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Cycas chenii (Cycadaceae), a new species from China, and its phylogenetic position

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Abstract

Cycas chenii X. Gong & W. Zhou sp. nov., a new species of Cycas L., is described and illustrated here. The morphological and karyomorpholoical comparisons are made between C. chenii and the closely related taxa for defining its taxonomical status as a new species. Moreover, the phylogenetic position of C. chenii within 16 Cycas species is determined using DNA sequences of two plastid regions, nuclear ribosomal ITS and two nuclear regions. Cycas chenii is readily distinguished from the related C. guizhouensis by an acaulescent stem. Phylogenetic evidence indicates that C. chenii is a distinct group related to C. guizhouensis in the Section Stangerioides. The distribution and conservation status of C. chenii are also discussed.

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... There are more than 14 Cycas species, of which 10 are endemic to the basin region of the Red River (Hill, 2008). Cycas chenii X. Gong & W. Zhou (Section Stangerioides) is a recently described species (Zhou et al., 2015). This species is distributed in Chuxiong and Honghe of Yunnan Province, China, along the upstream drainage areas of the Red River (also called Yuanjiang in China). ...
... This species is distributed in Chuxiong and Honghe of Yunnan Province, China, along the upstream drainage areas of the Red River (also called Yuanjiang in China). It occurs on a range of substrates from limestone to shale or schist, which is characteristic of steep slopes at altitudes ranging from 500 m to 1300 m (Zhou et al., 2015). Only six populations have been discovered, four at the northeast side of the Red River and two at the southwest side. ...
... Only six populations have been discovered, four at the northeast side of the Red River and two at the southwest side. To date, the total population size of C. chenii is estimated at less than 500 individuals across its geographic distribution , with all the know populations of the species being far from any protected areas (Zhou et al., 2015). This species is threatened by ongoing land-clearing and over-collection. ...
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Article
Geological activities and climate oscillations during the Quaternary period profoundly impacted the distribution of species in Southwest China. Some plant species may be harbored in refugia, such as the dry-hot valleys of Southwest China. Cycas chenii X. Gong & W. Zhou, a critically endangered cycad species, which grows under the canopy in subtropical evergreen broad-leaved forests along the upstream drainage area of the Red River, is endemic to this refugium. In this study, 60 individuals of C. chenii collected from six populations were analyzed by sequencing two chloroplast intergenic spacers (cpDNA: psbA-trnH and trnL-trnF) and two nuclear genes (PHYP and RBP-1). Results showed high genetic diversity at the species level, but low within-population genetic diversity and high interpopulation genetic differentiation. A Bayesian phylogenetic tree based on cpDNA showed that five chloroplast haplotypes were clustered into two clades, which corresponds to the division of the western and eastern bank of the Red River. These data indicate a possible role for the Red River as a geographic barrier to gene flow in C. chenii. Based on our findings, we propose appropriate in situ and ex situ conservation strategies for C. chenii.
... For conifers, we referenced A Handbook of the World's Conifers (Farjon, 2017); for cycads, The genus Cycas (Cycadaceae) in China (Hill, 2008); and for gnetophytes and ginkgos, Species Catalogue of China, Vol.1: Plants (Jin and Yang, 2015). New records, such as Xanthocyparis vietnamensis (Meng et al., 2013) and Calocedrus rupestris (Nong et al., 2011), and new species, such as Cycas chenii (Zhou et al., 2015), were also included. Only taxa at the species level were considered for this purpose, excluding hybrids, cultivated species and uncertain species. ...
... The three unprotected species include two Cycas and one conifer species. For these species, no detailed distribution records were found for Cunninghamia konishii (Farjon, 2017), Cycas chenii was a newly described species from Honghe and Shuangbai counties in Yunnan province (Zhou et al., 2015), which is not protected in any nature reserve (Zheng et al., 2017), and Cycas shanyaensis lacked distribution reports except for the records in the original literature (Fu, 2006;Liu, 1998). Therefore, to fill the conservation gap of threatened gymnosperms in China, we should place more attention on these unprotected species, such as Cycas chenii. ...
