Phylogeny of the gymnosperm genus Cycas L. (Cycadaceae) as inferred from plastid and nuclear loci based on a large-scale sampling: Evolutionary relationships and taxonomical implications

Liu, Jian; Zhang, Shouzhou; Nagalingum, Nathalie S.; Chiang, Yu–Chung; Lindström, Anders J.; Gong, Xun

doi:10.1016/j.ympev.2018.05.019

Cited by 34 publications

(56 citation statements)

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“…In comparison with the phylogeny reported in Liu et al (2018), our phylogeny is similar in terms of the topology and the node support. This is not surprising because we used their DNA sequences.…”

Section: Phylogenetic Tree Of Cycassupporting

confidence: 64%

“…This is not surprising because we used their DNA sequences. Three of the six Sections of the genus are polyphyletic (Cycas, Stangerioides, Indosinense) and the remaining sections are monophyletic as previously reported (Xiao and Möller, 2015;Liu et al, 2018). There are a few points worth highlighting.…”

Section: Phylogenetic Tree Of Cycasmentioning

confidence: 61%

“…The full list of Cycas species is still a matter of debate. However, a recent study analyzed a large dataset of informative markers (DNA data) to estimate the total cycad diversity to 116 (100 accepted, 7 subspecies and 9 controversial species; Liu et al, 2018). To assemble a complete phylogeny for the 116 Cycas species, we retrieved from GenBank/EBI (accessed October 2018; Liu et al, 2018) DNA sequences of seven nuclear regions (PHYP, RPB1, HZP, AC3, F3H, SAMS, and GTP) and four plastid regions (including a complementary plant DNA barcode trnH-psbA as well as psbM-trnD, trnL-trnF and trnS-trnG) of Cycas species.…”

Section: A Complete List Of Cycas Species Used To Reconstruct a Datedmentioning

confidence: 99%

“…However, a recent study analyzed a large dataset of informative markers (DNA data) to estimate the total cycad diversity to 116 (100 accepted, 7 subspecies and 9 controversial species; Liu et al, 2018). To assemble a complete phylogeny for the 116 Cycas species, we retrieved from GenBank/EBI (accessed October 2018; Liu et al, 2018) DNA sequences of seven nuclear regions (PHYP, RPB1, HZP, AC3, F3H, SAMS, and GTP) and four plastid regions (including a complementary plant DNA barcode trnH-psbA as well as psbM-trnD, trnL-trnF and trnS-trnG) of Cycas species. The molecular matrix is available as Supplementary Material (DNA matrix; available at https://doi.org/10.5061/dryad.1g1jwstrn, Mankga et al, 2020b); accession numbers as well as the species names are presented in Supplementary Table S1.…”

Section: A Complete List Of Cycas Species Used To Reconstruct a Datedmentioning

confidence: 99%

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The Cycad Genus Cycas May Have Diversified From Indochina and Occupied Its Current Ranges Through Vicariance and Dispersal Events

et al. 2020

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Biogeographically, cycads were once widely distributed but the extant cycads are restricted to tropical and subtropical regions. They originated ∼ 300 Ma and rediversified recently around 12 Ma, with the genus Cycas being the most rapidly diversified and largely distributed lineage. However, the forces that shaped the diversification and biogeography of the genus remain to be fully understood. Here, we first retrieved and used DNA sequences from GenBank (nuclear: PHYP, RPB1, HZP, AC3, F3H, SAMS, and GTP; chloroplasts: plant barcode trnH-psbA, trnL-trnF, trnS-trnG, and psbM-trnD) to assemble a complete dated phylogeny of Cycas. Then, we employed the Bayesian Binary Method to reconstruct the historical biogeography of the extant Cycas and finally, using the Bayesian approach for diversification analysis, we explored the evolutionary events that might have shaped the rapid diversification and large distribution of Cycas across the Pacific Islands. Our analysis pointed to Indo-China as the origin of the genus, which may have dispersed firstly across the Pacific Islands during the late Miocene aided by multiple excursions of sea levels and the development of a key innovation, i.e., a spongy endocarp particularly in the seeds of the subsection Rumphiae. The colonization of South China, which was thought to be the origin of the genus, may have occurred more recently aided by both dispersal and vicariance events. However, no significant shifts in the evolutionary events (speciation, extinction, mass extinction) that shaped the diversity of the genus were observed. Overall, our study reclarifies the historical biogeography and the evolutionary forces that shaped the current diversity of the genus Cycas.

