For all researches, please visit our "Peer-reviewed publications" page.
Aliabadian M, Alaei-Kakhki N, Mirshamsi O, Nijman V, Roulin A (2016)
Biological Journal of the Linnean Society.
The existence of substantial morphological variation has resulted in the description of numerous subspecies of the cosmopolitan barn owl, Tyto alba. However, preliminary studies have revealed a high degree of genetic variation between Old and New World barn owls, suggesting that the T. alba complex may consist of several species. We present a comprehensive study of its taxonomy and propose a spatiotemporal framework to explain the origin and patterns of dispersal and diversification within these cosmopolitan owls. We used a Bayesian relaxed molecular clock approach to assess the timing of diversification. To evaluate the biogeographical pattern, we considered dispersal in addition to temporal connectivity between areas. Finally, we used ecological niche modelling to evaluate their ecological niches. Our phylogenetic analyses suggest that barn owls of the Old and New World show a high degree of genetic divergence, and the barn owls of South and South-east Asia (Tyto alba stertens and Tyto alba javanica) cluster with the Australian barn owl Tyto delicatula. We propose to treat the T. alba complex as three species: T. alba (Africa, Europe), Tyto furcata (New World), and Tyto javanica (Australasia). The dating analyses indicate that the early divergence among the species of the T. alba complex took place in the Middle Miocene and we hypothesize that a common ancestor of the T. alba complex lived in Africa. A potential scenario suggests that T. alba dispersed to Europe and south-western Asia during the interglacial periods of the Miocene/Pliocene, and dispersed into the New World either via an eastern Asian route or a western north Atlantic one.
Bellot S, Cusimano N, Luo S, Sun G, Zarre S, Gröger A et al. (2016)
Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales
Genome Biology and Evolution 8(7) 2214-2230.
Cynomoriaceae, one of the last unplaced families of flowering plants, comprises one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence. Cynomorium has large genomes of 13.70-13.61 (Italy) to 13.95-13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.
Keywords: Chondriome, Cynomorium, Mediterranean-Irano-Turanian, horizontal gene transfer, parasitic plants, plastome
Shabani F, Kumar L, Solhjouy-fard S (2016)
Variances in the projections, resulting from CLIMEX, Boosted Regression Trees and Random Forests techniques
Theoretical and Applied Climatology.
The aim of this study was to have a comparative investigation and evaluation of the capabilities of correlative and mechanistic modeling processes, applied to the projection of future distributions of date palm in novel environments and to establish a method of minimizing uncertainty in the projections of differing techniques. The location of this study on a global scale is in Middle Eastern Countries. We compared the mechanistic model CLIMEX (CL) with the correlative models MaxEnt (MX), Boosted Regression Trees (BRT), and Random Forests (RF) to project current and future distributions of date palm (Phoenix dactylifera L.). The Global Climate Model (GCM), the CSIRO-Mk3.0 (CS) using the A2 emissions scenario, was selected for making projections. Both indigenous and alien distribution data of the species were utilized in the modeling process. The common areas predicted by MX, BRT, RF, and CL from the CS GCM were extracted and compared to ascertain projection uncertainty levels of each individual technique. The common areas identified by all four modeling techniques were used to produce a map indicating suitable and unsuitable areas for date palm cultivation for Middle Eastern countries, for the present and the year 2100. The four different modeling approaches predict fairly different distributions. Projections from CL were more conservative than from MX. The BRT and RF were the most conservative methods in terms of projections for the current time. The combination of the final CL and MX projections for the present and 2100 provide higher certainty concerning those areas that will become highly suitable for future date palm cultivation. According to the four models, cold, hot, and wet stress, with differences on a regional basis, appears to be the major restrictions on future date palm distribution. The results demonstrate variances in the projections, resulting from different techniques. The assessment and interpretation of model projections requires reservations, especially in correlative models such as MX, BRT, and RF. Intersections between different techniques may decrease uncertainty in future distribution projections. However, readers should not miss the fact that the uncertainties are mostly because the future GHG emission scenarios are unknowable with sufficient precision. Suggestions towards methodology and processing for improving projections are included.
