our root prior is reasonable. We acknowledge that a more explicit discussion of these assumptions is valuable for communicating the findings of divergence time analyses. Roger and Susko1 correctly reiterate our observation2 that, for the ancient nodes under discussion, sequence data do not significantly contribute to age estimates, as is expected given the antiquity of the nodes under study, which will be associated with the greatest uncertainty11. Sequence data can only ‘overwhelm’ the user prior if there is conflict between constraints, causing truncation of the effective prior. In our paper2, we demonstrate that ancient HGT provides a calibration that improves our estimates for the effective prior and posterior of methanogens by ~400 Ma (ref. 2, Fig. 2a, Supplementary Fig. 8). Future studies including more HGT events, providing both relative time constraints and fossil calibrations, will further improve precision in these investigations. ❐

Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution

Archaeal methane production is a major component of the modern carbon cycle. It has been proposed that the metabolism of methanogenic Archaea also contributed to a “methane greenhouse” during the early Archaean Eon, a hypothesis requiring evidence for the evolution of methanogenesis at or before this time. Molecular clock models are frequently used to estimate divergence times of organismal lineages in phylogenies, as well as the order of character acquisition. However, estimating the timing of microbial evolutionary events, especially ones as ancient as the Archaean, is challenged by the lack of diagnostic fossils. Other methods are thus required to calibrate the ages of these clades. Horizontal gene transfers (HGTs) are ubiquitous evolutionary events throughout the Tree of Life, complicating phylogenomic inference by introducing topological conflicts between different gene families across taxa. As HGTs also convey relative timing information between lineages, they can be harnessed to provide geological age constraints for clades lacking a fossil record. We derive a valuable temporal constraint on the timing of the evolution of methanogenesis from a single HGT event from within archaeal methanogen lineages to the ancestor of Cyanobacteria, one of the few microbial clades with recognized crown group fossils. Results of molecular clock analyses using this HGT predict methanogens most likely diverging within Euryarchaeota no later than 3.51 Ga, and methanogenesis itself likely evolving substantially earlier. This timing provides independent support for scenarios wherein microbial methane production has a substantial role in maintaining temperatures on the early Earth. SIGNIFICANCE Methanogenic Archaea are the only organisms known to provide biogeochemically relevant sources of methane on Earth today. While this metabolism is undoubtedly ancient, the oldest geochemical evidence is too young to constrain the emergence of microbial methane, and there is a paucity of reliable microbial fossils to suggest the presence of methanogenic lineages. Molecular clock analyses of methanogenic Archaea, with age constraints derived from an HGT from within methanogens to the ancestor of Cyanobacteria, provide independent support for the hypothesis of an Eoarchaean biogenic methane greenhouse. This approach has broad implications for estimating the ages of microbial clades across the entire Tree of Life, a critical yet largely unexplored frontier of natural history.