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25 October 2017, Volume 39 Issue 05
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  • Reviews
    Tibet, the Himalaya, Asian monsoons and biodiversity-In what ways are they related?
    Robert A. Spicer
    2017, 39(05):  233-244.  doi:10.1016/j.pld.2017.09.001
    Abstract ( 44 )   HTML ( )   PDF (8785KB) ( 17 )   Save
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    Prevailing dogma asserts that the uplift of Tibet, the onset of the Asian monsoon system and high biodiversity in southern Asia are linked, and that all occurred after 23 million years ago in the Neogene. Here, spanning the last 60 million years of Earth history, the geological, climatological and palaeontological evidence for this linkage is reviewed. The principal conclusions are that:1) A proto-Tibetan highland existed well before the Neogene and that an Andean type topography with surface elevations of at least 4.5 km existed at the start of the Eocene, before final closure of the Tethys Ocean that separated India from Eurasia. 2) The Himalaya were formed not at the start of the IndiaeEurasia collision, but after much of Tibet had achieved its present elevation. The Himalaya built against a pre-existing proto-Tibetan highland and only projected above the average height of the plateau after approximately 15 Ma. 3) Monsoon climates have existed across southern Asia for the whole of the Cenozoic, and probably for a lot longer, but that they were of the kind generated by seasonal migrations of the Inter-tropical Convergence Zone. 4) The projection of the High Himalaya above the Tibetan Plateau at about 15 Ma coincides with the development of the modern South Asia Monsoon. 5) The East Asia monsoon became established in its present form about the same time as a consequence of topographic changes in northern Tibet and elsewhere in Asia, the loss of moisture sources in the Asian interior and the development of a strong winter Siberian high as global temperatures declined. 6) New radiometric dates of palaeontological finds point to southern Asia's high biodiversity originating in the Paleogene, not the Neogene.
    Iran supports a great share of biodiversity and floristic endemism for Fritillaria spp. (Liliaceae):A review
    Mahmoud Kiani, Shirin Mohammadi, Alireza Babaei, Fatemeh Sefidkon, Mohamad Reza Naghavi, Mojtaba Ranjbar, Seyed Ali Razavi, Keramatollah Saeidi, Hadi Jafari, Davoud Asgari, Daniel Potter
    2017, 39(05):  245-262.  doi:10.1016/j.pld.2017.09.002
    Abstract ( 66 )   HTML ( )   PDF (8945KB) ( 24 )   Save
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    Iran supports a great share of exotic and/or endemic plant genera and species. The genus Fritillaria (Liliaceae) is a precious part of this botanical richness with 19 species, of which 10 are endemic to the country. However, signs are mounting that the country is truly at a crossroads when it comes to preservation of this national wealth. In this regard, an effective conservation strategy should thoroughly consider the classification of Fritillaria, as conservation practices are compromised by knowledge gaps in systematics and taxonomy. As published studies on Fritillaria in Iran have been sporadic and limited in scope, the aim of this review is to provide information necessary to help bridge these information gaps. Our objective is to facilitate increased understanding of the geographic, taxonomic, cytogenetic and phylogenetic status of Iranian Fritillaria, which is vital to meeting the goal of sustainable conservation of the genus in Iran and neighboring areas.
    Assigning conservation value and identifying hotspots of endemic rattan diversity in the Western Ghats, India
    Mukta Joshi, Bipin Charles, G. Ravikanth, N. A. Aravind
    2017, 39(05):  263-272.  doi:10.1016/j.pld.2017.08.002
    Abstract ( 59 )   HTML ( )   PDF (2327KB) ( 10 )   Save
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    Rattans, or canes, are one of the most important non-timber forest products supporting the livelihood of many forest-dwelling communities in South and North-eastern India. Due to increased demand for rattan products, rattans have been extracted indiscriminately from the Western Ghats, a 1600-km mountain chain running parallel to the west coast of India. Extensive harvesting, loss of habitat and poor regeneration has resulted in dwindling rattan populations, necessitating an urgent attempt to conserve existing rattan resources. In this study, using niche-modelling tools, an attempt has been made to identify areas of high species richness of rattans in the Western Ghats, one of the mega-diversity regions of the world. We have also developed conservation values for 21 economically important and endemic rattans of the Western Ghats. We identified at least two to three sites of extremely high species richness outside the existing protected area network that should be prioritized for in situ conservation. This study emphasizes the need to develop strategies for the long-term conservation of rattans in the Western Ghats, India.
