Genetically distinct island populations of the Egyptian vulture (Neophron percnopterus)

The Egyptian vulture (Neophron percnopterus) is a species in decline throughout Europe, with the largest remaining breeding populations found in northern Spain. Iberian Peninsula populations of this species (about 1000 pairs) migrate to Africa in winter, while small populations in both the Canary and Balearic Islands (less than 40 pairs in each case) are apparently sedentary. We found that Egyptian vultures from both of these island groups were significantly differentiated from Iberian Peninsula populations (R _ST = 0.065–0.129, p = 0.000–0.007), using nine microsatellite loci isolated in a related species, the bearded vulture. The greatest degree of genetic differentiation was observed between the two island groups (R _ST = 0.279, p = 0.000). These island populations were more distinct from mainland groups than was a small sample of a well-defined separate subspecies from India (N. p. ginginianus; R _ST = 0.083–0.091, p = 0.023–0.024). This implies that these two island populations have been isolated from peninsular populations for many generations, despite the long-distance migration capabilities of the species. In constrast, populations within the Peninsula were not differentiated from one another at these microsatellite loci (R _ST = $-$0.004–0.007, p = 0.442–0.675). Introductions of Egyptian vultures from the larger northern breeding groups might therefore be appropriate in southern Spain, if necessary, but mainland birds should not be introduced to the islands if the genetic distinctiveness of these groups is to be preserved. Independent conservation plans are urgently required to protect these two island populations from extinction. This revised version was published online in July 2006 with corrections to the Cover Date.     

Isolation and characterization of 18 microsatellite loci in the Egyptian vulture (Neophron percnopterus)

We developed 18 new microsatellite loci for the endangered Egyptian vulture (Neophron percnopterus). Microsatellite loci were screened for variation in two different populations belonging to separate subspecies: the nominal N. p. percnopterus and the Canarian N. p. majorensis. Mean expected heterosygosities were respectively 0.51 and 0.46, while the mean number of alleles per locus was 4.7 and 3.9. These new markers allow further genetic studies for the endangered Canarian Egyptian Vulture.     

Rapid population declines of Egyptian vulture (Neophron percnopterus) and red-headed vulture (Sarcogyps calvus) in India

Since the early 1990s, large and rapid population declines of three species of vulture ( Gyps spp.) endemic to south Asia have occurred on the Indian subcontinent and have led to these species being listed by IUCN as critically endangered. Evidence of rates of population decline, cause of death and toxicity is consistent with these declines being caused by poisoning of vultures through the ingestion of tissues from livestock treated with the anti-inflammatory drug diclofenac. In this paper, analysis of repeated surveys in and near protected areas widely spread across India shows that populations of two other vulture species, Egyptian vulture Neophron percnopterus and red-headed vulture Sarcogyps calvus , have also declined markedly and rapidly, but probably with a later onset than Gyps vultures in the same region. The declines continued at least up to 2003. It is recommended that these two species are considered for inclusion in the IUCN Red List and for urgent remedial conservation measures. Research is needed to determine whether or not the principal cause of these declines is diclofenac poisoning and to establish population trends in other scavenging birds in the Indian subcontinent.     

Plumage colour and feather structure of the bearded vulture (Gypaetus barbatus)

The rufous colouring on the feathers of the under parts of adult bearded vultures Gypaetus barbatus , studied by scanning electron microscopy, energy-dispersive X-ray microanalysis and X-ray diffraction analysis, is caused by an external deposit of iron oxide in the ferrihydrite state. Unstained feathers, e.g. in captive birds, are pure white. The feathers of young birds have similar coatings of iron oxide to those of adults, but because the feathers are pigmented pale to dark brown (dependent on age), the rusty colour is partly or totally obscured. The intensity of the colour in adult birds varies between individuals and within individuals with time; the more worn the feathers the more iron oxide they can hold. After heavy rainfall up to 30% of adult birds can become appreciably paler. Birds take about 6 days (range–9 days) to regain normal colouring. Iron oxide accumulates mainly in the axes of shafts and barbs, barbs and barbules and barbules and hamuli, and forms blob-like deposits at the ends of barbs and barbules on the outer layers of feathers. Iron oxide is probably acquired passively when bearded vultures come into contact with deposits in caves and on ledges on cliffs. The colour is then spread by preening. Iron oxide imparts camouflage to adult birds, but also reduces wear on the outer layer of feathers, makes feathers more rigid and probably helps control ectoparasites.     

