Transcriptome Sequences Resolve Deep Relationships of the Grape Family

Wen, Jun; Xiong, Zhiqiang; Nie, Ze Long; Mao, Likai; Zhu, Yabing; Kan, Xianzhao; Ickert‐Bond, Stefanie M.; Gerrath, Jean M.; Zimmer, Elizabeth A.; Fang, Xiao Dong

doi:10.1371/journal.pone.0074394

Cited by 105 publications

(132 citation statements)

References 57 publications

(81 reference statements)

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“…Cissus origins, phylogeny, and Miocene diversity in Africa -Relationships among genera in the Vitaceae are mostly comparable between our study and the most recent previous studies of Cissus ( Liu et al, 2013( Liu et al, , 2016Rodrigues et al, 2014 ), with limited support for the backbone of the trees (but see Wen et al, 2013 andZhang et al, 2015 ). Cissus species are found in three distinct clades in all analyses, identifi ed by Rodrigues et al (2014) as the Cissus striata clade (clade III of Liu et al, 2013 ), the C .…”

Section: Discussionsupporting

confidence: 80%

X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early-diverging members of the genus

Adams¹,

Collinson²,

Smith³

et al. 2017

Preprint

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Premise of the study: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments. Methods: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy. Virtual taphonomy, using SRXTM data sets, produced digital fossils to elucidate seed taphonomy. Phylogenetic relationships within Cissus were reconstructed using existing and newly produced DNA sequences for African species. Paleobiology and paleoecology were inferred from African nearest living relatives. Key results: The fossils were assigned to four new Cissus species, related to four modern clades. The fossil plants were interpreted as climbers inhabiting a mosaic of riverine woodland and forest to more open habitats. Virtual taphonomy explained how complex mineral infill processes concealed key seed features, causing the previous taxonomic misidentification. Newly sampled African species, with seeds most similar to the fossils, belong to four clades within core Cissus, two of which are early diverging. Conclusions: Virtual taphonomy, combined with X-ray imaging, has enabled recognition of the first fossil Cissus and Vitaceae from Africa. Early-divergent members of the core Cissus clade were present in Africa by at least the early Miocene, with an African origin suggested for the Cissus sciaphila clade. The fossils provide supporting evidence for mosaic paleoenvironments inhabited by early Miocene hominoids.

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Section: Discussionsupporting

confidence: 80%

X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early-diverging members of the genus

Adams¹,

Collinson²,

Smith³

et al. 2017

Preprint

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“…A phylogenomic approach targeting thousands of independently evolved nuclear loci may be the only way to assess the current taxonomy of this group, and dissect the roles of hybridization and introgression in the origin and rapid diversification of this insular lineage. Phylogenomic methods based on markers identified from, e.g., restriction site associated DNA sequencing (RADseq) (Cruaud et al, 2014;Eaton and Ree, 2013;Smith et al, 2014), targeted enrichment of ultraconserved elements (UCEs) or conserved ortholog sequences (COS) (Mandel et al, 2014;Smith et al, 2014), and RNA-Seq (Wen et al, 2013;Wickett et al, 2014) could be suitable methods to resolve Hawaiian mint relationships. However, these approaches are also associated with challenges, including accurately inferring orthology in high polyploid plants, slow mutation rates in exonic regions, which may be too low to resolve recent radiations (Giarla and Esselstyn, 2015), and the need to obtaining high quality RNA and DNA.…”

Section: Discussionmentioning

confidence: 99%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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(2016) 'The quest to resolve recent radiations : plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).', Molecular phylogenetics and evolution., 99 . pp. 16-33. Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractThe Hawaiian mints (Lamiaceae), one of the largest endemic plant lineages in the archipelago, provide an excellent system to study rapid diversification of a lineage with a remote, likely paleohybrid origin. Since their divergence from New World mints 4-5 million years ago the members of this lineage have diversified greatly and represent a remarkable array of vegetative and reproductive phenotypes. Today many members of this group are endangered or already extinct, and molecular phylogenetic work relies largely on herbarium samples collected during the last century. So far a gene-by-gene approach has been utilized, but the recent radiation of the Hawaiian mints has resulted in minimal sequence divergence and hence poor phylogenetic resolution. In our quest to trace the reticulate evolutionary history of the lineage, a resolved maternal phylogeny is necessary. We applied a high-throughput approach to sequence 12 complete or nearly complete plastid genomes from multiple Hawaiian mint species and relatives, including extinct and rare taxa. We also targeted 108 hypervariable regions from throughout the chloroplast genomes in nearly all of the remaining Hawaiian species, and relatives, using a nextgeneration amplicon sequencing approach. This procedure generated ~20Kb of sequence data for each taxon and considerably increased the total number of variable sites over previous analyses. Our results demonstrate the potential of high-throughput sequencing of historic material for evolutionary studies in rapidly evolving lineages. Our study, however, also highlights the challenges of resolving relationships within recent radiations even at the genomic level.

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“…A previously identified clade based on molecular data (V. aestivalis, V. cinerea, V. labrusca and V. vulpina) is divided here between Groups II and III. Although Vitis is well known to be a monophyletic genus (Wen et al, , 2013, on the basis of leaf shape, three species of Ampelopsis cluster in three different groups, together with Vitis species. These data suggest that, although leaf shape may bear signatures of recent evolutionary events, leaf shape does not appear to track with phylogeny at larger scales; distantly related species, even from distinct genera, resemble each other in leaf shape through evolutionary convergence.…”

Section: Morphological Differences Between Domesticated Grape and Wilmentioning

confidence: 99%

Latent developmental and evolutionary shapes embedded within the grapevine leaf

Chitwood

Klein

O'Hanlon

et al. 2015

Preprint

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SummaryAcross plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences.Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a single leaf. Here, we measured the shapes of > 3200 leaves representing > 270 vines from wild relatives of domesticated grape (Vitis spp.) to determine whether leaf shapes attributable to genetics and development are separable from each other.We isolated latent shapes (multivariate signatures that vary independently from each other) embedded within the overall shape of leaves. These latent shapes can predict developmental stages independent from species identity and vice versa. Shapes predictive of development were then used to stage leaves from 1200 varieties of domesticated grape (Vitis vinifera), revealing that changes in timing underlie leaf shape diversity.Our results indicate that distinct latent shapes combine to produce a composite morphology in leaves, and that developmental and evolutionary contributions to shape vary independently from each other.

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Transcriptome Sequences Resolve Deep Relationships of the Grape Family

Cited by 105 publications

References 57 publications

X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early-diverging members of the genus

X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early-diverging members of the genus

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Latent developmental and evolutionary shapes embedded within the grapevine leaf

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