Keywords: Chondriome, Cynomorium, Mediterranean-Irano-Turanian, horizontal gene transfer, parasitic plants, plastome
Shabani F, Kumar L, Ahmadi M (2016)
A comparison of absolute performance of different correlative and mechanistic species distribution models in an independent area
Ecology and Evolution 6(16) 5973-5986.
To investigate the comparative abilities of six different bioclimatic models in an independent area, utilizing the distribution of eight different species available at a global scale and in Australia. Global scale and Australia. We tested a variety of bioclimatic models for eight different plant species employing five discriminatory correlative species distribution models (SDMs) including Generalized Linear Model (GLM), MaxEnt, Random Forest (RF), Boosted Regression Tree (BRT), Bioclim, together with CLIMEX (CL) as a mechanistic niche model. These models were fitted using a training dataset of available global data, but with the exclusion of Australian locations. The capabilities of these techniques in projecting suitable climate, based on independent records for these species in Australia, were compared. Thus, Australia is not used to calibrate the models and therefore it is as an independent area regarding geographic locations. To assess and compare performance, we utilized the area under the receiver operating characteristic (ROC) curves (AUC), true skill statistic (TSS), and fractional predicted areas for all SDMs. In addition, we assessed satisfactory agreements between the outputs of the six different bioclimatic models, for all eight species in Australia. The modeling method impacted on potential distribution predictions under current climate. However, the utilization of sensitivity and the fractional predicted areas showed that GLM, MaxEnt, Bioclim, and CL had the highest sensitivity for Australian climate conditions. Bioclim calculated the highest fractional predicted area of an independent area, while RF and BRT were poor. For many applications, it is difficult to decide which bioclimatic model to use. This research shows that variable results are obtained using different SDMs in an independent area. This research also shows that the SDMs produce different results for different species; for example, Bioclim may not be good for one species but works better for other species. Also, when projecting a “large” number of species into novel environments or in an independent area, the selection of the “best” model/technique is often less reliable than an ensemble modeling approach. In addition, it is vital to understand the accuracy of SDMs' predictions. Further, while TSS, together with fractional predicted areas, are appropriate tools for the measurement of accuracy between model results, particularly when undertaking projections on an independent area, AUC has been proved not to be. Our study highlights that each one of these models (CL, Bioclim, GLM, MaxEnt, BRT, and RF) provides slightly different results on projections and that it may be safer to use an ensemble of models.
Keywords: Bioclimatic model, correlative model, distribution model, fundamental niche, mechanistic niche model, modeling methods, realized niche, species
Soares de Oliveira I, Rödder D, Capinha C, Ahmadzadeh F, Karlokoski Cunha de Oliveira A, Toledo L (2016)
Assessing future habitat availability for coastal lowland anurans in the Brazilian Atlantic rainforest
Studies on Neotropical Fauna and Environment 51(1) 45-55.
ABSTRACTGlobal warming is expected to cause several modifications to physical environments, and sea level rise is a certain outcome. However, assessment of the potential impacts caused by sea level rise on biodiversity is still emerging. Therefore, we assessed the combined impact of global warming and sea level rise on the potential distribution of 19 coastal lowland anurans in the biodiversity hotspot Atlantic Forest. We applied a correlative species distribution model (SDM) (BIOCLIM) and GIS-based spatial analyses. We evaluated the extent of changes of potential distributions under extreme and moderate global warming scenarios as well as two extreme sea level rise scenarios. Our results suggest wide areas of suitable habitat for most species in the future. However, for 15% of these species the SDMs predict massive losses of range extent as a result of a combination of global warming and sea level rise. Such observations highlight an immediate need to consider the potential effects of sea level rise in c...
Keywords: Amphibian conservation, biodiversity hotspot, global warming, habitat suitability, species distribution model
Liede-Schumann S, Khanum R, Mumtaz A, Gherghel I, Pahlevani A (2015)
Going West - a subtropical lineage (Vincetoxicum, Apocynaceae: Asclepiadoideae) expanding into Europe.
Molecular phylogenetics and evolution.