Organization and variation of the mitochondrial DNA control region in five Caprinae species

The complete mitochondrial DNA (mtDNA) control region was analyzed from five species of the subfamily Caprinae; Naemorhedus caudatus, N. goral, Capra hircus, Capricornis swinhoei, and Capricornis crispus. Among these species, the control region ranged from 1,096 to 1,212 bp in length. Our results were compatible with the scheme of three domains (ETAS, Central, and CSB) within the control region. A + T < G + C was observed in all the domains. In the Korean gorals, of the 31 variable sites in the whole control region resulting in 15 haplotypes, 27 variable sites were in the ETAS domain. We found two to three tandem repeat in all five species examined in this study, three in N. caudatus and N. goral, two in Capra hircus and C. crispus, and one in C. swinhoei, respectively. All of these repeat units include two short sections of mirror symmetry (TACAT and ATGTA). Short mirror symmetries were well-resolved among five different species, although left domain has high substitution rates. By Kimura’s two parameter method, the genetic distances between the genera Naemorhedus and Capricornis were calculated and divergence time between Naemorhedus and Capricornis may be nearly 2Myr.     

Analysis of relatedness and determination of the source of founders in the captive bearded vulture, Gypaetus barbatus, population

Genetic relatedness among founders is a vitalparameter in the management of captivepopulations as kin structure can have asignificant effect on subsequent populationstructure. Methods for inferring relatednessfrom microsatellite markers have all beendeveloped for natural populations; theirapplicability to captive populations withunknown founder origins needs thereforetesting. We used information derived from 14microsatellites in 177 individuals and Quellerand Goodnight's approach, to estimaterelatedness in the captive bearded vulturepopulation and to test the assumption ofunrelated founders. Mean relatedness of knownparent–offspring, full-sib and half-sib pairswithin the captive population were in agreementwith theoretical distributions. Pairwiserelatedness values among the founders had amean of –0.051 (SE ± 0.007) and theirdistribution did only differ marginally fromthe one found in the natural Pyreneanpopulation. A maximum likelihood approach wasused to determine the likelihood of founderpairs to be as closely related as full-sibs orparent–offspring. These results were combinedwith data from 268 bp mitochondrial DNA controlregion sequences and studbook information. Wecould exclude a close relationship among themajority of the 36 successfully reproducingfounders. Our study therefore removesmanagement concerns about hidden problems ofinbreeding and inbreeding depression. Itdemonstrates the applicability of relatednessestimates based on microsatellite allelefrequency data even in captive populations.Furthermore, we verified studbook informationon the origin of two founders from thePyrenees, and show the value of assignmenttests based on microsatellites for deducingfounder origins and their important role infuture monitoring projects.     

Breeding site selection by bearded vulture (Gypaetus barbatus) and Eurasian griffon (Gyps fulvus) in the Caucasus

Occupied and unoccupied sites of bearded vulture Gypaetus barbatus and Eurasian griffon Gyps fulvus were located in the Caucasus (mainly Georgia). Habitat variables related to nest-site characteristics, climate, terrain, human disturbance and food availability were used to construct predictive models of vulture breeding site selection by using a geographic information system (GIS), logistic regression and Bayesian statistical inference. The probability of bearded vulture occupancy of a cliff ledge that was safe from climatic adversity, human disturbance and predation was positively correlated with the following variables measured within a 20-km radius of the ledge: mean elevation, mean slope, the percentage of open areas, mean distance to roads, number of globally threatened wild goats Capra cylindricornis, C. caucasica and C. aegargus , and annual biomass of dead livestock. The probability of such a cliff ledge being occupied by Eurasian griffon was negatively correlated with annual rainfall at the ledge and positively correlated with the percentage of open areas and annual biomass of dead livestock within 20 km of the ledge. Provided that GIS coverage of the habitat variables is available, these models can be of help in various areas of the Caucasus and elsewhere to predict possible nest occurrence areas, and highlight sites where vultures may occur in the future if the population grows because of conservation or other activities.     

