Non-referenced genome assembly from epigenomic short-read data

Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.     

First sighting of a tropical benthic reef shark species at Rapa Nui: chance dispersal or a sign of things to come?

On 20 December 2017, a mature Triaenodon obesus was observed at Hanga Roa Bay, Rapa Nui (Easter Island) at c.18 m depth. This observation increases both the range of T. obesus in the Pacific Ocean and the number of elasmobranch species at Rapa Nui. In combination with other recent sightings further extending the southern range of this species during the Austral summer, sea surface temperature is suggested as key to southern dispersal.     

Human introduction or natural dispersion? Atlantic Ocean occurrence of the Indo‐Pacific whitetip reef shark Triaenodon obesus

Occurrence of multiple whitetip reef sharks Triaenodon obesus in the Atlantic Ocean is reported for the first time from near a sunken ferry off the Paraná coast in south‐eastern Brazil. This occurrence is hypothesized to have been caused by either a human introduction or a remarkably long oceanic displacement.     

印度洋中西部和大西洋西部水域大眼金枪鱼的食性比较

根据2004年8月至2005年3月大西洋西部水域及2003年12月份至2004年5月份在印度洋中西部水域金枪鱼延绳钓渔业所获取的大眼金枪鱼数据,对两个诃查区域内的大眼金枪鱼食性进行了研究。结果表明,印度洋中西部水域大眼金枪鱼的食物组成包括沙丁鱼、鱿鱼、乌贼等13个饵料类群,其中主要摄食鱿鱼和沙丁鱼;大西洋西部水域大眼金枪鱼主要摄食沙丁鱼、鱿鱼、虾类等13种饵料类群,主要以沙丁鱼为饵,其次为鱿鱼。印度洋中西部水域大眼金枪鱼空胃率非常高,基本上维持在60％以上;大西洋西部水域大眼金枪鱼空胃率相对较低,基本上都在30％以下。印度洋中西部水域大眼金枪鱼平均饱满指数变化不大,基本上维持在0．40～0．55之间。大西洋西部水域大眼金枪鱼平均饱满指数变化也不太大。印度洋中西部水域大眼金枪鱼各月平均饱满指数高于大西洋西部水域,且各月空胃率高于后者。印度洋中西部和大西洋西部水域大眼金枪鱼Shannon-Weiner多样性指数H’基本上都1．50～2．00之间变化。相同调查月份内,印度洋中西部水域大眼金枪鱼食物Pielou均匀度指数J’均高于大西洋西部水域。     

Geographic variation in sexual selection among populations of an iguanid lizard,Sauromalus obesus (=ater)

Abstract.— Geographic variation in selection pressures may result in population divergence and speciation, especially if sexual selection varies among populations. Yet spatial variation in targets and intensity of sexual selection is well studied in only a few species. Even more rare are simultaneous studies of multiple populations combining observations from natural settings with controlled behavioral experiments. We investigated how sexual selection varies among populations of the chuckwalla, Sauromalus obesus. Chuckwallas are sexually dimorphic in color, and males vary in coloration among populations. Using field observations and multiple regression techniques, we investigated how sexual selection acts on various male traits in three populations in which males differed in coloration. The influence of sexual selection on male coloration was then investigated in more detail using controlled experiments. Results from field observations indicate that phenotypic selection was acting on territory quality in all three populations. In two populations, selection was also acting either directly or indirectly on male coloration. Male color likely functions as an indicator of food resources to females because male color is based partly on carotenoid pigments. In controlled experiments, significantly more females from these two populations chose males with brighter colors over dull males, a result consistent with studies on carotenoid pigments in other taxa. In a third population, no evidence of sexual selection on male coloration was found in either the field study or controlled experiment. Lack of female preferences for male color in this population, in which chuckwalla densities are low and home ranges are large, may result from searching costs to females.     

The effect of vegetation cover on vigilance and foraging tactics in the fat sand rat Psammomys obesus

The combination of the visual obstruction and protection properties of vegetation is considered to be one of the most important factors determining the trade-off between vigilance and foraging in a prey species. In the Negev desert, diurnal fat sand rats construct their burrows in the ephemeral river beds ("wadis"), under dense and tall shrubs of Atriplex halimus, or on the open first fluvial terrace, covered with scattered low shrubs of Anabasis articulata. We tested the hypothesis that properties of the vegetation would affect the time budget of female sand rats. Sand rats spent more time aboveground, rested more, were less vigilant, and moved more slowly under the dense cover in the wadi than at the open terrace. No differences in the total foraging time were revealed, but foraging tactics varied between habitats: individuals in the wadi mainly fed aboveground, whereas those at the terrace mainly hoarded. Our results indicate that sand rats perceive the dense vegetation cover as good protection despite its visual obstructive nature, and that vigilance in Psammomys obesus is performed at the cost of resting rather than at the cost of foraging. Received: January 15, 2001 / Accepted: April 17, 2001     

