scholarly journals Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics

2017 ◽  
Author(s):  
Marek L. Borowiec
Keyword(s):  
Convergent Evolution ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Taxon Sampling ◽  
Data Sets ◽  
Sequence Evolution ◽  
Army Ants ◽  
Data Set ◽  
Army Ant ◽  
Ant Behavior

AbstractThe evolution of the suite of morphological and behavioral adaptations underlying the ecological success of army ants has been the subject of considerable debate. This “army ant syn-drome” has been argued to have arisen once or multiple times within the ant subfamily Dorylinae. To address this question I generated data from 2,166 loci and a comprehensive taxon sampling for a phylogenetic investigation. Most analyses show strong support for convergent evolution of the army ant syndrome in the Old and New World but certain relationships are sensitive to analytics. I examine the signal present in this data set and find that conflict is diminished when only loci less likely to violate common phylogenetic model assumptions are considered. I also provide a temporal and spatial context for doryline evolution with timecalibrated, biogeographic, and diversification rate shift analyses. This study underscores the need for cautious analysis of phylogenomic data and calls for more efficient algorithms employing better-fitting models of molecular evolution.SignificanceRecent interpretation of army ant evolution holds that army ant behavior and morphology originated only once within the subfamily Dorylinae. An inspection of phylogenetic signal in a large new data set shows that support for this hypothesis may be driven by bias present in the data. Convergent evolution of the army ant syndrome is consistently supported when sequences violating assumptions of a commonly used model of sequence evolution are excluded from the analysis. This hypothesis also fits with a simple scenario of doryline biogeography. These results highlight the importance of careful evaluation of signal and conflict within phylogenomic data sets, even when taxon sampling is comprehensive.

scholarly journals Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

2020 ◽  
Author(s):  
Dario Karmeinski ◽  
Karen Meusemann ◽  
Jessica A. Goodheart ◽  
Michael Schroedl ◽  
Alexander Martynov ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Transcriptome Assembly ◽  
Phylogenetic Signal ◽  
Taxon Sampling ◽  
Data Sets ◽  
Transcriptome Data ◽  
Data Set ◽  
Sea Slugs ◽  
History Of

AbstractBackgroundCladobranch sea slugs represent roughly half of the biodiversity of soft-bodied, marine gastropod molluscs (Nudibranchia) on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as bioindicators and providers of medical drug leads), the evolutionary history of cladobranch sea slugs is not yet fully understood. Here, we amplify the current knowledge on the phylogenetic relationships by extending the cladobranch and outgroup taxon sampling using transcriptome data.ResultsWe generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa. We complemented our taxon sampling with previously published transcriptome data, resulting in a final supermatrix covering 56 species from all but one accepted cladobranch superfamilies. Transcriptome assembly using six different assemblers, selection of those assemblies providing the largest amount of potentially phylogenetically informative sites, and quality-driven compilation of data sets resulted in three different supermatrices: one with a full coverage of genes per species (446 single-copy protein-coding genes) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1,767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximum statistical support for all major splits and phylogenetic relationships on family level. The only discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal.ConclusionsOur data matrices and the inferred trees inferred can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The correct placement of E. pulchra, however, proves challenging, even with large data sets. Moreover, quartet mapping shows that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

scholarly journals Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa

2015 ◽  
Author(s):  
Marek L Borowiec ◽  
Ernest K Lee ◽  
Joanna C Chiu ◽  
David C Plachetzki
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Data Sets ◽  
Sequence Evolution ◽  
Systematic Bias ◽  
Whole Genome ◽  
Data Partition ◽  
Data Set ◽  
Genome Data ◽  
Computationally Intensive

Transcriptome-enabled phylogenetic analyses have dramatically improved our understanding of metazoan phylogeny in recent years, although several important questions remain. The branching order near the base of the tree is one such outstanding issue. To address this question we assemble a novel data set comprised of 1,080 orthologous loci derived from 36 publicly available genomes and dissect the phylogenetic signal present in each individual partition. The size of this data set allows for a closer look at the potential biases and sources of non-phylogenetic signal. We assessed a range of measures for each data partition including information content, saturation, rate of evolution, long-branch score, and taxon occupancy and explored how each of these characteristics impacts phylogeny estimation. We then used these data to prepare a reduced set of partitions that fit an optimal set of criteria and are amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. All of our analyses support Ctenophora as the sister lineage to other Metazoa, although support for this relationship varies among analyses. We find no support for the traditional view uniting the ctenophores and Cnidaria (jellies, anemones, corals, and kin). We also examine phylogenetic placement of myriapods (centipedes and millipedes) and find it more sensitive to the type of analysis and data used. Our study provides a workflow for minimizing systematic bias in whole genome-based phylogenetic analyses.

