How territoriality affects the density of an egg predator： Habitat renovation and reintroduction as a method of conserving two endangered desert spring fish

Conservation of endangered sympatric species must be carefully executed to ensure that the protection of one species does not negatively impact the survival of another. Critically endangered Pecos gambusia Gambusia nobilis and Leon Springs pupfish Cyprinodon bovinus, which are endemic to a threatened desert spring habitat, exemplify one such scenario. Recently, this habitat has been expanded, and captively bred C. bovinus were released to repopulate an area historically known to contain this species. A previous study suggested that G. nobilis are detrimental to C. bovinus populations, due to their tendency to congregate near spawning pairs and feed on their eggs. Whether G. nobilis are attracted to territorial C. bovinus, regardless of spawning behavior, remains unclear. To determine this, the number of G. nobilis in occupied and unoccupied breeding territories of both wild and captively bred C. bovinus was measured. Gambusia nobilis densities were similar between unoccupied and occupied territorial sites, suggesting that they do not show a preference for C. bovinus territories. Regardless of habitat location or prior captivity, territorial C. bovinus significantly excluded G. nobilis within their direct vicinity （5 cm）, but not from their entire territory. Decreased G. nobilis density within the habitat may allow C. bovinus to defend their breeding territories more readily during the summer spawning season. This study provides empirical evidence of captively raised individuals behaving similarly to wild indi- viduals upon reintroduction to their natural habitat and support for conservation methods that focus on common limiting factors between endangered species [Current Zoology 60 （4）： 527-533, 2014].     

Validation of the binary designation Symbiodinium thermophilum (Dinophyceae)

The binary designation Symbiodinium thermophilum was invalid due to the absence of an illustration as required by Article 44.2 of the ICN. Herein, it is validated. This species is the most common symbiont in reef corals in the southern Persian/Arabian Gulf, the world's hottest body of water sustaining reef coral growth.     

Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry

Background

The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversity. The Kuwait Genome Project an initiative to sequence individual genomes from the three subgroups of Kuwaiti population namely, Saudi Arabian tribe; “tent-dwelling” Bedouin; and Persian, attributing their ancestry to different regions in Arabian Peninsula and to modern-day Iran (West Asia). These subgroups were in line with settlement history and are confirmed by genetic studies. In this work, we report whole genome sequence of a Kuwaiti native from Persian subgroup at >37X coverage.

Results

We document 3,573,824 SNPs, 404,090 insertions/deletions, and 11,138 structural variations. Out of the reported SNPs and indels, 85,939 are novel. We identify 295 ‘loss-of-function’ and 2,314 ’deleterious’ coding variants, some of which carry homozygous genotypes in the sequenced genome; the associated phenotypes include pharmacogenomic traits such as greater triglyceride lowering ability with fenofibrate treatment, and requirement of high warfarin dosage to elicit anticoagulation response. 6,328 non-coding SNPs associate with 811 phenotype traits: in congruence with medical history of the participant for Type 2 diabetes and β-Thalassemia, and of participant’s family for migraine, 72 (of 159 known) Type 2 diabetes, 3 (of 4) β-Thalassemia, and 76 (of 169) migraine variants are seen in the genome. Intergenome comparisons based on shared disease-causing variants, positions the sequenced genome between Asian and European genomes in congruence with geographical location of the region. On comparison, bead arrays perform better than sequencing platforms in correctly calling genotypes in low-coverage sequenced genome regions however in the event of novel SNP or indel near genotype calling position can lead to false calls using bead arrays.

Conclusions

We report, for the first time, reference genome resource for the population of Persian ancestry. The resource provides a starting point for designing large-scale genetic studies in Peninsula including Kuwait, and Persian population. Such efforts on populations under-represented in global genome variation surveys help augment current knowledge on human genome diversity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1233-x) contains supplementary material, which is available to authorized users.     