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Article
China is one of the diversity centers of gymnosperms. Nearly one-fifth (195 species) of gymnosperms are located in China, but 69 species are threatened. To date, the conservation status of gymnosperms, especially threatened gymnosperms in China, remains largely unknown, which seriously restricts the comprehensive protection of gymnosperms. Understanding the distribution pattern of species richness and exploring the relationships between species richness and environmental factors are key steps for their protection. In this study, we first constructed a database for the 69 threatened species of gymnosperms with 13 270 distribution records. It is found that 31 of the grid cells (50 km × 50 km) cover all threatened gymnosperm species in China, and the grid cells of threatened gymnosperms are mainly distributed in the southern area of the Yellow River, with a distribution center in the Western Sichuan Plateau. Then, we evaluated the conservation status of threatened gymnosperms, and the results indicate that 9 (13%) threatened gymnosperms are distributed outside of nature reserves. Therefore, there are still conservation gaps in the protection of threatened gymnosperms in China. We should give more attention to unprotected threatened gymnosperms and conduct taxonomic studies on the species without detailed distribution records. Finally, conservation priority areas and priority conservation levels of threatened gymnosperms in China were proposed. The Western Sichuan Plateau is the most important conservation priority area of threatened gymnosperms. This study will shed light on plant protection and forest management in China.
... Furthermore, the dioecious habit and rarity of reproductive organs in the wild has also caused ambiguity when circumscribing species (e.g. (Averyanov et al., 2014;Zhou et al., 2015)). The number of species of Cycas has increased from less than 20 in the early 20th century (Pilger, Hill and sect. ...
... A previous phylogenetic study had proposed that it was close to sect. Indosinenses, although the authors explained it by long-branch attraction (Zhou et al., 2015). Given that our results are equivocal, the classification of this species remains unclear. ...
Article
The gymnosperm genus Cycas is the sole member of Cycadaceae, and is the largest genus of extant cycads. There are about 115 accepted Cycas species mainly distributed in the paleotropics. Based on morphology, the genus has been divided into six sections and eight subsections, but this taxonomy has not yet been tested in a molecular phylogenetic framework. Although the monophyly of Cycas is broadly accepted, the intrageneric relationships inferred from previous molecular phylogenetic analyses are unclear due to insufficient sampling or uninformative DNA sequence data. In this study, we reconstructed a phylogeny of Cycas using four chloroplast intergenic spacers and seven low-copy nuclear genes and sampling 90% of extant Cycas species. The maximum likelihood and Bayesian inference phylogenies suggest: (1) matrices of either concatenated cpDNA markers or of concatenated nDNA lack sufficient informative sites to resolve the phylogeny alone, however, the phylogeny from the combined cpDNA-nDNA dataset suggests the genus can be roughly divided into 13 clades and six sections that are in agreement with the current classification of the genus; (2) although with partial support, a clade combining sections Panzhihuaenses + Asiorientales is resolved as the earliest diverging branch; (3) section Stangerioides is not monophyletic because the species resolve as a grade; (4) section Indosinenses is not monophyletic as it includes Cycas macrocarpa and C. pranburiensis from section Cycas; (5) section Cycas is the most derived group and its subgroups correspond with geography.
... However, molecular phylogenetic analyses indicated that the extant cycads underwent a synchronous global re-diversification and are not much more than 12 million years old (Nagalingum et al., 2011). In recent years, researchers have studied cycad phylogeny Wei et al., 2015), conservation (Feng et al., 2014;Feng et al., 2016;Feng et al., 2017;Gregory and Lopez-Gallego, 2018;Tang et al., 2018a;Zheng et al., 2017), biogeography (Gutiérrez-Ortega et al., 2017;Meerow et al., 2018;Cabrera-Toledo et al., 2019), pollination biology (Tang et al., 2018b;Santiago-Jimnez et al., 2019), and physiology (Vovides and Galicia, 2016). Cycads comprise two families (Cycadaceae and Zamiaceae), with 10 genera and 355 accepted species (Calonje et al., 2019). ...
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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.
... This genus was recently classified into six sections (Hill, 2008;Lindstrom et al., 2008), which is inconsistent with the previous infrageneric classification by De Laubenfels and Adema (1998), which divided Cycas into four subgenera containing 30 species. In addition, a few new species have been documented in recent years, and several species complexes were also proposed ( Zhou et al., 2015;Singh, 2017), all of which further complicated the classifications within the genus. A comprehensive infrageneric classification incorporating both molecular phylogeny and morphological characters is therefore needed; however, the genetic diversity and classification of Cycas species remain unclear due to the lack of informative markers ( Liu et al., 2018). ...
