Multilocus marker-based delimitation of Salicornia persica and its population discrimination assisted by supervised machine learning approach.

The Salicornia L. has been considered one of the most taxonomically challenging genera due to high morphological plasticity, intergradation between related species, and lack of diagnostic features in preserved herbarium specimens. In the United Arab Emirates (UAE), only one species of this genus, Salicornia europaea, has been reported, though investigating its identity at the molecular level has not yet been undertaken. Moreover, based on growth form and morphology variation between the Ras-Al-Khaimah (RAK) population and the Umm-Al-Quwain (UAQ) population, we suspect the presence of different species or morphotypes. The present study aimed to initially perform species identification using multilocus DNA barcode markers from chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA), followed by the genetic divergence between two populations (RAK and UAQ) belonging to two different coastal localities in the UAE. The analysis resulted in high-quality multilocus barcode sequences subjected to species discrimination through the unsupervised OTU picking and supervised learning methods. The ETS sequence data from our study sites had high identity with the previously reported sequences of Salicornia persica using NCBI blast and was further confirmed using OTU picking methods viz., TaxonDNAs Species identifier and Assemble Species by Automatic Partitioning (ASAP). Moreover, matK sequence data showed a non-monophyletic relationship, and significant discrimination between the two populations through alignment-based unsupervised OTU picking, alignment-free Co-Phylog, and alignment & alignment-free supervised learning approaches. Other markers viz., rbcL, trnH-psbA, ITS2, and ETS could not distinguish the two populations individually, though their combination with matK (cpDNA & cpDNA+nrDNA) showed enough population discrimination. However, the ITS2+ETS (nrDNA) exhibited much higher genetic divergence, further splitting both the populations into four haplotypes. Based on the observed morphology, genetic divergence, and the number of haplotypes predicted using the matK marker, it can be suggested that two distinct populations (RAK and UAQ) do exist. Further extensive morpho-taxonomic studies are required to determine the inter-population variability of Salicornia in the UAE. Altogether, our results suggest that S. persica is the species that grow in the present study area in UAE, and do not support previous treatments as S. europaea.

Long-term forest vegetation dynamics in Nanda Devi Biosphere Reserve, Indian west Himalaya: evidence from repeat studies on compositional patterns.

It has been established that resurvey of historical vegetation stands, even those not marked permanently, could foster our understanding of vegetation dynamics and changes in structure and composition over time. However, such studies are poorly available, particularly in remote landscapes of the Indian Himalaya. There exists a complete lack of resurveys, which has limited our ability to provide reliable evidence of changes over the decades. This study, for the first time in the Indian Himalaya, considered repeat surveys (nearly after 25 years) of vegetation stands in eleven forest communities of the buffer zone of NDBR (Nanda Devi Biosphere Reserve). Thirty historical forest stands, earlier studied in 1988-1990, were revisited during 2012-2014 and investigated using the same survey methods as used in the previous study. We found that previously reported dominant tree species, i.e., Alnus nepalensis, Acer cappadocicum, Quercus floribunda, Quercus semecarpifolia, Hippophae salicifolia, and Betula utilis, in nine out of eleven communities in the study area are continuing to exhibit dominance in the community. However, a significant increase in species richness and density in the seedling and sapling layer in Quercus floribunda, Quercus semecarpifolia, Rhododendron arboreum, and Abies pindrow is indicative of the ongoing process of change in forest composition. The compositional features of plant communities, when analyzed through Community Change Sensitivity (CCS) approach, identified Quercus floribunda, mixed Quercus-deciduous spp., Hippophae salicifolia, and Abies pindrow as the most change-sensitive communities in the study area and thus can be prioritized as the long-term ecological monitoring sites in the west Himalaya to understand intensity and patterns of changes. The potential changes based on the ecological information from two time period compositional data sets, having conservation and management implications, should be accommodated in the long-term perspective plans of the reserve.

Evaluating germinability of eight desert halophytes under long-term seed storage: Implications for conservation.

