Phylogenetic analysis of sequences of the 12S and 16S rRNA mitochondrial genes in the family Bovidae: new evidence

The phylogeny of the family Bovidae has been inferred from our data on the 12S and 16S rRNA gene sequences and from the results of other authors. A considerable (2,460 bp) length of the analyzed fragments of these conserved genes and the use of different methods of cladogram construction allowed us to verify the systematic position of the genera Saiga, Pantholops, Procarpa, and Oreamnos. Saigas were shown to be phylogenetically far closer to gazelles than black-tailed gazelles and pygmy antelopes. In general, the genetic analysis data are in agreement with the results of morphological studies.     

Diversification and subspecies patterning of the goitered gazelle (Gazella subgutturosa) in Iran

Goitered gazelles, Gazella subgutturosa, exist in arid and semiarid regions of Asia from the Middle to the Far East. Although large populations were present over a vast area until recently, a decline of the population as a result of hunting, poaching, and habitat loss led to the IUCN classification of G. subgutturosa as “vulnerable." We examined genetic diversity, structure, and phylogeny of G. subgutturosa using mitochondrial cytochrome b sequences from 18 geographically distant populations in Iran. The median‐joining network of cyt b haplotypes indicated that three clades of goitered gazelles can be distinguished: a Middle Eastern clade west of the Zagros Mountains (and connected to populations in Turkey and Iraq), a Central Iranian clade (with connection to Azerbaijan), and an Asiatic clade in northeastern Iran (with connection to Turkmenistan, Uzbekistan, and other Asian countries as far as northeastern China and Mongolia). Based on our results, we argue that Iran is the center of diversification of goitered gazelles, due to the presence of large mountain ranges and deserts that lead to the separation of populations. In accordance with previous morphological studies, we identified the Asiatic clade as the subspecies G. s. yarkandensis, and the other two clades as the nominate form G. s. subgutturosa. The new genetic information for goitered gazelles in Iran provides the basis for future national conservation programs of this species.     

A Cladistic Analysis of Mitochondrial Ribosomal DNA from the Bovidae

There is a huge data base of genetic information for the domestic artiodactyl speciesBos taurus(cow),Ovis aries(sheep), andCapra hircus(goat). However, the phylogenetic relationships of these economically critical taxa and their close relatives, family Bovidae, remain for the most part unresolved. In this report, we aligned new mitochondrial (mt) 12S and 16S ribosomal (r) DNA sequences from 26 bovid taxa with published sequences. Phylogenetic analyses of the more than 64 kilobases of mt rDNA from 57 taxa support a basal division in the Bovidae that separatesBosand its close relatives fromCapra, Ovis,and their kin. As suggested by previous molecular and morphological studies, “antelopes” are a paraphyletic assemblage. Caprinae (sheep, goats, goat antelopes, and musk oxen) groups consistently with hippotragine and alcelaphine antelopes, while Bovini (cattle and buffaloes) clusters with tragelaphine and boselaphine antelopes. The traditional tribal subdivisions of Bovidae are supported in most cases, but there are exceptions within Caprinae and Antilopinae (gazelles and close relatives). The rDNA data consistently place the enigmatic generaPelea, Pantholops,andSaiga,but the origin ofAepyceros,the impala, remains obscure. Combined phylogenetic analyses of the rDNA data with the skeletal characters of Gentry (1992) were used to assess the stability of the molecular results.     

Dietary Overlap of Przewalski's Gazelle,Tibetan Gazelle,and Tibetan Sheep on the Qinghai-Tibet Plateau

Abstract: We studied food composition and overlap among sympatric Przewalski's gazelle (Procapra przewalskii), Tibetan gazelle (P. picticaudata), and Tibetan domestic sheep (Ovis aries) in the Upper Buha River, Qinghai-Tibet Plateau, using microscopic fecal analysis. The 2 gazelles forage mainly on plants from Leguminosae and Compositae families and domestic sheep feed mainly on Gramineae and Cyperaceae. The dietary overlap index between the 2 gazelles and Tibetan domestic sheep increased from 0.43 to 0.58 during the plant-growing period to 0.76–0.77 during the plant-withering period, which indicated competition for foods intensified during the food-limited season. Although the 2 gazelle ate similar diets, they might avoid food competition by occupying different foraging areas. We suggest reducing numbers of overwintering Tibetan domestic sheep on pastures to lessen survival pressure on the endangered gazelles during winters.     