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Section: Phylogenetic Tree Of Cycassupporting

confidence: 64%

Section: Phylogenetic Tree Of Cycasmentioning

confidence: 61%

Section: A Complete List Of Cycas Species Used To Reconstruct a Datedmentioning

confidence: 99%

Section: A Complete List Of Cycas Species Used To Reconstruct a Datedmentioning

confidence: 99%

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The Cycad Genus Cycas May Have Diversified From Indochina and Occupied Its Current Ranges Through Vicariance and Dispersal Events

et al. 2020

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“…Cycas L. is the sole genus of the Cycadaceae, and its 117 species are mainly distributed in tropical and subtropical regions of Southeast and East Asia, East Africa, Oceania, and Madagascar (Fragniere et al, 2015). Cycas is monophyletic and is sister to all of the other extant cycad genera (Salas-Leiva et al, 2013;Liu et al, 2018). South China is viewed as the origin of Cycas (Xiao and Moeller, 2015).…”

Section: Introductionmentioning

confidence: 99%

Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

Wang

Zhang

et al. 2019

Front. Genet.

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Historical geology, climatic oscillations, and seed dispersal capabilities are thought to influence the population dynamics and genetics of plants, especially for distribution-restricted and threatened species. Investigating the genetic resources within and among taxa is a prerequisite for conservation management. The Cycas taiwaniana complex consists of six endangered species that are endemic to South China. In this study, we investigated the relationship between phylogeographic history and the genetic structure of the C. taiwaniana complex. To estimate the phylogeographic history of the complex, we assessed the genetic structure and divergence time, and performed phylogenetic and demographic historical analyses. Two chloroplast DNA intergenic regions (cpDNA), two single-copy nuclear genes (SCNGs), and six microsatellite loci (SSR) were sequenced for 18 populations. The SCNG data indicated a high genetic diversity within populations, a low genetic diversity among populations, and significant genetic differentiation among populations. Significant phylogeographical structure was detected. Structure and phylogenetic analyses both revealed that the 18 populations of the C. taiwaniana complex have two main lineages, which were estimated to diverge in the Middle Pleistocene. We propose that Cycas fairylakea was incorporated into Cycas szechuanensis and that the other populations, which are mainly located on Hainan Island, merged into one lineage. Bayesian skyline plot analyses revealed that the C. taiwaniana complex experienced a recent decline, suggesting that the complex probably experienced a bottleneck event. We infer that the genetic structure of the C. taiwaniana complex has been affected by Pleistocene climate shifts, sea-level oscillations, and human activities. In addition to providing new insights into the evolutionary legacy of the genus, the genetic characterizations will be useful for the conservation of Cycas species.

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Transcriptome analysis of two radiated Cycas species and the subsequent species delimitation of the Cycas taiwaniana complex

Wang

Jian

2019

Appl Plant Sci

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Premise Cycas is an important gymnosperm genus, and the most diverse of all cycad genera. The C. taiwaniana complex of species are morphologically similar and difficult to distinguish due to a lack of genomic resources.MethodsWe characterized the transcriptomes of two closely related and endangered Cycas species endemic to Hainan, China: C. hainanensis and C. changjiangensis. Three single‐copy nuclear genes in the C. taiwaniana complex were sequenced based on these transcriptomes, enabling us to evaluate the species boundaries using the multispecies coalescent method implemented in the Bayesian Phylogenetics and Phylogeography program.ResultsWe obtained 68,184 and 81,561 unigenes for C. changjiangensis and C. hainanensis, respectively. We identified six positively selected genes that are mainly involved in stimulus responses, suggesting that environmental adaptation may have played an important role in the relatively recent divergence of these species. The similar KS distribution peaks at 1.0 observed for the paralogs in the two species indicate a common whole‐genome duplication event. Our species delimitation analysis indicated that the C. taiwaniana complex consists of three distinct species, which correspond to the previously reported morphological differences.DiscussionOur study provides valuable genetic resources for Cycas species and guidance for the taxonomic treatment of the C. taiwaniana complex, as well as new insights into evolution of species within Cycas.

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Phylogeny of the gymnosperm genus Cycas L. (Cycadaceae) as inferred from plastid and nuclear loci based on a large-scale sampling: Evolutionary relationships and taxonomical implications

Cited by 34 publications

References 32 publications

The Cycad Genus Cycas May Have Diversified From Indochina and Occupied Its Current Ranges Through Vicariance and Dispersal Events

The Cycad Genus Cycas May Have Diversified From Indochina and Occupied Its Current Ranges Through Vicariance and Dispersal Events

Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

Transcriptome analysis of two radiated Cycas species and the subsequent species delimitation of the Cycas taiwaniana complex

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