The efficiency of mitochondrial DNA markers in constructing genetic relationship among Oryx species

To date, only parts of mitochondrial DNA from cytochrome b, 12S rRNA, 16S rRNA and non-coding Dloop had been sequenced for different species of Oryx. Discrepancy in the genetic relationship among Oryx species was previously revealed when combinations of these sequences were analyzed. In the present study, various combinations of these data sets and different sampling sizes of the closely related tribes of the family Bovidae were manipulated using bioinformatics. These data were used to provide the genetic kinship among different Oryx species. The complete cytochrome b gene sequence was also used alone for the same purpose after excluding the third position of its codons. Using Bayesian (BA), maximum-parsimony (MP), maximum-likelihood (ML) and neighbor-joining (NJ) analytical methods, a single relationship was obtained in which the different Oryx species were sisters and the Arabian Oryx was the oldest. Our results demonstrated that, the molecular markers and the samples size were more robust and efficient in building the relationship than computational methods.Key words: Conservation, endangered species, Oryx, mitochondrial DNA (mtDNA) markers

Environmental proxies of antigen exposure explain variation in immune investment better than indices of pace of life.

Investment in immune defences is predicted to covary with a variety of ecologically and evolutionarily relevant axes, with pace of life and environmental antigen exposure being two examples. These axes may themselves covary directly or inversely, and such relationships can lead to conflicting predictions regarding immune investment. If pace of life shapes immune investment then, following life history theory, slow-living, arid zone and tropical species should invest more in immunity than fast-living temperate species. Alternatively, if antigen exposure drives immune investment, then species in antigen-rich tropical and temperate environments are predicted to exhibit higher immune indices than species from antigen-poor arid locations. To test these contrasting predictions we investigated how variation in pace of life and antigen exposure influence immune investment in related lark species (Alaudidae) with differing life histories and predicted risks of exposure to environmental microbes and parasites. We used clutch size and total number of eggs laid per year as indicators of pace of life, and aridity, and the climatic variables that influence aridity, as correlates of antigen abundance. We quantified immune investment by measuring four indices of innate immunity. Pace of life explained little of the variation in immune investment, and only one immune measure correlated significantly with pace of life, but not in the predicted direction. Conversely, aridity, our proxy for environmental antigen exposure, was predictive of immune investment, and larks in more mesic environments had higher immune indices than those living in arid, low-risk locations. Our study suggests that abiotic environmental variables with strong ties to environmental antigen exposure can be important correlates of immunological variation.Financial support came from the Schure-Beijerinck-Poppings Fonds (to NPCH and AH), BirdLife Netherlands (to BIT), NSF grant IBN 0212587 (to JBW), and VENI and VIDI grants from the Netherlands Organisation for Scientific Research (to KDM and BIT).This is the accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007%2Fs00442-014-3136-y

