Biology subjects

Matzke, N. J.

Publications and source records attributed to Matzke, N. J..

12 recordsLinked to original sources

bioRxiv2026

Statistical Model Comparison Supports a Pitcher Origin of Utricularia Suction Traps

Carnivorous plants have been the subject of fascination and research ever since Darwin codified the subject in his 1875 book Insectivorous Plants. The origin of complex trapping mechanisms from structures adapted for photosynthesis is of particular interest. While Darwin proposed a plausible scenario for the origin of the snap traps of the Venus flytrap from simpler adhesive traps, the origin of the tiny and complex bladder traps of the genus Utricularia mystified Darwin and many subsequent workers, despite Utricularia being the most diverse genus of carnivorous plants. In this study, we test the "pitcher hypothesis," which proposes that Utricularia bladder traps evolved gradually from an adhesive trap ancestor, via an extinct pitcher trap intermediate. To overcome the lack of any fossil evidence for this scenario, we constructed a variety of continuous-time Markov chain (CTMC) models, each of which consists of a transition matrix allowing or disallowing certain transitions between 11 types of traps. We assembled available phylogenetic trees for 436 carnivorous plant species and noncarnivorous outgroups, classified each species by trap type, and statistically compared the fit of 18 CTMC models using Maximum Likelihood and statistical model comparison with Akaike Information Criterion. The best-fitting model (PH-7R-AAI), consistent with our pitcher hypothesis, had an AIC weight of 60%, with two similar models accounting for the remaining 40%. These results support a circuitous stepwise evolutionary pathway to the bladder trap, and demonstrate how a detailed stepwise evolutionary scenario may be statistically tested even without direct fossil evidence of key intermediate stages.

evolutionary biology↗

bioRxiv2025

Phylogenomics and Fossilized Birth-Death Dating Reveals Gondawanan Origin and Extensive Post-Cretaceous Diversification of Worldwide Cicadidae.

The Cretaceous-Paleogene (K-Pg) mass extinction resulted in a massive turnover in biodiversity. The oldest fossils of the globally-distributed insect family Cicadidae date to the Paleocene, suggesting that this family diversified after the K-Pg boundary. We analyzed 490 nuclear Anchored Hybrid Enrichment loci as well as mitochondrial genomes for the Cicadidae, sampling all five subfamilies and 82% of tribes, using concatenated maximum-likelihood and multi-species coalescent approaches to resolve the phylogenetic relationships of Cicadidae subfamilies. We estimated divergence times of Cicadidae lineages using a fossilized birth-death model augmented into the multispecies coalescent with 44 fossil taxa. We estimated a Cretaceous origin for Cicadidae with four of the five subfamilies diversifying shortly after the K-Pg extinction event. Our fossilized birth-death tip-dating approach improved the precision of age estimates for many cicada clades compared to dates based on node-calibration from previous studies. Our results augment insight into how the K-Pg mass extinction shaped present-day diversity.

evolutionary biology↗

bioRxiv2025

Adding 3Di characters to amino acid datasets can improve resolution, but the effect is weaker in shorter and alpha-helical proteins such as histones

The recent introduction of Foldseeks 3Di character alphabet to encode 3D protein structure has opened up new possibilities for structural phylogenetics. These characters, like protein structure, are more conserved than amino acids, raising the possibility of better resolution of very deep branches on the tree of life. As 3Di characters have a 20-letter alphabet, they are readily treatable with off-the-shelf algorithms for model-based phylogenetic inference and related methods such as bootstrapping. However, it remains to be seen if 3Di phylogenies are broadly more resolved than sequence-based phylogenies. We present data using samples from nine protein superfamilies showing that 3Di combines with sequence to produce better resolved phylogenies than either sequence or 3Di alone. We also show that information-theoretic measures, applied to superfamily alignments, significantly correlate with resolution in phylogenies derived from these alignments. Further, we identify the proportion of alpha helices in proteins as a major driver in reducing the information carried by 3Di character alignments, explaining the relatively poor performance of 3Di characters on superfamilies with highly-conserved structure but high alpha helical content. Our results provide encouragement for the further use of 3Di to address challenging questions in deep history, but also sound a note of caution about which proteins it is most suitable for. SIGNIFICANCE3Di characters have been suggested as a method to generate well-resolved deep phylogenies. Our results show that 3Di characters combined with sequences can improve resolution in the deepest nodes of protein superfamily trees. However, our results also show that 3Di characters may not be suitable for all protein types.

