Nematodes (Longidorus sp. andTylenchorhynchus microphasmis loof) in growth and nodulation of sea buckthorn (Hippophaë rhamnoides L.)

Summary Hippophaë rhamnoides seedlings were grown in sterilized and unsterilized soil from a decliningH. rhamnoides scrub, to which different numbers ofLongidorus sp. andTylenchorhynchus microphasmis were added. In sterilized and unsterilized soil, retardation of growth, content of dry matter in the shoots, and incidence of deformed short lateral roots of test plants were positively correlated with counts of both nematode species. Nitrogen content in the shoots, nodulation on the roots of test plants and increase increase in nematodes were negatively correlated with the initial number of both nematode species in sterilized soil. In unsterilized soil, an unknown biotic factor was present that reduces growth ofH. rhamnoides, nodulation and multiplication of the nematodes. This factor seems to interact with the nematodes in reducing growth ofH. rhamnoides.Deceased.     

Separation of D- and L-amino acids by ion exchange column chromatography in the form of alanyl dipeptides

Summary A method of ion exchange column chromatography was developed for the determination of D- and L-amino acids in the form of diastereomeric dipeptide. First the protein containing samples were hydrolyzed with 6 molar hydrochloric acid, then the single amino acids were separated in an LKB automated amino acid analyzer with the LKB fraction collector. Following lyophilization, the single amino acids were transformed into alanyl dipeptides with tertiary-butyloxycarbonil-L-alanine-N-hydroxy-succinimide (t-BOC-L-Ala-ONSu) active ester. The alanyl dipeptides were easily separated from one another and the initial amino acids. Determination of the D- and L-amino acids in this form is relatively accurate and reproducible but takes some time (33–38 min). Accuracy of the determination is satisfactory. The coefficient of variation amounts to 3–5%. The use of the method is suggested to laboratories having an amino acid analyzer and wish to determine D-and L-amino acids in synthetic-amino acids complements, peptides or natural materials.     

Oceanographic barriers,divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short‐finned pilot whale

Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short‐finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the “Naisa” and “Shiho” forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short‐finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short‐finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally‐distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.     

A new fourier transform approach for protein coding measure based on the format of the Z curve

MOTIVATION: At the core of most protein gene-finding algorithms are the coding measures used to make a decision on coding/non-coding. Of the protein coding measures, the Fourier measure is one of the most important. However, due to the limited length of the windows usually used, the accuracy of the measure is not satisfactory. This paper is devoted to improving the accuracy by lengthening the sequence to amplify the periodicity of 3 in the coding regions. RESULTS: A new algorithm is presented called the lengthen-shuffle Fourier transform algorithm. For the same window length, the percentage accuracy of the new algorithm is 6-7% higher than that of the ordinary Fourier transform algorithm. The resulting percentage accuracy (average of specificity and sensitivity) of the new measure is 84.9% for the window length 162 bp. AVAILABILITY: The program is available on request fromC.- T. Zhang. Contact: ctzhang@tju.edu.cn      

Phylogenetic identification and population differentiation of bottlenose dolphins (Tursiops spp.) in Melanesia,as revealed by mitochondrial DNA

The taxonomic status of many dolphin populations remains uncertain in poorly studied regions of the world's ocean. Here we attempt to clarify the phylogenetic identity of two distinct forms of bottlenose dolphins (Tursiops spp.) described in the Melanesian region of the Pacific Ocean. Mitochondrial DNA control region sequences from samples collected in New Caledonia (n = 88) and the Solomon Islands (n = 19) were compared to previously published sequences of Tursiops spp., representing four phylogenetic units currently recognized within the genus. Phylogenetic reconstructions confirm that the smaller coastal form in Melanesia belongs to the same phylogenetic unit as T. aduncus populations in the Pacific, but differs from T. aduncus in Africa, and that the larger more oceanic form belongs to the species T. truncatus. Analyses of population diversity reveal high levels of regional population structuring among the two forms, with contrasting levels of diversity. From a conservation perspective, genetic isolation of T. aduncus in the Solomon Islands raises further concern about recent impacts of the commercial, live‐capture export industry. Furthermore, the low level of mtDNA diversity in T. aduncus of New Caledonia suggests a recent population bottleneck or founder effect and isolation. This raises concerns for the conservation status of these local populations.     