Parent-offspring Conflict during the Post-fledging Period in the Egyptian Vulture Neophron percnopterus (Aves,Accipitridae)

Egyptian vultures were studied during their post-fledging dependence period in northern Spain in order to detect if there were parent-offspring and sibling tensions during the transition of young to independence. The frequency of parental feedings and the frequency of movements of the parents towards their young decreased during the post-fledging period, especially in its final part. At the same time, the frequency of movements and of aggression by the young towards their parents increased. Aggression by adults to their young was not observed. Siblings disputed feedings, but there was no other evidence for sibling conflict. The results suggest that parent-offspring and sibling conflict exists and that its development is broken by the departure of young on migration. Some behavioural traits of adults (maintenance of distance from young and of intensity of nest-defence, tolerance of young during foraging trips through the home range) do not accord with parent-offspring conflict perhaps because they are related to factors other than family tension.     

Egyptian Vultures Neophron percnopterus and Ostrich Struthio camelus eggs: the origins of stone-throwing behaviour

Experiments were carried out on wild and hand-reared Egyptian Vultures to investigate the origins of the stone-throwing this species uses to break into Ostrich eggs. There was no evidence of cultural transmission for stone-throwing through copying experienced birds. A naïve captive-reared bird threw stones once an Ostrich egg had been linked with a food reward. The origins of aimed stone-throwing are probably related to the unaimed throwing of small eggs, since the actions are similar, and all tested birds strongly preferred to throw rounded or egg-like stones, rather than jagged ones, at Ostrich eggs.     

Generation of VNTRs and heteroplasmy by sequence turnover in the mitochondrial control region of two elephant seal species

We describe an unusual repetitive DNA region located in the 3′ end of the light (L)-strand in the mitochondrial control region of two elephant seal species. The array of tandem repeats shows both VNTR (variable-number tandem repeat) and sequence variation and is absent from 12 compared mammalian species, except for the occurrence in the same location of a distinct repetitive region in rabbit mtDNA and a similar repeat in the harbor seal. The sequence composition and arrangement of the repeats differ considerably between the northern elephant seal (Mirounga angustirostris) and the southern species (M. leonina) despite an estimated divergence time of 1 MY (based on an mtDNA-RNA gene and the nonrepetitive control region). Analysis of repeat sequence relationships within and between species indicate that divergence in sequence and structure of repeats has involved both slippagelike and unequal crossingover processes of turnover, generating very high levels of divergence and heteroplasmy. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

First cases of polygyny for the Bearded Vulture Gypaetus barbatus in the central Pyrenees

We report the first cases of polygyny for the Bearded Vulture Gypaetus barbatus in the central Pyrenees, Spain. Although polyandry is frequent in the study area (31.8% of all reproductive units in 2016), we only observed the occurrence of three cases of polygyny over the period 1994–2017. Polygyny in Bearded Vultures is possibly a consequence of habitat saturation.     