The development of the refractive state in the newborn Thomson gazelle

Changes in refractive error during the first 3 months of life were studied retinoscopically in six Thomson gazelles (Gazella thomsoni). Animals were hand-raised to allow repeat testing over time without chemical restraint. Refraction results were correlated with ultrasound measurements of intraocular dimensions, and with values in adult gazelles. Gazelles are born hyperopic with a mean refractive error of 3.44±0.31 D. By day 50, the animals are virtually emmetropic (0.13±0.21 D) and remain so in adulthood (0.03±0.09 D). The refractive error is highly correlated with the axial length (r²=0.96) and with the vitreous chamber depth (r²=0.83), but not with anterior chamber depth. Significant with-the-rule astigmatism was recorded (P<0.001).     

Modified netting technique for capturing gazelles in Serengeti,Ngorongoro and Loliondo,Tanzania

During serological surveillance of peste des petits ruminants (PPR) disease, it required capture of randomly selected herds of gazelles as part of a study to determine the epidemiological role of these species in the circulation of peste des petits ruminants virus (PPRV). The study targeted capturing 135 Grant's gazelles (Gazella granti) from the Serengeti ecosystem, Tanzania. A modified netting technique was used aiming at providing safe, efficient and cost‐effective method for capture of gazelles. Locally available materials were used, and wildlife professionals guided the process of manufacturing supporting frame for the nets. Twenty (20) black metal pipes, 20 metal bars, four nets and three vehicles were used in the procedure. A total of 136 Grant's gazelles and nine Thomson's gazelles were captured in three missions. The Grant's gazelles were captured as per sample size calculated in all locations: Loliondo (n = 25), Serengeti National Park (n = 44) and Ngorongoro Conservation Area (NCA) (n = 67) using less time and minimum cost than estimated. Injuries of three fawns (2%) inadvertently captured with the groups of adults and sub‐adult animals were recorded. Comparing with 2014 and other studies, modified netting technique showed high animal and operator safety levels with minimal injuries. With this technique, it was possible to capture even flighty animals that behave nervously because of hunting and other human activities, including Thomson's gazelles, a species previously found to be difficult to capture by netting.     

Population development of Arabian Gazelles,Gazella arabica,on the Farasan Islands,Saudi Arabia (Mammalia: Bovidae)

The population of the Arabian Gazelle (Gazella arabica) was assessed on Farasan Kebir, the main island of the Farasan Archipelago (Saudi Arabia), from June 2010 to January 2013, using road strip counts. Two methods of estimating the population size were applied to analyse data obtained from the road strip count: (i) the traditional technique after Bothma, with a fixed strip width, and (ii) distance sampling using DISTANCE 6.0. Estimates varied between 483 gazelles (95% CI: 44) in November 2010 and 1070 gazelles (95% CI: 63) in June 2010. The number of gazelles estimated for Farasan Kebir using distance sampling is 2388 gazelles (95% CI: 921) in December 2011, 1199 gazelles (95% CI: 1372) in June 2012, and 1048 gazelles (95% CI:1524) in January 2013. Taking into account previous counts (1988–2009) the population seems, despite considerable variations, surprisingly stable. This may be attributed to a prevailing fishing culture among local residents and thus the absence of traditional hunting as well as the ranger activities on the islands. The disparity between the two estimation methods decreased to only 270 gazelles in January 2013 and provides additional confidence in the future application of both estimation techniques.The traditional technique is recommended as the more practical method for rangers and conservation mangers to determine population changes.     

Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant’s gazelles

The intraspecific phylogeography of Grant’s gazelles Nanger granti was assessed with mitochondrial DNA control region sequences. Samples of 177 individuals from 17 Kenyan and Tanzanian populations were analysed. Three highly divergent, reciprocally monophyletic lineages were found, with among group net nucleotide distances of 8–12%. The three lineages—notata, granti and petersii—grouped populations according to their geographic origin, encompassing populations in the north, southwest, and east, respectively. The mtDNA lineages reflected distinct evolutionary trajectories, and the data are discussed in reference to the four currently recognised subspecies. We suggest Grant’s gazelles be raised to the superspecies Nanger (granti) comprising three taxonomic units corresponding to the three mtDNA lineages. There was no evidence of gene flow between the notata and granti lineages, despite their geographic proximity, suggesting reproductive isolation. These constitute evolutionary significant units within the adaptive evolutionary framework. Due to its restricted geographic distribution and genetic and morphological distinctiveness, we suggest the petersii lineage be raised to the species Nanger (granti) petersii within the Grant’s gazelles superspecies.     