Vincetoxicum sensu lato is a tropical lineage comprising two clades that have reached high northern latitudes. Of the temperate clades, one is restricted to the Far East, the other one (Vincetoxicum s. str. Clade) extends into Europe, but their ranges overlap in Central China and Japan. Three species invasive in North America, V. hirundinaria, V. nigrum and V. rossicum, are members of the Vincetoxicum s. str. Clade. We explore the prerequisites for the range expansion in the Vincetoxicum s. str. Clade performing Bayesian and Maximum Likelihood phylogenetic analyses on sequences of the nuclear internal transcribed spacer (ITS) region, the nuclear external transcribed spacer region (ETS), and five plastid markers. The resulting phylogeny is used to conduct biogeographic analysis using BioGeoBEARS to reconstruct ancestral species ranges. Moreover, we map the known occurrences of two rare characters in Asclepiadoideae, the possession of phenanthroindolizidine alkaloids and reported cases of autogamy onto our phylogeny. Finally, we have conducted ecological niche modelling using Maxent on a total of 220 spatially unique occurrences of nine Vincetoxicum s. str. species spanning more than 4,000 km along the east-west gradient to learn about the climatic conditions along the presumed migration route. Our results indicate a north-westward migration in Vincetoxicum s. str. along the Asian mountain chains to Europe. Climatic preferences of the nine species sampled are dissimilar, except for the common exposure to at least one month of subfreezing temperatures, indicating a rather wide climatic tolerance for the clade as a whole. The three species invasive in North America belong to the northern Eurasian subclade and show the rare combination of phenanthroindolizidine alkaloids and autogamy.
Keywords: Ancestral area reconstruction, Biogeography, Climatic niches, Invasive species, Maxent, Molecular phylogeny
Shabani F, Kumar L, Esmaeili A (2015)
A modelling implementation of climate change on biodegradation of Low-Density Polyethylene (LDPE) by Aspergillus niger in soil
Global Ecology and Conservation 4 388-398.
Aim: To model the areas becoming and remaining highly suitable for Aspergillus niger growth over the next ninety years by future climate alteration, in relation to the species’ potential enhancement of Low Density Polyethylene (LDPE) biodegradation in soil. Location: Global scale Methods: Projections of A. niger growth suitability for 2030, 2050, 2070 and 2100 were made using the A2 emissions scenario together with two Global Climate Models (GCMs): the CSIRO-Mk3.0 (CS) model and the MIROC-H (MR) model through CLIMEX software. Subsequently the outputs of the two GCMs were overlaid to extract common areas in each period of time, providing higher certainty concerning areas which will become highly suitable to A. niger in the future. Afterwards, GIS software was employed to extract sustainable regions for this species growth from present time up to 2100. Results: Central and eastern Argentina, Uruguay, southern Brazil, eastern United States, southern France, northern Spain, central and southern Italy, southern Hungary, eastern Albania, south western Russia, central and eastern China, eastern Australia, south east of South Africa, central Zambia, Rwanda, Burundi, central Kenya, central Ethiopia and north eastern Oman will be highly suitable for A. niger growth from present time up to 2100. Main conclusions: Accurately evaluating the impact of landfilling on land use and predicting future climate are vital components for effective long-term planning of waste management. From a social and economic perspective, utilization of our mapped projections to detect suitable regions for establishing landfills in areas highly sustainable for microorganisms like A. niger growth will allow a significant cost reduction and improve the performance of biodegradation of LDPE over a long period of time, through making use of natural climatic and environmental factors.
Keywords: Aspergillus niger, CLIMEX, Climate change, Microbial degradation, Polyethylene
Shabani F, Kumar L, Nojoumian A, Esmaeili A, Toghyani M (2015)
Projected future distribution of date palm and its potential use in alleviating micronutrient deficiency.
Journal of the science of food and agriculture.