Observations of stranded and swimming whale sharks Rhincodon typus in Khor Al-Zubair,NW Arabian Gulf and Shatt Al-Arab Estuary,Iraq

This study is the first record of a whale shark Rhincodon typus in Iraqi waters and the second record from the Arabian (Persian) Gulf portion of the north-west Indian Ocean. The stranding and sighting events were documented by photos of three individuals: the stranded specimen was 6.5 m total length (L_T) and the free-swimming individuals were c. 1–2 and 2–3 m L_T respectively_. An appeal is made for Iraqi policy makers to participate in regional and international organizations for the conservation of this endangered species.     

Fish communities on the world's warmest reefs: what can they tell us about the effects of climate change in the future?

To examine the role of climatic extremes in structuring reef fish communities in the Arabian region, reef fish communities were visually surveyed at four sites within the southern Persian Gulf (also known as the Arabian Gulf and The Gulf), where sea-surface temperatures are extreme (range: 12-35° C annually), and these were compared with communities at four latitudinally similar sites in the biogeographically connected Gulf of Oman, where conditions are more moderate (range: 22-31° C annually). Although sites were relatively similar in the cover and composition of coral communities, substantial differences in the structure and composition of associated fish assemblages were apparent. Fish assemblages in the southern Persian Gulf held significantly lower estimates of abundance, richness and biomass, with significantly higher abundances of smaller sized individuals than Gulf of Oman assemblages. Functionally, southern Persian Gulf sites held significantly lower abundances of nearly all the common fish trophic guilds found on Gulf of Oman sites, although higher abundances of herbivorous grazers were apparent. These results suggest the potential for substantial changes in the structure of reef-associated fish communities, independent of changes in habitat within an environment of increasing fluctuations in oceanic climate.     

Vegetation Mapping of the Mond Protected Area of Bushehr Province （South-west Iran）

Arid regions of the world occupy up to 35% of the earth＇s surface, the basis of various definitions of climatic conditions, vegetation types or potential for food production. Due to their high ecological value, monitoring of arid regions is necessary and modern vegetation studies can help in the conservation and management of these areas. The use of remote sensing for mapping of desert vegetation is difficult due to mixing of the spectral reflectance of bright desert soils with the weak spectral response of sparse vegetation. We studied the vegetation types in the semiarid to arid region of Mond Protected Area, south-west Iran, based on unsupervised classification of the Spot XS bands and then produced updated maps. Sixteen map units covering 12 vegetation types were recognized in the area based on both field works and satellite mapping. Halocnemum strobilaceum and Suaeda fruticosa vegetation types were the dominant types and Ephedra foliata, Salicornia europaea-Suaeda heterophylla vegetation types were the smallest. Vegetation coverage decreased sharply with the increase in salinity towards the coastal areas of the Persian Gulf. The highest vegetation coverage belonged to the riparian vegetation along the Mond River, which represents the northern boundary of the protected area. The location of vegetation types was studied on the separate soil and habitat diversity maps of the study area, which helped in final refinements of the vegetation map produced.     

The dispersal of Halimeda in northern hemisphere mid-latitudes: Palaeobiogeographical insights

The bryopsidalean alga Halimeda gained an important role as carbonate producer in Cenozoic tropical coral reefs and became a significant constituent of the modern Mediterranean seaweed flora. There are, however, open questions at which time the thermophile alga appeared in the cooler Mediterranean Sea and why it is not detected in coral reefs of the modern Persian Gulf. To unravel the biogeography and ecology of Halimeda at its northern margin of distribution, we use fossil Halimeda records of the Central Paratethys/Medditerranean for comparison of the geological, (palaeo)ecological and evolutionary dispersal constraints of the alga in the Miocene and Holocene Persian Gulf. The revealed spatial and temporal distribution patterns of Halimeda in the regions of the Mediterranean and Arabian seas identify water temperature as the major ecological constraint and the extreme Plio-Pleistocene climate changes as the motor for the dispersal and evolution of Halimeda in higher latitudes. Generally, the distribution of tropical species in higher latitudes was related to warm climate intervals during the Neogene. Accordingly, the available (palaeo)biogeographic data implies that the warm-adapted ancestors of the present-day Mediterranean H. tuna population possibly entered the Mediterranean Sea during the mid-Pliocene global warmth and became isolated during subsequent cooling. It also implies that the warm Persian Gulf water is probably unsuitable for the cool-adapted H. discoidea population in the Gulf of Oman and that its tropical ancestors could have reached the Gulf of Oman only during a Pleistocene glacial phase when monsoon-induced upwelling of cold water in the Arabian Sea was reduced and the Persian Gulf fell dry. This example demonstrates the limitation of the actualistic palaeontological approach when using biota at the edges of their distribution range as palaeoclimate proxy.     