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Article
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. Methods: We 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. Results: We 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. Discussion: Our 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.
... They have survived through periods of dramatic tectonic activity, climate fluctuation and environmental variations, making this plant group of great significance for research (Zheng et al., 2017). Cycas chenii X. Gong & W. Zhou was described and illustrated to honor Professor Jiarui Chen (Chia-Jui Chen), a botanist from the Institute of Botany, Chinese Academy of Sciences, for his significant work on the genus Cycas in China (Zhou et al., 2015). Research by Feng et al. (2016) involving species of the Cycas segmentifida D.Y. Wang & C.Y. Deng complex significantly altered our understanding of this group. ...
Article
The development of new taxonomical theories and approaches, particularly molecular phylogenetics, has led to the expansion of traditional morphology-based taxonomy into the concept of “integrative taxonomy.” Taxonomic knowledge has assumed greater significance in recent years, particularly because of growing concerns over the looming biodiversity crisis. Since its establishment in 1938, the Kunming Institute of Botany (KIB), which is located in Yunnan province in Southwest China, has focused attention on the taxonomy and conservation of the flora of China. For the forthcoming 80th anniversary of KIB, we review the achievements of researchers at KIB and their associates with respect to the taxonomy of land plants, fungi, and lichen. Major taxonomic advances are summarized for families of Calymperaceae, Cryphaeaceae, Lembophyllaceae, Neckeraceae, Polytrichaceae and Pottiaceae of mosses, Pteridaceae and Polypodiaceae of ferns, Taxaceae and Cycadaceae of gymnosperms, Asteraceae, Begoniaceae, Ericaceae, Euphorbiaceae, Gesneriaceae, Lamiaceae, Orchidaceae, Orobanchaceae, Poaceae, Theaceae and Urticaceae of angiosperms, Agaricaceae, Amanitaceae, Boletaceae, Cantharellaceae, Physalacriaceae Russulaceae, Suillaceae and Tuberaceae of fungi, and Ophioparmaceae and Parmeliaceae of lichens. Regarding the future development of taxonomy at KIB, we recommend that taxonomists continue to explore the biodiversity of China, integrate new theories and technologies with traditional taxonomic approaches, and engage in creative monographic work, with support from institutions, funding agencies, and the public.
... Phan from Xishuangbanna of China is the synonym of C. simplicipinna (Smitinand) K.D. Hill based on field surveys and data reference (Hill, 2008). In addition, the newly published species, C. chenii X. Gong & Wei Zhou, is affiliated with section Stangerioides (Zhou, Guan, & Gong, 2015 ...
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As ancient gymnosperm and woody plants, cycads have survived through dramatic tectonic activities, climate fluctuation, and environmental variations making them of great significance in studying the origin and evolution of flora biodiversity. However, they are among the most threatened plant groups in the world. The principal aim of this review is to outline the distribution, diversity, and conservation status of Cycas in China and provide suggestions for conservation practices. In this review, we describe the taxonomy, distribution, and conservation status of Cycas in China. By comparing Chinese Cycas species with its relatives worldwide, we then discuss the current genetic diversity, genetic differentiation of Cycas, and try to disentangle the potential effects of Quaternary climate changes and topographical events on Cycas. We review conservation practices from both researchers and practitioners for these rare and endangered species. High genetic diversity at the species level and strong genetic differentiation within Cycas have been observed. Most Cycas species in southwest China have experienced population retreats in contrast to the coastal Cycas's expansion during the Quaternary glaciation. Additionally, human activities and habitat fragmentation have pushed these endangered taxa to the brink of extinction. Although numerous efforts have been made to mitigate threats to Cycas survival, implementation and compliance monitoring in protection zones are currently inadequate. We outline six proposals to strengthen conservation measures for Cycas in China and anticipate that these measures will provide guidelines for further research on population genetics as well as conservation biology of not only cycads but also other endangered species worldwide.
... Primers used for the sequences were listed in Table 2. The PCR protocols for cpDNA and nDNA amplification were referred to Sangin et al. (2010) and Zhou et al. (2015) respectively. Purified PCR products were then sequenced with the same primers used for PCR amplifications in an ABI 3770 automated sequencer at Shanghai Sangon Biological Engineering Technology & Services Co, Ltd. ...
