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Donald J Brightsmith - One of the best experts on this subject based on the ideXlab platform.
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predation on Scarlet Macaw ara macao cyanoptera chicks by collared forest falcons micrastur semitorquatus in the maya biosphere reserve guatemala
Ornitologia Neotropical, 2017Co-Authors: Rony Garciaanleu, Donald J Brightsmith, Gabriela Poncesantizo, Steve Gulick, Janice D Boyd, Roan McnabAbstract:Abstract ∙ Through efforts of the Wildlife Conservation Society, poaching in an important Scarlet Macaw ( Ara macao cyanoptera ) nesting area in the Maya Biosphere Reserve in Guatemala had been reduced to zero by 2004. However, during long‐term monitoring of the nesting success of Scarlet Macaws in the Maya Biosphere Reserve, unexplained or unknown disappearance of chicks from nests was common despite the aforementioned reduction in poaching. To determine the cause of these disappearances, we installed five video camera surveillance systems in the nest cavities during the 2008 nesting season. Fatal attacks on chicks by Collared Forest Falcons ( Micrastur semitorquatus ) were recorded at three of these nests. This result highlights natural predation as a limiting factor for the recruitment of new individuals into the Scarlet Macaw population in the Maya Biosphere Reserve even when poaching is suppressed. Resumen ∙ Depredacion de pichones de Guacamayas Rojas ( Ara macao cyanoptera ) por Halcones Selvaticos de Collar ( Micrastur semitorquatus ) en la Reserva de la Biosfera Maya, Guatemala A traves de los esfuerzos de la Wildlife Conservation Society, el robo de pichones de Guacamayas Rojas ( Ara macao cyanoptera ) en una importante zona de anidacion de la Reserva de la Biosfera Maya en Guatemala ha sido reducido a cero desde el ano 2004. Sin embargo, durante el monitoreo a largo plazo del exito de anidacion de las guacamayas rojas en la Reserva de la Biosfera Maya, la desaparicion por razones desconocidas de pichones de los nidos fue comun a pesar de la reduccion de robos anteriormente mencionada. Para determinar la causa de estas desapariciones, instalamos cinco sistemas de vigilancia de camaras de video en los nidos durante la temporada de anidacion de 2008. En tres de estos cinco nidos se registraron ataques fatales contra pichones por parte del Halcon Selvatico de Collar ( Micrastur semitorquatus ). Este resultado destaca la depredacion natural como un factor limitante para el reclutamiento de nuevos individuos en la poblacion de Guacamayas Rojas en la Reserva de la Biosfera Maya, incluso cuando se suprime el robo de pichones.
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A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)
2016Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Poul Liboriussen, Colleen A Fisher, Elaine Owens, Ganesh Viswanathan, Yvette Halley, Ian R. TizardAbstract:Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (.1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two Scarlet Macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the Scarlet Macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the Scarlet Macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence fo
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A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene
2016Co-Authors: Yvette A Halley, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Ian R. Tizard, Jared E. Decker, Eric Bhattarai, Charles D. Johnson, Dale Rollins, Markus J. PetersonAbstract:Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., Scarlet Macaw; Ara macao). More than 90 % of the assembled bobwhite genome was captured within,40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for.14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the Scarlet Macaw provided evidence for population bottlenecks which wer
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Blood Biochemical Values of Wild Scarlet Macaw (Ara macao macao) Nestlings and Adults
Journal of avian medicine and surgery, 2016Co-Authors: Lauren Peruffo, Janice D Boyd, Sharman Hoppes, Donald J BrightsmithAbstract:Abstract Blood biochemical values are useful as indicators of disease in veterinary practice and for health assessments of free-ranging animal populations. We analyzed blood biochemical values for free-living nestling and adult Scarlet Macaws (Ara macao macao) in southeastern Peru with an Abaxis VetScan VS2 portable analyzer with Avian/Reptilian Profile Plus rotors. The resulting data were used to create provisional age-independent reference intervals for this instrument for wild Scarlet Macaw nestlings, calculate blood biochemical ranges for this instrument for wild adults, and examine age-related trends in nestlings. Levels of 11 parameters were studied: albumin, aspartate aminotransferase, calcium, creatine kinase, globulin, glucose, phosphorus, potassium, total protein, sodium, and uric acid. Bile acid levels were generally below the instrument detection level and were not evaluated. Most values and their trends with bird age were comparable to those observed in captive large Macaw nestlings. Albumin,...