Ex situ conservation in seed banks is a potential complementary conservation strategy for native plant species. It is well established that ex situ seed banking of native wild plants prolongs seed viability and thereby preserves genetic and species diversity for future use. We evaluated ex situ storage potential of eight halophytic species from deserts in the United Arab Emirates (UAE) by studying seed germination. Specifically, we examined the germinability of freshly collected seeds and seeds stored for three years in a seed bank. We also examined the effect of light conditions on fresh and stored seed germination. Fresh seeds of seven of the eight species tested had a higher germination rates under 12/12 h light/dark fluctuations than did those exposed to total darkness. Storage reduced light sensitivity in Halocnemum strobilaceum, Suaeda aegyptiaca, Salsola drummondii and Salsola imbricata, but increased the requirement for light in Arthrocnemum macrostachyum. In Anabasis setifera, storage decreased germination percentage when there was a 12-hour light/dark fluctuation, but increased germination rate when exposed to the dark treatment. Storage significantly reduced germination in both the light/dark and dark treatments in Suaeda vermiculata and S. aegyptiaca. Germination speed also responded differently to storage; whereas Timson's index significantly increased in A. macrostachyum and H. strobilaceum, it significantly decreased for S. drummondii, S. aegyptiaca and S. vermiculata. Germination of these species at a range of temperatures requires further testing; additionally, we strongly suggest that these laboratory findings be complemented by field studies.

Prospects of genomic resources available at the global databases for the flora of United Arab Emirates.

This article emphasizes available genomic resources at the global databases National Center for Biotechnology Information (NCBI) GenBank, Gramene and Phytozome for the selected 378 plant taxa of the United Arab Emirates (UAE). Germplasm of these species was collected and banked at the Sharjah Seed Bank and Herbarium (SSBH) along with their related information on habit, habitat and occurrence. The occurrence statistics exhibits almost 19.84% species under rare-to-very rare category, the GenBank search statistics for this category indicates 17.72% species as studied and 2.11% as not studied. Overall, from the global search statistics for 378 plant species, it seems that about 40 (10.58%) species remained unstudied. Most of the unstudied species were herbaceous plants belonging to the mountainous habitat. Moreover, full genomes were recorded for 7 species at NCBI GenBank, 2 species at Phytozome and 1 species at Gramene database. The local search statistics (for UAE) exhibits about 10.58% of the flora that still remained unstudied and only 11 (2.90%) of the recorded species were having genomic information at NCBI GenBank. It is necessary to prioritize studies on such species that could provide valuable insight on their genetic composition in order to understand their adaptation to the natural environment. At present, the SSBH is cataloguing UAE's flora using core barcode and assisted markers that could provide a robust DNA barcode library for native plants of UAE. Our study appeals researchers to recognize and prioritize the species that need attention to enrich their genomic resources at the global databases by supporting nucleotide libraries with their conspecifics. At present, genomic resources for UAE plant taxa are limited, but with the advent of low-cost sequencing technologies these resources would flourish in the near future. Nevertheless, the information generated through genomic studies could be utilized for conservation and management of threatened and endangered plant species, Crop Wild Relatives and medicinal plants. We hope this article will promote interest in conducting additional studies in genomics of desert plants by encouraging researchers to participate in this emerging field.

Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint.

The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora.

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

Seed colour affects light and temperature requirements during germination in two Lotus species (Fabaceae) of the Arabian subtropical deserts / El color de la semilla afecta los requerimientos de luz y temperatura durante la germinación en dos especies de Lotus (Fabaceae) de los desiertos subtropicales árabes

AbstractHeterogeneity in seeds mostly occurs due to physiological, environmental and genetic factors, and these could affect seed dormancy and germination. Therefore, the aim of our study was to assess the effect of seed colour on germination behavior. For this, both light and temperature requirements were assessed in Lotus glinoides and Lotus halophilus (Fabaceae) from the hyper-arid deserts of the United Arab Emirates. Germination was assessed in terms of both final germination level (percentage) and germination rate, as expressed by Timson’s germination velocity index. Lotus glinoides produces black and yellow-colored seeds, and L. halophilus produces green and yellow seeds. Different seed lots were germinated in both light and darkness at different temperatures. Yellow seeds of the two species attained significantly lower germination, compared to black and green seeds. There was no specific light or temperature requirements for the germination of the two coloured seeds of L. glinoides; the effect of interactions between seed colour and both light and incubation temperature, were not significant on the final germination percentage. in L. halophilus, green seeds germinated significantly more in both light and darkness at lower temperatures (15/25 °C) and in light at higher temperatures (25/35 °C), compared to yellow seeds. Yellow seeds germinated faster, compared to black at 15/25 °C in L. glinoides and compared to green seeds at 15/25 °C and 25/35 °C in L. halophilus. Seed colour variation, at least in L. halophilus, could be a survival strategy that would determine the time of germination throughout the year in the unpredictable desert environment. Rev. Biol. Trop. 64 (2): 483-492. Epub 2016 June 01.