scholarly journals Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny

2000 ◽  
Vol 355 (1398) ◽  
pp. 769-793 ◽  
Author(s):  
Karen Sue Renzaglia ◽  
R. Joel Duff ◽  
Daniel L. Nickrent ◽  
David J. Garbary
Keyword(s):  
Phylogenetic Signal ◽  
Phenotypic Variability ◽  
Land Plant ◽  
Land Plants ◽  
Total Evidence ◽  
Data Sets ◽  
Data Set ◽  
Plant Phylogeny ◽  
Male Gametes ◽  
Early Land

As the oldest extant lineages of land plants, bryophytes provide a living laboratory in which to evaluate morphological adaptations associated with early land existence. In this paper we examine reproductive and structural innovations in the gametophyte and sporophyte generations of hornworts, liverworts, mosses and basal pteridophytes. Reproductive features relating to spermatogenesis and the architecture of motile male gametes are overviewed and evaluated from an evolutionary perspective. Phylogenetic analyses of a data set derived from spermatogenesis and one derived from comprehensive morphogenetic data are compared with a molecular analysis of nuclear and mitochondrial small subunit rDNA sequences. Although relatively small because of a reliance on water for sexual reproduction, gametophytes of bryophytes are the most elaborate of those produced by any land plant. Phenotypic variability in gametophytic habit ranges from leafy to thalloid forms with the greatest diversity exhibited by hepatics. Appendages, including leaves, slime papillae and hairs, predominate in liverworts and mosses, while hornwort gametophytes are strictly thalloid with no organized external structures. Internalization of reproductive and vegetative structures within mucilage–filled spaces is an adaptive strategy exhibited by hornworts. The formative stages of gametangial development are similar in the three bryophyte groups, with the exception that in mosses apical growth is intercalated into early organogenesis, a feature echoed in moss sporophyte ontogeny. A monosporangiate, unbranched sporophyte typifies bryophytes, but developmental and structural innovations suggest the three bryophyte groups diverged prior to elaboration of this generation. Sporophyte morphogenesis in hornworts involves non–synchronized sporogenesis and the continued elongation of the single sporangium, features unique among archegoniates. In hepatics, elongation of the sporophyte seta and archegoniophore is rapid and requires instantaneous wall expandability and hydrostatic support. Unicellular, spiralled elaters and capsule dehiscence through the formation of four regular valves are autapomorphies of liverworts. Sporophytic sophistications in the moss clade include conducting tissue, stomata, an assimilative layer and an elaborate peristome for extended spore dispersal. Characters such as stomata and conducting cells that are shared among sporophytes of mosses, hornworts and pteridophytes are interpreted as parallelisms and not homologies. Our phylogenetic analysis of three different data sets is the most comprehensive to date and points to a single phylogenetic solution for the evolution of basal embryophytes. Hornworts are supported as the earliest divergent embryophyte clade with a moss/liverwort clade sister to tracheophytes. Among pteridophytes, lycophytes are monophyletic and an assemblage containing ferns, Equisetum and psilophytes is sister to seed plants. Congruence between morphological and molecular hypotheses indicates that these data sets are tracking the same phylogenetic signal and reinforces our phylogenetic conclusions. It appears that total evidence approaches are valuable in resolving ancient radiations such as those characterizing the evolution of early embryophytes. More information on land plant phylogeny can be found at: http://www.science.siu.edu/landplants/index.html.

scholarly journals Phylogenomic analysis of echinoderm class relationships supports Asterozoa

2014 ◽  
Vol 281 (1786) ◽  
pp. 20140479 ◽  
Author(s):  
Maximilian J. Telford ◽  
Christopher J. Lowe ◽  
Christopher B. Cameron ◽  
Olga Ortega-Martinez ◽  
Jochanan Aronowicz ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Phylogenomic Analysis ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
Complete Dataset ◽  
Type Larva ◽  
Molecular Phylogenetic

While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used ‘phylogenetic signal dissection’ to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.

scholarly journals Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants

2019 ◽  
Author(s):  
Ting Yang ◽  
Xuezhu Liao ◽  
Lingxiao Yang ◽  
Yang Liu ◽  
Weixue Mu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Structure ◽  
Strong Support ◽  
Gc Content ◽  
Taxon Sampling ◽  
Data Sets ◽  
Green Plants ◽  
Comparative Analyses ◽  
Chloroplast Genomes ◽  
The Matrix

AbstractBackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.ResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.ConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.

scholarly journals Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3941 ◽  
Author(s):  
Alejandra Panzera ◽  
Adam D. Leaché ◽  
Guillermo D’Elía ◽  
Pedro F. Victoriano
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
Molecular Systematic ◽  
Data Set ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenomic Analyses

The genusLiolaemusis one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless,Liolaemuslizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenusLiolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic.Liolaemus tenuis tenuisis difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion ofL. t. tenuisfrom analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships betweenL. fuscus,L. monticola,L. nigroviridisandL. nitidus, andL. plateiandL. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade ofLiolaemusthat will help future work aimed at resolving theLiolaemusphylogeny.

scholarly journals Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dario Karmeinski ◽  
Karen Meusemann ◽  
Jessica A. Goodheart ◽  
Michael Schroedl ◽  
Alexander Martynov ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Set Covering ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Transcriptome Data ◽  
Data Set ◽  
Sea Slugs ◽  
History Of

Abstract Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

scholarly journals Lower statistical support with larger datasets: insights from the Ochrophyta radiation

2021 ◽  
Author(s):  
Arnaud Di Franco ◽  
Denis Baurain ◽  
Gernot Glöckner ◽  
Michael Melkonian ◽  
Hervé Philippe
Keyword(s):  
Evolutionary Rate ◽  
Phylogenetic Signal ◽  
Signal Extraction ◽  
Taxon Sampling ◽  
Sequence Evolution ◽  
Internal Branch ◽  
Statistical Support ◽  
Dataset Size ◽  
Fitting Model ◽  
Heterogeneous Size

AbstractIt is commonly assumed that increasing the number of characters has the potential to resolving radiations. We studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous size and origin (6,762 sites for mitochondrion, 21,692 sites for plastid and 209,105 sites for nucleus). While statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion and plastid trees, it decreases in the nuclear tree. Statistical support is not simply related to the dataset size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that proper signal extraction is difficult to attain, as demonstrated by conflicting results obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid dataset provided higher statistical support for the ochrophyte radiation than the larger nucleus dataset. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear dataset. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of datasets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.

scholarly journals Polygenic dissection of the bipolar phenotype

2011 ◽  
Vol 198 (4) ◽  
pp. 284-288 ◽  
Author(s):  
M. L. Hamshere ◽  
M. C. O'Donovan ◽  
I. R. Jones ◽  
L. Jones ◽  
G. Kirov ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Genetic Susceptibility ◽  
Strong Support ◽  
Psychotic Symptoms ◽  
Data Sets ◽  
Data Set ◽  
Risk Alleles ◽  
Score Analysis ◽  
Primary Sample ◽  
Psychotic Bipolar Disorder

BackgroundRecent data provide strong support for a substantial common polygenic contribution (i.e. many alleles each of small effect) to genetic susceptibility for schizophrenia and overlapping susceptibility for bipolar disorder.AimsTo test hypotheses about the relationship between schizophrenia and psychotic types of bipolar disorder.MethodUsing a polygenic score analysis to test whether schizophrenia polygenic risk alleles, en masse, significantly discriminate between individuals with bipolar disorder with and without psychotic features. The primary sample included 1829 participants with bipolar disorder and the replication sample comprised 506 people with bipolar disorder.ResultsThe subset of participants with Research Diagnostic Criteria schizoaffective bipolar disorder (n = 277) were significantly discriminated from the remaining participants with bipolar disorder (n = 1552) in both the primary (P = 0.00059) and the replication data-sets (P = 0.0070). In contrast, those with psychotic bipolar disorder as a whole were not significantly different from those with non-psychotic bipolar disorder in either data-set.ConclusionsGenetic susceptibility influences at least two major domains of psychopathological variation in the schizophrenia–bipolar disorder clinical spectrum: one that relates to expression of a ‘bipolar disorder-like’ phenotype and one that is associated with expression of ‘schizophrenia-like’ psychotic symptoms.

scholarly journals Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

2020 ◽  
Vol 69 (4) ◽  
pp. 613-622 ◽  
Author(s):  
Rong Zhang ◽  
Yin-Huan Wang ◽  
Jian-Jun Jin ◽  
Gregory W Stull ◽  
Anne Bruneau ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Strong Support ◽  
Molecular Data ◽  
Data Sets ◽  
Plastome Evolution ◽  
The Family ◽  
Phylogenetic Resolution ◽  
History Of ◽  
Phylogenomic Analyses ◽  
Almost All

Abstract Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae’s thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family’s complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.]

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