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Cycas hongheensis was firstly proposed as a distinct taxon in 1994 and formally described two years later based on vegetative materials only. Here, the reproductive organs of this species, namely, the female cone, male cone and seeds are supplemented for description as these fertile materials were found for the first time at the type locality. Furthermore, the phylogenetic position of this species as being the only endemic member of Cycas sect. Indosinenses in China was investigated. The conflicting phylogenic results between chloroplastic (cpDNA) and nuclear DNA (nDNA) are corresponded with the inconformity characters of morphology of this species. The characters of lacking indumentum on ovules and the distinct apical spine of megasporophyll are corresponding to nDNA result while the characters such as the soft and rudimentary apical spine of the microsporophyll and the absence of fibrous layer inside the sarcotesta comform to cpDNA result. For the taxonomy, we agree this species to be classified into Cycas sect. Indosinenses for the obvious morphological characters of megasporophyll and ovule as well as deeper evidence from phylogeny based on nuclear data, as biparental inherited nuclear genes could offer more comprehensive genetic information than maternal inherited cpDNA.
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Chapter
This procedure has been used with success on a wide variety of plant groups and even some animals. The method is used to isolate total genomic DNA (nuclear, chloroplast, and mitochondrial). It is a rapid, inexpensive method that is suitabie for use in conjunction with other protocois, such as isolation of DNA enriched for cpDNA. it is also easy to scale down for use in population sampling, using 0.01g or less of fresh tissue. Other applications include isolation of DNA from herbarium specimens (Doyle & Dickson, 1987. Taxon 36:715–722), and isolation of RNA. A brief word on the history of the protocol is in order. This procedure was modified by us (Doyle and Doyle, 1987. Phytochemical Bulletin 19:11–15) for use with fresh plant tissue from a method of Saghai-Maroof et al. (1984, PNAS USA 81:8014–8019) who used lyophilized tissue. They in turn had developed their procedure from earlier protocols. We were recently asked to publish a slightly modified version of our procedure (Doyle and Doyle, 1990 Focus 12:13–15). We recently learned from Brian Taylor (Texas A&M University, USA) that he had published a virtually identical procedure for fresh tissue, also in Focus, in 1982 (Taylor & Powell, Focus 4:4–6) of which we (and apparently the editors of Focus!) were entirely unaware. It is indeed a useful procedure, thus independently confirmed.
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— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
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The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Article
N the inorphologic identification of chromosomes, the location of the I centromere is the most useful landmark, and one which is characterized by great constancy. It would seem that not much could be added to the definitions by E. B. WILSON (1928) of the locations on the chromosome of the centrornere or, in the terminology of that time, the spindle attachment: “Attachment of the chromosome to the spindle is commonly limited to a small area, and is of two general types, namely: (1) terminnl or telomitic and (2) non-ferminal or atelomitic, being in the former case at one end, and in the latter at some other point or points. Non-terminal attachment may be at the middle point (median) or at an intermediate point (submedian, sub-terminal). All gradations exist between these various cases;” (I.c., p. 130-131). In the acconipanying picture (l.c., Fig. 56, p. 132), here reprinted as Fig. l., the four locations of median, submedian, subterminal and terminal are represented, and, in addition, “lateral”, which corresponds to the modern term “diffuse centromere”. Nevertheless, at the present time, with the immense increase in research activity in mammalian cytology, the terminology of the centromeric position has become burdened by much obscurity and confusion. One cause of confusion is that different authors, and even the same author on different occasions, have used the terms median, submedian etc. with great amplitude, and it is often difficult to know in a specific case what each term signifies. Another cause of confusion is that a set of terms for chromosomes with specific centromeric positions, such as metacentric, acrocentric, telocentric, have come into wide usage without being clearly defined in relation to the positional terms median, submedian, subterminal and terminal. During the spring of 1963 the present writers exchanged epistolary
Article
Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/31361/1/0000273.pdf
Article
The history of long-branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA-artifacts include excluding long-branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long-branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall waSPS are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic “the guinea-pig is not a rodent” hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition-specific GTR + Γ + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long-branch attraction to the outgroup. © The Willi Hennig Society 2005.
Article
A list of the 305 currently recognized cycad species is given, along with citations of the original place of publication and the location of type specimens when known. Included in the list are currently recognized infraspecific taxa, brief geographical ranges, and a partial list of synonyms for each taxon.
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