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Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 2024; 31:dsae005. [PMID: 38366840 PMCID: PMC10917472 DOI: 10.1093/dnares/dsae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.
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Affiliation(s)
- Katarina C Stuart
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | | | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- School of Life and Environmental Sciences,University of Sydney, Sydney, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
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2
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Global invasion history and native decline of the common starling: insights through genetics. Biol Invasions 2023. [DOI: 10.1007/s10530-022-02982-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
AbstractFew invasive birds are as globally successful as the Common or European Starling (Sturnus vulgaris). Native to the Palearctic, the starling has been intentionally introduced to North and South America, South Africa, Australia, and the Pacific Islands, enabling us to explore species traits that may contribute to its invasion success. Coupling the rich studies of life history and more recent explorations of genomic variation among invasions, we illustrate how eco-evolutionary dynamics shape the invasion success of this long-studied and widely distributed species. Especially informative is the comparison between Australian and North American invasions, because these populations colonized novel ranges concurrently and exhibit shared signals of selection despite distinct population histories. In this review, we describe population dynamics across the native and invasive ranges, identify putatively selected traits that may influence the starling’s spread, and suggest possible determinants of starling success world-wide. We also identify future opportunities to utilize this species as a model for avian invasion research, which will inform our understanding of species’ rapid evolution in response to environmental change.
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Stuart KC, Edwards RJ, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL, Rollins LA. Transcript- and annotation-guided genome assembly of the European starling. Mol Ecol Resour 2022; 22:3141-3160. [PMID: 35763352 PMCID: PMC9796300 DOI: 10.1111/1755-0998.13679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/10/2022] [Indexed: 01/01/2023]
Abstract
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.
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Affiliation(s)
- Katarina C. Stuart
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Richard J. Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Yuanyuan Cheng
- School of Life and Environmental SciencesThe University of Sydney, SydneyNew South WalesAustralia
| | - Wesley C. Warren
- Department of Animal Sciences, Institute for Data Science and InformaticsThe University of MissouriColumbiaMissouriUSA
| | - David W. Burt
- Office of the Deputy Vice‐Chancellor (Research and Innovation)The University of QueenslandBrisbaneAustralia
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Natalie R. Hofmeister
- Department of Ecology and Evolutionary BiologyCornell UniversityNew YorkUSA,Fuller Evolutionary Biology ProgramCornell Lab of OrnithologyNew YorkUSA
| | - Scott J. Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | | | - Melissa Bateson
- Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Matthew C. Brandley
- Section of Amphibians and ReptilesCarnegie Museum of Natural HistoryPittsburghPennsylvaniaUSA
| | - Katherine L. Buchanan
- School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Phillip Cassey
- Invasion Science & Wildlife Ecology LabUniversity of AdelaideAdelaideAustralia
| | - David F. Clayton
- Department of Genetics & BiochemistryClemson UniversitySouth CarolinaUSA
| | - Tim De Meyer
- Department of Data Analysis & Mathematical Modelling, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Simone L. Meddle
- The Roslin Institute, The Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia,School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
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4
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A recent invasive population of the European starling sturnus vulgaris has lower genetic diversity and higher fluctuating asymmetry than primary invasive and native populations. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02653-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Bodt LH, Rollins LA, Zichello JM. Contrasting mitochondrial diversity of European starlings ( Sturnus vulgaris) across three invasive continental distributions. Ecol Evol 2020; 10:10186-10195. [PMID: 33005374 PMCID: PMC7520211 DOI: 10.1002/ece3.6679] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/30/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022] Open
Abstract
European starlings (Sturnus vulgaris) represent one of the most widespread and problematic avian invasive species in the world. Understanding their unique population history and current population dynamics can contribute to conservation efforts and clarify evolutionary processes over short timescales. European starlings were introduced to Central Park, New York in 1890, and from a founding group of about 100 birds, they have expanded across North America with a current population of approximately 200 million. There were also multiple introductions in Australia in the mid-19th century and at least one introduction in South Africa in the late 19th century. Independent introductions on these three continents provide a robust system to investigate invasion genetics. In this study, we compare mitochondrial diversity in European starlings from North America, Australia, and South Africa, and a portion of the native range in the United Kingdom. Of the three invasive ranges, the North American population shows the highest haplotype diversity and evidence of both sudden demographic and spatial expansion. Comparatively, the Australian population shows the lowest haplotype diversity, but also shows evidence for sudden demographic and spatial expansion. South Africa is intermediate to the other invasive populations in genetic diversity but does not show evidence of demographic expansion. In previous studies, population genetic structure was found in Australia, but not in South Africa. Here we find no evidence of population structure in North America. Although all invasive populations share haplotypes with the native range, only one haplotype is shared between invasive populations. This suggests these three invasive populations represent independent subsamples of the native range. The structure of the haplotype network implies that the native-range sampling does not comprehensively characterize the genetic diversity there. This study represents the most geographically widespread analysis of European starling population genetics to date.
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Affiliation(s)
- Louise Hart Bodt
- Educational Laboratory for Comparative Genomics and Human OriginsAmerican Museum of Natural HistoryNew YorkNYUSA
- Cold Spring Harbor LaboratoryDNA Learning CenterCold Spring HarborNYUSA
- Department of BiologyNew York UniversityNew YorkNYUSA
| | - Lee Ann Rollins
- Evolution & Ecology Research CentreSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNSWAustralia
| | - Julia M. Zichello
- Educational Laboratory for Comparative Genomics and Human OriginsAmerican Museum of Natural HistoryNew YorkNYUSA
- Division of AnthropologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Division of Natural SciencesCollege of Mt. St. VincentBronxNYUSA
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Bentz AB, Thomas GWC, Rusch DB, Rosvall KA. Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly. Sci Rep 2019; 9:15849. [PMID: 31676844 PMCID: PMC6825141 DOI: 10.1038/s41598-019-52312-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, transcriptomic resources are scarce. To further advance the utility of this system for biologists across disciplines, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,739 transcripts, which we aligned to 14,717 high confidence protein-coding genes. We then characterized each tissue with regard to its unique genes and processes and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird and advance our understanding of fundamental questions in evolutionary and organismal biology.
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Affiliation(s)
- Alexandra B Bentz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA. .,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA.
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Kimberly A Rosvall
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
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Richardson MF, Sherwin WB, Rollins LA. De Novo Assembly of the Liver Transcriptome of the European Starling, Sturnus vulgaris. J Genomics 2017; 5:54-57. [PMID: 28529652 PMCID: PMC5436464 DOI: 10.7150/jgen.19504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The European starling, Sturnus vulgaris, is a prolific and worldwide invasive species that also has served as an important model for avian ecological and invasion research. Although the genome sequence recently has become available, no transcriptome data have been published for this species. Here, we have sequenced and assembled the S. vulgaris liver transcriptome, which will provide a foundational resource for further annotation and validation of the draft genome. Moreover, it will be important for ecological and evolutionary studies investigating the genetic factors underlying rapid evolution and invasion success in this global invader.
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Affiliation(s)
- Mark F Richardson
- Deakin University, Bioinformatics Core Research Group, 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia.,Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - William B Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,Cetacean Research Unit, Murdoch University, South Road, Murdoch, Western Australia 6150, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia
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