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Rothfels, C.

Publications and source records attributed to Rothfels, C..

6 recordsLinked to original sources
bioRxiv2024

The nitrogen-fixing fern Azolla has a complex microbiome characterized by multiple modes of transmission

Azolla is a floating fern that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont--Anabaena azollae--that performs nitrogen fixation in specialized Azolla leaf pockets. This cyanobac-terium has a greatly reduced genome and appears to be in the "advanced" stages of symbiosis, potentially evolving into a nitrogen-fixing organelle. However, there are also other lesser-known inhabitants of the leaf pocket whose role and mode of transmission are unknown. We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes in order to identify the common bacterial endosymbionts of the leaf pocket and assess their patterns of co-diversification. Four taxa were found across all samples, establishing that there are multiple endosymbionts that consistently inhabit the Azolla leaf pocket. We found varying degrees of co-diversification across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which implies that the endosymbiotic community is transmitted by a mix of horizontal and vertical mechanisms, and that some members of the microbiome are more facultative symbionts than others. These results show that the Azolla symbiotic community is complex, featuring members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.

ecology↗
bioRxiv2021

PURC v2.0: a program for improved sequence inference for polyploid phylogenetics and other manifestations of the multiple-copy problem

Inferring the true biological sequences from amplicon mixtures remains a difficult bioinformatic problem. The traditional approach is to cluster sequencing reads by similarity thresholds and treat the consensus sequence of each cluster as an "operational taxonomic unit" (OTU). Recently, this approach has been improved upon by model-based methods that correct PCR and sequencing errors in order to infer "amplicon sequence variants" (ASVs). To date, ASV approaches have been used primarily in metagenomics, but they are also useful for identifying allelic or paralogous variants and for determining homeologs in polyploid organisms. To facilitate the usage of ASV methods among polyploidy researchers, we incorporated ASV inference alongside OTU clustering in PURC v2.0, a major update to PURC (Pipeline for Untangling Reticulate Complexes). In addition to preserving original PURC functions, PURC v2.0 allows users to process PacBio CCS/HiFi reads through DADA2 to generate and annotate ASVs for multiplexed data, with outputs including separate alignments for each locus ready for phylogenetic inference. In addition, PURC v2.0 features faster demultiplexing than the original version and has been updated to be compatible with Python 3. In this chapter we present results indicating that PURC v2.0 (using the ASV approach) is more likely to infer the correct biological sequences in comparison to the earlier OTU-based PURC, and describe how to prepare sequencing data, run PURC v2.0 under several different modes, and interpret the output. We expect that PURC v2.0 will provide biologists with a method for generating multi-locus "moderate data" datasets that are large enough to be phylogenetically informative and small enough for manual curation.

bioinformatics↗
bioRxiv2021

Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

Premise of study"El Chango" is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants. MethodsWe collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e.,, including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions. ResultsWe obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most-parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest. ConclusionsOur findings contribute to the understanding of Cenomanian equatorial regions, and support the hypothesis of a geographically and ecologically structured "rise of angiosperms", with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

paleontology↗
bioRxiv2021

Mistreating birth-death models as priors in phylogenetic analysis compromises our ability to compare models

Time-calibrated phylogenetic trees are a tremendously powerful tool for studying evolutionary, ecological, and epidemiological phenomena. Such trees are predominantly inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a "tree prior"). However, we show that the tree "parameter" consists, in part, of data, in the form of taxon samples. Treating the tree as a parameter fails to account for these data and compromises our ability to compare among models. Since accuracy of the inferred phylogeny strongly depends on how well the tree prior approximates the true diversification process that gave rise to the tree, the inability to accurately compare competing tree priors has broad implications for applications based on time-calibrated trees. We outline potential remedies to this problem, and provide guidance for researchers interested in assessing the fit of tree models.

evolutionary biology↗
bioRxiv2017

Origin and evolution of the nuclear auxin response system

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

genomics↗
bioRxiv2017

Inferring the evolutionary reduction of corm lobation in Isoëtes using Bayesian model-averaged ancestral state reconstruction

Inferring the evolution of characters in Isoetes has been problematic, as these plants are morphologically conservative and yet highly variable and homoplasious within that conserved base morphology. However, molecular phylogenies have given us a valuable tool to test hypothesis of character evolution within the genus. One such hypothesis is that extant Isoetes have undergone a morphological reduction from larger arborescent lycophyte ancestors. In this work we examine the reduction in lobe numbers on the underground trunk, or corm, over evolutionary time. Using reversible-jump MCMC and Bayesian inference, our results support the hypothesis of a directional reduction in lobe number in Isoetes, with the best-supported model of character evolution being one of irreversible reduction. Furthermore, the most probable ancestral corm lobe number of extant Isoetes is three, and a reduction to two lobes has occurred at least six times. From our results, we can infer that corm lobation, like many other traits in Isoetes, shows a degree of homoplasy, yet also shows ongoing evolutionary reduction.

evolutionary biology↗