Genetic diversity and relations of the Goitered gazelle (<Emphasis Type="Italic">Gazella subgutturosa</Emphasis>) groups from Uzbekistan,Turkmenistan, and Azerbaijan: Analysis of the D-loop of mitochondrial DNA

Polymorphism of the nucleotide sequence of a hypervariable fragment of the D-loop (985 bp) of mtDNA in 76 Goitered gazelles of subspecies Gazella subgutturosa subgutturosa from Uzbekistan, Turkmenistan, and Azerbaijan was studied. The genetic similarity of gazelles from Turkmenistan and Uzbekistan has been identified. The population of gazelles from Shirvanskaya steppe reserve (Azerbaijan) is unique and strictly isolated from other groups studied. A high haplotypic (H = 0.9649 ± 0.0091) and relatively low nucleotide diversity (π = 0.0212 ± 0.0105) were noted for all investigated groups of gazelle based on this mtDNA fragment, which is probably related to ecological peculiarities of the species and the history of formation of regional populations.     

Molecular Support for the Placement of Saiga and Procapra in Antilopinae (Artiodactyla, Bovidae)

The evolutionary history of the bovid subfamily Antilopinae is unclear. Traditionally, this subfamily is subdivided into two tribes: Neotragini (dwarf antelopes) and Antilopini (gazelles and their relatives). Here, we report new sequences for the 12S and 16S rRNA genes in the enigmatic antilopine taxa Procapra gutturosa and Saiga tatarica and analyze the phylogenetic relationships of these taxa relative to other antilopines. Our study demonstrates the close affinity of the saiga antelope to Gazella despite the conventional systematic allocation of Saiga to the Caprinae subfamily. The second member of the Saigini tribe, Pantholops hodgsoni (Tibetan gazelle), falls within Caprinae. In all of our analyses, Procapra gutturosa occupied a basal position in the Antilopinae clade or was a sister-group to the dwarf antelope Madoqua. This suggests early separation of Procapra from other antelopes.     

A phylogeographic framework for the conservation of Saharan and Arabian Dorcas gazelles (Artiodactyla: Bovidae)

Many species of gazelles (Gazella spp.) are nowadays threatened by hunting, poaching, habitat loss and habitat deterioration. Conservation efforts for this group not only face the problem of maintaining remnant populations, but often natural populations have been extirpated from the wild. In some cases, though, captive breeding programs exist that might provide a valuable source for future reintroductions. A major problem in this context is that phylogeographic relationships among different (potentially locally adapted) populations, and even basic phylogenetic relationships between species, are poorly understood, thus hampering the assignment of management units, breeding groups or stocks for reintroduction projects. Our present study focused on Dorcas gazelles (G. dorcas and G. saudiya) from the species’ entire distribution range, with samples originating from western Saharan Africa into Saudi Arabia. In stark contrast to previous studies reporting on pronounced genetic structure in taxa such as Mountain gazelles (G. gazella), we detected low genetic diversity and no evidence for major phylogenetic lineages when analyzing two mitochondrial genetic markers. Using a coalescent approach we infer a steep population decline that started approximately 25,000 years before present and is still ongoing, which coincides with human activities in Saharan Africa. Our phylogenetic analyses, statistical parsimony network analysis and inferred colonization patterns shed doubt on the validity of various described subspecies of G. dorcas.     

Just another island dwarf? Phenotypic distinctiveness in the poorly known Soemmerring's Gazelle,Nanger soemmerringii (Cetartiodactyla: Bovidae), of Dahlak Kebir Island

The gazelles of Dahlak Kebir are the only population of Nanger soemmerringii Cretzschmar, 1828 living on an island. Little is known on the biology of these animals, except that they are evidently smaller than their conspecifics living on the continent. We took advantage of a recently acquired collection of crania, probably the largest available study sample of the Dahlak Kebir population worldwide, to explore the phenotypic variation of this island endemism. To this aim, we employed state of the art geometric morphometrics techniques and multivariate statistics to compare the insular population with samples of two out of three subspecies of N. soemmerringii from continental Africa. We found that not only is the size of the animal remarkably smaller in Dahlak Kebir gazelles, but their cranial shape is also highly distinctive, and this might be only partly explained by allometry. We also showed that phenotypic variance might have been reduced in the island population, likely as a consequence of genetic bottlenecks. This unique population is part of a species vulnerable to extinction. Our results suggest that the Dahlak Kebir Island gazelles might represent a significant component of its variation and potential for adaptive change and evolution. More information, including molecular data, and an accurate assessment of its taxonomic relevance and conservation status, is urgently needed. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 603–620.     

