Reduction of species identification errors in surveys of marine wildlife abundance utilising unoccupied aerial vehicles (UAVs)

The advent of unoccupied aerial vehicles (UAVs) has enhanced our capacity to survey wildlife abundance, yet new protocols are still required for collecting, processing, and analysing image-type observations. This paper presents a methodological approach to produce informative priors on species misidentification probabilities based on independent experiments. We performed focal follows of known dolphin species and distributed our imagery amongst 13 trained observers. Then, we investigated the effects of reviewer-related variables and image attributes on the accuracy of species identification and level of certainty in observations. In addition, we assessed the number of reviewers required to produce reliable identification using an agreement-based framework compared with the majority rule approach. Among-reviewer variation was an important predictor of identification accuracy, regardless of previous experience. Image resolution and sea state exhibited the most pronounced effects on the proportion of correct identifications and the reviewers’ mean level of confidence. Agreement-based identification resulted in substantial data losses but retained a broader range of image resolutions and sea states than the majority rule approach and produced considerably higher accuracy. Our findings suggest a strong dependency on reviewer-related variables and image attributes, which, unless considered, may compromise identification accuracy and produce unreliable estimators of abundance

New Data on the Origin of Modern Man in the Levant

Anthropolog

Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns

Over the past decade, fluorescent proteins (FPs) have become ubiquitous tools in biological research. Yet, little is known about the natural function or evolution of this superfamily of proteins that originate from marine organisms. Using molecular phylogenetic analyses of 102 naturally occurring cyan fluorescent proteins, green fluorescent proteins, red fluorescent proteins, as well as the nonfluorescent (purple-blue) protein sequences (including new FPs from Lizard Island, Australia) derived from organisms with known geographic origin, we show that FPs consist of two distinct and novel regions that have evolved under opposite and sharply divergent evolutionary pressures. A central region is highly conserved, and although it contains the residues that form the chromophore, its evolution does not track with fluorescent color and evolves independently from the rest of the protein. By contrast, the regions enclosing this central region are under strong positive selection pressure to vary its sequence and yet segregate well with fluorescence color emission. We did not find a significant correlation between geographic location of the organism from which the FP was isolated and molecular evolution of the protein. These results define for the first time two distinct regions based on evolution for this highly compact protein. The findings have implications for more sophisticated bioengineering of this molecule as well as studies directed toward understanding the natural function of FPs

Climate change promotes parasitism in a coral symbiosis.

Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with the dinoflagellate alga, Symbiodinium. Together, the coral holobiont has dominated oligotrophic tropical marine habitats. However, warming destabilizes this association and reduces coral fitness. It has been theorized that, when reefs become warm and eutrophic, mutualistic Symbiodinium sequester more resources for their own growth, thus parasitizing their hosts of nutrition. Here, we tested the hypothesis that sub-bleaching temperature and excess nitrogen promotes symbiont parasitism by measuring respiration (costs) and the assimilation and translocation of both carbon (energy) and nitrogen (growth; both benefits) within Orbicella faveolata hosting one of two Symbiodinium phylotypes using a dual stable isotope tracer incubation at ambient (26 °C) and sub-bleaching (31 °C) temperatures under elevated nitrate. Warming to 31 °C reduced holobiont net primary productivity (NPP) by 60% due to increased respiration which decreased host %carbon by 15% with no apparent cost to the symbiont. Concurrently, Symbiodinium carbon and nitrogen assimilation increased by 14 and 32%, respectively while increasing their mitotic index by 15%, whereas hosts did not gain a proportional increase in translocated photosynthates. We conclude that the disparity in benefits and costs to both partners is evidence of symbiont parasitism in the coral symbiosis and has major implications for the resilience of coral reefs under threat of global change

The IGF1 small dog haplotype is derived from Middle Eastern grey wolves

<p>Abstract</p> <p>Background</p> <p>A selective sweep containing the insulin-like growth factor 1 (<it>IGF1</it>) gene is associated with size variation in domestic dogs. Intron 2 of <it>IGF1 </it>contains a SINE element and single nucleotide polymorphism (SNP) found in all small dog breeds that is almost entirely absent from large breeds. In this study, we surveyed a large sample of grey wolf populations to better understand the ancestral pattern of variation at <it>IGF1 </it>with a particular focus on the distribution of the small dog haplotype and its relationship to the origin of the dog.</p> <p>Results</p> <p>We present DNA sequence data that confirms the absence of the derived small SNP allele in the intron 2 region of <it>IGF1 </it>in a large sample of grey wolves and further establishes the absence of a small dog associated SINE element in all wild canids and most large dog breeds. Grey wolf haplotypes from the Middle East have higher nucleotide diversity suggesting an origin there. Additionally, PCA and phylogenetic analyses suggests a closer kinship of the small domestic dog <it>IGF1 </it>haplotype with those from Middle Eastern grey wolves.</p> <p>Conclusions</p> <p>The absence of both the SINE element and SNP allele in grey wolves suggests that the mutation for small body size post-dates the domestication of dogs. However, because all small dogs possess these diagnostic mutations, the mutations likely arose early in the history of domestic dogs. Our results show that the small dog haplotype is closely related to those in Middle Eastern wolves and is consistent with an ancient origin of the small dog haplotype there. Thus, in concordance with past archeological studies, our molecular analysis is consistent with the early evolution of small size in dogs from the Middle East.</p> <p>See associated opinion by Driscoll and Macdonald: <url>http://jbiol.com/content/9/2/10</url></p