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an evaluation of primers for microsatellite markers in Scarlet Macaw ara macao and their performance in a peruvian wild population
Conservation Genetics Resources, 2015Co-Authors: George Olah, Robert Heinsohn, Jose R Espinoza, Donald J Brightsmith, Rod PeakallAbstract:Primer pairs were designed for 41 di-nucleotide microsatellite loci identified from across the full genome of the Scarlet Macaw (Ara macao). We present the best 30 polymorphic loci with 5–22 alleles, 3–14 effective alleles and expected heterozygosities of 0.669–0.930. These markers will facilitate population genetic and conservation genetic studies on Macaws.
Christopher Vaughan - One of the best experts on this subject based on the ideXlab platform.
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Scarlet Macaw, Ara macao, (Psittaciformes: Psittacidae) diet in Central Pacific Costa Rica
2016Co-Authors: Christopher Vaughan, Nicole Nemeth, Leonel MarinerosAbstract:Costa Rica. Feeding data acquired in this study were not collected systematically, but opportunistically when-ever Macaws were observed feeding. To supplement feeding observations, we conducted interviews with local residents. Scarlet Macaws fed on seeds, fruits, leaves, flowers and/or bark of 43 plant species. Various plant parts eaten by Macaws from several tree species contain secondary compounds toxic to humans, and additional species included in their diet are nonnative, introduced for agricultural purposes. Important Macaw feeding tree species are Ceiba pentandra, Schizolobium parahybum, and Hura crepitans; these species are also crucial to this Macaw population because of nest cavities they provide. The results of this study contribute to the conservation of Scarlet Macaws in Central Pacific Costa Rica through promoting protection of individual trees, and through local elementary school reforestation programs focusing on tree species that Macaws use for feeding and/or nesting. Scarlet Macaw conservation is extremely important, as numerous population pressures have cause
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genetic patterns and conservation of the Scarlet Macaw ara macao in costa rica
Conservation Genetics, 2016Co-Authors: Christopher Vaughan, Otto Monge, Kari Schmidt, Gustavo A GutierrezespeletaAbstract:Once widely distributed throughout the lowland forests of Costa Rica, Scarlet Macaws (Ara macao) have been reduced to two major, geographically separated, populations along the Pacific slope. Past demographic declines raise conservation concerns regarding the detrimental effects of population fragmentation. This investigation aimed to evaluate the current status of Scarlet Macaws along the Pacific slope by examining levels of genetic variation and patterns of genetic structure within and among remnant populations. Statistical analyses using multilocus genotypes revealed strong differentiation between Central and South Pacific populations, suggesting local geographic barriers have historically restricted gene flow between these localities. High genetic diversity suggests neither population suffers from genetic erosion, likely resulting from relatively large population sizes and high dispersal capacity and longevity. However, evidence of disequilibrium within the Central Pacific population infers anthropogenic threats have disrupted natural population dynamics. These results advocate on focusing available resources on habitat restoration and nest protection, as a means to assist in reestablishing demographic stability and maintain the genetic health of wild Scarlet Macaws in Costa Rica.