Factors affecting growth and nodulation ofHippophaë rhamnoides L. ssp.Rhamnoides in soils from two successional stages of dune formation

Summary To explain the decline of Hippopha? scrub in the vegetation succession in the dunes of The Netherlands, the growth and nodulation of Hippopha? plants grown in pots, using soil from an early stage (site AH) and a post-optimum stage (site HP), were investigated. In HP-soil nodulation, yield, and the nitrogen and phosphorus content of test plants were always lower and the number of necrotic nodules and the dry matter content were always higher than in AH-soil, even after inoculation with crushed nodules and the addition of a nutrient solution. Plants in HP-soil also had darker roots, less root hairs, a higher number of short lateral roots and a higher percentage of dead roots than those in AH-soil. These characteristics of adverse growth conditions disappeared upon ignition or gamma-irradiation of HP-soil. Possible explanations of these results are discussed. The degeneration of Hippopha? scrub cannot be ascribed to the age of the plants, the absence of sufficient infective endophyte particles or to abiotic factors such as unfavourable physical (particle size) or chemical soil conditions but is caused by biotic factors. No indications were obtained that plant-pathogenic fungi and bacteria are involved. HP-soil in contrast to AH-soil, however, contained large numbers of the nematodeLongidorus sp., a species known to cause root deformations. The conclusion was that this nematode is one of the biotic factors involved in the degeneration of the Hippopha? scrub. This degeneration is due to a restriction of the root system resulting in a low phosphate uptake, a low nodulation capacity and, as a consequence, a low nitrogen content. The results demonstrate that biotic soil factors are important in influencing succession in higher plant communities.     

Assessment of the efficiency of a hand-held suction device for sampling spiders: improved density estimation or oversampling?

In the study a comparison is made between the results of two sampling procedures, both based on the application of the same hand-held suction apparatus. Sampling was aimed at spiders, and was carried out on two alfalfa fields. In the first method suction sampling was applied to an enclosure of 0.48 m². The enclosed area was sampled intensively, which was facilitated by the removal of the vegetation. The second method was a transect sampling procedure during which the suction apparatus with a 0.01 m² nozzle was applied to single unenclosed sampling points 1 m apart. A linear series of 48 such subsamples comprised a transect, thus the total area covered in a transect equalled the area of the enclosure. In the transect samples three times more spiders were caught than in the enclosures. This result was consistent on different occasions and at both fields. This basic trend was found in all spider families that were present in significant numbers in the samples. Species composition in the samples collected by the two methods was similar, and species abundance ranks were highly correlated across dates. We propose that an “edge effect” can explain higher catches in transect samples. This edge effect is caused by lateral suction at the edges, which inflated the number of animals caught in the transect application.     

Long‐range movement by Hector's dolphins provides potential genetic enhancement for critically endangered Maui's dolphin

For endangered populations with low genetic diversity, low levels of immigration could lead to genetic rescue, reducing the risk of inbreeding depression and enhancing chances of long‐term species survival. Our genetic monitoring of Maui's dolphins revealed the first contemporary dispersal of their sister subspecies, Hector's dolphin, from New Zealand's South Island into the Maui's dolphin distribution along ~300 km of the North Island's northwest coast. From 2010 to 2012, 44 individuals were sampled within the Maui's dolphin distribution, four of which were genetically identified as Hector's dolphins (two living females, one dead female, one dead male). We also report two Hector's dolphins (one dead female neonate, one living male) sampled along the North Island's southwest coast, outside the presumed range of either subspecies. Together, these records demonstrate long‐distance dispersal by Hector's dolphins (≥400 km) and the possibility of an unsampled Hector's dolphin population along the southwest coast of the North Island. Although two living Hector's dolphins were found in association with Maui's dolphins, there is currently no evidence of interbreeding between the subspecies. These results highlight the value of genetic monitoring for subspecies lacking distinctive physical appearances as such discoveries are not detected by other means, but have important conservation implications.     

A mass stranding of seven Longman's beaked whales (Indopacetus pacificus) in New Caledonia,South Pacific

Seven Longman's beaked whales (Indopacetus pacificus) stranded together in southern New Caledonia on 16 November 2013 (one adult male, two adult females, two subadult females, one calf, and one unknown). At this time, we have no evidence to suggest that this event was an “atypical” mass stranding associated with active naval sonar or other anthropogenic activities. The adult females were slightly larger (618–640 cm) than the adult male (590 cm). The length of the calf (ca. 300 cm) suggests it was less than a year old. Five of the whales were sampled for mitochondrial (mt) DNA analysis to confirm species identification. All shared the same haplotype over 680 bp of the mtDNA control region. High concentrations of Hg, Fe, Se, Zn (all in the liver), and Cd (in the kidneys) were detected. Necropsies revealed plastic debris in the stomach of two of the whales. One of these same whales had chronic gastritis while the other had acute pleurisy and also tested positive for morbillivirus. This infection may have been a major factor behind this mass stranding event.