Victorian Alpine Plot Network (Alpine Long Term Monitoring - Community Changes): Multi-taxa Phylogenomic Data, 2012–2013
Abstract: Global change poses significant and urgent challenges for biodiversity conservation. Species persistence under a rapidly changing environment ultimately depends on abilities to disperse to favourable habitats or adapt in situ by plastic or evolutionary mechanisms. Conservation strategies preserving endemism and adaptive potential are critical.
This study aims to investigate the phylogeographic history of Victorian Alpine plants using high-density genetic markers. Multi-taxa genomic data was compared to determine common phylogeographic patterns and identify evolutionary processes shaping biodiversity. Spatial patterns of genetic structure were used to delineate evolutionary bioregions and refugia of high conservation value.
Life-history traits have seldom been explicitly within a landscape genetic framework. Spatial isolation is a key component of genetic structure for sessile organisms. This study demonstrates that life-history traits are primary drivers of inter-population connectivity and genetic structure. Differences across taxa impacted on patterns of genetic structure on fine spatial scales, while common patterns were observed at broad scales regardless of life-history
traits. These findings complement other Australian Alpine genetic studies indicate that flora and fauna in Victorian Alps share a common genetic structure and phylogeographic history driven by unique processes. The geomorphology of the Victorian Alps has clearly driven the evolutionary trajectories of the native flora and fauna. This approach could inform evidence based conservation policy. Previously undelineated cryptic species were revealed by this study highlighting limitations of traditional taxonomy and the utility of new approaches. This project demonstrates how genomic technologies can characterise evolutionary processes at landscape scales, and detect important patterns in at-risk ecosystems. Sampling method: As per "Materials and Methods" section of the Honours thesis. Study extent: Leaf tissue was collected over the summer 2012-2013, with additional sampling at Mount Stirling and Mount Howitt in October 2013. A summary of the spatial and taxonomic extent of the study can be found in the "Tables" section of the Honours thesis. Project funding: Between 2012 and 2018 this project was part of the Long Term Ecological Research Network (LTERN) supported by the Australian Government’s Terrestrial Ecosystems Research Network (www.tern.org.au) – an Australian research infrastructure facility established under the National Collaborative Research Infrastructure Strategy and Education Infrastructure Fund–Super Science Initiative through the Department of Industry, Innovation, Science, Research and Tertiary Education.
traits. These findings complement other Australian Alpine genetic studies indicate that flora and fauna in Victorian Alps share a common genetic structure and phylogeographic history driven by unique processes. The geomorphology of the Victorian Alps has clearly driven the evolutionary trajectories of the native flora and fauna. This approach could inform evidence based conservation policy. Previously undelineated cryptic species were revealed by this study highlighting limitations of traditional taxonomy and the utility of new approaches. This project demonstrates how genomic technologies can characterise evolutionary processes at landscape scales, and detect important patterns in at-risk ecosystems. Sampling method: As per "Materials and Methods" section of the Honours thesis. Study extent: Leaf tissue was collected over the summer 2012-2013, with additional sampling at Mount Stirling and Mount Howitt in October 2013. A summary of the spatial and taxonomic extent of the study can be found in the "Tables" section of the Honours thesis. Project funding: Between 2012 and 2018 this project was part of the Long Term Ecological Research Network (LTERN) supported by the Australian Government’s Terrestrial Ecosystems Research Network (www.tern.org.au) – an Australian research infrastructure facility established under the National Collaborative Research Infrastructure Strategy and Education Infrastructure Fund–Super Science Initiative through the Department of Industry, Innovation, Science, Research and Tertiary Education.
