ORCID Profile
0000-0002-0861-0191
Current Organisations
Zhejiang University of Technology
,
Newcastle University
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Publisher: Wiley
Date: 18-07-2022
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.
Publisher: The Royal Society
Date: 06-2016
Abstract: Humans and animals show increased attention towards threatening stimuli when they are in increased states of anxiety. The few animal studies that have examined this phenomenon, known as attention bias, have applied environmental manipulations to induce anxiety but the effects of drug-induced anxiety levels on attention bias have not been demonstrated. Here, we present an attention bias test to identify high and low anxiety states in sheep using pharmacological manipulation. Increased anxiety was induced using 1-methyl-chlorophenylpiperazine (m-CPP) and decreased anxiety with diazepam, and then we examined the behaviour of sheep in response to the presence of a dog as a threat. Increased attention towards the threat and increased vigilance were shown in sheep that received the m-CPP and reduced in sheep receiving the diazepam. The modulated attention towards a threat displayed by the m-CPP and diazepam animals suggests that attention bias can assess different levels of anxiety in sheep. Measuring attention bias has the potential to improve animal welfare assessment protocols.
Publisher: Elsevier BV
Date: 11-2020
DOI: 10.1016/J.NEUBIOREV.2020.07.012
Abstract: Just as happy people see the proverbial glass as half-full, 'optimistic' or 'pessimistic' responses to ambiguity might also reflect affective states in animals. Judgement bias tests, designed to measure these responses, are an increasingly popular way of assessing animal affect and there is now a substantial, but heterogeneous, literature on their use across different species, affect manipulations, and study designs. By conducting a systematic review and meta-analysis of 459 effect sizes from 71 studies of non-pharmacological affect manipulations on 22 non-human species, we show that animals in relatively better conditions, assumed to generate more positive affect, show more 'optimistic' judgements of ambiguity than those in relatively worse conditions. Overall effects are small when considering responses to all cues, but become more pronounced when non-ambiguous training cues are excluded from analyses or when focusing only on the most ergent responses between treatment groups. Task type (go/no-go go/go active choice), training cue reinforcement (reward-punishment reward-null reward-reward) and sex of animals emerge as potential moderators of effect sizes in judgement bias tests.
Publisher: Cold Spring Harbor Laboratory
Date: 23-08-2021
DOI: 10.1101/2021.08.22.457241
Abstract: 1. During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species’ ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species’ invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and ergent evolutionary change between contemporary native and invasive range s les and their common ancestral population. To do this, we use reduced-representation sequencing of native s les collected recently in north-western Europe and invasive s les from Australia, together with museum specimens s led in the UK during the mid-19 th Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants (e.g. TCDD) and food carbohydrate content. We also identified ergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary s les. Our results demonstrate the value of including historical s les in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.
Publisher: Cold Spring Harbor Laboratory
Date: 08-04-2021
DOI: 10.1101/2021.04.07.438753
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 genome ( S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (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. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. 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 counter-intuitive behaviour in traditional BUSCO metrics, and present B uscomp , a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.
Publisher: Elsevier BV
Date: 2020
Publisher: Elsevier BV
Date: 10-2020
Publisher: Cold Spring Harbor Laboratory
Date: 19-05-2021
DOI: 10.1101/2021.05.19.442026
Abstract: A species’ success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings ( Sturnus vulgaris ) established populations in Australia and North America in the 19 th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations from three continents to determine how demographic processes interact with rapid adaptive evolution to generate similar genetic patterns in these recent and replicated invasions. Our results confirm that a post-bottleneck expansion may in fact support local adaptation. We find that specific genomic regions have differentiated even on this short evolutionary timescale, and suggest that selection best explains differentiation in at least two of these regions. This infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors), perhaps in part due to the demographic boom intrinsic to many invasions.
Publisher: Elsevier BV
Date: 05-2020
Publisher: Wiley
Date: 06-02-2022
DOI: 10.1111/MEC.16353
Abstract: During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species’ ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species’ invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris , to identify parallel and ergent evolutionary change between contemporary native and invasive range s les and their common ancestral population. To do this, we use reduced‐representation sequencing of native s les collected recently in northwestern Europe and invasive s les from Australia, together with museum specimens s led in the UK during the mid‐19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified ergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary s les. Our results demonstrate the value of including historical s les in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.
Publisher: American Chemical Society (ACS)
Date: 15-01-2021
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Melissa Bateson.