Darwin review: angiosperm phylogeny and evolutionary radiations
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ABSTRACT:
SUBMITTER: Soltis P
PROVIDER: S-EPMC6452062 | biostudies-literature | 2019 Mar
REPOSITORIES: biostudies-literature
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Project description:Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology.
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Project description:The cellular architecture of ciliates is one of the most complex known within eukaryotes. Detailed systematic schemes have thus been constructed through extensive comparative morphological and ultrastructural analysis of the ciliature and of its internal cytoskeletal derivatives (the infraciliature), as well as of the architecture of the oral apparatus. In recent years, a consensus was reached in which the phylum was divided in eight classes as defined by Lynn and Corliss [Lynn, D. H. & Corliss, J. O. (1991) in Microscopic Anatomy of Invertebrates: Protozoa (Wiley-Liss, New York), Vol. 1, pp. 333-467]. By comparing partial sequences of the large subunit rRNA molecule, and by using both distance-matrix and maximum-parsimony-tree construction methods (checked by boot-strapping), we examine the phylogenetic relationships of 22 species belonging to seven of these eight classes. At low taxonomic levels, the traditional grouping of the species is generally confirmed. At higher taxonomic levels, the branching pattern of these seven classes is resolved in several deeply separated major branches. Surprisingly, the first emerging one contains the heterotrichs and is strongly associated with a karyorelictid but deeply separated from hypotrichs. The litostomes, the oligohymenophorans, and the hypotrichs separate later in a bush-like topology hindering the resolution of their order of diversification. These results show a much more ancient origin of heterotrichs than was classically assumed, indicating that asymmetric, abundantly ciliated oral apparatuses do not correspond to "highly evolved" traits as previously thought. They also suggest the occurrence of a major radiative explosion in the evolutionary history of the ciliates, yielding five of the eight classes of the phylum. These classes appear to differ essentially according to the cytoskeletal architecture used to shape and sustain the cellular cortex (a process of essential adaptative and morphogenetic importance in ciliates).
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Project description:In The Descent of Man, Darwin speculated that our capacity for musical rhythm reflects basic aspects of brain function broadly shared among animals. Although this remains an appealing idea, it is being challenged by modern cross-species research. This research hints that our capacity to synchronize to a beat, i.e., to move in time with a perceived pulse in a manner that is predictive and flexible across a broad range of tempi, may be shared by only a few other species. Is this really the case? If so, it would have important implications for our understanding of the evolution of human musicality.
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Project description:Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.
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Project description:PIN-FORMED 1 (PIN1) is an important secondary transporter and determines the direction of intercellular auxin flow. As PIN1 performs the conserved function of auxin transport, it is expected that the sequence and structure of PIN1 is conserved. Therefore, we hypothesized that PIN1 evolve under pervasive purifying selection in the protein-coding sequences in angiosperm. To test this hypothesis, we performed detailed evolutionary analyses of 67 PIN1 sequences from 35 angiosperm species. We found that the PIN1 sequences are highly conserved within their transmembrane regions, part of their hydrophilic regions. We also found that there are two or more PIN1 copies in some of these angiosperm species. PIN1 sequences from Poaceae and Brassicaceae are representative of the modern clade. We identified 12 highly conserved motifs and a significant number of family-specific sites within these motifs. One family-specific site within Motif 11 shows a different residue between monocots and dicots, and is functionally critical for the polarity of PIN1. Likewise, the function of PIN1 appears to be different between monocots and dicots since the phenotype associated with PIN1 overexpression is opposite between Arabidopsis and rice. The evolution of angiosperm PIN1 protein-coding sequences appears to have been primarily driven by purifying selection, but traces of positive selection associated with sequences from certain families also seem to be present. We verified this observation by calculating the numbers of non-synonymous and synonymous changes on each branch of a phylogenetic tree. Our results indicate that the evolution of angiosperm PIN1 sequences involve strong purifying selection. In addition, our results suggest that the conserved sequences of PIN1 derive from a combination of the family-specific site variations and conserved motifs during their unique evolutionary processes, which is critical for the functional integrity and stability of these auxin transporters, especially in new species. Finally, functional difference of PIN1 is likely to be present in angiosperm because the positive selection is occurred in one branch of Poaceae.
| S-EPMC3938449 | biostudies-literature
Project description:The genus Liriodendron belongs to the family Magnoliaceae, which resides within the magnoliids, an early diverging lineage of the Mesangiospermae. However, the phylogenetic relationship of magnoliids with eudicots and monocots has not been conclusively resolved and thus remains to be determined1-6. Liriodendron is a relict lineage from the Tertiary with two distinct species-one East Asian (L. chinense (Hemsley) Sargent) and one eastern North American (L. tulipifera Linn)-identified as a vicariad species pair. However, the genetic divergence and evolutionary trajectories of these species remain to be elucidated at the whole-genome level7. Here, we report the first de novo genome assembly of a plant in the Magnoliaceae, L. chinense. Phylogenetic analyses suggest that magnoliids are sister to the clade consisting of eudicots and monocots, with rapid diversification occurring in the common ancestor of these three lineages. Analyses of population genetic structure indicate that L. chinense has diverged into two lineages-the eastern and western groups-in China. While L. tulipifera in North America is genetically positioned between the two L. chinense groups, it is closer to the eastern group. This result is consistent with phenotypic observations that suggest that the eastern and western groups of China may have diverged long ago, possibly before the intercontinental differentiation between L. chinense and L. tulipifera. Genetic diversity analyses show that L. chinense has tenfold higher genetic diversity than L. tulipifera, suggesting that the complicated regions comprising east-west-orientated mountains and the Yangtze river basin (especially near 30° N latitude) in East Asia offered more successful refugia than the south-north-orientated mountain valleys in eastern North America during the Quaternary glacial period.