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doi:10.1017/S0959270905000092 Printed in the United Kingdom Response of a Scarlet Macaw Ara macao population to conservation practices in Costa
2015Co-Authors: Christopher Vaughan, Nicole M Nemeth, John Cary, Stanley TempleAbstract:The Central Pacific Conservation Area contains one of Costa Rica’s two viable, but threatened Scarlet Macaw Ara macao populations. For 14 years (1990–2003), we monitored the size of this population. Non-linear models fitted to 1990–1994 observations revealed seasonal and long-term changes in population size. The peak of annual population size occurred in August, with a cyclic range of about 90 birds between the lowest and highest points of the annual cycle. The best model also revealed a decline in population size of approximately eight birds counted per year or 4 % of the total population per year (1990–1994). Young-to-adult ratios calculated for the month of August during this study fluctuated around a baseline that averaged 6.1 % a year (1990–2003). These ratios exceeded 8 % for three different years (1995, 1996 and 2000). All three of these “good ” recruitment years occurred after management began, and two of them were associated with zealous anti-poaching efforts that ultimately could not be sustained. After intensive management practices began in 1995, the August counts increased by about 37 indi-viduals in two years (1995–1996) to an average 243 individuals, which remained almost constant up to 2003. Management practices included creation of a local conservation organization that coordinated environmental education, artificial nest construction, networking among stakehold-ers and with governmental authorities, and artificial and natural nest protection. Although Scarlet Macaw conservation efforts have been inconsistent since 1997, our study demonstrates that collaborative conservation by local stakeholders increased the population of this threatened species in 1995–1996, and from 1996 to present the population has sustained itself
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Beach almond (Terminalia catappa, Combretaceae) seed production and predation by Scarlet Macaws (Ara macao) and variegated squirrels (Sciurus variegatoides)
Revista de biologia tropical, 2014Co-Authors: Jonathan J. Henn, Michael B. Mccoy, Christopher VaughanAbstract:Knowledge of ecological impacts of exotic beach almond (Terminalia catappa) in the central Pacific of Costa Rica are little known, but studies have found this species to be a potentially important food source for endangered Scarlet Macaws (Ara macao). In this study, reproductive phenology and seed predation by variegated squirrels (Sciurus variegatoides) and Scarlet Macaws were measured during March and April 2011 on beaches of central Pacific coastal Costa Rica. Seed productivity and predation levels were quantified on a weekly basis for 111 beach almond trees to assess the importance of beach almond as a food source for Scarlet Macaws and the extent of resource partitioning between seed predators. Seed production of the trees was great (about 194 272 seeds) and approximately 67% of seeds were predated by seed predators. Macaws consumed an estimated 49% of seeds while squirrels consumed 18%. Additionally, evidence of resource partitioning between squirrels and Macaws was found. Scarlet Macaws preferred to feed on the northern side and edge of the canopy while squirrels preferred to feed on the southern and inside parts of the canopy. Both species ate most seeds on the ocean side of the tree. Despite the status of this tree as an exotic species, the beach almond appears to be an important resource for Scarlet Macaw population recovery. The resource produced by this tree should be taken into account as reforestation efforts continue in Costa Rica.
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Scarlet Macaw ara macao psittaciformes psittacidae diet in central pacific costa rica
Revista De Biologia Tropical, 2014Co-Authors: Christopher Vaughan, Nicole M Nemeth, Leonel MarinerosAbstract:From 1993 to 1997, we observed Scarlet Macaw (Ara macao) feeding behavior in Central Pacific Costa Rica. Feeding data acquired in this study were not collected systematically, but opportunistically when- ever Macaws were observed feeding. To supplement feeding observations, we conducted interviews with local residents. Scarlet Macaws fed on seeds, fruits, leaves, flowers and/or bark of 43 plant species. Various plant parts eaten by Macaws from several tree species contain secondary compounds toxic to humans, and additional species included in their diet are nonnative, introduced for agricultural purposes. Important Macaw feeding tree species are Ceiba pentandra, Schizolobium parahybum, and Hura crepitans; these species are also crucial to this Macaw population because of nest cavities they provide. The results of this study contribute to the conservation of Scarlet Macaws in Central Pacific Costa Rica through promoting protection of individual trees, and through local elementary school reforestation programs focusing on tree species that Macaws use for feeding and/or nesting. Scarlet Macaw conservation is extremely important, as numerous population pressures have caused significant declines in Macaw numbers in Costa Rica. Rev. Biol. Trop. 54 (3): 919-926. Epub 2006 Sept. 29.
George Olah - One of the best experts on this subject based on the ideXlab platform.
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an evaluation of primers for microsatellite markers in Scarlet Macaw ara macao and their performance in a peruvian wild population
Conservation Genetics Resources, 2015Co-Authors: George Olah, Robert Heinsohn, Jose R Espinoza, Donald J Brightsmith, Rod PeakallAbstract:Primer pairs were designed for 41 di-nucleotide microsatellite loci identified from across the full genome of the Scarlet Macaw (Ara macao). We present the best 30 polymorphic loci with 5–22 alleles, 3–14 effective alleles and expected heterozygosities of 0.669–0.930. These markers will facilitate population genetic and conservation genetic studies on Macaws.
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nest site selection and efficacy of artificial nests for breeding success of Scarlet Macaws ara macao macao in lowland peru
Journal for Nature Conservation, 2014Co-Authors: George Olah, Robert Heinsohn, Gabriela Vigo, Donald J BrightsmithAbstract:Psittacidae (parrots) have the most threatened species of any bird family in the world. Most parrots are obligate secondary cavity nesters, and can be limited in their breeding success by the availability and quality of nest hollows. However, nesting opportunities for parrots can be increased by provision of artificial nest boxes. The Tambopata Macaw Project has been studying the breeding ecology and natural history of the Scarlet Macaw Ara macao macao in the south-eastern Peruvian Amazon for over 20 years by monitoring natural nest hollows and two types of artificial nest (wooden and PVC). We present data for breeding success in natural and artificial nests over 12 consecutive breeding seasons. The aims of this study were to: (a) determine the nesting requirements and reproductive success of breeding Macaws; and, (b) compare the efficacy of the two types of artificial nests and natural nest cavities. Our data showed a high rate of reoccupation of successful nests in consecutive years and that nests in artificial and natural nests had very similar reproductive parameters. Our results indicate that artificial nest types can be used by conservation managers seeking to assist A. macao populations where nest hollows are in short supply, and that artificial nests can contribute important data to natural history studies of species where access to natural nests is limited.
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philornis sp bot fly larvae in free living Scarlet Macaw nestlings and a new technique for their extraction
Veterinary Parasitology, 2013Co-Authors: George Olah, Gabriela Vigo, Lizzie Ortiz, Lajos Rozsa, Donald J BrightsmithAbstract:Abstract Bot fly larvae (Philornis genus) are obligate subcutaneous blood-feeding parasites of Neotropical birds including psittacines. We analyze twelve years of data on Scarlet Macaw (Ara macao) nestlings in natural and artificial nests in the lowland forests of southeastern Peru and report prevalence and intensity of Philornis parasitism. Bot fly prevalence was 28.9% while mean intensity was 5.0 larvae per infected chick. Prevalence in natural nests (11%, N = 90 nestlings) was lower than in wooden nest-boxes (39%, N = 57) and PVC boxes (39%, N = 109). We describe a new technique of removing Philornis larvae using a reverse syringe design snake bite extractor. We compare this new technique to two other methods for removing bots from Macaw chicks and find the new method the most suitable.
Ganesh Viswanathan - One of the best experts on this subject based on the ideXlab platform.
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A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)
2016Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Poul Liboriussen, Colleen A Fisher, Elaine Owens, Ganesh Viswanathan, Yvette Halley, Ian R. TizardAbstract:Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (.1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two Scarlet Macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the Scarlet Macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the Scarlet Macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence fo
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a multi platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw ara macao
PLOS ONE, 2013Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Terje Raudsepp, Poul Liboriussen, Yvette A Halley, Colleen A Fisher, Elaine Owens, Ganesh ViswanathanAbstract:Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 highquality putative single nucleotide polymorphisms, the final genome assembly (.1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two Scarlet Macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the Scarlet Macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the Scarlet Macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.
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Consensus Scarlet Macaw (Ara macao) Karyotype.
2013Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Terje Raudsepp, Poul Liboriussen, Colleen A Fisher, Elaine Owens, Yvette Halley, Ganesh ViswanathanAbstract:Cytogenetic analyses indicate that the Scarlet Macaw diploid chromosome number is 2n = 62–64, as inferred from chromosome counts of multiple cells derived from three individuals, including the sequenced female Macaw (Neblina). All investigated Scarlet Macaws had 22 macrochromosomes, which included 10 pairs of autosomes and the sex chromosomes, and approximately 40–42 microchromosomes, the numbers of which varied due to technical reasons such as metaphase overlaps, variation in staining, and chromosome spreading.
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Chicken-Scarlet Macaw (Ara macao) Comparative Chromosome Painting (ZooFISH).
2013Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Terje Raudsepp, Poul Liboriussen, Colleen A Fisher, Elaine Owens, Yvette Halley, Ganesh ViswanathanAbstract:Using chicken flow sorted macrochromosomes (GGA1-GGA9) as well as GGAZ and GGAW, the homologous chromosome segments of the Scarlet Macaw were established via fluorescent in situ hybridization. All flow sorted probes were validated via hybridization to chicken metaphase spreads (see Figure S1).
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Major repetitive content predicted by RepeatMasker within the Scarlet Macaw first generation de novo genome assembly (SMACv1.0, SMACv1.1).
2013Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Terje Raudsepp, Poul Liboriussen, Colleen A Fisher, Elaine Owens, Yvette Halley, Ganesh ViswanathanAbstract:Major repetitive content predicted by RepeatMasker within the Scarlet Macaw first generation de novo genome assembly (SMACv1.0, SMACv1.1).
Scot E Dowd - One of the best experts on this subject based on the ideXlab platform.
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A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)
2016Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Poul Liboriussen, Colleen A Fisher, Elaine Owens, Ganesh Viswanathan, Yvette Halley, Ian R. TizardAbstract:Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (.1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two Scarlet Macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the Scarlet Macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the Scarlet Macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence fo
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A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene
2016Co-Authors: Yvette A Halley, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Ian R. Tizard, Jared E. Decker, Eric Bhattarai, Charles D. Johnson, Dale Rollins, Markus J. PetersonAbstract:Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., Scarlet Macaw; Ara macao). More than 90 % of the assembled bobwhite genome was captured within,40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for.14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the Scarlet Macaw provided evidence for population bottlenecks which wer
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A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene.
PloS one, 2014Co-Authors: Yvette A Halley, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Jared E. Decker, Charles D. Johnson, Dale Rollins, Eric K. Bhattarai, Ian Tizard, Markus J. PetersonAbstract:Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., Scarlet Macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within 14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the Scarlet Macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the Scarlet Macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.
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Comparative Demographic History Analysis and PSMC Effective Population Size Estimates for Bobwhite (Colinus virginianus) (A) and Scarlet Macaw (Ara macao) (B).
2014Co-Authors: Yvette A Halley, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Ian R. Tizard, Jared E. Decker, Eric Bhattarai, Charles D. Johnson, Dale Rollins, Markus J. PetersonAbstract:Estimates of effective population size are presented on the y-axis as the scaled mutation rate. The bottom x-axis represents per-site pairwise sequence divergence and the top x-axis represents years before present, both on a log scale. Generation intervals of 1.22 years for the bobwhite (Colinus virginianus) and 12.7 years for the Scarlet Macaw (Ara macao) were used (See Methods). In the absence of known per-generation de novo mutation rates for the bobwhite and the Scarlet Macaw, we used the two human mutation rates (μ) of 1.1×10−8 and 2.5×10−8 per generation [124], [125] (see Methods). Darker lines represent the population size inference, and lighter, thinner lines represent 100 bootstraps to quantify uncertainty of the inference.
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a multi platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw ara macao
PLOS ONE, 2013Co-Authors: C M Seabury, Donald J Brightsmith, Scot E Dowd, Paul M Seabury, Terje Raudsepp, Poul Liboriussen, Yvette A Halley, Colleen A Fisher, Elaine Owens, Ganesh ViswanathanAbstract:Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 highquality putative single nucleotide polymorphisms, the final genome assembly (.1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two Scarlet Macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the Scarlet Macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the Scarlet Macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.
