Biology subjects

Walker, J. F.

Publications and source records attributed to Walker, J. F..

At least 19 recordsLinked to original sources

bioRxiv2026

Real-time measurement of short-chain fatty acids via microwave sensing: A pilot study

BackgroundShort-chain fatty acids (SCFAs) - acetate, propionate, and butyrate - are key microbial metabolites that influence host metabolism, barrier function, and immune tone. Yet, in vivo measurements of SCFAs remain poorly characterized because stool measurements only capture a small, spatially averaged fraction of luminal production. PurposeTo evaluate whether label-free microwave sensing using a vector network analyzer (VNA) can differentiate SCFA identity, concentration, and their ratios via unique dielectric signatures. MethodsSodium acetate, sodium propionate, and sodium butyrate solutions (10 uM - 1M) were prepared by measuring their electrochemical properties (pH and mV). Using a 2-port VNA interfaced with a high-frequency copper plate (1 - 3 GHz), scattering and impedance parameters were measured for SCFAs and their ratios. A per-frequency ANOVA was employed to identify discriminatory frequency bands, and supervised machine learning (random forest) was employed to identify additional features differentiating SCFAs. ResultsSCFAs displayed distinct (ANOVA, p < 0.05) electrochemical signatures for both pH and mV. The 21 transmission spectrum revealed discriminatory frequencies with prominent bands at 1.38 - 1.40 GHz and 1.79 - 1.85 GHz. For SCFA ratios, the random forest model achieved up to 80.6% accuracy (k = 0.72) with S11 (77.7%) and S22 (69.9%) unwrapped phases observed as the top two important features contributing to the models performance. ConclusionVNA-based microwave sensing resolves SCFA-specific, frequency-dependent dielectric signatures across biologically relevant concentrations and classifies SCFA-like mixtures with high accuracy. These findings support microwave sensing as a foundation for real-time, non-invasive monitoring of gut microbial metabolism. IMPORTANCEShort-chain fatty acids (SCFAs) are central to host-microbe interactions, yet conventional stool assays provide only snapshots of microbial metabolism and poorly reflect real-time intestinal production of these microbial metabolites. SCFAs mediate intestinal barrier integrity, immune regulation, energy availability, and energy metabolism. Alterations in SCFA production and composition are increasingly recognized as biomarkers of gut microbial dysbiosis, with strong connections to conditions such as inflammatory bowel disease, metabolic syndrome, obesity, and neurodegenerative disorders. As such, the dynamic and quantitative assessment of SCFA profiles in vivo may provide valuable insight into gut health, disease progression, and therapeutic response. Despite large technological advances in the past decade, there is a limited understanding of in vivo SCFA dynamics within the gut, largely due to the inaccessibility and limitation of developing non-invasive diagnostic tools. Furthermore, the spatiotemporal resolution of microbial-derived metabolites in the gut is also very limited, with most current research methods relying on utilizing stool samples, which only contain a fraction of produced SCFA concentrations. In this pilot study, SCFA solutions of known concentrations and identity were measured and analyzed via their capacitance to use as an emerging diagnostic tool in clinical and/or athletic research and to further practice assessing gut microbial dynamics. We demonstrate that microwave sensing - a label-free, electrical approach - can distinguish among SCFAs and their concentrations by exploiting their dielectric differences and frequency-resolved behavior. Using a Vector Network Analyzer and a low-loss dielectric sensor, we identify reproducible GHz-scale bands that separate acetate, propionate, and butyrate. Results indicated that these metabolites can be differentiated via their S parameter (frequency response) electrical signals and pH values. Additionally, we classify physiological SCFA mixtures with strong performance.The study will be repeated by measuring various fluid media, starting with acidic solutions and testing with fluid mixes such as mock carbohydrate solutions that best mimic gut microbial conditions in hopes of developing a diagnostic tool (i.e., swallowable sensor) that can be used to monitor real-time human gut environments. This establishes a practical path toward dynamic, non-invasive readouts of gut microbial activity with potential applications in clinical monitoring.

bioengineering↗

bioRxiv2025

Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae

Background and AimsThe flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite the available transcriptomic data, no focused phylotranscriptomic study has been conducted to characterize the patterns of molecular evolution in this group. In this study, we leverage a dataset composed predominately of publicly available transcriptomes to infer relationships within Apocynaceae and explore the molecular processes that have shaped their divergences. MethodsWe extracted nuclear, chloroplast, and mitochondrial genes from 47 publicly available and one newly sequenced transcriptome to assemble and infer species relationships across Apocynaceae. Leveraging the gene-rich nuclear phylotranscriptomic data, we inferred molecular dates and investigated the complex history of gene tree conflict, molecular rate shifts, and gene duplications. To investigate the genomic basis of adaptations, we analyzed the inferred 14,838 gene duplications at the base of Apocynaceae for shared functional enrichment of genes related to evolutionary innovations. Key ResultsThe Apocynaceae topology inferred from our phylotranscriptomic analysis is highly concordant with the current consensus. Notably, a genome-wide acceleration in molecular rate subtends the Ceropegieae tribe. We observed that a decreased time between divergences is associated with a higher rate of gene tree conflict, a pattern especially prevalent across the Apocynaceaes historically recalcitrant backbone relationships. Furthermore, gene duplications may underlie evolutionary innovations, such as immunity-related gene expansion in the genus Asclepias and duplications associated with trichome modifications in the epiphytic Hoya. Finally, we discuss the contentious history of whole-genome duplication (WGD) within the Apocynaceae and emphasize the need for further investigation into the placement of WGDs. ConclusionsRepurposing transcriptomes is a powerful means of accumulating data for novel insights in plant evolution, especially during uncertain funding and cases where budget restrictions exist. Leveraging this gene-dense dataset, we obtained novel insights into the molecular evolution of Apocynaceae and identified areas for future investigations.

evolutionary biology↗

bioRxiv2025

Recurrent Emergence of Boundary Cell Types During Evolution of Floral Bullseye Patterns

Petal patterns play an important role in the reproductive success of flowering plants by attracting pollinators and protecting reproductive organs from environmental factors. Some transcription factors (TFs) that control pigment production and cuticle elaboration in petal epidermal cells have been identified. However, little is known about the upstream developmental processes that pre-pattern the petal surface to first establish the different domains where these regulators will later be expressed. Here, we developed a computational model of the evolution and development of petal patterns to investigate this early pre-patterning phase. We selected for gene regulatory networks (GRNs) that could divide the petal surface into proximal and distal domains to create a bullseye, a very common type of petal pattern across the angiosperms. The evolved GRNs showed robust patterning dynamics and could generate a variety of bullseye proportions. We found that the evolution of bullseye patterns was often accompanied by the spontaneous emergence of a third cell type with a unique gene expression profile at the boundary between the proximal and distal regions. These bullseye boundary cells appeared in most simulations despite not being explicitly selected for, and we validated their presence experimentally in Hibiscus trionum, a model system whose flowers display a bullseye pattern. Although boundary cell types emerged spontaneously in our simulations, they evolved more often and were more important for pattern formation when gene expression was modelled as a noisy process. This suggests that GRNs producing this emergent cell type may support reproducible bullseye formation by buffering against developmental variability. Altogether, the results from our evolutionary simulations illuminate the early steps of petal pattern formation and demonstrate that novel cell types can arise spontaneously and repeatedly from selection on other cell types when developmental robustness is considered.

systems biology↗

bioRxiv2025

Herbaria provide a valuable resource for obtaining informative mRNA

While DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative to DNA, this has effectively precluded the use of herbaria for transcriptomics. Here, we challenge the assumption that herbaria cannot be used for transcriptomics by assembling transcriptomes from RNA extracted from herbarium specimens. Through systematic comparison of transcriptomes from fresh-collected, silica-dried, and archival specimens, we demonstrate the suitability of herbarium-derived RNA for transcriptomics. We show the practical applicability of archival mRNA by functionally validating a plant immune receptor synthesized from a specimen collected in 1956. These results contradict the community consensus regarding archival RNA and open the door to subsequent transcriptomic explorations of rare and extinct plant species. Our findings highlight the importance of preserving and utilizing the diversity embedded within herbarium collections.

