Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum , Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
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Target‐enrichment sequencing reveals for the first time a well‐resolved phylogeny of the core Bromelioideae (family Bromeliaceae)
A phylogenomic analysis of the so far phylogenetically unresolved subfamily Bromelioideae (Bromeliaceae) was performed to infer species relationships as the basis for future taxonomic treatment, stabilization of generic concept, and further analyses of evolution and biogeography of the subfamily. A target‐enrichment approach was chosen, using the Angiosperms353 v.4 kit RNA‐baits and including 86 Bromelioideae species representing previously identified major evolutionary lineages. Phylogenetic analyses were based on 125 target nuclear loci, assembled off‐target plastome as well as mitogenome reads. A Bromelioideae phylogeny with a mostly well‐resolved backbone is provided based on nuclear (194 kbp), plastome (109 kbp), and mitogenome data (34 kbp). For the nuclear markers, a coalescent‐based analysis of single‐locus gene trees was performed as well as a supermatrix analysis of concatenated gene alignments. Nuclear and plastome datasets provide well‐resolved trees, which showed only minor topological incongruences. The mitogenome tree is not sufficiently resolved. A total of 26 well‐supported clades were identified. The genera
- Award ID(s):
- 2110875
- NSF-PAR ID:
- 10496620
- Publisher / Repository:
- John Wiley & Sons
- Date Published:
- Journal Name:
- TAXON
- Volume:
- 72
- Issue:
- 1
- ISSN:
- 0040-0262
- Page Range / eLocation ID:
- 47 to 63
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Background Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far.
Methods Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes.
Key Results Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny.
Conclusions Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
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Abstract Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas
MP ‐EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with many traditionally recognized clades. Here, we evaluate this discrepancy via improved coalescence analyses with reference to the rich history of phylogenetic studies on mammals. This integration clearly demonstrates that both supermatrix and coalescence analyses of just 26 loci yield a congruent, well‐supported phylogenetic hypothesis for Mammalia. Discrepancies between published studies are explained by implementation of overly simpleDNA substitution models, inadequate tree‐search routines and limitations of theMP ‐EST method. We develop a simple measure,partitioned coalescence support (PCS ), which summarizes the distribution of support and conflict among gene trees for a given clade. Extremely highPCS scores for outlier gene trees at two nodes in the mammalian tree indicate a troubling bias in theMP ‐EST method. We conclude that in this age of phylogenomics, a solid understanding of systematics fundamentals, choice of valid methodology and a broad knowledge of a clade's taxonomic history are still required to yield coherent phylogenetic inferences. -
Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selectionmore » « less
Summary Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of
Populus , a model tree genus in the Northern Hemisphere.We constructed phylogenetic trees of 29
Populus taxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence.We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance.
Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genus
Populus . These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies. -
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Summary The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR‐lacking clade (IRLC) and the plant model
Medicago truncatula . The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non‐papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early‐branching papilionoid clades. A number of IR‐related and repeat‐mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated withycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non‐IR repeats in the progression of plastome change is discussed.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1002/tax.12831
