Biology subjects

Soltis, D. E.

Publications and source records attributed to Soltis, D. E..

28 records · Page 2Linked to original sources

bioRxiv2021

Transcriptome-based phylogeny and whole-genome duplication in Theaceae

Theaceae, with three tribes and nine genera, is a family of great economic and ecological importance. Recent phylogenetic analyses based on plastid genome resolved the relationship among three tribes and the intergeneric relationships within Gordonieae and Stewartieae. However, generic level relationships within the largest tribe Theeae were not fully resolved and potential hybridization among genera within Theeae revealed previously also remains to be tested further. Here we conducted a comprehensive phylogenomic study of Theaceae based on transcriptomes and low-depth whole-genome sequencing of 57 species as well as additional plastome sequence data from previous work. Phylogenetic analyses suggested that Stewartieae was the first-diverging clade in Theaceae, consistent with previous study using plastomic data. Within Theeae, the highly supported Apterosperma-Laplacea clade grouped with Pyrenaria with maximum support based on the partitioned and unpartitioned concatenation analyses using the 610 low-copy nuclear genes, leaving Camellia and Polyspora as another sister genera in the tribe. PhyloNet analyses suggested one reticulation event within Camellia and Pyrenaria respectively, but no intergeneric reticulations were detected in Theeae. Another introgression was found between Gordonia lasianthus and the common ancestor of Gordonieae during the Late Oligocene. The existing land bridges (e.g. Bering land bridge) might have facilitated this ancient introgression. Further researches need to be conducted to uncover the interspecific introgression pattern within Camellia. Ks distribution analyses supported the tea family shared one whole-genome duplication (WGD) event Ad-{beta}, which was recently mapped to the clade containing core Ericales, Primuloids, Polemonioids and Lecythidaceae.

evolutionary biology↗

bioRxiv2021

Gene duplications and genomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the Tree of Life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation1, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here we examine the relationship of various facets of genomic evolution--including gene and genome duplication, genome size, and chromosome number--with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.

evolutionary biology↗

bioRxiv2020

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity and endemism. We also undertook the first direct, quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants in North America. We expected concordance between butterflies and angiosperms based on both shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants in some regions of the continent. In particular, the warm desert regions of the southwestern United States and Mexico showed surprisingly high butterfly phylogenetic diversity and endemism, in contrast to much lower values for angiosperms. Butterflies did not show patterns of phylogenetic clustering as found in flowering plants, suggesting differences in habitat conservation between the two groups. Finally, we found weak relationships and spatially structured biases in relative branching timing between angiosperms and butterflies. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as an important North American butterfly biodiversity hotspot.

ecology↗

bioRxiv2019

Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids

Premise of the StudyRecent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification rates. These now-common approaches typically (1) are characterized by incomplete coverage without explicit sampling methodologies, and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. Here we use an empirical example to examine effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionists based on those results.\n\nMethodsWe used a supermatrix for rosids, a large clade of angiosperms, and its well-sampled subclade Cucurbitaceae, as empirical case studies. We compared results using this large phylogeny with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA, BAMM) and semiparametric (DR).\n\nKey ResultsWe find the impact of sampling on diversification estimates is idiosyncratic and often strong. As compared to full empirical sampling, representative and random sampling schemes either depress or exaggerate speciation rates depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.\n\nConclusionsWe (1) urge caution in use of summary backbone trees containing only higher-level taxa, (2) caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees, and (3) stress the importance of explicit sampling methodologies in macroevolutionary studies.

evolutionary biology↗

bioRxiv2019

Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

Current advances in sequencing technology have greatly increased the availability of sequence data from public genetic databases. With data from GenBank, we assemble and phylogenetically investigate a 19,740-taxon, five-locus supermatrix (i.e., atpB, rbcL, matK, matR, and ITS) for rosids, a large clade containing over 90,000 species, or approximately a quarter of all angiosperms (assuming an estimate of 400,000 angiosperm species). The topology and divergence times of the five-locus tree generally agree with previous estimates of rosid phylogeny, and we recover greater resolution and support in several areas along the rosid backbone, but with a few significant differences (e.g., the placement of the COM clade, as well as Myrtales, Vitales, and Zygophyllales). Our five-locus phylogeny is the most comprehensive DNA data set yet compiled for the rosid clade. Yet, even with 19,740 species, current sampling represents only 16-22% of all rosids, and we also find evidence of strong phylogenetic bias in the accumulation of GenBank data, highlighting continued challenges for species coverage. These limitations also exist in other major angiosperm clades (e.g., asterids, monocots) as well as other large, understudied branches of the Tree of Life, highlighting the need for broader molecular sampling. Nevertheless, the phylogeny presented here improves upon sampling by more than two-fold and will be an important resource for macroevolutionary studies of this pivotal clade.