plant biology↗

bioRxiv2024

The genetic basis of replicated bullseye pattern reduction across the Trionum Complex

Angiosperm flowers exhibit a wide diversity of colorful motifs on their petals. Such patterns fulfill both biotic and abiotic functions, mediating plant-pollinator communication and providing protection against damaging UV rays or desiccation. These motifs are often evolutionary labile, varying in size, shape and hue between closely related species and constitute excellent systems to illuminate the evolutionary processes that generate morphological diversity or instead lead to the repetitive emergence of similar forms. Hibiscus trionum flowers have a prominent bullseye pattern combining a purple center contrasting against a white margin. H. trionum belongs to a small clade of Hibiscus known as the Trionum Complex that displays a range of petal patterns within and between species. Here, we integrate phylogenomic approaches, molecular techniques and genetic manipulation to solve species relationships across the Trionum Complex, identify key genes involved in the production of bullseye pigmentation, and reveal molecular events underpinning pattern variation during the evolution of the group. We find that repetitive bullseye reduction events primarily occur through independent modifications of a single genetic locus encoding BERRY1, an R2R3 MYB that regulates anthocyanin pigment production in petals. Moreover, we demonstrate that buff-tailed bumblebees (Bombus terrestris) discriminate against flowers with smaller bullseye sizes suggesting that a reduction in bullseye proportions potentially impacts plant fitness and contributes to trait distribution across the group. Collectively, our results demonstrate how repeated mutations in a single locus led to morphological variation in petal patterning, a trait that contributes to angiosperm reproductive isolation and speciation.

plant biology↗

bioRxiv2024

A Necrotizing Toxin Promotes Pseudomonas syringae Infection Across Evolutionarily Divergent Plant Lineages

The Pseudomonas syringae species complex harbors a diverse range of plant pathogenic bacteria. While much of the current understanding of P. syringae is centered on interactions with flowering plants, much less is known about infection in evolutionarily divergent non-flowering lineages. Here, we took a comparative evolutionary approach to understand how P. syringae infects distantly related plants. We identify broad host P. syringae isolates causing significant disease in the liverwort Marchantia polymorpha, the fern Ceratopteris richardii, and the flowering plant Nicotiana benthamiana, which last shared a common ancestor over 500 million years ago. We demonstrate that phytotoxin enriched isolates belonging to the phylogroup 2 clade of the P. syringae species complex are particularly virulent in non-flowering plants, relying on a combination of type-3 secreted effector proteins and the lipopeptide phytotoxin syringomycin. The application of purified syringomycin promotes necrosis in diverse host tissues and activates conserved genes associated with redox regulation and cell death. Toxin-deficient phylogroups normally unable to infect Marchantia thalli exhibit enhanced bacterial growth when supplemented with exogenous syringomycin, further highlighting its role as a host-range defining factor in Pseudomonas. Collectively our research reveals a key role for the lipopeptide syringomycin in promoting Pseudomonas colonization, which works in concert with type-3 effector proteins to antagonize an exceptionally wide spectrum of land plants.

plant biology↗

bioRxiv2023

Investigating Phylogenetic Conflict using Homolog Trees reveals the Genetic Basis of Phenotypic Convergence in Carnivorous Sundews

Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analysing conflict on entire homolog trees can aid in inferring the genetic basis of trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development.

evolutionary biology↗

bioRxiv2023

Transcriptome data from silica-preserved leaf tissue reveals gene flow patterns in a Caribbean bromeliad