    Soil seed banks along elevational gradients in tropical, subtropical and subalpine forests in Yunnan Province, southwest China
    Xiaqin Luo, Min Cao, Min Zhang, Xiaoyang Song, Jieqiong Li, Akihiro Nakamura, Roger Kitching
    2017, 39(05):  273-286.  doi:10.1016/j.pld.2017.10.001
    Abstract ( 58 )   HTML ( )   PDF (1757KB) ( 12 )   Save
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    Soil seed banks are a vital part of ecosystems and influence community dynamics and regeneration. Although soil seed banks in different habitats have been reported, how soil seed banks vary with elevational gradients in different climatic zones is still unknown. This paper investigates seed density, species composition and nonconstituent species of forest soil seed banks in Yunnan Province, southwest China. Similarity between the soil seed bank and standing vegetation was also examined. We collected soil samples from sites spanning 12 elevations in tropical rain forests, subtropical evergreen broadleaved forests and subalpine coniferous forests, and transported them to a glasshouse for germination trials for species identification. The soil seed banks of tropical and subtropical forests had much higher seed densities and species richness than those of subalpine forests. Seeds of woody species dominated the soil seed banks of tropical and subtropical forests, while herbs dominated those of subalpine forests. The nonconstituent species in the soil seed banks were all herbs and were most abundant in tropical forests, followed by subtropical forests but were completely absent from subalpine forests.
    Identification of massive molecular markers in Echinochloa phyllopogon using a restriction-site associated DNA approach
    Guoqi Chen, Wei Zhang, Jiapeng Fang, Liyao Dong
    2017, 39(05):  287-293.  doi:10.1016/j.pld.2017.08.004
    Abstract ( 36 )   HTML ( )   PDF (777KB) ( 6 )   Save
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    Echinochloa phyllopogon proliferation seriously threatens rice production worldwide. We combined a restriction-site associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for E. phyllopogon. RAD tags were generated from the genomic DNA of two E. phyllopogon plants, and sequenced to produce 5197.7 Mb and 5242.9 Mb high quality sequences, respectively. The GC content of E. phyllopogon was 45.8%, which is high for monocots. In total, 4710 putative SSRs were identified in 4132 contigs, which permitted the design of PCR primers for E. phyllopogon. Most repeat motifs among the SSRs identified were dinucleotide (>82%), and most of these SSRs were four motif-repeats (>75%). The most frequent motif was AT, accounting for 36.3%-37.2%, followed by AG and AC. In total, 78 putative polymorphic SSR loci were found. A total of 49,179 SNPs were discovered between the two samples of E. phyllopogon, 67.1% of which were transversions and 32.9% were transitions. We used eight SSRs to study the genetic diversity of four E. phyllopogon populations collected from rice fields in China and all eight loci tested were polymorphic.
    Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species
    Hantao Qin, Guoqian Yang, Jim Provan, Jie Liu, Lianming Gao
    2017, 39(05):  294-299.  doi:10.1016/j.pld.2017.05.008
    Abstract ( 49 )   HTML ( )   PDF (1207KB) ( 8 )   Save
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    Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (~1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (~18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean=4.875), and within-population expected heterozygosity from zero to 0.789 (mean=0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
    Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean
    Shan He, Wei Xu, Fei Li, Yue Wang, Aizhong Liu
    2017, 39(05):  300-307.  doi:10.1016/j.pld.2017.05.007
    Abstract ( 40 )   HTML ( )   PDF (1950KB) ( 7 )   Save
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    Investigation of the relationships of phenotypic and epigenetic variations might be a good way to dissect the genetic or molecular basis of phenotypic variation and plasticity in plants. Castor bean (Ricinus communis L.), an important non-edible oilseed crop, is a mono-species genus plant in the family Euphorbiaceae. Since it displays rich phenotypic variations with low genetic diversity, castor bean is a good model to investigate the molecular basis of phenotypic and epigenetic variations. Cytosine DNA methylation represents a major molecular mechanism of epigenetic occurrence. In this study, epigenetic diversity of sixty landrace accessions collected worldwide was investigated using the methylationsensitive amplification polymorphism (MSAP) technique. Results showed that the epigenetic diversity (based on the polymorphism of DNA methylated loci) exhibited a medium variation (Ne=1.395, He=0.242, I=0.366) at the population level though the variation was great, ranging from 3.80% to 34.31% among accessions. Both population structure analysis and the phylogenetic construction (using the neighbor-joining criteria) revealed that the two main clades were identified, but they did not display a distinct geographic structure. After inspecting the location of polymorphic methylated loci on genome we identified that the polymorphic methylated loci occur widely in nuclear and organelle genomes. This study provides new data to understand phenotypic and epigenetic variations in castor bean.