Wild Gazelles of the Southern Levant: Genetic Profiling Defines New Conservation Priorities

The mountain gazelle (Gazella gazelle), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia) were historically abundant in the southern Levant, and more specifically in Israel. Anthropogenic and natural changes have caused a rapid decline in gazelle populations, raising concerns about their conservation status and future survival. The genetic profile of 111 wild gazelles from Israel was determined based on three regions of mitochondrial DNA (control region, Cytochrome b and 12S ribosomal RNA) and nine nuclear microsatellite markers. Genetic analysis of the mountain gazelle population, the largest known population of this rare species, revealed adequate diversity levels and gene flow between subpopulations. Nevertheless, ongoing habitat degradation and other human effects, such as poaching, suggest the need for drastic measures to prevent species extinction. Dorcas gazelles in Israel displayed inbreeding within subpopulations while still maintaining considerable genetic diversity overall. This stable population, represented by a distinctive genetic profile, is fragmented and isolated from its relatives in neighboring localities. Based on the genetic profile of a newly sampled subpopulation in Israel, we provide an alternative hypothesis for the historic dispersal of Dorcas gazelle, from the Southern Levant to northern Africa. The small acacia gazelle population was closest to gazelles from the Farasan Islands of Saudi Arabia, based on mitochondrial markers. The two populations did not share haplotypes, suggesting that these two populations may be the last remnant wild gazelles of this species worldwide. Only a dozen acacia gazelles survive in Israel, and urgent steps are needed to ensure the survival of this genetically distinctive lineage. The genetic assessments of our study recognize new conservation priorities for each gazelle species in the Southern Levant.     

Restriction polymorphisms in the internal transcribed spacers and 5.8S rDNA ofSaccharomyces

Polymorphism in enzymatically amplified ribosomal DNA (rDNA) were examined in 18 strains ofSaccharomyces. Restriction patterns generated from the region spanning the internal transcribed spacers (ITS) and the 5.8S rDNA produced two clusters corresponding toS. bayanus andS. cerevisiae. The type culture ofS. carlsbergensis (ATCC 76529), which could not be separated from theS. cerevisiae group by small subunit (SSU) rDNA patterns, showed aScrfI profile that was distinct from all the other strains. The type culture ofs. intermedius var.turicensis (ATCC 76519) is assigned toS. bayanus on the basis of the combined results of SSU and ITS restriction analyses.S. kluyveri occurred at a separate branch of the distance tree and is unrelated to any of the strains. Results were in general agreement with reported DNA homologies and are discussed in relation to other molecular and genetic data.     

Utility of island populations in re‐introduction programmes – relationships between Arabian gazelles (Gazella arabica) from the Farasan Archipelago and endangered mainland populations

Understanding local adaptation and population differentiation is vital to the success of re‐introduction initiatives. As other mammals living on islands, Arabian gazelles (G. arabica) show reduced body size on the Farasan archipelago, which we corroborated in this study through morphometric analyses of skulls. In the light of the steep population decline on the Arabian Peninsula – but stable population development on the archipelago – we tested the potential suitability of Farasan gazelles as a source for re‐introductions on the mainland. We therefore investigated genetic differentiation between Farasan and mainland populations using eleven nuclear microsatellite loci and detected a distinct genetic cluster exclusively present on the archipelago, which we inferred to be separated from the mainland cluster for less than 2000 years. About 30% of sampled individuals from Farasan Islands showed assignment to a mainland cluster with signs of ongoing introgression. Analyses using the isolation‐with‐migration model confirmed recent (probably human‐induced) bidirectional exchange of gazelles between mainland and island populations. Hence, the surprisingly uniform island dwarfism most likely reflects phenotypic plasticity, that is, altered morphology as a direct consequence of harsh environmental conditions and resource limitation on the archipelago. Should a further decline of Arabian gazelles on the mainland necessitate restocking in the future, Farasan gazelles may thus become an additional source for captive breeding programmes.     