Sequence variation and evolution of the mitochondrial DNA control region in the musk shrew, Suncus murinus

The complete mitochondrial DNA (mtDNA) control region was cloned and sequenced in the musk shrew, Suncus murinus, Insectivora. The general aspect was similar to that found in other mammals. We have found in two locations of this region the presence of arrays of tandem repeats like those in other shrew species. One array was located in the left domain containing the termination-associated sequences (TAS) and the length of a copy was 77 bp. The other repeats were situated upstream from the recognition site for the end of H-strand replication in the right domain and were 20 bp long. The left halves of the control region containing the former repeats were sequenced and compared in several laboratory lines and wild animals from different localities, variations in copy number of repeated sequences were found both among individuals and within an individual. A comparative study of repeated sequences provides useful indication for the origin and evolution of tandem repeated sequences. Strand slippage and mispairing during replication of mtDNA with concerted manner is currently regarded as a dominant theory to account molecular mechanism for tandemly repeated sequences, and the pattern of sequence and length variation in our study supports this theory. Our results, however, suggest that the evolution of the repeated sequences containing the TAS in the musk shrew might go through the process of two steps; at the first step one complete repeated and several incomplete repeated sequences had reproduced in common ancestor of the shrew, and the second stage step-up of complete repeated sequences occurred with concerted evolution after differentiation into continental and insular groups.     

Structure and patterns of sequence variation in the mitochondrial DNA control region of the great cats

Mitochondrial DNA control region structure and variation were determined in the five species of the genus Panthera. Comparative analyses revealed two hypervariable segments, a central conserved region, and the occurrence of size and sequence heteroplasmy. As observed in the domestic cat, but not commonly seen in other animals, two repetitive sequence arrays (RS-2 with an 80-bp motif and RS-3 with a 6-10-bp motif) were identified. The 3' ends of RS-2 and RS-3 were highly conserved among species, suggesting that these motifs have different functional constraints. Control region sequences provided improved phylogenetic resolution grouping the sister taxa lion (Panthera leo) and leopard (Panthera pardus), with the jaguar (Panthera onca).     

DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys)

The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 bp in length. Our data were compatible with the proposal of three domains (extended terminal associated sequences [ETAS], central, conserved sequence blocks [CSB]) within the control region. The most conserved region in the control region was the central domain (12% of nucleotide positions variable), whereas in the ETAS and CSB domains, 22% and 40% of nucleotide positions were variable, respectively. Tandem repeats were encountered only in the ETAS domain of Clethrionomys rufocanus. This tandem repeat found in C. rufocanus was 24 bp in length and was located at the 5' end of the control region. Only two of the proposed CSB and ETAS elements appeared to be supported by our data; however, a "CSB1-like" element was also documented in the ETAS domain.     

DNA sequence variation in the mitochondrial control region of subterranean mole rats,Spalax ehrenbergi superspecies,in Israel

The complete mitochondrial control region was sequenced for 60 individuals representing different populations for each of the four species of the subterranean mole rat Spalax ehrenbergi superspecies in Israel: Spalax galili (2n = 52), S. golani (2n = 54), S. carmeli (2n = 58), and S. judaei (2n = 60). The control region of all species and populations is very similar both in length (979 to 983 bp) and in base composition. As in agreement with previous surveys on mitochondrial control regions on mammals, the mole rat control region can be divided into a central domain and two flanking domains, ETAS (extended termination associated sequences) and CSB (conserved sequence blocks). Along with the common conserved blocks found in these domains (ETAS1, ETAS2, CSB1, CSB2, and CSB3), we have also detected in all individuals an ETAS1-like and a CSB1-like element, both in the ETAS domain. The most conserved region was the central domain, followed by the CSB and ETAS domains, showing important differences in the four species analyzed. Phylogenetic analysis supported the existence of two clades. One clade contained individuals belonging to Spalax galili (2n = 52) and S. golani (2n = 54), separated in two different branches depending on the species. The other clade contained individuals belonging to S. carmeli (2n = 58) and S. judaei (2n = 60) mixed together, suggesting a more recent event of speciation. Within species we have observed a southward trend of increasing variability. These results have been explained as a consequence of the adaptation of the species to ecological factors such as aridity and temperature stresses.     

Universal primers for amplification of the complete mitochondrial control region in marine fish species

Through multiple alignment analysis of mitochondrial tRNA-Thr and tRNA-Phe sequences from 161 fishes, new universal primers specially targeting the entire mitochondrial control region were designed. This new primer set successfully amplified the expected PCR products from various kinds of marine fish species, belonging to various families, and the amplified segments were confirmed to be the control region by sequencing. These primers provide a useful tool to study the control region diversity in economically important fish species, the possible mechanism of control region evolution, and the functions of the conserved motifs in the control region.     