evolutionary biology↗

bioRxiv2024

Easy come, easier go: mapping the loss of flagellar motility across the tree of life

Bacterial swimming is mostly powered by the bacterial flagellar motor and the number of proteins involved in the flagellar motor can vary. Quantifying the proteins present in flagellar motors from a range of species delivers insight into how motility has changed throughout history and provides a platform for estimating from its genome whether a species is likely to be motile. We conducted sequence and structural homology searches for 54 flagellar pathway proteins across 11,365 bacterial genomes and developed a classifier with up to 95% accuracy that could predict whether a strain was motile or not. We then mapped the evolution of flagellar motility across the GTDB bacterial tree of life. We confirmed that the last common bacterial ancestor had flagellar motility and that the rate of loss of this motility was four-fold higher than the rate of gain. We showed that the presence of filament protein homologues was highly phylogenetically correlated with motility and that all species classified as motile contained at least one filament homologue. We calculated the rate of gain and loss for each flagellar protein and that the filament protein FliC was highly correlated with motility across the tree of life. We then measured the correlation of each flagellar motor protein with FliC and showed that the filament, rotor, and rod and hook proteins were all highly correlated with FliC, and thus with motility. We calculated the differential rates of gain and loss for each flagellar protein and quantified which genomes encoded for partial sets of flagellar proteins, indicating potential pathways by which motility could be lost. Overall, we show that filament, rod and hook and rotor proteins are conserved when flagellar motility is preserved and that the presence or absence of a FliC homologue is a good, simple predictor of whether or not a species has flagellar motility.

microbiology↗

bioRxiv2024

Molecular and structural innovations of the stator motor complex at the dawn of flagellar motility

The rotation of the bacterial flagellum is powered by the MotAB stator complex, which converts ion flux into torque. The origin and evolution of this remarkable complex is understudied. Here, we perform the first phylogenetic and structural characterisation and classification of MotAB and nonflagellar relatives. Using 193 genomes sampled across 27 bacterial phyla, we estimated phylogenies and ancestral sequences, and generated AlphaFold predictions for all extant and reconstructed proteins. We then mapped them onto the phylogeny to determine patterns of diversity and distribution of structural innovations. We identify two discrete groups: the Flagellar Ion Transporters (FIT) and the Generic Ion Transporters (GIT). The FIT proteins are structurally conserved and have a square fold domain and a torque-generating interface (TGI). FIT proteins are divided into two clades, termed TGI4 and TGI5, referring to whether there have 4 or 5 short helices in the TGI. TGI5 motors are predominantly found in Proteobacteria and include the well-studied E. coli K12 system, while TGI4 motors are found in diverse phyla and include the Na+-powered polar motors of Vibrio (PomAB). The GIT proteins, on the other hand, are structurally diverse and lack these attributes. The interaction between the A and B subunits is conserved across the FIT and GIT proteins. The two subunits are jointly necessary for function, with the genes typically adjacent within an operon. Motility assays in E. coli show that the structural elements unique to FIT play an important role in flagellar motility. Our results indicate that the stator motor complex has a single origin and shares unique motility-related structural traits. Significance StatementFlagellar motility is a key feature in bacterial pathogenicity and survival. It allows bacteria to propel themselves and direct movement according to environmental conditions. We investigated the molecular and structural diversity of the stator motor proteins that provide the ion motive force to power flagellar rotation. This study integrates phylogenetics, 3D protein structure modeling, motility assays and ancestral state reconstruction (ASR) to provide insights into the structural mechanisms that first powered the flagellar motor. We provide the first phylogenetic and structural characterisation and classification of MotAB and relatives.

