Biology subjects

Tank, D. C.

Publications and source records attributed to Tank, D. C..

7 recordsLinked to original sources

bioRxiv2026

Painting the evolutionary history of a multicompartmentalized syngameon in North American Castilleja (Orobanchaceae)

Understanding the evolutionary history of recent rapidly radiating groups remains a major challenge in systematics, especially when incomplete reproductive isolation and rampant interspecific gene flow obscure phylogenetic signal. Here, we present a comprehensive phylogenomic study of the genus Castilleja (the paintbrushes, Orobanchaceae), integrating nuclear and chloroplast data to investigate patterns of diversification, hybridization, and geographic structure across its range. Our results provide the first evidence that Castilleja functions as a multicompartmentalized syngameon-a network of closely related species with ongoing or historical gene flow among non-sister lineages within and between geographically structured compartments. High nuclear gene tree discordance, coupled with strong cpDNA geographic compartment structuring and nuclear network analysis, supports the hypothesis that recent rapid radiation and Plio-Pleistocene climatic fluctuations created alternating periods of range expansion and contraction. These dynamics likely promoted localized hybridization within isolated compartments during contraction and further introgression between compartments during range expansion. Our findings not only clarify the evolutionary relationships within Castilleja but also demonstrate the importance of genome-scale data and syngameon theory in understanding diversification in lineages where hybridization is rampant.

evolutionary biology↗

bioRxiv2021

Phylogenomic analyses using genomes and transcriptomes do not resolve relationships among major clades in Phrymaceae

Premise of the studyPhylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons. MethodsWe sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events. Key resultsMost gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. ConclusionsWe show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that genome-scale data do not always fully "resolve" phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.

evolutionary biology↗

bioRxiv2020

Phylogeny, classification, and character evolution of tribe Citharexyleae (Verbenaceae)

Premise of the studyTribe Citharexyleae comprises three genera: Baillonia, Citharexylum, and Rehdera. While there is good support for these genera as a clade, relationships between genera remain unresolved due to low sampling of the largest genus, Citharexylum. A molecular phylogenetic approach was taken to resolve intergeneric relationships in Citharexyleae and infrageneric relationships in Citharexylum. MethodsSeven chloroplast regions, two nuclear ribosomal spacers, and six low-copy nuclear loci were analyzed for 64 species of Citharexyleae. Phylogenetic analyses were conducted using maximum likelihood, Bayesian inference, and Bayesian multi-species coalescent approaches. Habit, presence/absence of thorns, inflorescence architecture, flower color, fruit color, and geography were examined to identify diagnostic characters for clades within Citharexylum. Key resultsIntergeneric relationships resolved Rehdera as sister to Citharexylum and Baillonia nested within Citharexylum. Two species, C. oleinum and C. tetramerum, fell outside of Citharexyleae close to tribe Duranteae. There is strong support for seven clades within Citharexylum, each characterized by a unique combination of geography, fruit color/maturation, and inflorescence architecture. ConclusionsBaillonia is included in Citharexylum; Rehdera is retained as a distinct genus. A subgeneric classification for Citharexylum is proposed.

evolutionary biology↗

bioRxiv2020

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment datasets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here we use an automated approach for orthology inference in a target enrichment dataset of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic datasets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment datasets.

evolutionary biology↗

bioRxiv2018

Phylogeny of the Australian Solanum dioicum group using seven nuclear genes: testing Symons fruit and seed dispersal hypotheses

The dioecious and andromonoecious Solanum taxa (previously described as the \"S. dioicum group\") of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first intron-containing nuclear gene dataset in the genus Solanum and the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed dispersal (strongly linked to calyx accrescence) is far more common among Australian Solanum than previously thought and support the hypothesis that the combination of large fleshy fruits and endozoochorous dispersal represents a reversal in this study group. The general lack of direct evidence related to biotic dispersal (epizoochorous or endozoochorous) may be a function of declines and/or extinctions of vertebrate dispersers. Because of this, some taxa might now rely on secondary dispersal mechanisms (e.g. shakers, tumbleweeds, rafting) as a means to maintain current populations and establish new ones.

evolutionary biology↗

bioRxiv2018

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

PREMISE OF THE STUDYAt the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high-alpine flora of the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities.\n\nMETHODSWe used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assed how maximum elevation explains phylogenetic structure. To evaluate similarities between summits we quantified phylogenetic turnover, taking into consideration micro-habitats (talus vs. meadows).\n\nKEY RESULTSWe found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely no different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: significant overdispersion degraded as elevation increased. Between summits we found high phylogenetic turnover, which was driven by greater niche heterogeneity on summits with alpine meadows.\n\nCONCLUSIONSThis study provides further evidence that stochastic processes shape the assembly of vascular plant communities in the high-alpine at regional scales. However, order-specific patterns suggest adaptations may be important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important to disentangle the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.

evolutionary biology↗

bioRxiv2018

Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Premise of the studyTargeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies.\n\nMethods and ResultsWe present Fluidigm2PURC, an open source Python utility for processing paired-end Illumina data from double-barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling Reticulate Complexes), our scripts process raw FASTQ files for analysis with PURC and use its output to infer haplotypes for diploids, polyploids, and samples with unknown ploidy. We demonstrate the use of the pipeline with an example data set from the genus Thalictrum L. (Ranunculaceae).\n\nConclusionsFluidigm2PURC is freely available for Unix-like operating systems on GitHub [https://github.com/pblischak/fluidigm2purc] and for all operating systems through Docker [https://hub.docker.com/r/pblischak/fluidigm2purc].

bioinformatics↗