Polymorphism of the mitochondrial DNA control region in eight sturgeon species and development of a system for DNA-based species identification

Intraspecific and interspecific nucleotide sequence variations of the mtDNA control region (D-loop) were studied with mtDNAs isolated from tissue specimens of more than 1400 sturgeons of nine species: Russian sturgeon Acipenser gueldenstaedtii, Persian sturgeon A. persicus, Siberian sturgeon A. baerii, Amur sturgeon A. schrenkii, Fringebarbel sturgeon A. nudiventris, sterlet A. ruthenus, stellate sturgeon A. stellatus, beluga Huso huso, and kaluga H. dauricus. The results were used to analyze the interspecific variation of the mtDNA control region in the given set of species and to develop a test system of ten species-specific primers, which allowed species identification from noninvasive tissue samples, spawn, and food products of eight species. The system proved suitable for multiplex PCR. A method was developed for the first time to reliably differentiate the A. baerii mitotype and the baerii-like mitotype of A. gueldenstaedtii. It was found that, although genetically separate, A. gueldenstaedtii and A. persicus are relatively young species and have common mitochondrial haplotypes, precluding their identification via mtDNA analysis alone. To develop a system for species identification of A. gueldenstaedtii and A. persicus, it is necessary to study the polymorphism of nuclear markers.     

Sequence variation in the guillemot (Alcidae: Cepphus) mitochondrial control region and its nuclear homolog

We describe sequence variation in the mitochondrial control region and its nuclear homolog in three species and seven subspecies of guillemots (Cepphus spp.). Nuclear homologs of the 5' end of the control region were found in all individuals. Nuclear sequences were approximately 50% divergent from their mitochondrial counterparts and formed a distinct phylogenetic clade; the mitochondrial-nuclear introgression event must have predated the radiation of Cepphus. As in other vertebrates, the guillemot control region has a relatively conserved central block flanked by hypervariable 5' and 3' ends. Mean pairwise interspecific divergence values among control regions were lower than those in other birds. All individuals were heteroplasmic for the number of simple tandem nucleotide repeats (A(n)C) at the 3' end of the control region. Phylogenetic analyses suggest that black guillemots are basal to pigeon and spectacled guillemots, but evolutionary relationships among subspecies remain unresolved, possibly due to incomplete lineage sorting. Describing molecular variation in nuclear homologs of mitochondrial genes is of general interest in phylogenetics because, if undetected, the homologs may confound interpretations of mitochondrial phylogenies.      

利用线粒体DNA控制区序列分析细鳞鲑种群的遗传结构

细鳞鲑(Brachymystaxlenok)是我国重要的经济鱼类,由于过度捕捞、环境污染及其他因素的影响,其种群已处于濒危状态。研究细鳞鲑种群的遗传结构对于探讨这一物种的形成与演化及其有效保护等问题具有十分重要的意义。本文测定了我国东部水系的细鳞鲑7个种群71个个体的线粒体DNA控制区序列片段(835bp),发现43个变异位点,共计15个单倍型。AMOVA分析结果表明,不同的地理区域之间存在显著的遗传分化(63.55%),而区域内和种群内的遗传变异分别只有24.17%和12.28%。采用邻接法(NJ)构建分子系统树,结果表明,单倍型被分成3个与各自的地理区域相对应的族群,各地理区域之间没有共享的单倍型。细鳞鲑的这种独特的遗传结构与其进化历史(例如地理隔离造成基因流的长期中断)和生物学特性(例如有限的散布能力和基因交换能力)有密切的关系。根据上述研究结果,我们建议对这3个遗传分化显著的地理区域加以保护,并按照不同的水系来保护种群,避免不同区域的种群之间发生基因交流。