evolutionary biology↗

bioRxiv2023

Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone

Protein structure is more conserved than protein sequence, and therefore may be useful for phylogenetic inference beyond the "twilight zone" where sequence similarity is highly decayed. Until recently, structural phylogenetics was constrained by the lack of solved structures for most proteins, and the reliance on phylogenetic distance methods which made it difficult to treat inference and uncertainty statistically. AlphaFold has mostly overcome the first problem by making structural predictions readily available. We address the second problem by redeploying a structural alphabet recently developed for Foldseek, a highly-efficient deep homology search program. For each residue in a structure, Foldseek identifies a tertiary interaction closest-neighbor residue in the structure, and classifies it into one of twenty "3Di" states. We test the hypothesis that 3Dis can be used as standard phylogenetic characters using a dataset of 53 structures from the ferritin-like superfamily. We performed 60 IQtree Maximum Likelihood runs to compare structure-free, PDB, and AlphaFold analyses, and default versus custom model sets that include a 3DI-specific rate matrix. Analyses that combine amino acids, 3Di characters, partitioning, and custom models produce the closest match to the structural distances tree of Malik et al. (2020), avoiding the long-branch attraction errors of structure-free analyses. Analyses include standard ultrafast bootstrapping confidence measures, and take minutes instead of weeks to run on desktop computers. These results suggest that structural phylogenetics could soon be routine practice in protein phylogenetics, allowing the re-exploration of many fundamental phylogenetic problems.

evolutionary biology↗

bioRxiv2022

Ancestral reconstruction of the MotA stator subunit reveals that conserved residues far from the pore are required to drive flagellar motility

The bacterial flagellar motor (BFM) is a rotary nanomachine powered by the translocation of ions across the inner membrane through the stator complex. The stator complex consists of two membrane proteins: MotA and MotB (in H+ powered motors), or PomA and PomB (in Na+ powered motors). In this study we used ancestral sequence reconstruction (ASR) to probe which residues of MotA correlate with function and may have been conserved to preserve motor function. We reconstructed ten ancestral sequences of MotA and found four of them were motile in combination with contemporary E. coli MotB and in combination with our previously published functional ancestral MotBs. Sequence comparison between wild-type (WT) E. coli MotA and MotA-ASRs revealed 30 critical residues across multiple domains of MotA that were conserved among all motile stator units. These conserved residues included pore-facing, cytoplasm-facing and MotA-MotA intermolecular facing sites. Overall, this work demonstrates the role of ASR in assessing conserved variable residues in a subunit of a molecular complex.

microbiology↗

bioRxiv2021

A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations

Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs (rRNA) and in eukaryotic genomes are typically present as one or more arrays of tandem repeats. Species have characteristic rDNA copy numbers, ranging from tens to thousands of copies, with the number thought to be redundant for rRNA production. However, the tandem rDNA repeats are prone to recombination-mediated changes in copy number, resulting in substantial intra-species copy number variation. There is growing evidence that these copy number differences can have phenotypic consequences. However, we lack a comprehensive understanding of what determines rDNA copy number, how it evolves, and what the consequences are, in part because of difficulties in quantifying copy number. Here, we developed a genomic sequence read approach that estimates rDNA copy number from the modal coverage of the rDNA and whole genome to help overcome limitations in quantifying copy number with existing mean coverage-based approaches. We validated our method using strains of the yeast Saccharomyces cerevisiae with previously-determined rDNA copy numbers, and then applied our pipeline to investigate rDNA copy number in a global sample of 788 yeast isolates. We found that wild yeast have a mean copy number of 92, consistent with what is reported for other fungi but much lower than in laboratory strains. We also show that different populations have different rDNA copy numbers. These differences can partially be explained by phylogeny, but other factors such as environment are also likely to contribute to population differences in copy number. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations. Author summaryThe ribosomal RNA gene repeats (rDNA) form large tandem repeat arrays in most eukaryote genomes. Their tandem arrangement makes the rDNA prone to copy number variation, and there is increasing evidence that this copy number variation has phenotypic consequences. However, difficulties in measuring rDNA copy number hamper investigation into rDNA copy number dynamics and their significance. Here we developed a novel bioinformatics method for measuring rDNA copy number from whole genome sequence data that is based on the modal sequence read coverage. We established parameters for optimal performance of the method and validated it using yeast strains of known rDNA copy numbers. We then applied the method to a dataset of almost 800 global yeast isolates and demonstrate that yeast populations have different rDNA copy numbers that partially correlate with phylogeny. Our work provides a simple and accurate method for determining rDNA copy number that leverages the growing number of whole genome datasets, and highlights the dynamic nature of rDNA copy number.

genomics↗

bioRxiv2021

Homology between the flagellar export apparatus and ATP synthetase: evidence from synteny predating the Last Universal Common Ancestor