First record of mudskipper Boleophthalmus dussumieri (Gobiidae: Oxudercinae) on the coast of Mozambique and evidence of two putative lineages along its known distribution range

Boleophthalmus dussumieri is one of the most widely distributed mudskippers and is native to the Persian Gulf in Iran down to the northeast of the Arabian Sea and the coast of India. Nonetheless, the present study is the first to confirm the presence of B. dussumieri in the marine areas of the Mozambique coast. In addition, molecular analysis revealed strong evidence for the existence of two lineages with a high level of nucleotide divergence along the sampled area, revealing a still-neglected taxonomic condition for this lineage/species.     

Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Bracbypodium distacbyon

This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight （R2 〉 0.92） and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response tonitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determina- tion of genomic regions associated with superior nutrient use efficiency.     

Male size does not correlate with fertilization success in two bufonid toads that show size-assortative mating

We examined sexual size dimorphism （SSD）, mating pattem, fertilization efficiency and female reproductive traits in two bufonid toads （Bufo gargarizans and Duttaphrynus melanostictus） to test the idea that importance of male body size for egg fertilization success depends on the mating pattern. Female-biased SSD was evident only in D. melanostictus. Female B. gar- garizans laid fewer larger eggs nearly three months earlier than did female D. melanostictus. Fertilization efficieneies on average were higher in B. gargarizans （95%） than in D. melanostictus （91%）. Though differing in the degree of SSD, body size, breeding season, clutch size, egg size and fertilization efficiency, the two toads were similar in four aspects： （1） both showed size-assortative mating; （2） females did not tradeoff egg size against egg number; （3） male size, clutch size and clutch dry mass were greater in male-larger than in female-larger pairs after accounting for female snout-vent length （SVL）; and （4） the ratio of male to female SVL did not affect fertilization efficiency. Our data show that： （1） a female preference for large males is likely not important in terms of egg fertilization success; （2） a male preference for large females is likely important because larger females are more fecund; and （3） size-assortative mating arises from a male preference for large females. Our study demonstrates that male size is not always important for egg fertilization success in anurans that show size-assortative mating.     

Antipredator deception in terrestrial vertebrates

Abstract Deceptive antipredator defense mechanisms fall into three categories： depriving predators of knowledge of prey＇s presence, providing cues that deceive predators about prey handling, and dishonest signaling. Deceptive defenses in terrestrial vertebrates include aspects of crypsis such as background matching and countershading, visual and acoustic Batesian mimicry, active defenses that make animals seem more difficult to handle such as increase in apparent size and threats, feigning injury and death, distractive behaviours, and aspects of flight. After reviewing these defenses, I attempt a preliminary evaluation of which aspects of antipredator deception are most widespread in amphibians, reptiles, mammals and birds     

Identification and characterization of genes involved in the jasmonate biosynthetic and signaling pathways in mulberry （Morus notabilis）

Jasmonate （JA） is an important phytohormone regulating growth, development, and environmental response in plants, particularly defense response against herbivorous insects. Recently, completion of the draft genome of the mulberry （Morus notabilis） in conjunction with genome sequencing of silkworm （Bombyx mori） provides an opportuni-ty to study this unique plant-herbivore interaction. Here, we identified genes involved in JA biosynthetic and signaling pathways in the genome of mulberry for the first time, with the majority of samples showing a tissue-biased expression pattern. The analysis of the representative genes 12-oxophy-todienoic acid reductase （OPRs） and jasmonate ZIM-domain （JAZs） was performed and the results indicated that the mulberry genome contains a relatively smal number of JA biosynthetic and signaling pathway genes. A gene encoding an＆amp;nbsp;important repressor, MnNINJA, was identified as an alternative splicing variant lacking an ethylene-responsive element binding factor-associated amphiphilic repression motif. Having this fundamental information wil facilitate future functional study of JA-related genes pertaining to mulberry-silkworm interactions.     