Leishmaniasis in the Jordan Valley. V. Dispersal characteristics of the sandfly Phlebotomus papatasi

Several characteristics of dispersing and non-dispersing Phlebotomus papatasi (Scopoli) were quantified and compared. The majority of dispersing sandflies, trapped crossing fallow fields, were females (68.5% v. 51.1%); of the dispersing females, 55.4% were parous, 48.1% were inseminated and 11.6% were gravid. In the population of sandflies sampled exiting from burrows of the sand rat Psammomys obesus Cretschmar, these categories, respectively, represented 39%, 90% and 26% of the females examined. Leishmania promastigotes were found in 9% of females exiting from P. obesus burrows, and in 2.7% of the dispersing females. The anthrone test established that the reason for activity of gravid females is sugar feeding. These females do not disperse and are suitable targets for future control measures.     

Effect of seed extracts of <Emphasis Type="Italic">Withania somnifera,Croton tiglium</Emphasis> and <Emphasis Type="Italic">Hygrophila auriculata</Emphasis> on behavior and physiology of <Emphasis Type="Italic">Odontotermes obesus</Emphasis> (Isoptera,Termitidae)

In addition to antibiotic properties, medicinal plants are important sources of chemicals with potential application as pesticides. The present study deals with antitermitic potential of seed extracts of Withania somnifera (Indian ginseng), Croton tiglium (jamalgoota) and Hygrophila auriculata (talimkhana). The seed extracts caused changes in tunneling behaviour, number of bacterial colonies in hindgut and activities of enzymes in midgut of Odontotermes obesus. C. tiglium showed the lowest LT₅₀ (12.85 and 2.65 h) among the three seed extracts at concentrations of 50% (half dilution of the extract) and 100% (extract without dilution), respectively. There was no tunneling in soil treated with 100% concentration of seed extracts of W. somnifera and C. tiglium. Numbers of bacterial colonies in the gut of termites from soils treated with 50% and 100% concentrations of the three plants did not differ significantly, but they differed from those in termites from untreated soil. At 50% concentrations of seed extracts of the tested plants, the difference in hindgut enzyme activities was not obvious, however, at 100% concentrations the enzyme activities in the termites from soils treated with seed extracts significantly differed from controls and differences were also recorded between the plants.     

Leptin and the Development of Obesity and Diabetes in Psammomys obesus

COLLIER, GREG R, KEN WALDER, PAUL LEWAN DOWSJCI, ANDREW SANIGORSKI, PAUL ZIMMET. Leptin and the development of obesity and diabetes in Psammomys obesus. The recently discovered ob gene and its circulating product, leptin, may be critical factors in the control of energy balance. Recent studies in ob/ob mice, which lack circulating leptin, have shown dramatic reductions in food intake and bodyweight after leptin treatment. In addition, studies in both humans with obesity and animal models of obesity have demonstrated hyperleptinemia. Here, we report a longitudinal study examining changes in circulating leptin during the development of obesity and diabetes in Psammomys obesus. Over the 8 weeks of the study, lean animals increased their bodyweight by 154% and leptin levels remained essentially unchanged. In contrast, animals that developed obesity (223 % increase in bodyweight), hyperglycemia, and hyperinsulinemia also developed hyperleptinemia between 4 weeks and 8 weeks of age. These results demonstrate that the development of hyperleptinemia is associated with the development of obesity and subsequent metabolic abnormalities.     

Incrimination of Phiebotomus papatasi as vector of Leishmania major in the southern Jordan Valley

he status of sandflies as vectors of cutaneous leishmaniasis in the southern Jordan Valley was investigated during 1992. Sandflies were collected from domestic habitats and from burrows of Psammomys obesus . Of 686 Phlebotomus papatasi females collected from burrows, fourteen harboured promastigotes in their guts. On the other hand, none of 1446 P.papatasi females collected from domestic habitats were found infected. The highest infection rate (5.5%) was recorded in November at the end of the sandfly season. Six leishmanial stocks isolated from P.papatasi females were typed by cellulose acetate electrophoresis using the six enzymes G6PDH, 6PGDH, PGI, PGM, FK and ME. Five of the leishmanial stocks were identical to a Leishmania major reference strain (MHOMISU/73/5-ASKH). The sixth isolate was a 6PGDH variant of L.major . These findings present the first direct evidence of the role of P.papatasi as a vector of L.major in Jordan.