Restricted range of ocular accommodation in barn owls (Aves:Tytonidae)

Summary In an examination of the focusing abilities of 15 species of owls, the North American barn owl, Tyto alba pratincola (Bonaparte 1838), was an outstanding accommodator, having a range of accommodation exceeding 10 diopters (Murphy and Howland 1983). Using comparable methods, we examined the accommodation of 4 specimens of the Australian barn owl, Tyto alba delicatula (Gould 1837). We failed to elicit accommodation greater than two diopters, and most stimuli failed to evoke any discernable accommodation at all. Furthermore, examination of other Australian tytonid owls, the grass owl, T. longimembris, the sooty owl, T. tenebricosa, and both the mainland and Tasmanian subspecies of the masked owl, T. novaehollandiae novaehollandiae and T. novaehollandiae castanops, also failed to reveal anything but very moderate accommodative ranges. We conclude that the outstanding accommodative ability of the American barn owl is truly an exception to the modest accommodative abilities of the tytonid owls generally.     

Novel microsatellite markers obtained from Gansu zokor (Eospalax cansus) and cross-species amplification in Plateau zokor (Eospalax baileyi)

Zokor (Mysopalacinae) is a group of subterranean rodents. Although they are regarded as important components in the ecosystems they belong to, due to their underground lifestyle, very little is known about their ecology and behavior. Development of microsatellite markers can potentially assist in addressing behavioral and ecological questions such as dispersal, mating and social systems. Here we report the development of 11 polymorphic microsatellite loci from the genome of Eospalax cansus using 454 shot-gun sequencing. Genetic diversity was assessed using DNA samples of 47 individuals of E. cansus from a single location. Cross-amplification in Eospalax baileyi was also tested, with five polymorphic markers being amplified successfully. These markers are the first published microsatellites loci from E. cansus and will be invaluable for studies addressing ecological and behavioral questions involving E. cansus and E. baileyi, and potentially other species in Mysopalacinae.     

Genetic diversity estimation and core collection construction of Sinojackia huangmeiensis based on novel microsatellite markers

Sinojackia huangmeiensis is a critically endangered tree species in the Styracaceae endemic to China. To create tools to better evaluate the genetic diversity of this species, we used a modified genomic library enrichment method, the PETUER (Probe Extension and TEACl Universal EnRichment) method, to develop genetic markers. The resulting 18 microsatellite loci had high polymorphism with 3–12 alleles per locus and showed negligible stutter. Observed (H_O) heterozygosities were 0.057–0.724, and polymorphism information content (PIC) was 0.109–0.794. No significant linkage disequilibrium between pairs of loci was found. All 123 individuals found in the National Natural Reserve of Longgan Lake was genotyped at the 18 loci and used to estimate a UPGMA dendrogram. Using an iterative clustering method, a set of 18 individuals was established as a core collection to represent genetic diversity and would be useful to facilitate the conservation for S. huangmeiensis. In addition, we tested the 18 loci for cross-species amplification in three other Sinojackia species and the closely related Changiostyrax dolichocarpa. These polymorphic loci will be valuable for future population genetic and phylogenetic studies of S. huangmeiensis and congeneric species, as well as in closely related Styracaceae.     

近缘种扩增法对黑叶猴微卫星位点的筛选及特征分析(英文)

微卫星位点近缘种筛选法使得在探讨各种灵长类种群遗传结构和生殖策略上更加便捷。我们利用138条人类微卫星引物在黑叶猴中进行筛选,得到了23个具有多态性位点。在28个检测个体中,每个位点的等位基因数为3到9个,期望杂合度为0.62,观测杂合度为0.50,其中有7个位点偏离Hardy-Weinberg平衡,9个位点存在无效等位基因现象。但是各位点之间均未检测到连锁不平衡现象。这些位点将在黑叶猴种群遗传结构的研究中发挥重要作用。     

鲤科鱼蓝黑鲮微卫星位点的种间扩增(英文)