Genealogy and phylogeography of Cyprinid fish Labeo rohita （Hamilton, 1822） inferred from ATPase 6 and 8 mitochondrial DNA gene analysis

ATPase 6/8 gene （842 bp） of mitochondrial DNA was sequenced in Labeo rohita samples （n = 253） collected from nine rivers belonging to four river basins; Indus, Ganges, Brahmaputra and Mahanadi. Analysis revealed 44 haplotypes with high haplotype diversity （Hd） 0.694 and low nucleotide diversity （π） 0.001. The within population variation was larger （83.44%） than among population differences （16.56%）. The mean Fsv value （0.166; P 〈 0.05） for overall populations revealed moderate level of genetic structuring in the wild L. rohita populations. The haplotype network presented a single clade for wild L. rohita population, from different rivers. Negative values for Fu＇s index （Fs）, mismatch distribution analysis indicated period of expansion in L. rohita population. The time after recent expansion was estimated for each population, between 0.042 to 0.167 mya. The pattern of Isolation by Distance （IBD） was not significant （r = -0.113, P 〈 0.287）, when all the sampling locations were compared （Mantel test）, however, when an outlier （Indus, Brahmaputra and Mahanadi） was removed from the whole population set, a clear positive correlation between pairwise Fsv and geographic distance （Km） was seen. The analysis of data demonstrated that ATPase6/8 gene polymorphism is a potential marker to understand genetic population structure of wild L. rohita existing in different rivers. The study identified population substructure in wild L. rohita with common ancestral origin [Current Zoology 60 （4）： 460--471, 2014].     

Molecular mechanisms of insect adaptation to plant defense： Lessons learned from a Bruchid beetle

Plants can accumulate, constitutively and/or after induction, a wide variety of defense compounds in their tissues that confer resistance to herbivorous insects. The naturally occurring plant resistance gene pool can serve as an arsenal in pest management via transgenic approaches. As insect-plant interaction research rapidly advances, it has gradually become clear that the effects of plant defense compounds are determined not only by their toxicity toward target sites, but also by how insects respond to the challenge. Insect digestive tracts are not passive targets of plant defense, but often can adapt to dietary challenge and successfully deal with various plant toxins and anti-metabolites. This adaptive response has posed an obstacle to biotechnology-based pest control approaches, which underscores the importance of understanding insect adaptive mechanisms. Molecular studies on the impact of protease inhibitors on insect digestion have contributed significantly to our understanding of insect adaptation to plant defense. This review will focus on exposing how the insect responds to protease inhibitors by both qualitative and quantitative remodeling of their digestive proteases using the cowpea bruchid-soybean cysteine protease inhibitor N system.     

Modulating Wnt signaling to improve cell replacement therapy for Parkinson＇s disease

Clinical trials have demonstrated the capacity for dopamine neurons, transplanted ectopicaUy into the striatum, to structurally inte- grate, restore dopamine transmission, and induce long-term functional benefits for Parkinson＇s disease （PD） patients. Despite this proof of principle, a number of limitations have hindered the development of cell replacement therapy over the past 20 years, particu- larly tissue availability, graft survival, and adequate reinnervation of the host brain. With a greater understanding of failure in prior clinical trials, increased knowledge of midbrain dopamine development （now including Wnts）, and the development of pluripotent stem cell technologies, we are better equipped than ever to re-address a number of these challenges. This review summarizes the trials, tribulations, and progress in cell replacement therapy for PD. We discuss the prospects of modulating canonical and non-canon- ical Wnt signalingto improve cell therapy based upon their roles in dopamine neural development and the adult brain. This will include the potential of Wnts to （i） expand fetaUy derived tissue in vitro and foUowing transplantation, （ii） promote the differentiation of pluripotent stem cells, （iii） increase graft integration and restoration of neural circuitry, and finally （iv） enhance graft survival.     