BACKGROUND: Micronutrient deficiency develops when nutrient intake does not match nutritional requirements for maintaining healthy tissue and organ functions which may have long-ranging effects on health, learning ability and productivity. Inadequacy of iron, zinc and vitamin A are the most important micronutrient deficiencies. Consumption of a 100 g portion of date flesh from date palm (Phoenix dactylifera L.) has been reported to meet approximately half the daily dietary recommended intake of these micronutrients. This study investigated the potential distribution of P. dactylifera under future climates to address its potential long-term use as a food commodity to tackle micronutrient deficiencies in some developing countries. RESULTS: Modelling outputs indicated large shifts in areas conducive to date palm cultivation, based on global-scale alteration over the next 60 years. Most of the regions suffering from micronutrient deficiencies were projected to become highly conducive for date palm cultivation. CONCLUSIONS: These results could inform strategic planning by government and agricultural organizations by identifying areas to cultivate this nutritionally important crop in the future to support the alleviation of micronutrient deficiencies. © 2015 Society of Chemical Industry.
Keywords: Phoenix dactylifera L, climate change, global climate models, micronutrient deficiency
Ihlow F, Ahmadzadeh F, Ghaffari H, Taşkavak E, Hartmann T, Etzbauer C et al. (2014)
Assessment of genetic structure, habitat suitability and effectiveness of reserves for future conservation planning of the Euphrates soft-shelled turtle Rafetus euphraticus (Daudin, 1802)
Aquatic Conservation: Marine and Freshwater Ecosystems Forthcoming.
1. The endangered Euphrates soft-shelled turtle, Rafetus euphraticus, is endemic to the Mesopotamian River Basin in the Middle East. Within recent decades, populations of this aquatic species have been heavily depleted and severely fragmented owing to habitat alteration and destruction by drainage and hydroelectricity dam constructions. Continuing habitat loss and fragmentation are considered the main drivers for the population decline of R. euphraticus. 2. Intraspecific genetic variability was investigated using two mitochondrial gene fragments for 31 specimens covering most of the distributional range of the species. Habitat suitability models were computed using a combination of bioclimatic and remote sensing variables as environmental predictors to assess habitat suitability, habitat fragmentation and coverage by designated protected areas across the range of R. euphraticus. 3. Beyond single substitutions in two sequences, no significant genetic variation could be detected in R. euphraticus. Models show habitat suitability to be high throughout the range of the species, although only a fraction is currently covered by reserves. Habitat suitability and coverage of reserves is highly variable among countries. South-western Iran appears to be ofmajor importance for future conservation strategies. Suitabilitymodels are in concordance with the habitat selection patterns of R. euphraticus. 4. The existing reserve system is considered insufficient and has to be significantly improved in order to sustain viable populations of R. euphraticus. To counter continuing fragmentation and alteration by dam construction, future conservation measures should focus on highlighted priority areas.
Keywords: conservation planning, genetic variation, habitat fragmentation, habitat suitability modelling, protected areas
Shabani F, Kumar L, Esmaeili A (2014)
Future distributions of Fusarium oxysporum f. spp. in European, Middle Eastern and North African agricultural regions under climate change
Agriculture, Ecosystems & Environment 197 96-105.
The levels of inaccuracy in projections of global climate model outputs can be reduced by identification of the correlations between the output results of a number of models, which include common assumptions. Some of the invasive pathogen of Fusarium oxysporum f. spp. pose risks to a number of cash crops such as banana, tomato, palm and garlic while some have a symbiotic relation varying from pathogenic to commensal (null effect), up to beneficial effect. Limitation of occurrence records of many single species such as F. oxysporum f. sp. cubense, F. oxysporum f. sp. albedinis, F. oxysporum f. sp. lycopersici and F. oxysporum f. sp. vasinfectum necessitated this study to model the future distribution of F. oxysporum f. spp. rather than individual species. The future distribution of F. oxysporum f. spp. was modeled by CSIRO-Mk3.0 (CS) and MIROC-H (MR) GCMs, and the results were correlated to identify areas suitable for F. oxysporum f. spp. growth for North Africa, Middle Eastern and European countries for the years 2050 and 2100. The projections established that a number of countries will become highly conducive to this fungus, while others are projected to produce marginal levels of conduciveness by 2050 and 2100. We also demonstrate that refining CLIMEX outputs with a combination of a number of alternative GCMs results ensures that modeled projections become more robust, rather than producing purely hypothetical findings.
Keywords: CLIMEX, Climate change, Fusarium oxysporum f. spp., GIS