evolutionary biology↗

bioRxiv2019

Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae

BackgroundA major goal of phylogenetic systematics is to understand both the patterns of diversification and the processes by which these patterns are formed. Few studies have focused on the ancient, species-rich Magnoliales clade and its diversification pattern. Within Magnoliales, the pantropically distributed Annonaceae are by far the most genus-rich and species-rich family-level clade, with c. 110 genera and c. 2,400 species. We investigated the diversification patterns across Annonaceae and identified traits that show varied associations with diversification rates using a time-calibrated phylogeny of 835 species (34.6% sampling) and 11,211 aligned bases from eight regions of the plastid genome (rbcL, matK, ndhF, psbA-trnH, trnL-F, atpB-rbcL, trnS-G, and ycf1). Two hypotheses that might explain patterns of diversification--the museum model and heterogeneous diversification rates--are also evaluated.\n\nResultsTwelve rate shifts were identified using BAMM: in Annona, Artabotrys, Asimina, Drepananthus, Duguetia, Goniothalamus, Guatteria, Uvaria, Xylopia, the tribes Miliuseae and Malmeeae, and the Desmos-Dasymaschalon-Friesodielsia-Monanthotaxis clade (which collectively account for over 80% of the total species richness in the family). TurboMEDUSA and method-of-moments estimator analyses showed largely congruent results. A positive relationship between species richness and diversification rate is revealed using PGLS. We further explore the possible role of selected traits (habit, pollinator trapping, floral sex expression, pollen dispersal unit, anther septation, and seed dispersal unit) in shaping diversification patterns, based on inferences of BiSSE, MuSSE, HiSSE, and FiSSE analyses. Our results suggest that the liana habit, the presence of circadian pollinator trapping, androdioecy, and the dispersal of seeds as single-seeded monocarp fragments are closely correlated with higher diversification rates; pollen aggregation and anther septation, in contrast, are associated with lower diversification rates.\n\nConclusionOur results show that the high species richness in Annonaceae is likely the result of recent increased diversification rather than the steady accumulation of species via the museum model. BAMM, turboMEDUSA, and the method-of-moments estimator all indicate heterogeneity in diversification rates across the phylogeny, with different traits associated with shifts in diversification rates in different Annonaceae clades.

evolutionary biology↗

bioRxiv2018

For comparing phylogenetic diversity among communities, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagels {lambda} and Blombergs K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearmans{rho} > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blombergs K or close to Pagels {lambda} from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

ecology↗

bioRxiv2018

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost associated with developing targeted sequencing approaches is preliminary data needed for identifying orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm lineage. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order lineages of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order lineages, including all angiosperms.

evolutionary biology↗

bioRxiv2017

Divergent gene expression levels between diploid and autotetraploid Tolmiea (Saxifragaceae) relative to the total transcriptome, the cell, and biomass

O_LIStudies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Integrating multiple methods of transcript analysis, we document a difference in transcriptome size, and make multiple comparisons of transcript abundance in diploid and autotetraploid Tolmiea.\nC_LIO_LIWe use RNA spike-in standards to identify and correct for differences in transcriptome size, and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass.\nC_LIO_LIIn total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. A shift in total transcriptome size resulted in only ~58% of the total DEGs being identified as differentially expressed following a per transcriptome normalization. When transcript abundance was normalized per cell, ~82% of the total DEGs were recovered. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size.\nC_LIO_LIWhile each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.\nC_LI

genomics↗

bioRxiv2017

Geographic range dynamics drove ancient hybridization in a lineage of angiosperms

Factors explaining global distribution patterns have been central to biology since the 19th century, yet failure to combine dispersal-based biogeography with shifts in habitat suitability remains a present-day setback in understanding geographic distributions present and past, and time-extended trajectories of lineages. The lack of methods in a suitable integrative framework stands as a conspicuous shortcoming for reconstructing these dynamics. Here we showcase novel methods to overcome these methodological gaps, broadening the prospects for phyloclimatic modeling. We focus on a clade in the angiosperm genus Heuchera endemic to southern California that experienced ancient introgression from circumboreally distributed species of Mitella, testing hypotheses regarding biotic contact in the past between ancestral species lacking a fossil record. We obtain strong support for a past contact zone in northwestern North America, resolving this paradox of hybridization between ancestors of taxa currently separated by [~]1300 km.

evolutionary biology↗