caBIG™ VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data

Background

We sketch our species identification tool for palm sized computers that helps knowledgeable observers with census activities. An algorithm turns an identification matrix into a minimal length series of questions that guide the operator towards identification. Historic observation data from the census geographic area helps minimize question volume. We explore how much historic data is required to boost performance, and whether the use of history negatively impacts identification of rare species. We also explore how characteristics of the matrix interact with the algorithm, and how best to predict the probability of observing a previously unseen species.

Results

Point counts of birds taken at Stanford University's Jasper Ridge Biological Preserve between 2000 and 2005 were used to examine the algorithm. A computer identified species by correctly answering, and counting the algorithm's questions. We also explored how the character density of the key matrix and the theoretical minimum number of questions for each bird in the matrix influenced the algorithm. Our investigation of the required probability smoothing determined whether Laplace smoothing of observation probabilities was sufficient, or whether the more complex Good-Turing technique is required.

Conclusion

Historic data improved identification speed, but only impacted the top 25% most frequently observed birds. For rare birds the history based algorithms did not impose a noticeable penalty in the number of questions required for identification. For our dataset neither age of the historic data, nor the number of observation years impacted the algorithm. Density of characters for different taxa in the identification matrix did not impact the algorithms. Intrinsic differences in identifying different birds did affect the algorithm, but the differences affected the baseline method of not using historic data to exactly the same degree. We found that Laplace smoothing performed better for rare species than Simple Good-Turing, and that, contrary to expectation, the technique did not then adversely affect identification performance for frequently observed birds.     

Molecular sexing of monomorphic endangered Ara birds

Survival of most endangered birds may depend on breeding programs where sex identification plays an important role. Molecular sexing has shown to be a rapid and safe procedure. In this work we established sex identification of monomorphic endangered Ara birds using a chromosome W-linked DNA marker, the Chromo-helicase-DNA-Binding 1 (CHD) gene. Most birds have two CHD sex-linked genes, one W-linked (CHD-W) and one Z-linked (CHD-Z). These markers were characterized from Ara militaris and gender sex was determined by PCR and restriction analyzes. The procedure here reported was successfully applied to five different species of the genus Ara and confirmed the validity of the technique. To our knowledge, this is the first report of molecular sexing of the Ara species. This molecular sexing is currently been used in breeding programs of Ara birds.     

青海三江源玛可河保护分区发现棕腹啄木鸟

<正>2013年4月24日、6月9日和6月27日,在青海省三江源国家级自然保护区玛可河地区友谊林场(32°40′N,101°2′E,海拔3 240 m)、格日则沟原始林区(32°44′N,101°10′E,海拔3 480 m)针叶树干以及玛可河干流岸边(32°40′N,100°57′E,海拔3 270 m)杨树上共观察到7只?形目鸟类,并拍摄到清晰数码照片。该鸟体形中等,     

Ascaridoidea: a simple DNA assay for identification of 11 species infecting marine and freshwater fish,mammals, and fish-eating birds

Eleven species belonging to superfamily Ascaridoidea, which infect marine and freshwater fish, mammals, and fish-eating birds, were analyzed using a PCR-RFLP method. The following species were investigated: Anisakis pegreffi, A. physeteris, and A. simplex (parasites of fish and mammals), Contracaecum osculatum, C. radiatum, and C. rudolphi (parasites of mammals and fish-eating birds), Hysterothylacium aduncum (a parasite of fish), Porrocaecum angusticolle, P. crassum, P. depressum, and P. ensicaudatum (parasites of fish-eating birds). PCR-amplified rDNA regions encompassing ITS1, 5.8S rDNA, and ITS2 produced on templates of genomic DNA isolated from all investigated species were digested with TaqI, AluI, BsuRI, and RsaI endonucleases. Restriction patterns showed that endonuclease TaqI is the most useful enzyme for identification of all investigated species. No variations in restriction patterns within each species were detected. Therefore, we propose that the PCR-RFLP assay described in this report may be used for identification of marine and freshwater parasites from superfamily Ascaridoidea.     