The Red Sea, Coastal Landscapes, and Hominin Dispersals

This chapter provides a critical assessment of environment, landscape and resources in the Red Sea region over the past five million years in relation to archaeological evidence of hominin settlement, and of current hypotheses about the role of the region as a pathway or obstacle to population dispersals between Africa and Asia and the possible significance of coastal colonization. The discussion assesses the impact of factors such as topography and the distribution of resources on land and on the seacoast, taking account of geographical variation and changes in geology, sea levels and palaeoclimate. The merits of northern and southern routes of movement at either end of the Red Sea are compared. All the evidence indicates that there has been no land connection at the southern end since the beginning of the Pliocene period, but that short sea crossings would have been possible at lowest sea-level stands with little or no technical aids. More important than the possibilities of crossing the southern channel is the nature of the resources available in the adjacent coastal zones. There were many climatic episodes wetter than today, and during these periods water draining from the Arabian escarpment provided productive conditions for large mammals and human populations in coastal regions and eastwards into the desert. During drier episodes the coastal region would have provided important refugia both in upland areas and on the emerged shelves exposed by lowered sea level, especially in the southern sector and on both sides of the Red Sea. Marine resources may have offered an added advantage in coastal areas, but evidence for their exploitation is very limited, and their role has been over-exaggerated in hypotheses of coastal colonization

A New Horned Crocodile from the Plio-Pleistocene Hominid Sites at Olduvai Gorge, Tanzania

BACKGROUND: The fossil record reveals surprising crocodile diversity in the Neogene of Africa, but relationships with their living relatives and the biogeographic origins of the modern African crocodylian fauna are poorly understood. A Plio-Pleistocene crocodile from Olduvai Gorge, Tanzania, represents a new extinct species and shows that high crocodylian diversity in Africa persisted after the Miocene. It had prominent triangular "horns" over the ears and a relatively deep snout, these resemble those of the recently extinct Malagasy crocodile Voay robustus, but the new species lacks features found among osteolaemines and shares derived similarities with living species of Crocodylus. METHODOLOGY/PRINCIPAL FINDINGS: The holotype consists of a partial skull and skeleton and was collected on the surface between two tuffs dated to approximately 1.84 million years (Ma), in the same interval near the type localities for the hominids Homo habilis and Australopithecus boisei. It was compared with previously-collected material from Olduvai Gorge referable to the same species. Phylogenetic analysis places the new form within or adjacent to crown Crocodylus. CONCLUSIONS/SIGNIFICANCE: The new crocodile species was the largest predator encountered by our ancestors at Olduvai Gorge, as indicated by hominid specimens preserving crocodile bite marks from these sites. The new species also reinforces the emerging view of high crocodylian diversity throughout the Neogene, and it represents one of the few extinct species referable to crown genus Crocodylus

Особенности полиморфизма генов вирулентности Helicobacter pylori и генов ИЛ-1 при язвенной болезни желудка и двенадцатиперстной кишки, ассоциированной с Helicobacter pylori

The prevalence of H.pylori virulence genes (iceA, cagA, babA2, vacA) as well as the distribution of the IL-1 genes was studied in patients with H.pylori-associated gastric and duodenal ulcer disease. VacA s1/m2 iceA1 cagA+ и vacA s1/m2 iceA1 cagA+ babA2 genotypes of H. pylori were shown to be prevalent in the clinic isolates. Four patients were found to be infected with Ureaplasma urealyticum. The combination of the IL‑1B ‑511*Т / IL‑1B +3954*C / IL-1RN*2 alleles was shown to be prevalent among the patients with gastric and duodenal ulcer disease. The correlation between the H. pylori genotypes, the IL-1 genes and the peculiarities of ulcer disease was not found.Исследовали особенности распределения генов вирулентности (iceA, cagA, babA2, vacA) и генов ИЛ-1 в клинических изолятах Helicobacter pylori (H.p.), полученных от пациентов с эндоскопически подтвержденными диагнозами язвенной болезни двенадцатиперстной кишки (ЯБД) и язвенной болезни желудка (ЯБЖ). Обнаружено, что в биоптатах превалируют штаммы H.p. с генотипом vacA s1/m2 iceA1 cagA+ и vacA s1/m2 iceA1 cagA+ babA2. При этом у больных ЯБЖ и ЯБД наиболее часто встречается комбинация аллелей IL‑1B‑511*Т/IL‑1B +3954*C/IL-1RN*2. У 4 пациентов в биоптатах обнаружены микоплазмы (Ureaplasma urealyticum). Связь между разновидностью комбинации генов вирулентности H.p., генов ИЛ-1 и особенностью течения язвенной болезни не установлена

A Unique Human-Fox Burial from a Pre-Natufian Cemetery in the Levant (Jordan)

New human burials from northern Jordan provide important insights into the appearance of cemeteries and the nature of human-animal relationships within mortuary contexts during the Epipalaeolithic period (c. 23,000–11,600 cal BP) in the Levant, reinforcing a socio-ideological relationship that goes beyond predator-prey. Previous work suggests that archaeological features indicative of social complexity occur suddenly during the latest Epipalaeolithic phase, the Natufian (c. 14,500–11,600 cal BP). These features include sedentism, cemeteries, architecture, food production, including animal domestication, and burials with elaborate mortuary treatments. Our findings from the pre-Natufian (Middle Epipalaeolithic) cemetery of ‘Uyun al-Hammam demonstrate that joint human-animal mortuary practices appear earlier in the Epipalaeolithic. We describe the earliest human-fox burial in the Near East, where the remains of dogs have been found associated with human burials at a number of Natufian sites. This is the first time that a fox has been documented in association with human interments pre-dating the Natufian and with a particular suite of grave goods. Analysis of the human and animal bones and their associated artefacts provides critical data on the nature and timing of these newly-developing relationships between people and animals prior to the appearance of domesticated dogs in the Natufian