O_LITranscriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept under special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from six-month-old, field collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genus Pitcairnia (Bromeliaceae) in the Dominican Republic and infer barriers to gene flow. C_LIO_LIWe extracted RNA from silica-dried leaf tissue from 19 Pitcairnia individuals collected across the Dominican Republic. We used a series of macro-and micro-evolutionary approaches to examine the relationships and patterns of gene flow among individuals. C_LIO_LIWe produced high-quality transcriptomes from silica-dried material and demonstrated that evolutionary relationships on the island match geography more closely than species delimitation methods. A population genetic examination indicates that a combination of ecological and geographic features are barriers to gene flow in Pitcairnia. C_LIO_LIHigh-quality transcriptomes can be obtained from silica-preserved tissue. The genetic diversity among Pitcairnia populations does not warrant classification as separate species, but the Dominican Republic contains several barriers to gene flow, notably the Cordillera Central mountain range. C_LI

evolutionary biology↗

bioRxiv2020

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

The genomic data revolution has enabled biologists to develop innovative ways to infer key episodes in the history of life. Whether genome-scale data will eventually resolve all branches of the Tree of Life remains uncertain. However, through novel means of interrogating data, some explanations for why evolutionary relationships remain recalcitrant are emerging. Here, we provide four biological and analytical factors that explain why certain genes may exhibit "outlier" behavior, namely, rate of molecular evolution, alignment length, misidentified orthology, and errors in modeling. Using empirical and simulated data we show how excluding genes based on their likelihood or inferring processes from the topology they support in a supermatrix can mislead biological inference of conflict. We next show alignment length accounts for the high influence of two genes reported in empirical datasets. Finally, we also reiterate the impact misidentified orthology and short alignments have on likelihoods in large scale phylogenetics. We suggest that researchers should systematically investigate and describe the source of influential genes, as opposed to discarding them as outliers. Disentangling whether analytical or biological factors are the source of outliers will help uncover new patterns and processes that are shaping the Tree of Life.

evolutionary biology↗

bioRxiv2020

When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships

Phylogenies inferred using both concatenation- and coalescent-based analyses typically render highly congruent trees. However, when they disagree, they often differ with respect to historically contentious and evolutionarily important relationships. These relationships may also involve etiolated lineages where increased sampling is not possible. Recently, methods aimed at interrogating single relationships or trees have emerged as promising investigative tools to examine these cases. Although recent methods such as "Edge-based Phylogenomic Support analYsis" (EPSY) led to insights into both systematic error and real biological signal, whether they are consistent with the coalescent in cases with high Incomplete Lineage Sorting (ILS) has yet to be characterized. Here, we use simulations and an empirical dataset to test the performance of EPSY, concatenation, and coalescent-based summary analyses under high levels of ILS. We focused on high-ILS scenarios because these represent the typical difficult cases that researchers often face due to the prevalence of ILS in phylogenomic datasets. ILS is known to be a major cause of phylogenomic conflict, which confounds many biological conclusions that depend on a resolved phylogeny, such as inferring ancestral character states, biogeographic reconstructions, and domestication histories. Our study found that EPSY was consistent with the coalescent in a high-ILS empirical dataset. In high-ILS simulations EPSY infers the correct edge more than half the time, whereas coalescent based methods and concatenation methods inferred the actual tree 37.8% and 25% of the time, respectively. All methods have conditions under which they generate the most accurate inferences. Given the levels of ILS in simulations, 26.2% of the time no method recovered the true tree. This zone where no current method can infer the true topology is likely due to properties of the species tree, such as the length of internal edges adjacent to a conflict and/or the length of the shortest branch. Nevertheless, the EPSY approach proves to be a valuable complement to phylogenomic analyses for interrogating regions of the tree with conflicting hypotheses generated from past studies or alternative inference methods. Our analyses highlight that robust phylogenetic trees may not be possible under some scenarios regardless of method and data source.

genomics↗

bioRxiv2019

A consensus phylogenomic approach highlights the ancient rapid radiation of Ericales

Premise of studyLarge genomic datasets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. MethodsWe used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods and is summarized in a consensus framework. Key ResultsOur consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships due to lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole genome duplication before the radiation of all or most ericalean families and demonstrate that tree topology and heterogeneous evolutionary rates impact the inferred placement of genome duplications. ConclusionsOur approach provides a novel hypothesis regarding the history of Ericales and confidently resolves most nodes. We demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

evolutionary biology↗

bioRxiv2019

Characterizing gene tree conflict in plastome-inferred phylogenies

Premise of the studyEvolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict.\n\nMethodsUsing a broad sampling of angiosperm plastomes, we characterized gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type).\n\nKey resultsWe uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find gene length is the strongest correlate to concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes.\n\nConclusionsOur results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given the documented cases of heteroplasmic recombination. We suggest rpoC2 as a useful marker for reconstructing angiosperm phylogeny, reducing the effort and expense of assembling and analyzing entire plastomes.