DNA barcode divergence among species and genera of birds and fishes

COI DNA barcoding is increasingly recognized as a significant new tool for the recognition and identification of animal species. Here, publicly available barcode data are compiled and analysed for birds (657 species) and fishes (1088 species). The proportion of species that cannot be barcode-distinguished by this marker is approximately 6.4% for birds and 2.1-2.5% for fishes. At all hierarchical taxonomic levels (species, genera, family, order, class), fish show greater mean COI divergence than birds. If two samples are barcode-identical, then for both birds and fishes, the probability that they are from the same species is 98-99%. The probability of conspecificity rapidly drops as divergence increases. At 2% COI divergence, this probability approximates to 1% for birds and 3% for fishes. The apparent difference between birds and fishes might partially reflect currently unrecognized cryptic species complexes in the latter. These probability estimates derive from pooled samples of birds and pooled samples of fishes, and will not apply in all situations. Recently evolved species complexes will have higher proportions of species that are barcode-identical. As barcode data accumulate, more refined statistical analyses will become possible.     

New DNA barcodes for identification of Korean birds

DNA barcode is a short sequence of standardized genomic region that is specific to a species and therefore, helps in species identification. According to studies of animal species, the 648-bp sequence of the mitochondrial gene encoding cytochrome c oxidase 1 (CO1) is extremely useful for species identification. Several studies of birds have already ascertained the reliability of CO1 barcodes. In this study, we investigated the validity of DNA barcoding in Korean bird species by using additional barcode records. We analyzed the CO1 barcodes of 154 species of Korean birds, and discovered that the average genetic distance between congeneric species was 25 times higher than the average genetic distance within species. Most (98.7 %) bird species possessed a barcode distinct from that of other bird species. However, among the remaining 1.3 %, species had overlapping barcode clusters. Thus, we reemphasize that CO1 barcodes are an effective identification tool for Korean bird species.     

Using molt cycles to categorize the age of tropical birds: an integrative new system

ABSTRACT Accurately differentiating age classes is essential for the long‐term monitoring of resident New World tropical bird species. Molt and plumage criteria have long been used to accurately age temperate birds, but application of temperate age‐classification models to the Neotropics has been hindered because annual life‐cycle events of tropical birds do not always correspond with temperate age‐classification nomenclature. However, recent studies have shown that similar molt and plumage criteria can be used to categorize tropical birds into age classes. We propose a categorical age‐classification system for tropical birds based on identification of molt cycles and their inserted plumages. This approach allows determination of the age ranges (in months) of birds throughout plumage succession. Although our proposed cycle‐based system is an improvement over temperate calendar‐based models, we believe that combining both systems provides the most accurate means of categorizing age and preserving age‐related data. Our proposed cycle‐based age‐classification system can be used for all birds, including temperate species, and provides a framework for investigating molt and population dynamics that could ultimately influence management decisions.     

A DNA microarray for identification of selected Korean birds based on mitochondrial cytochrome c oxidase I gene sequences

DNA barcoding with the gene encoding cytochrome c oxidase I (COI) in the mitochondrial genome has been proposed as a standard marker to identify and discover animal species. Some migratory wild birds are suspected of transmitting avian influenza and pose a threat to aircraft safety because of bird strikes. We have previously reported the COI gene sequences of 92 Korean bird species. In the present study, we developed a DNA microarray to identify 17 selected bird species on the basis of nucleotide diversity. We designed and synthesized 19 specific oligonucleotide probes; these probes were arrayed on a silylated glass slide. The length of the probes was 19-24 bps. The COI sequences amplified from the tissues of the selected birds were labeled with a fluorescent probe for microarray hybridization, and unique hybridization patterns were detected for each selected species. These patterns may be considered diagnostic patterns for species identification. This microarray system will provide a sensitive and a high-throughput method for identification of Korean birds.     

Monitoring wild greenfinch (Carduelis chloris) for Salmonella enterica typhimurium

The identification and monitoring of emerging infectious diseases in free living wild birds is a challenge to wildlife biologists. In this study, a non-invasive methodology for identifying salmonellosis in wild garden birds was developed. We focussed on greenfinch, Carduelis chloris, which were found to have a seasonal pattern in the occurrence of Salmonella Typhimurium DT 56(v). Principal components analysis of biometric data indicated that low fat and low weight could be useful indicators of Salmonella positive greenfinch. A combination of biometrics taken from live birds, faecal analysis, and behavioural observations provide an effective and efficient system for identifying the presence of salmonellosis within greenfinch.     