Evolution of deceit by worthless donations in a nuptial gift-giving spider

Males of the nursery web spider Pisaura mirabil usually offer an insect prey wrapped in white silk as a nuptial gift to facilitate copulation. Males exploit female foraging preferences in a sexual context as females feed on the gift during copula- tion. It is possible for males to copulate without a gift, however strong female preference for the gift leads to dramatically higher mating success for gift-giving males. Females are polyandrous, and gift-giving males achieve higher mating success, longer copulations, and increased sperm transfer that confer advantages in sperm competition. Intriguingly, field studies show that ap- proximately one third of males carry a worthless gift consisting of dry and empty insect exoskeletons or plant fragments wrapped in white silk. Silk wrapping disguises gift content and females are able to disclose gift content only after accepting and feeding on the gift, meanwhile males succeed in transferring sperm. The evolution of deceit by worthless gift donation may be favoured by strong intra-sexual competition and costs of gift-construction including prey capture, lost foraging opportunities and investment in silk wrapping. Females that receive empty worthless gifts terminate copulation sooner, which reduces sperm transfer and likely disadvantages males in sperm competition. The gift-giving trait may thus become a target of sexually antagonistic co-evolution, where deceit by worthless gifts leads to female resistance to the trait. We discuss factors such as female mating rate and intensity of sperm competition that may shape the evolution of male deception, and how ecological factors may influence the evolution and maintenance of worthless gifts as an evolutionarily stable alternative mating strategy by frequency dependent selection     

Uropygial gland volatiles may code for olfactory information about sex,individual, and species in Bengalese finches Lonchura striata

Over-shadowed by eye-catching vocal and visual signals, chemical communication has long been overlooked in birds. This study aimed at exploring whether volatile composition of the uropygial gland secretion （UGS） of birds was associated with the information about sex, individual and species. By using dichloromethane extraction and gas chromatography-mass spectrometry （GC-MS）, we analyzed the UGS volatiles of domesticated Bengalese finches （ Lonchura striata, Estrildiea） which is also known as white-rumped munias. We characterized 16 volatile molecules from the UGS, including eight n-alkanols, five diesters, an ester, an aldehyde and a fatty acid, and quantified them in terms of GC peak area percentages （relative abundances） . Among these compounds, hexadecanol and octadecanol were major components in both sexes. The former was richer in males than in females and the latter richer in females than in males, suggesting that they might be male and female pheromone candidates, respectively. The high inter-individual variations, in relative abundance, of the UGS volatiles implied that these compounds might carry information about individuality. The similarity between GC profiles of the UGS and wing feather from same individuals indicates that the birds might preen the secretion to their feathers to transmit chemical cues. Additionally, by comparing with three sympatric passerine species, i. e., zebra finches Taeniopygia guttata, yellow-bowed buntings Emberiza chrysophrys and rooks Corvus frugilegus, we found that the composition of C13 - C18 alkanols in the UGS might code for information about species. Our study also showed that quantitative differences （degree） of same UGS volatiles might be the key for the Bengalese finch to code for information about sex and individuality whereas both the kind and degree of UGS constituents could be utilized to code for information about species [ Current Zoology 55 （5）： 357-365, 2009].     

New Replacement Name for Rana paradoxa Mocquard, 1890 with Designations of Lectotypes for Rana paradoxa and Rana conspicil- lata Giinther, 1872： Both Synonymized with Limnonectes kuhlii （Tschudi, 1838） （Dicroglossidae： Dicroglossinae）

Fanged frogs, now called Limnonectes kuhlii, from Borneo are remotely related to true Javanese L. kuhliL For future taxonomy of Bornean fanged frogs, we fix the nomenclatural status of two existing names, Rana conspicillata Giunther, 1872 and Rana paradoxa Mocquard, 1890. Morphological comparison of the type-series revealed heterospecific relationships of the two species. For R. conspicillata, we designate BMNH 1947.2.29.20 as the lectotype, and for R. para doxa, we also designate MNHN 1889.222 as the lectotype and propose a replacement name Limnonectes mocquardi, in order to stabilize their nomenclature.