本研究使用105对微卫星引物对7种鲤科鱼类进行跨越种间PCR扩增,共得到14个多态性微卫星位点.其中9个扩增效果较好的位点用于分析来自帕吉勒提河(Bhagirathi, n=20)和戈达瓦里河(Godavari, n=25)的蓝黑鲮(Labeo calbasu)样品的遗传多样性.结果显示,前者在每个位点的平均等位基因数为7.33,而后者为8 1,期望杂合度介于0.795(Bhagirathi)和0.801(Godavari)之间;4个位点MFW11* (Godavari)、R1*(Godavari)、R3* (Bhagirathi) 和 Lr38*(Bhagirathi和Godavari)都表现出明显的杂合子缺失和哈迪温伯格平衡偏离;而任意两位点间都未观测到连锁不平衡现象;位点R3*极可能存在无效等位基因.上述结果表明这些多态性微卫星位点作为共显性标记在蓝黑鲮群体遗传学研究中有着较好的应用前景.     

Development and optimization of microsatellite DNA primers for boreal owls (Aegolius funereus)

We developed 22 microsatellite loci for boreal owls (Aegolius funereus). We genotyped 275 unrelated boreal owls (Aegolius f. richardsoni) and 36 unrelated Tengmalm's owls (Aegolius f. funereus) using seven loci that were polymorphic and did not have detectable null alleles. Among North American and Scandinavian boreal owls, respectively, allelic diversity ranged from three to 11 alleles and from one to 11 alleles, observed heterozygosity ranged from 0.31 to 0.80 and from 0.00 to 0.81, and expected heterozygosity ranged from 0.28 to 0.81 and from 0.00 to 0.81. These markers appeared to amplify DNA in six other Strigidae species.     

Directional evolution of size coupled with ascertainment bias for variation in Drosophila microsatellites

Species-specific differences in microsatellite locus length and ascertainment bias have both been proposed to explain differences in microsatellite variability and length usually observed when loci isolated in one species are used to survey variation in a related species. Here we provide a simple algebraic approach to independently estimate the contributions of true species-specific length differences and ascertainment bias. We apply this approach to a reciprocal-isolation microsatellite study and show contributions of both ascertainment bias and a true longer average microsatellite length in Drosophila melanogaster compared with D. simulans.     

Quantifying ascertainment bias and species-specific length differences in human and chimpanzee microsatellites using genome sequences

Surveys of variability of homologous microsatellite loci among species reveal an ascertainment bias for microsatellite length where microsatellite loci isolated in one species tend to be longer than homologous loci in related species. Here, we take advantage of the availability of aligned human and chimpanzee genome sequences to compare length difference of homologous microsatellites for loci identified in humans to length difference for loci identified in chimpanzees. We are able to quantify ascertainment bias for a range of motifs and microsatellite lengths. Because ascertainment bias should not exist if a microsatellite selected in one species is as likely to be longer as it is to be shorter than its homologue, we propose that the nature of ascertainment bias can provide evidence for understanding how microsatellites evolve. We show that bias is greater for longer microsatellites but also that many long microsatellites have short homologues. These results are consistent with the notion that growth of long microsatellites is constrained by an upper length boundary that, when reached, sometimes results in large deletions. By evaluating ascertainment bias separately for interrupted and uninterrupted repeats we also show that long microsatellites tend to become interrupted, thereby contributing a second component of ascertainment bias. Having accounted for ascertainment bias, in agreement with results published elsewhere, we find that microsatellites in humans are longer on average than those in chimpanzees. This length difference is similar among repeat motifs but surprisingly comprises two roughly equal components, one associated with the repeats themselves and one with the flanking sequences. The differences we find can only be explained if microsatellites are both evolving directionally under a biased mutation process and are doing so at different rates in different closely related species.     

Standardizing for microsatellite length in comparisons of genetic diversity

Mutation rates at microsatellites tend to increase with the number of repeats of the motif, leading to higher levels of polymorphism at long microsatellites. To standardize levels of diversity when microsatellites differ in size, we investigate the relationship between tract length and variation and provide a formula to adjust allelic richness to a fixed mean number of repeats in the specific case of chloroplast microsatellites. A comparison between 39 loci from eight species of conifers (where chloroplast DNA is paternally inherited) and 64 loci from 12 species of angiosperms (where chloroplast DNA is generally predominantly maternally inherited) indicates that the greater allelic richness found in conifers remains significant after controlling for number of repeats. The approach stresses the advantage of reporting variation in number of repeats instead of relative fragment sizes.     