evolutionary biology↗

bioRxiv2018

Nested phylogenetic conflicts and deep phylogenomics in plants

Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a dataset in order to resolve recalcitrant relationships and, importantly, identify what the dataset is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant dataset. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific dataset to address deep phylogenetic relationships while also identifying the inferential boundaries of the dataset.

evolutionary biology↗

bioRxiv2018

Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae of Madagascar, and high altitude Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examine potential correlates between molecular evolution within this clade and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we presented detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and identified a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche and did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and while these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

evolutionary biology↗

bioRxiv2017

Quartet Sampling distinguishes lack of support from conflicting support \newline in the plant tree of life

Premise of the StudyPhylogenetic support has been difficult to evaluate within the plant tree of life partly due to the difficulty of distinguishing conflicted versus poorly informed branches. As datasets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.\n\nMethodsWe describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide datasets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We test QS with simulations and recent plant phylogenies inferred from variously sized datasets.\n\nKey ResultsQS scores demonstrate convergence with increasing replicates and are not strongly affected by branch depth. Patterns of QS support from different phylogenies leads to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA grade angiosperms, major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.\n\nConclusionsThe QS method represents an efficient and effective synthesis of phylogenetic tests that offer more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted to reconstruct the complex evolutionary histories surrounding in particular ANA grade angiosperms, monocots, and non-vascular plants.

evolutionary biology↗

bioRxiv2017

Disparity, Diversity, And Duplications In The Caryophyllales

O_LIThe role whole genome duplication (WGD) plays in the history of lineages is actively debated. WGDs have been associated with advantages including superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates.\nC_LIO_LIUsing seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5,036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic niche and lineage diversification rate.\nC_LIO_LIThirteen putative WGDs and twenty-seven diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic niches.\nC_LIO_LIWhile we find that many diversification shifts occur after WGDs it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic niche, or rate of evolution.\nC_LI

evolutionary biology↗

bioRxiv2017

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

O_LIThe carnivorous members of the large, hyperdiverse Caryophyllales (e.g. Venus flytrap, sundews and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved.\nC_LIO_LITo explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced ten transcriptomes, including all the carnivorous genera except those in the rare West African liana family (Dioncophyllaceae). We used a variety of methods to infer the species tree, examine gene tree conflict and infer paleopolyploidy events.\nC_LIO_LIPhylogenomic analyses support the monophyly of the carnivorous Caryophyllales, with an origin of 68-83 mya. In contrast to previous analyses recover the remaining non-core Caryophyllales as non-monophyletic, although there are multiple reasons this result may be spurious and node supporting this relationship contains a significant amount gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously debated nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set.\nC_LIO_LIOur data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.\nC_LI

evolutionary biology↗

bioRxiv2017

Site and gene-wise likelihoods unmask influential outliers in phylogenomic analyses

Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Here, we examined two datasets where supermatrix and coalescent-based species trees conflict. We identified two highly influential \"outlier\" genes in each dataset. When removed from each dataset, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the outlier genes in the vertebrate dataset have been shown in a previous study to be the result of errors in orthology detection, the outlier genes from a plant dataset did not exhibit any obvious systematic error and therefore may be the result of some biological process yet to be determined. While topological comparisons among a small set of alternate topologies can be helpful in discovering outlier genes, they can be limited in several ways, such as assuming all genes share the same topology. Coalescent species tree methods relax this assumption but do not explicitly facilitate the examination of specific edges. Coalescent methods often also assume that conflict is the result of incomplete lineage sorting (ILS). Here we explored a framework that allows for quickly examining alternative edges and support for large phylogenomic datasets that does not assume a single topology for all genes. For both datasets, these analyses provided detailed results confirming the support for coalescent-based topologies. This framework suggests that we can improve our understanding of the underlying signal in phylogenomic datasets by asking more targeted edge-based questions.

evolutionary biology↗