A place to land: spatiotemporal drivers of stopover habitat use by migrating birds

Migrating birds require en route habitats to rest and refuel. Yet, habitat use has never been integrated with passage to understand the factors that determine where and when birds stopover during spring and autumn migration. Here, we introduce the stopover‐to‐passage ratio (SPR), the percentage of passage migrants that stop in an area, and use 8 years of data from 12 weather surveillance radars to estimate over 50% SPR during spring and autumn through the Gulf of Mexico and Atlantic coasts of the south‐eastern US, the most prominent corridor for North America’s migratory birds. During stopovers, birds concentrated close to the coast during spring and inland in forested landscapes during autumn, suggesting seasonal differences in habitat function and highlighting the vital role of stopover habitats in sustaining migratory communities. Beyond advancing understanding of migration ecology, SPR will facilitate conservation through identification of sites that are disproportionally selected for stopover by migrating birds.     

重庆市涪陵区春季城市园林鸟类及其群落结构研究

2009年2月至4月, 采用样线调查法对重庆市涪陵区城市园林的鸟类及其群落结构进行了初步研究。结果表明:重庆市涪陵区城市园林春季共调查40次, 记录鸟类37种, 2245只, 隶属于2目、17科、30属, 其中26种鸟类物种被列入“三有”名录, 1种列入CITES名录;从区系类型看, 东洋种25种、古北种8种、广布种4种;从居留类型看, 留鸟31种, 夏候鸟4种, 冬候鸟2种;从多样性分析看, 太极森林公园的鸟类物种多样性指数和均匀性指数最大(2.3239, 0.6974), 易家坝广场园林则最小(1.0307, 0.4691), 其与堡子城公园的相似程度最高(63.16%);涪陵区城市园林鸟类G-F多样性指数为0.5100。     

Frequency of virulence genes and antibiotic resistances in Enterococcus spp. isolates from wastewater and feces of domesticated mammals and birds, and wildlife

Enterococci are gastrointestinal tract residents and also an important cause of nosocomial infections. To understand which species, virulence determinants, and antibiotic resistances are prevalent in enterococci shed by various hosts groups, a total of 1460 strains isolated from 144 fecal samples obtained from wastewater, domesticated mammals and birds, and wildlife were characterized. Identification of isolates to the species level showed that Enterococcus faecalis was dominant in domesticated mammals and birds and wildlife feces, whereas Enterococcus faecium was dominant among wastewater isolates, and that no single Enterococcus species could be associated with a specific host group. The frequency of 12 virulence determinants was evaluated among isolates, but no single virulence determinant could be associated with a specific host group. Resistance to 12 antibiotics was evaluated among isolates, and it was shown that the highest frequency of resistance at breakpoint concentration was found in domesticated mammals and birds (P?≤ 0.05 for 4 antibiotics). Our results suggests that (1) species identification and virulence typing of Enterococcus spp. isolates are not useful for the identification of the host groups responsible for fecal contamination of water by microbial source tracking and that (2) antibiotic use for clinical, veterinary, or animal husbandry practices is promoting resistance.     

Effectiveness of mobile apps in teaching field-based identification skills

It has been suggested that few students graduate with the skills required for many ecological careers, as field-based learning is said to be in decline in academic institutions. Here, we asked if mobile technology could improve field-based learning, using ability to identify birds as the study metric. We divided a class of ninety-one undergraduate students into two groups for field-based sessions where they were taught bird identification skills. The first group has access to a traditional identification book and the second group were provided with an identification app. We found no difference between the groups in the ability of students to identify birds after three field sessions. Furthermore, we found that students using the traditional book were significantly more likely to identify novel species. Therefore, we find no evidence that mobile technology improved students’ ability to retain what they experienced in the field; indeed, there is evidence that traditional field guides were more useful to students as they attempted to identify new species. Nevertheless, students felt positively about using their own smartphone devices for learning, highlighting that while apps did not lead to an improvement in bird identification ability, they gave greater accessibility to relevant information outside allocated teaching times.     

