Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.     

Gone with the wind: Seasonal distribution and habitat use by the reef manta ray (Mobula alfredi) in the Maldives,implications for conservation

1. Reef manta rays (Mobula alfredi) are one of the ocean's largest and most charismatic species. Pressure from targeted and bycatch fisheries coupled with their conservative life‐history traits including slow growth, late maturity, and low fecundity has led to catastrophic declines of the global population. The species is now listed as Vulnerable to Extinction on IUCN Red List of Threatened Species.
2. The global M. alfredi population is widely distributed in highly fragmented subpopulations. The Maldives supports the world's largest known subpopulation that undergoes seasonal migrations which are thought to be linked to peaks in ocean productivity induced by the South Asian Monsoon. Although the species is protected from targeted fisheries in the region, increasing pressures from habitat degradation and unsustainable tourism activities mean their effective conservation relies upon knowledge of the species' habitat use, seasonal distribution, and the environmental influences on such movements.
3. Photo‐ID sighting records collected between 2005 and 2017 were used to identify key aggregation sites throughout the archipelago, and multiple linear regression and prediction analysis identified the environmental variables affecting variations in the intra‐annual sighting frequency of M. alfredi.
4. Mobula alfredi were recorded at 273 different sites, 48 of which, with >100 sightings at each, were classified as key areas of habitat use. South‐west monsoon winds and chlorophyll‐a concentration predominantly affected the monthly percentage of M. alfredi sighted on the down‐current side of the atolls.
5. In a country where climate change and touristic pressure are increasingly threatening this species and its habitat, the identification of key areas of habitat use and temporal changes in the use of these sites highlight the areas that should be prioritized for protection enabling more effective conservation management.

     

Effects of suboptimal low temperature on yield,fruit appearance and quality in muskmelon (Cucumis melo L.) cultivars

Summary

The effects of suboptimal low temperature were investigated on an array of yield, fruit appearance and fruit quality characters in 23 cultivars of melon, Cucumis melo L. The cultivars were grown in two temperature regimes: (I) a heated greenhouse (T1) with temperatures similar to those used in commercial cultivation in the winter in Israel; and (ii) an unheated greenhouse (T2) that had significantly lower night temperatures than T1. Significant differences were found among the cultivars in all characters. Plants from T2 showed an extended fruiting period, more fruits and higher total yield but smaller and lighter fruits than in T1. Fruits from T2 also had significantly more netting and higher amounts of total soluble sugars (TSS), sucrose and fructose than fruits from T1. Hybrid cultivars showed significantly higher electrical conductivity (EC), pH, acidity, TSS, sucrose, fructose and total sugars than open pollinated cultivars. Three trends were found among the characters in respect to the performance of the cultivars between T1 and T2: (a) most cultivars had significantly higher amounts in T2 than T1 (fruit/plant, yield/plant and fructose); (b) only cultivars with amounts below the pooled mean in T1 had higher amounts in T2 (percent dry weight, sucrose, TSS and total sugars); (c) no trend was found between T1 and T2 (mean fruit weight, pH, EC, glucose). Suboptimal low temperatures, when used appropriately, can aid in improving fruit quality.     

Fishing groupers towards extinction: a global assessment of threats and extinction risks in a billion dollar fishery

Groupers are a valuable fishery resource of reef ecosystems and are among those species most vulnerable to fishing pressure because of life history characteristics including longevity, late sexual maturation and aggregation spawning. Despite their economic importance, few grouper fisheries are regularly monitored or managed at the species level, and many are reported to be undergoing declines. To identify major threats to groupers, the International Union for Conservation of Nature (IUCN) Red List criteria were applied to all 163 species. Red List assessments show that 20 species (12%) risk extinction if current trends continue, and an additional 22 species (13%) are considered to be Near Threatened. The Caribbean Sea, coastal Brazil and Southeast Asia contain a disproportionate number of Threatened species, while numerous poorly documented and Near Threatened species occur in many regions. In all, 30% of all species are considered to be Data Deficient. Given that the major threat is overfishing, accompanied by a general absence and/or poor application of fishery management, the prognosis for restoration and successful conservation of Threatened species is poor. We believe that few refuges remain for recovery and that key biological processes (e.g. spawning aggregations) continue to be compromised by uncontrolled fishing. Mariculture, through hatchery‐rearing, increases production of a few species and contributes to satisfying high market demand, but many such operations depend heavily on wild‐caught juveniles with resultant growth and recruitment overfishing. Better management of fishing and other conservation efforts are urgently needed, and we provide examples of possible actions and constraints.     

Reproductive ecology of Pinus nigra in an invasive population: individual- and population-level variation in seed production and timing of seed release

? Context

The details of fecundity, such as its distribution and timing, can have important consequences for forest dynamics.

? Aims

We detail two aspects of the reproductive ecology of an exotic population of Pinus nigra in New Zealand. We compare our findings with those reported for P. nigra in southern France and Britain.

? Methods

We describe variation in fecundity, both within the population and through time, and relate seed release to climatic conditions.

? Results

On average, trees entered reproduction earlier than reported in European studies. Although the mean number of cones per tree varied through time, the distribution of cone production among trees was consistently best described using a negative binomial or mixed gamma-exponential distribution. Both distributions are right skewed and trees maintained fecundity hierarchies over time, suggesting that some trees in the population have much higher lifetime reproduction than others. We found that trees released significantly more seeds when conditions were dry and windy, potentially increasing the proportion of seeds that disperse long distances.

? Conclusions

Right-skewed fecundity distributions have the potential to slow spread rates, while preferentially releasing seeds in dry windy conditions is likely to increase spread rates. The net effect of these processes is an open question.     

Soil properties and tree growth along an altitudinal transect in Ecuadorian tropical montane forest

In tropical montane forests, soil properties change with increasing altitude, and tree‐growth decreases. In a tropical montane forest in Ecuador, we determined soil and tree properties along an altitudinal transect between 1960 and 2450 m asl. In different vegetation units, all horizons of three replicate profiles at each of eight sites were sampled and height, basal area, and diameter growth of trees were recorded. We determined pH and total concentrations of Al, C, Ca, K, Mg, Mn, N, Na, P, S, Zn, polyphenols, and lignin in all soil horizons and in the mineral soil additionally the effective cation‐exchange capacity (CEC). The soils were Cambisols, Planosols, and Histosols. The concentrations of Mg, Mn, N, P, and S in the O horizons and of Al, C, and all nutrients except Ca in the A horizons correlated significantly negatively with altitude. The C : N, C : P, and C : S ratios increased, and the lignin concentrations decreased in O and A horizons with increasing altitude. Forest stature, tree basal area, and tree growth decreased with altitude. An ANOVA analysis indicated that macronutrients (e.g., N, P, Ca) and micronutrients (e.g., Mn) in the O layer and in the soil mineral A horizon were correlated with tree growth. Furthermore, lignin concentrations in the O layer and the C : N ratio in soil affected tree growth. These effects were consistent, even if the effect of altitude was accounted for in a hierarchical statistical model. This suggests a contribution of nutrient deficiencies to reduced tree growth possibly caused by reduced organic‐matter turnover at higher altitudes.