ResumenLa heterogeneidad en las semillas se produce principalmente debido a factores fisiológicos, genéticos y ambientales, y esto podría afectar latencia de las semillas y la germinación. Por lo tanto, el objetivo de nuestro estudio fue evaluar el efecto del color de la semilla en el comportamiento de la germinación. Para ello, tanto los requisitos de luz y temperatura fueron evaluados en Lotus glinoides y Lotus halophilus (Fabaceae) desde los desiertos hiper-árida de los Emiratos Árabes Unidos. La germinación se evaluó en términos de nivel final de germinación (porcentaje) y la tasa de germinación, expresado por el índice de velocidad de germinación de Timson. L. glinoides produce semillas negro y de color amarillo, y L. halophilus produce semillas verdes y amarillas. Los diferentes lotes de semillas fueron germinadas en luz y oscuridad a diferentes temperaturas. Semillas amarillas de las dos especies alcanzaron significativamente menor germinación, en comparación con las semillas negras y verdes. No había requisitos específicos de luz o temperatura para la germinación de las semillas de dos colores de L. glinoides; el efecto de las interacciones entre color de la semilla y la luz y la temperatura de incubación, no fueron significativas en el porcentaje final de germinación. En L. halophilus, semillas verdes germinados significativamente más en la luz y la oscuridad a temperaturas más bajas (15/25 °C) ya la luz a temperaturas más altas (25/35 °C), en comparación con semillas amarillas. Semillas amarillas germinaron más rápido, en comparación con el negro a 15/25 °C en L. glinoides y en comparación con semillas verdes a 15/25 °C y 25/35 °C en L. halophilus. La variación del color de la semilla, al menos en L. halophilus, podría ser una estrategia de supervivencia que determinaría el momento de la germinación durante todo el año en el entorno del desierto impredecible.

Seed colour affects light and temperature requirements during germination in two Lotus species (Fabaceae) of the Arabian subtropical deserts.

Heterogeneity in seeds mostly occurs due to physiological, environmental and genetic factors, and these could affect seed dormancy and germination. Therefore, the aim of our study was to assess the effect of seed colour on germination behavior. For this, both light and temperature requirements were assessed in Lotus glinoides and Lotus halophilus (Fabaceae) from the hyper-arid deserts of the United Arab Emirates. Germination was assessed in terms of both final germination level (percentage) and germination rate, as expressed by Timson's germination velocity index. Lotus glinoides produces black and yellow-colored seeds, and L. halophilus produces green and yellow seeds. Different seed lots were germinated in both light and darkness at different temperatures. Yellow seeds of the two species attained significantly lower germination, compared to black and green seeds. There was no specific light or temperature requirements for the germination of the two coloured seeds of L. glinoides; the effect of interactions between seed colour and both light and incubation temperature, were not significant on the final germination percentage. In L. halophilus, green seeds germinated significantly more in both light and darkness at lower temperatures (15/25 °C) and in light at higher temperatures (25/35 °C), compared to yellow seeds. Yellow seeds germinated faster, compared to black at 15/25 °C in L. glinoides and compared to green seeds at 15/25 °C and 25/35 °C in L. halophilus. Seed colour variation, at least in L. halophilus, could be a survival strategy that would determine the time of germination throughout the year in the unpredictable desert environment.

Global hotspots in the present-day distribution of ancient animal and plant lineages.

The current distribution of biotic lineages that emerged in the deep time has both theoretical and practical implications, in particular for understanding the processes that have forged present-day biodiversity and informing local and regional-scale conservation efforts. To date however, there has been no examination of such patterns globally across taxa and geological time. Here we map the diversity of selected extant seed plant and tetrapod vertebrate lineages that were already in existence either in the latest Triassic or latest Cretaceous. For Triassic-age lineages, we find concentrations in several regions - both tropical and temperate - parts of North America, Europe, East and South-east Asia, northern South America, and New Zealand. With Cretaceous-age lineages, high values are relatively uniformly distributed across the tropics, with peak the values along the Andes, in South-east Asia and Queensland, but also in the temperate Cape Mountains. These patterns result from a combination of factors, including land area, geographic isolation, climate stability and mass extinction survival ability. While the need to protect many of these lineages has been long recognised, a spatially-explicit approach is critical for understanding and maintaining the factors responsible for their persistence, and this will need to be taken forward across finer scales.