Plant regeneration from protoplasts of Solanum species with potential agricultural value (S. hjertingii,S. polyadenium,S. capsicibaccatum)

Protoplasts have been isolated from three tuber-bearing Solanum species, S. hjertingii, S. polyadenium and S. capsicibaccatum, that are sexually incompatible with S. tuberosum, but possess potentially useful characters. For isolating protoplasts from leaves of in vitro shoot cultures of S. hjertingii and S. capsicibaccatum growth was improved by including silver thiosulfate in the medium. However, for S. polyadenium, leaves of pot-grown plants were the best source for protoplasts. Following protoplast division and culture, plants were regenerated from protoplasts of each of the species. The pattern of chromosome variation in regenerants was similar to that observed for other diploid and tetraploid Solanum species. The results indicate that it should be possible to introduce the potentially useful germplasm from these wild species into somatic hybrids with S. tuberosum by protoplast fusion.Abbreviations STS silver thiosulfate - BAP benzylaminopurine - GA₃ gibberellic acid - NAA naphthalene acetic acid - IAA indole-3-acetic acid     

Functional heterogeneity of the 30S ribosomal subunit of Escherichia coli. II. Effect of S21 on initiation

Summary Native 30S ribosomal subunits fromEscherichia coli are deficient in fractional protein S21, which is present on the monosome and polysome-derived 30S subunits. The presence of S21 prevents the binding of Fmet-tRNA if and only if 50S subunits are present. In contrast, proteins S2, S3 and S14 stimulate the binding of Fmet-tRNA. These results have been used to rationalize other data concerning the mechanism of Fmet-tRNA binding by ribosomes. In addition, the present data indicate that the 30S ribosomal subunits are heterogeneousin vivo as well asin vitro.Dedicated to Professor H. Veldstra on the occasion of his retirement from the chair of biochemistry of the University of Leiden.     

Sequences of the cDNAs and genomic DNAs encoding the S1, S7, S8, and Sf alleles from almond, Prunus dulcis

Partial genomic and cDNA sequences of the RNase alleles S1, S7, S8 and Sf were obtained from Prunus dulcis cvs ’Ne Plus Ultra’, ’Ferragnes’ and ’Nonpareil’ 15–1, and IRTA Selection 12–2. Total DNA was extracted from leaves, and cDNA was prepared from total RNA extracted from styles. The partial cDNA sequences of the S1 allele from ’Ferragnes’, and the S7 and S8 alleles from ’Nonpareil’ 15–1, matched those reported in the literature for the alleles Sb, Sc and Sd respectively. The sequences of the S1, S7, S8 and Sf alleles found in genomic DNA contained introns of 562, 1,530, 2,208 and 689 bp respectively. The exon/intron splice junction sites of all alleles followed the GT/AG consensus sequence rule, and the sequences were found to be highly conserved. Received: 18 October 2000 / Accepted: 8 March 2001     

Assessing the Biodiversity of Monoraphidium Using 18S rDNA Sequences

The taxonomy of the genus Monoraphidium is unclear due in part to the absence of morphological features to clearly distinguish one species from another. Phytoplankton samples collected from lakes in the Arrowwood National Refuge in eastern North Dakota were found to contain several morphological species of Monoraphidium. Eighteen Monoraphidium isolates were examined with light microscopy and six morphological species were identified. PCR–RFLP of the 18S rDNA was used to type the isolates. Following digestion by Hae III and Taq I, the 18S rDNA PCR–RFLP patterns indicated 10 different types. Presently, the 18S rDNA product is being sequenced for each of the 10 types. By examining morphological characters and 18S rDNA sequences, congruence between morphology and sequence data may be compared. Also, because there is a lack of morphological characters defining Monoraphidium species, diversity within the 18S rDNA sequences may aid in the taxonomy of the genus and its place within the Chlorococcales. Supported by National Science Foundation Grants MCB‐0084188 and DBI‐0070387.     

ORIGINS OF SOLANUM LASIOCARPUM AND S. REPANDUM

Solanum candidum of tropical America is very similar to S. lasiocarpum of southeastern Asia and S. sessiliflorum, a wild and domesticated plant of the Amazon basin, is very similar to S. repandum, a weed and domesticated plant of Oceania. Artificial hybrids between S. candidum and S. lasiocarpum are fertile, and it is postulated that S. lasiocarpum resulted from a Spanish introduction of S. candidum to Asia. Hybrids between S. repandum and S. sessiliflorum show considerable reduction in fertility and abnormalities at meiosis, whereas hybrids of both S. candidum and S. lasiocarpum with S. repandum are fertile. It is concluded that it is likely that S. repandum did not arise from S. sessiliflorum but from S. lasiocarpum or S. candidum. This would mean that the similarity of S. repandum to S. sessiliflorum results from convergence.