| S-EPMC6784881 | biostudies-literature
Project description:BackgroundA large number of taxa have undergone evolutionary radiations in mountainous areas, rendering alpine systems particularly suitable to study the extrinsic and intrinsic factors that have shaped diversification patterns in plants. The species-rich genus Saxifraga L. is widely distributed throughout the Northern Hemisphere, with high species numbers in the regions adjacent to the Qinghai-Tibet Plateau (QTP) in particular the Hengduan Mountains and the Himalayas. Using a dataset of 297 taxa (representing at least 60% of extant Saxifraga species), we explored the variation of infrageneric diversification rates. In addition, we used state-dependent speciation and extinction models to test the effects of geographic distribution in the Hengduan Mountains and the entire QTP region as well as of two morphological traits (cushion habit and specialized lime-secreting glands, so-called hydathodes) on the diversification of this genus.ResultsWe detected two to three rate shifts across the Saxifraga phylogeny and two of these shifts led to radiations within two large subclades of Saxifraga, sect. Ciliatae Haworth subsect. Hirculoideae Engl. & Irmsch. and sect. Porphyrion Tausch subsect. Kabschia Engl. GEOSSE analyses showed that presence in the Hengduan Mountains had a positive effect on diversification across Saxifraga. Influence of these mountains was strongest in Saxifraga sect. Ciliatae subsect. Hirculoideae given its pronounced distribution there, and thus the radiation in this group can be classified at least partially as geographic. In contrast, the evolution of the cushion life form and lime-secreting hydathodes had positive effects on diversification only in selected Saxifraga sections, including sect. Porphyrion subsect. Kabschia. We therefore argue that radiation in this group was likely adaptive.ConclusionsOur study underlines the complexity of processes and factors underpinning plant radiations: Even in closely related lineages occupying the same life zone, shifts in diversification are not necessarily governed by similar factors. In conclusion, alpine plant radiations result from a complex interaction among geographical settings and/or climatic modifications providing key opportunities for diversification as well as the evolution of key innovations.
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Project description:The evolutionary processes that drive rapid species diversification are poorly understood. In particular, it is unclear whether Darwinian adaptation or non-adaptive processes are the primary drivers of explosive species diversifications. Here we show that repeated rapid radiations within New World lupins (Lupinus, Leguminosae) were underpinned by a major increase in the frequency of adaptation acting on coding and regulatory changes genome-wide. This contrasts with far less frequent adaptation in genomes of slowly diversifying lupins and all other plant genera analysed. Furthermore, widespread shifts in optimal gene expression coincided with shifts to high rates of diversification and evolution of perenniality, a putative key adaptation trait thought to have triggered the evolutionary radiations in New World lupins. Our results reconcile long-standing debate about the relative importance of protein-coding and regulatory evolution, and represent the first unambiguous evidence for the rapid onset of lineage- and genome-wide accelerated Darwinian evolution during rapid species diversification.
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Project description:BACKGROUND:Gibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the discussion of these issues we analyzed the complete mitochondrial cytochrome b gene from 85 individuals representing all gibbon species, including most subspecies. RESULTS:Based on phylogenetic tree reconstructions, several monophyletic clades were detected, corresponding to genera, species and subspecies. A significantly supported branching pattern was obtained for members of the genus Nomascus but not for the genus Hylobates. The phylogenetic relationships among the four genera were also not well resolved. Nevertheless, the new data permitted the estimation of divergence ages for all taxa for the first time and showed that most lineages emerged during four short time periods. In the first, between approximately 6.7 and approximately 8.3 mya, the four gibbon genera diverged from each other. In the second (approximately 3.0 - approximately 3.9 mya) and in the third period (approximately 1.3 - approximately 1.8 mya), Hylobates and Hoolock differentiated. Finally, between approximately 0.5 and approximately 1.1 mya, Hylobates lar diverged into subspecies. In contrast, differentiation of Nomascus into species and subspecies was a continuous and prolonged process lasting from approximately 4.2 until approximately 0.4 mya. CONCLUSIONS:Although relationships among gibbon taxa on various levels remain unresolved, the present study provides a more complete view of the evolutionary and biogeographic history of the hylobatid family, and a more solid genetic basis for the taxonomic classification of the surviving taxa. We also show that mtDNA constitutes a useful marker for the accurate identification of individual gibbons, a tool which is urgently required to locate hunting hotspots and select individuals for captive breeding programs. Further studies including nuclear sequence data are necessary to completely understand the phylogeny and phylogeography of gibbons.
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Project description:Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene-Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.
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