Biology subjects

Fullmer, M. S.

Publications and source records attributed to Fullmer, M. S..

5 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

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

Interaction range of common goods shapes Black Queen dynamics beyond the cheater-cooperator narrative

Dependencies among microorganisms often appear mutualistic in the lab, as microbes grow faster together than alone. However, according to the Black Queen (BQ) hypothesis, these dependencies are underpinned by the evolutionary benefits from loss-of-function mutations when others in the community can supply the necessary common goods. BQ dynamics often describe a cheater-cooperator scenario, where some ecotypes, the "cheaters," produce no common goods and rely on others, the "cooperators", for survival. We have previously proposed that in systems with multiple common goods, an alternative endpoint for BQ dynamics can emerge. This endpoint describes an ecosystem of interdependent ecotypes engaging in "mutual cheating", i.e. where common good production is distributed. However, even with multiple goods the common good production can be centralized, i.e. with one ecotype providing all common goods for the ecosystem. Here, we present an eco-evolutionary model that reveals that BQ dynamics can result in both distributed- or centralized common good production. The interaction range, i.e. the number of beneficiaries a producer can support, distinguishes between these two endpoints. While many ecosystems evolve to be maximally distributed or maximally centralized, we also find intermediate ecosystems, where ecotypes that appear redundant are coexisting for long periods of time. Due to the limited interaction range, these redundant ecotypes are unable to distribute the production of common goods fully due to the presence of non-producing types. Despite non-producers thus stalling the division of labor, we observe that sudden structural shifts can occur that purge the non-producers from the ecosystem. Overall, our findings broaden the understanding of BQ dynamics, unveiling complex interactions beyond the simple cheater-cooperator narrative.

evolutionary biology↗

bioRxiv2020

Expanding the utility of sequence comparisons using data from whole genomes

Whole genome comparisons based on Average Nucleotide Identities (ANI), and the Genome-to-genome distance calculator have risen to prominence in rapidly classifying taxa using whole genome sequences. Some implementations have even been proposed as a new standard in species classification and have become a common technique for papers describing newly sequenced genomes. However, attempts to apply whole genome divergence data to delineation of higher taxonomic units, and to phylogenetic inference have had difficulty matching those produced by more complex phylogenetics methods. We present a novel method for generating reliable and statistically supported phylogenies using established ANI techniques. For the test cases to which we applied the developed approach we obtained accurate results up to at least the family level. The developed method uses non-parametric bootstrapping to gauge reliability of inferred groups. This method offers the opportunity make use of whole-genome comparison data that is already being generated to quickly produce accurate phylogenies. Additionally, the developed ANI methodology can assist classification of higher order taxonomic groups. Significance StatementThe average nucleotide identity (ANI) measure and its iterations have come to dominate in-silico species delimitation in the past decade. Yet the problem of gene content has not been fully resolved, and attempts made to do so contain two metrics which makes interpretation difficult at times. We provide a new single based ANI metric created from the combination of genomic content and genomic identity measures. Our results show that this method can handle comparisons of genomes with divergent content or identity. Additionally, the metric can be used to create distance based phylogenetic trees that are comparable to other tree building methods, while also providing a tentative metric for categorizing organisms into higher level taxonomic classifications.

bioinformatics↗

bioRxiv2019

The Patchy Distribution of Restriction-Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.

Restriction-modification (RM) systems in Bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In Bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.

genomics↗