Comparing Multiple Criteria for Species Identification in Two Recently Diverged Seabirds

Correct species identification is a crucial issue in systematics with key implications for prioritising conservation effort. However, it can be particularly challenging in recently diverged species due to their strong similarity and relatedness. In such cases, species identification requires multiple and integrative approaches. In this study we used multiple criteria, namely plumage colouration, biometric measurements, geometric morphometrics, stable isotopes analysis (SIA) and genetics (mtDNA), to identify the species of 107 bycatch birds from two closely related seabird species, the Balearic (Puffinus mauretanicus) and Yelkouan (P. yelkouan) shearwaters. Biometric measurements, stable isotopes and genetic data produced two stable clusters of bycatch birds matching the two study species, as indicated by reference birds of known origin. Geometric morphometrics was excluded as a species identification criterion since the two clusters were not stable. The combination of plumage colouration, linear biometrics, stable isotope and genetic criteria was crucial to infer the species of 103 of the bycatch specimens. In the present study, particularly SIA emerged as a powerful criterion for species identification, but temporal stability of the isotopic values is critical for this purpose. Indeed, we found some variability in stable isotope values over the years within each species, but species differences explained most of the variance in the isotopic data. Yet this result pinpoints the importance of examining sources of variability in the isotopic data in a case-by-case basis prior to the cross-application of the SIA approach to other species. Our findings illustrate how the integration of several methodological approaches can help to correctly identify individuals from recently diverged species, as each criterion measures different biological phenomena and species divergence is not expressed simultaneously in all biological traits.     

Evolutionary genetics: the evolution of plumage patterns

The identification and sequencing of a gene affecting melanin production in the bananaquit, a bird species notable for its polymorphic plumage colour, paves the way for much greater understanding of the evolution of plumage patterns in birds, and the developmental modulations involved in producing new patterns.     

Persistence of Salmonella enteritidis phage type 4 in the environment and arthropod vectors on an empty free-range chicken farm

The persistence of S. Enteritidis PT4 was studied on a free-range breeding chicken farm which had been depopulated following identification of the organism in breeding birds. The site was sampled periodically for 26 months after depopulation and the organism was found to persist in litter, dried faeces and feed, but not in dust within empty poultry houses, for the whole of that period. Salmonella Enteritidis PT4 was also found in soil samples after 8 months but not 13 months and in faeces from wild mice, foxes and cats but not wild birds or badgers. The organism was also found in adult and larval forms of ground beetles and centipedes. Addition of pullets to a contaminated pen or inclusion of contaminated litter, feed or beetles/larvae to feed did not result in acquisition of infection by birds.     

Applications of radio frequency identification (RFID) in ornithological research: a review

ABSTRACT Radio frequency identification (RFID) technology allows the unique identification of individuals and automated recording of the presence of tagged birds at fixed locations. Investigators have used RFID technology to examine questions related to pair formation, feeding rates, incubation behavior, prospecting behavior by nonbreeding birds, temporal changes in body condition, postfledging movements, dispersal, homing behavior, and other areas of ornithological interest. This technology can enable researchers to explore novel areas of inquiry and gather previously unobtainable quantities of information, allowing birds to record their own behavior without repeated capture and handling. In addition, RFID technology can be linked with other instruments, such as automated weighing devices, video cameras, infrared beams to detect the direction of movement, and temperature loggers, to collect additional data. New, inexpensive RFID technology has removed cost as a major constraint to the wider implementation of RFID in ornithological research. Because the technology requires that focal individuals come near (<10 cm) a reading antenna, RFID is not appropriate for all study systems and research questions. However, integrating RFID technology with additional instrumentation platforms and external data sets will continue to revolutionize studies of avian biology and behavior.     

我国32种鸟类DNA条形码分析

DNA条形码是一种分子分类方法,近年来在物种鉴定方面得到迅速的发展和应用.本研究分析了我国27属32种鸟类(61只)的线粒体细胞色素c氧化酶亚基Ⅰ(COⅠ)基因的条形码片段,分别用阈值法、聚类法和诊断核苷酸进行了分析,探究DNA条形码鉴定我国鸟类的准确性.结果显示,种内CO Ⅰ序列变异很小,种间存在较多的变异位点,种间的遗传距离显著大于种内的遗传距离,DNA条形码序列能够鉴定所有鸟类.     

Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals

In recent years, DNA barcoding has emerged as a powerful tool for species identification. We report an extended validation of a universal DNA mini-barcode for amplification of 130-bp COI segments from 23 specimens collected from a desert environment, including 11 reptiles, five mammals and seven birds. Besides the standard double-annealing protocol, we also tested a more stringent single-annealing protocol. The PCR success rate for the amplification of the mini-barcode region was: mammals (4/5), reptiles (5/11) and birds (4/7). These findings demonstrate the limited utility of universal primers for mini-barcoding, at least for these vertebrate taxa that we collected from the Saudi Arabian desert.     

A Universal Method for the Study of CR1 Retroposons in Nonmodel Bird Genomes

Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.