Development of novel microsatellite loci and analyses of genetic diversity in the endangered Tanakia somjinensis

Somjin bitterling (Tanakia somjinensis), an endemic cyprinid on the Korean Peninsula, is critically endangered with only a few small populations found in limited areas in a single drainage, raising concerns that this species has likely suffered low levels of genetic variability. In the current study, 23 polymorphic microsatellite markers were developed using Illumina paired-end sequencing for quantification of the genetic diversity in this species and to determine their amplification efficiency in other bitterling species. A total of 50 somjin bitterlings collected from two localities were genotyped using these 23 loci. This species showed a remarkably high level of genetic variability, with an average number of alleles per locus of 17.30 and mean observed and expected heterozygosity values of 0.758 and 0.802, respectively. Our relatedness analyses for all pairs of individuals clearly indicated that the two somjin bitterling populations were completely outbred. No signature of drastic demographic decline was detected using our analytical methods. Many of our loci were validated as successfully transferable within and between genera and could potentially be used for genetic and demographic studies in other bitterling species.     

A new large barn owl (Aves, Strigiformes, Tytonidae) from the Middle Pleistocene of Sicily, Italy, and its taphonomical significance

A new species of Tytonidae, Tyto mourerchauvireae, is described from the Sicilian cave deposits of Spinagallo, Luparello and Marasà, which have yielded a common vertebrate fossil assemblages referred to the early Middle Pleistocene. T. mourerchauvireae nov. sp. shows a pronounced increase in body size compared to other congeneric taxa. It is larger than the extant Tyto alba and the extinct Tyto balearica and Tyto sanctialbani and comparable in size among the Mediterranean taxa only with the extinct Tyto robusta, which differs in some morphological characteristics of the long bones. The insular adaptations of T. mourerchauvireae nov. sp. and the differences from the other forms of the genus Tyto which spread through the Mediterranean area during Neogene and Pleistocene are discussed. The fossil assemblages of the early Middle Pleistocene of Sicily are dominated by extinct giant Gliridae of the genus Leithia and Maltamys; these taxa are regarded as the primary prey items of T. mourerchauvireae nov. sp. The Gliridae remains were analysed microscopically to detect possible modifications of bones and teeth caused by ingestion and digestion processes. This type of analysis, together with the qualitative study of the fossil assemblages, allows to show the taphonomical importance of T. mourerchauvireae nov. sp. as agent of accumulation in such Sicilian fossil assemblages. Incidentally the taxonomic validity of T. robusta is discussed and confirmed.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of starry flounder (Platichthys stellatus) and cross-species amplification

Starry flounder (Platichthys stellatus) is a rare fish species in China. Here, we reported 12 polymorphic microsatellite loci isolated from a dinucleotide-enriched genomic library of starry flounder (P. stellatus). The number of alleles, observed and expected heterozygosity per locus in 30 individuals ranged from two to six, from 0.2500 to 1.0000 and from 0.4512 to 0.7667, respectively. One locus significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium between pairs of loci was found. Cross-species amplification of these microsatellite loci in additional three fish species was performed. These polymorphic microsatellite loci would be useful for investigating genetic population structure and construction of genetic linkage map in P. stellatus. Guidong Miao and Changwei Shao have contributed equally.     

Characterization of novel microsatellite loci in the great leaf-nosed bat, Hipposideros armiger and cross-amplification in other related species

Eight microsatellite loci were isolated from an enriched genomic library of the great leaf-nosed bat, Hipposideros armiger. The polymorphism of these loci was tested on a population of 48 individuals from Anhui Province, China. All loci revealed the polymorphism ranging from three to 12 alleles. The observed heterozygosity values were from 0.213 to 0.875 and expected heterozygosity from 0.232 to 0.820. No significant linkage disequilibrium was detected. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. In addition, successful cross-amplification also suggested that these microsatellite markers will facilitate research on the population genetics and gene flow of H. armiger and other related species.     

Development of microsatellite loci for Pelophylax plancyi and cross-amplification in other ranid species

Thirteen polymorphic microsatellite loci were obtained from the gold-striped pond frog, Pelophylax plancyi. The number of alleles per locus ranged from 5 to 13 with an average of 8.38. The observed and expected heterozygosities (H _O and H _E) ranged from 0.533 to 0.890 and from 0.620 to 0.897, with averages of 0.686 and 0.751, respectively. In order to assess interspecific amplification, all primer pairs were tested with the same PCR conditions on three other Pelophylax species: Pelophylax hubeiensis, Pelophylax fukienensis, Pelophylax nigromaculata and two species from the genus Hylarana and Hoplobatrachus, respectively. All of these loci can be amplified successfully in the Pelophylax species, with eight loci amplified in all species tested.     

Characterization of novel microsatellite loci in rare minnow (<Emphasis Type="Italic">Gobiocypris rarus</Emphasis>) and amplification in closely related species in Gobioninae

Rare minnow (Gobiocypris rarus) is an endangered small fish endemic to upper reach of the Yangtze River. From a (GT)n enriched genomic library, 32 microsatellites were isolated and characterized. Nineteen of these loci were polymorphic in a test population with alleles ranging from 2–7, and observed and expected heterozygosities from zero to 0.8438, and 0.2679 to 0.8264, respectively. In the cross-species amplifications, 13 out of 19 polymorphic loci were found to be also polymorphic in at least one of the 7 closely related species of the subfamily Gobioninae. These polymorphic microsatellite loci should provide sufficient level of genetic diversity to evaluate the fine-scale population structure in rare minnow and its closely related species for the conservation purpose.     

Characterization of 11 novel polymorphic microsatellite loci in the threatened Korean loach,Iksookimia koreensis,isolated using a next-generation sequencing method

To investigate the genetic diversity and population structure of Iksookimia koreensis, we characterized 11 novel polymorphic microsatellite markers developed using next-generation sequencing. The number of alleles per locus ranged from 4 to 10 (average = 6.26). Observed and expected heterozygosities ranged from 0.333 to 0.866 and from 0.375 to 0.866, respectively. No loci showed significant deviation from Hardy–Weinberg equilibrium (HWE). These loci were also used successfully to study the genetic diversity of a closely related species, Iksookimia longicorpa. Four of the 11 loci amplified in the two species showed different allele frequency and distribution, indicating deep genetic divergence between I. koreensis and I. longicorpa. The newly developed microsatellite markers reported here will provide a useful tool for examining gene flow, population genetic structure, and genetic diversity of these species.     

Wing and tail myology of Tyto furcata (Aves,Tytonidae)

Barn Owls (Tytonidae) are nocturnal raptors with the largest geographical distribution among Strigiformes. Several osteological, morphometrical, and biomechanical studies of this species were performed by previous authors. Nevertheless, the myology of forelimb and tail of the Barn Owls is virtually unknown. This study is the first detailed myological study performed on the wing and tail of the American Barn Owl (Tyto furcata). A total of 11 specimens were dissected and their morphology and muscle masses were described. Although T. furcata has the wing and tail myological pattern present in other species of Strigiformes, some peculiarities were observed including a difference in the attachment of m. pectoralis propatagialis due to the lack of the os prominence, and the presence of an osseous arch in the radius that seems to widen the anchorage area of the mm. pronator profundus, extensor longus alulae, and extensor longus digiti majoris. Furthermore, the m. biceps brachii has an unusual extra belly that flexes the forearm. The interosseous muscles have a small size and lacks ossified tendons. This feature may be indicative of a lower specialization in the elevation and flexion of the digiti majoris. Forelimb and tail muscle mass account for 10.66 and 0.24% of the total body mass, respectively. Forelimb muscle mass value is similar to the nocturnal (Strigiformes) and diurnal (Falconidae and Accipitridae) raptors, while the tail value is lower than in the diurnal raptors (Falconidae and Accipitridae). The myological differences with other birds of prey are here interpreted in association with their “parachuting” hunting style. This work complements our knowledge of the axial musculature of the American Barn owls, and provides important information for future studies related to functional morphology and ecomorphology.