Evidence of homology between proteins in the ATP synthetase and the bacterial flagellar motor (BFM) has been accumulating since the 1980s. Specifically, the BFMs Type 3 Secretion System (T3SS) export apparatus FliH, FliI, and FliJ are considered homologous to FO-b + F1-{delta}, F1-/{beta}, and F1-{gamma}, and have similar structure and interactions. We review the discoveries that advanced the homology hypothesis and then conduct a further test by examining gene order in the two systems and their relatives. Conservation of gene order, or synteny, is often observed between closely related prokaryote species, but usually degrades with phylogenetic distance. As a result, observed conservation of synteny over vast phylogenetic distances can be evidence of shared ancestral coexpression, interaction, and function. We constructed a gene order dataset by examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar T3SS. We compared this to published surveys of gene order in the F1FO-ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-{delta}--{gamma}. The V/A-type ATPases have a similar conserved gene order shared for homologous components. Our results further strengthen the argument for homology between these systems, and suggest a rare case of synteny conserved over billions of years, dating back to well before the Last Universal Common Ancestor (LUCA).

evolutionary biology↗

bioRxiv2019

Evaluating species distribution models with discrimination accuracy is uninformative for many applications

AimSpecies distribution models are used across evolution, ecology, conservation, and epidemiology to make critical decisions and study biological phenomena, often in cases where experimental approaches are intractable. Choices regarding optimal models, methods, and data are typically made based on discrimination accuracy: a models ability to predict subsets of species occurrence data that were withheld during model construction. However, empirical applications of these models often involve making biological inferences based on continuous estimates of relative habitat suitability as a function of environmental predictor variables. We term the reliability of these biological inferences \"functional accuracy.\" We explore the link between discrimination accuracy and functional accuracy.\n\nMethodsUsing a simulation approach we investigate whether models that make good predictions of species distributions correctly infer the underlying relationship between environmental predictors and the suitability of habitat.\n\nResultsWe demonstrate that discrimination accuracy is only informative when models are simple and similar in structure to the true niche, or when data partitioning is geographically structured. However, the utility of discrimination accuracy for selecting models with high functional accuracy was low in all cases.\n\nMain conclusionsThese results suggest that many empirical studies and decisions are based on criteria that are unrelated to models usefulness for their intended purpose. We argue that empirical modeling studies need to place significantly more emphasis on biological insight into the plausibility of models, and that the current approach of maximizing discrimination accuracy at the expense of other considerations is detrimental to both the empirical and methodological literature in this active field. Finally, we argue that future development of the field must include an increased emphasis on simulation; methodological studies based on ability to predict withheld occurrence data may be largely uninformative about best practices for applications where interpretation of models relies on estimating ecological processes, and will unduly penalize more biologically informative modeling approaches.

ecology↗

bioRxiv2018

Mutations close to the peptidoglycan-binding region of the stators of the bacterial flagellar motor influence phenamil resistance

The bacterial flagellar motor (BFM) is a molecular complex which powers the rotation of the filament that propels swimming bacteria. Rotational torque is generated by harnessing the flow of ions through ion channels known as stators which couple the energy from the ion gradient across the inner membrane to rotation of the rotor. Here we used error-prone PCR to introduce single point mutations into the sodium-powered Vibrio alginolyticus/Eschrichia Coli chimeric stator PotB. We then selected for motors that exhibited resistance to the sodium-channel inhibitor phenamil. We found that single mutations that inferred resistance to phenamil occurred at two sites: 1) the transmembrane domain of PotB, corresponding to the TM region of the PomB stator from V. alginolyticus, and 2) near the peptidoglycan (PG) binding region that corresponds to the C-terminal region of the MotB stator from E. coli. We corroborated our swim plate observations with single cell rotation assays to confirm that individual cells could drive rotation of flagellar motors in the presence of up to 100 M phenamil. Our results demonstrate that it is not only the pore region of the stator that moderates the effect of motility in the presence of ion-channel blockers. We hypothesise that mutations in the PG region can allow motors to function in the presence of phenamil by allowing multiple semi-functioning stators to persist on the motor and drive flagellar rotation.

microbiology↗

bioRxiv2018

Inferring Species Trees Using Integrative Models of Species Evolution

Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.

evolutionary biology↗