Ecology of the lappet-faced vulture Torgos tracheliotus in Saudi Arabia

1- Food availability for the lappet-faced vultures was examined between 1993 and 1995. Several methods were used to estimate the number of ungulates in the area, such as aerial surveys, ground counts, questionnaires and the Ministry of Agriculture reports. The density of domestic livestock was estimated as 2.66 LSU's (LSU= Livestock Unit, one LSU equal one camel or ten sheep or ten goats). Based in studies in northern Saudi Arabia the expected carrying capacity of livestock in the study area is 0.3. This mean that the number of domestic livestock outside the reserve was nine times the predicted carrying capacity of the study area. A high mortality rate among the domestic herds provided a reliable food source for all the scavenging species in the study area. The wild ungulates were also examined, but their number was low, and their distribution was restricted to inside the reserve. There was no evidence of food shortage for the vulture population. 2- The pellets analysed from the lappet-faced vulture roost and nests sites at Mahazat as- Sayd reserve showed that they were heavily reliant on domestic ungulate carcasses. The birds might occasionally feed on live prey such as rodents and spiny-tailed lizards, but this was not a major source of food. However, there was no evidence of any seasonal variation in the type of carcasses used by the lappet-faced vultures. 3- The way in which different scavenging species located and exploited the carcasses was examined. Observations at carcasses placed in random sites showed that the brown-necked raven was the first species to arrive to the carcass. The lappet-faced vulture was the last species to find the carcass. They started foraging singly or in pairs and they moved in different directions, which would allow them to form a network in the sky and search effectively for food over a large areas. The number of vultures increased rapidly once the carcass had been discovered. The mammalian scavengers found few of the carcasses and were nocturnal. 4- The competition over the food supply was determined by measuring the amount of food removed by each of the scavenging species. Observations at the carcasses showed that the amount of food utilised by the avian scavengers was 30.4%, most of which was consumed by the lappet-faced vultures. The bill structures of the smaller scavenging birds are not adapted for tearing the skin of carcasses. However, different species of scavengers attended the carcasses at different times of the day. The small species fed in the early morning and late evening and the lappet-faced vulture concentrated on feeding in the midday. Therefore, there was no evidence that competition at the food sources had any effect on the lappet-faced vulture population. 5- The most important factor influencing the timing of breeding is probably the climate. Eggs are laid in winter to minimise the thermal stress on both the egg and the incubating adults. The number of active nests inside the reserve was far higher than outside the reserve, because the reserve provides an undisturbed area for breeding. Human disturbance is probably the main factor affecting the vulture population in the study area. 6- Observations at the nest suggested that the lappet-faced female may incubate the egg more than the male. The critical time in the lifetime of the lappet-faced vulture was probably the post-fledging dependence period, which could last up to 4-5 months. The majority of birds which died were found in this period. 7- During the first six months after fledging the distance covered by the fledging nestling increased significantly with age. There was a seasonal cycle of the lappet-faced vultures abundance at the reserve. The results from the movements of birds fitted with the satellite transmitters supported this cycle and suggested that some birds engage in short-distance migration within Saudi Arabia

DNA Barcodes of Arabian Partridge and Philby’s Rock Partridge: Implications for Phylogeny and Species Identification

Recently, DNA barcoding based on mitochondrial cytochrome c oxidase subunit I (COI) has gained wide attention because of simplicity and robustness of these barcodes for species identification including birds. The current GenBank records show the COI barcodes of only one species, chukar partridge (Alectoris chukar), of the Alectoris genus. In this study, we sequenced the 694 bp segment of COI gene of the two species including, Arabian partridge (Alectoris melanocephala) and Philby’s rock partridge (Alectoris philbyi) of the same genus. We also compared these sequences with earlier published barcodes of chukar partridge. The pair-wise sequence comparison showed a total of 53 variable sites across all the 9 sequences from 3 species. Within-species variable sites were found to be 4 (Alectoris chukar), 0 (Alectoris philbyi) and 3 (Alectoris melanocephala). The genetic distances among the 9 individuals varied from 0.000 to 0.056. Phylogenetic analysis using COI barcodes clearly discriminated the 3 species, while Alectoris chukar was found to be more closely related to Alectoris philbyi. Similar differentiation was also observed using 1155 bp mitochondrial control region (CR) sequences suggesting the efficiency of COI gene for phylogenetic reconstruction and interspecific identification. This is the first study reporting the barcodes of Arabian partridge and Philby’s rock partridge

Parental cooperation in an extreme hot environment: natural behaviour and experimental evidence

One of the most apparent examples of cooperation between unrelated individuals is biparental care whereby the male and the female parent share the rearing of the offspring. Theoretical models of care predict that selection should favour biparental care if it substantially improves the survival of the offspring. Although various ecological factors have been proposed to necessitate biparental care, experimental evidence is scant given the challenges of manipulating ecological factors in the natural habitat of animals. We carried out one such experiment in a small shorebird, the Kentish plover, Charadrius alexandrinus, that breeds in an extreme desert environment. Nest cover and thus exposure to solar radiation vary between nests, and we show that parents at exposed nests spent more time incubating than those at nests shaded by a bush (covered nests). Experimental removal and supplementation of nest cover gave results consistent with the observational data; at experimentally exposed nests both males and females increased incubation effort and relieved each other more frequently whereas at experimentally covered nests we observed the opposite. We conclude that exposure to extreme solar radiation influences biparental care and this necessitates parental cooperation in the Kentish plover. Furthermore, since parental care often coevolves with mating strategies, we conjecture that where the environment puts less pressure on the parents and provides the opportunity for reduced care, both mating systems and parental care can diversify over evolutionary time. (C) 2011 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved

Modelling the distribution of wetland birds on the Red Sea coast in the Kingdom of Saudi Arabia

Species distribution modelling is useful for addressing knowledge gaps for poorly studied geographical areas by identifying potentially suitable habitats for species across landscapes. This study was undertaken to identify areas containing wetland habitats to support actions aimed at the conservation of wetland bird species on the Red Sea coast of the Kingdom of Saudi Arabia (KSA). We used a maximum entropy approach to build habitat suitability models for 22 wetland bird species (gulls, shorebirds, and terns). Ten variables relating to topography, habitat, latitude, coast complexity, man-made structures, and human settlements were used to produce individual habitat suitability models for each of the bird species. The areas under the curve (AUC) for the final model were 0.9013 and 0.879 for the training and testing data, respectively, and the jackknife analyses suggested that the models generally performed well. Using the modelled distributions of the 22 species along the Red Sea coast, the analysis suggested 17 core areas where the habitat and landscape configuration were suitable for supporting high species richness. Of these 17 sites, one is already protected, and there is a need to protect the remaining sites. The use of these models to inform conservation strategies in the Red Sea region of the KSA is discussed

Use of remote sensing to identify suitable breeding habitat for the Kentish Plover and estimate population size along the western coast of Saudi Arabia

he identification of the environmental parameters affecting species’ habitat preferences is a key to understanding the relationships between habitat features and species’ distributions. This understanding provides the evidence base upon which to formulate guidelines for managing populations. We used distribution modelling to quantify habitat relationships and to estimate the population size during the breeding season of the Kentish Plover Charadrius alexandrinus, a poorly known species on the western coast of Saudi Arabia. We used a Generalised Linear Model (GLM) with four habitat variables derived from satellite data: elevation, distance to settlements, vegetation cover and soil moisture to produce a habitat suitability model. Validation of this model using a receiver operating characteristic plot suggests that it is at least 80% accurate in predicting suitable sites. We then used our estimate of total area of suitable habitat above a critical suitability threshold and data on Kentish Plover density, to estimate the total population size to be 9,955±1,388 individuals. Based on our model we recommend sites for potential protected areas to be established. Finally, we believe that our modelling approach can provide inputs for conservation planning and long-term population monitoring of Kentish Plover and other shorebirds in the region. We argue that conservation of Kentish Plover habitat will not only protect this species, but will benefit other species, particularly those with similar habitat requirements

Are antimicrobial defences in bird eggs related to climatic conditions associated with risk of trans-shell microbial infection?

INTRODUCTION: All bird eggs are exposed to microbes in the environment, which if transmitted to the developing embryo, could cause hatching failure. However, the risk of trans-shell infection varies with environmental conditions and is higher for eggs laid in wetter environments. This might relate to generally higher microbial abundances and diversity in more humid environments, including on the surface of eggshells, as well as the need for moisture to facilitate microbial penetration of the eggshell. To protect against microbial infection, the albumen of avian eggs contains antimicrobial proteins, including lysozyme and ovotransferrin. We tested whether lysozyme and ovotransferrin activities varied in eggs of larks (Alaudidae) living along an arid-mesic gradient of environmental aridity, which we used as a proxy for risk of trans-shell infection. RESULTS: Contrary to expectations, lysozyme activity was highest in eggs from hotter, more arid locations, where we predicted the risk of trans-shell infection would be lower. Ovotransferrin concentrations did not vary with climatic factors. Temperature was a much better predictor of antimicrobial protein activity than precipitation, a result inconsistent with studies stressing the importance of moisture for trans-shell infection. CONCLUSIONS: Our study raises interesting questions about the links between temperature and lysozyme activity in eggs, but we find no support for the hypothesis that antimicrobial protein deposition is higher in eggs laid in wetter environments

Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)

In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies