De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

GigaScience, Journal Year: 2017, Volume and Issue: 6(10)

Published: Aug. 28, 2017

Abstract Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest not completely or accurately assembled, leading unknown errors in analyses additional cloning efforts the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based sequencing diploid assembly potential improvements Sanger-based intermediate-read zebra finch reference Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied neuroscience genomics. With DNA same individuals used generate genomes, generated assemblies with FALCON-Unzip assembler, resulting contigs no gaps megabase range, representing 150-fold 200-fold over current references, respectively. These phased corrected resolved what discovered be numerous misassemblies including missing sequences gaps, erroneous flanking base call difficult-to-sequence regions, complex repeat structure errors, allelic differences between haplotypes. were validated by single long-genome transcriptome reads resulted first time protein-coding specialized species. findings demonstrate impact long reads, previously phasing haplotypes on generating high-quality necessary understanding

Language: Английский

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A Bigger Toolbox: Biotechnology in Biodiversity Conservation

Trends in biotechnology, Journal Year: 2016, Volume and Issue: 35(1), P. 55 - 65

Published: July 14, 2016

Language: Английский

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Avian SDMs: current state, challenges, and opportunities

Journal of Avian Biology, Journal Year: 2017, Volume and Issue: 48(12), P. 1483 - 1504

Published: Oct. 23, 2017

Quantifying species distributions using distribution models (SDMs) has emerged as a central method in modern biogeography. These empirical link occurrence data with spatial environmental information. Since their emergence the 1990s, thousands of scientific papers have used SDMs to study organisms across entire tree life, birds commanding considerable attention. Here, we review current state avian and point challenges future opportunities for specific applications, ranging from conservation biology, invasive predicting seabird distributions, more general topics such modeling diversity, niche evolution seasonal at biogeographic scale. While been criticized being phenomenological nature, inability explicitly account variety processes affecting populations, conclude that they remain powerful tool learn about past, current, – least when limitations assumptions are recognized addressed. We close our by providing an outlook on prospects synergies other disciplines which can play important role.

Language: Английский

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Genomic approaches to understanding population divergence and speciation in birds

Ornithology, Journal Year: 2015, Volume and Issue: 133(1), P. 13 - 30

Published: Oct. 22, 2015

The widespread application of high-throughput sequencing in studying evolutionary processes and patterns diversification has led to many important discoveries. However, the barriers utilizing these technologies interpreting resulting data can be daunting for first-time users. We provide an overview a brief primer relevant methods (e.g., whole-genome sequencing, reduced-representation sequence-capture methods, RNA sequencing), as well steps analysis pipelines loci clustering, variant calling, transcriptome assembly). also review number applications which researchers have used address questions related avian systems. highlight how genomic tools are advancing research by discussing their contributions 3 facets history. focus on (1) general inferences about biogeography biogeographic history, (2) gene flow isolation upon secondary contact hybridization, (3) quantifying levels divergence between closely taxa. find that cases, confirms previous work from traditional molecular markers, although there examples genome-wide genetic markers different biological interpretation. discuss new allow entirely novel questions, conclude outlining intellectual methodological challenges genomics era moves forward.

Language: Английский

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Avian introgression in the genomic era

Avian Research, Journal Year: 2017, Volume and Issue: 8(1)

Published: Nov. 21, 2017

Introgression, the incorporation of genetic material from one (sub)species into gene pool another by means hybridization and backcrossing, is a common phenomenon in birds can provide important insights speciation process. In last decade, toolkit for studying introgression has expanded together with development molecular markers. this review, we explore how genomic data, most recent step methodological progress, impacts different aspects study avian introgression. First, detection hybrids backcrosses improved dramatically. The widely used software package STRUCTURE. Phylogenetic discordance (i.e. loci resulting discordant trees) introgression, although it should be regarded as starting point further analyses, not definitive proof Specifically, disentangling other biological processes, such incomplete lineage sorting, remains challenging endeavour, new techniques, D-statistic, are being developed. addition, phylogenetics might require shift trees to networks. Second, hybrid zones geographical or cline analysis led complex interplay between speciation. However, because each zone just single snapshot continuously changing interaction, studied across temporal and/or spatial scales. A third powerful tool genome scan. debate on which evolutionary processes underlie landscape still ongoing, question whether involved reproductive isolation cluster 'islands speciation' they scattered throughout genome. Exploring landscapes tree life will an exciting field research. Finally, findings these methods incorporated specific scenarios, consequently tested using modelling approach. All all, perspective our understanding evolution general.

Language: Английский

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A history of hybrids? Genomic patterns of introgression in the True Geese

BMC Evolutionary Biology, Journal Year: 2017, Volume and Issue: 17(1)

Published: Aug. 22, 2017

The impacts of hybridization on the process speciation are manifold, leading to distinct patterns across genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered other regions by homogenizing gene flow, resulting a heterogeneous landscape. A consequence this heterogeneity that genomes mosaics different histories can be compared unravel complex and events. However, incomplete lineage sorting (often outcome rapid speciation) result similar patterns. New statistical techniques, such as D-statistic networks, applied disentangle contributions sorting. We during after diversification True Geese (family Anatidae, tribe Anserini, genera Anser Branta) using an exon-based network approach taking advantage discordant tree re-sequencing all taxa clade. In addition, we determine timing introgression reconstruct historical effective population sizes for goose species infer which demographic or biogeographic factors might explain observed introgression. find indications ancient interspecific flow were able pinpoint several putative Specifically, genus Branta, both ancestor White-cheeked (Hawaiian Goose, Canada Cackling Goose Barnacle Goose) Brent hybridized with Red-breasted Goose. One suggests hybrid origin but scenario seems unlikely it not supported analysis. complex, highly reticulated evolutionary history estimation events means networks. reconstruction shows most showed steady increase Pliocene Pleistocene. These large have facilitated contact between diverging species, establishment zones consequent flow. Our analyses suggest influenced introgressive hybridization. used, based genome-wide phylogenetic incongruence analyses, will useful procedure many naturally hybridizing groups.

Language: Английский

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Animal tracking meets migration genomics: transcriptomic analysis of a partially migratory bird species

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(12), P. 3204 - 3216

Published: March 19, 2017

Abstract Seasonal migration is a widespread phenomenon, which found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions exploit more favourable habitats. Migration has been intensively studied birds, display astonishing variation strategies, thus providing powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, genetic basis remains largely unknown. Here, we used state‐of‐the‐art radio‐tracking technology characterize partially population European blackbirds ( Turdus merula ) southern Germany. We compared gene expression resident migrant individuals using high‐throughput transcriptomics blood samples. Analyses sequence revealed nonsignificant structure between differing by their phenotype. detected only four differentially expressed genes migrants residents, might be associated with hyperphagia, moulting enhanced DNA replication transcription. The most pronounced changes occurred birds depending on when, relation date departure, was collected. Overall, this analysis may play crucial roles determining decision migrate, or controlling physiological required onset migration. These results provide new insights into, testable hypotheses for, molecular mechanisms phenotype its underlying other bird species.

Language: Английский

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Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era

Springer eBooks, Journal Year: 2019, Volume and Issue: unknown, P. 151 - 210

Published: Jan. 1, 2019

Language: Английский

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Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra

MycoKeys, Journal Year: 2018, Volume and Issue: 43, P. 91 - 113

Published: Dec. 12, 2018

Neuropogonoid species in the lichen-forming fungal genus Usnea exhibit great morphological variation that can be misleading for delimitation of species. We specifically focused on two closely-related, predominantly Antarctic differing reproductive mode and representing a so-called pair: asexual U.antarctica sexual U.aurantiacoatra . Previous studies have revealed contradicting results. While multi-locus based DNA sequence data provided evidence these taxa might conspecific, microsatellite suggested they represent distinct lineages. By using RADseq, we generated thousands homologous markers to build robust phylogeny Furthermore, successfully implemented fine-scale population genomic analyses such as DAPC fineRADstructure. Both are readily delimited phylogenetic inferences and, therefore, hypothesis both conspecific was rejected. Population also strongly confirmed separated genomes additionally, showed different levels co-ancestry substructure within each Lower than may derived from wider distributional range former Our results demonstrate utility this RADseq method tracing dynamics lichens future analyses.

Language: Английский

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Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

European Journal of Wildlife Research, Journal Year: 2017, Volume and Issue: 63(6)

Published: Nov. 30, 2017

Disruption of naturally evolved spatial patterns genetic variation and local adaptations is a growing concern in wildlife management conservation. During the last decade, releases native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, one few terrestrial migratory vertebrates subjected large-scale for hunting purposes. It most numerous widespread duck world, yet each year more than three million farmed mallard ducklings released into wild European Union alone increase harvestable population. study aimed determine effects such species, specifically if mallards differ genetically among subpopulations Europe, there signs admixture between two groups, structure population changed since began 1970s, current data matches global across Northern hemisphere. We used Bayesian clustering (Structure software) Discriminant Analysis Principal Components (DAPC) analyze historical present-day (n = 171 n 209, respectively) as well 211) from six countries inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed clear differentiation mallards. Admixed individuals were found population, implicating introgression despite low survival Such cryptic would alter composition populations may unknown long-term consequences

Language: Английский

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