Type
collection
Title
Victorian Alpine Plot Network (Alpine Long Term Monitoring - Community Changes): Multi-taxa Phylogenomic Data, 2012–2013
Alternate Title
Victorian Alpine Plot Network: Multi-taxa Phylogenomic Data Long Term Monitoring - Community Changes, 2012–2013
Collection Type
Dataset
Access Privileges
Long Term Ecological Research Network
DOI - Digital Object Identifier
10.25911/5c0df29c2fc1f
Metadata Language
English
Data Language
English
Brief Description
This study aims to investigate the phylogeographic history of Victorian Alpine plants using high-density genetic markers. Multi-taxa genomic data was compared to determine< common phylogeographic patterns and identify evolutionary processes shaping biodiversity. Spatial patterns of genetic structure were used to delineate evolutionary bioregions and refugia of high conservation value.
A synopsis of related data packages which have been collected as part of the Victorian Alpine Plot Network’s full program is provided at https://doi.org/10.25911/5c133088bc5b9.
Full Description
Abstract: Global change poses significant and urgent challenges for biodiversity conservation. Species persistence under a rapidly changing environment ultimately depends on abilities to disperse to favourable habitats or adapt in situ by plastic or evolutionary mechanisms. Conservation strategies preserving endemism and adaptive potential are critical.
This study aims to investigate the phylogeographic history of Victorian Alpine plants using high-density genetic markers. Multi-taxa genomic data was compared to determine common phylogeographic patterns and identify evolutionary processes shaping biodiversity. Spatial patterns of genetic structure were used to delineate evolutionary bioregions and refugia of high conservation value.
Life-history traits have seldom been explicitly within a landscape genetic framework. Spatial isolation is a key component of genetic structure for sessile organisms. This study demonstrates that life-history traits are primary drivers of inter-population connectivity and genetic structure. Differences across taxa impacted on patterns of genetic structure on fine spatial scales, while common patterns were observed at broad scales regardless of life-history
traits. These findings complement other Australian Alpine genetic studies indicate that flora and fauna in Victorian Alps share a common genetic structure and phylogeographic history driven by unique processes. The geomorphology of the Victorian Alps has clearly driven the evolutionary trajectories of the native flora and fauna. This approach could inform evidence based conservation policy. Previously undelineated cryptic species were revealed by this study highlighting limitations of traditional taxonomy and the utility of new approaches. This project demonstrates how genomic technologies can characterise evolutionary processes at landscape scales, and detect important patterns in at-risk ecosystems. Sampling method: As per "Materials and Methods" section of the Honours thesis. Study extent: Leaf tissue was collected over the summer 2012-2013, with additional sampling at Mount Stirling and Mount Howitt in October 2013. A summary of the spatial and taxonomic extent of the study can be found in the "Tables" section of the Honours thesis. Project funding: Between 2012 and 2018 this project was part of the Long Term Ecological Research Network (LTERN) supported by the Australian Government’s Terrestrial Ecosystems Research Network (www.tern.org.au) – an Australian research infrastructure facility established under the National Collaborative Research Infrastructure Strategy and Education Infrastructure Fund–Super Science Initiative through the Department of Industry, Innovation, Science, Research and Tertiary Education.
traits. These findings complement other Australian Alpine genetic studies indicate that flora and fauna in Victorian Alps share a common genetic structure and phylogeographic history driven by unique processes. The geomorphology of the Victorian Alps has clearly driven the evolutionary trajectories of the native flora and fauna. This approach could inform evidence based conservation policy. Previously undelineated cryptic species were revealed by this study highlighting limitations of traditional taxonomy and the utility of new approaches. This project demonstrates how genomic technologies can characterise evolutionary processes at landscape scales, and detect important patterns in at-risk ecosystems. Sampling method: As per "Materials and Methods" section of the Honours thesis. Study extent: Leaf tissue was collected over the summer 2012-2013, with additional sampling at Mount Stirling and Mount Howitt in October 2013. A summary of the spatial and taxonomic extent of the study can be found in the "Tables" section of the Honours thesis. Project funding: Between 2012 and 2018 this project was part of the Long Term Ecological Research Network (LTERN) supported by the Australian Government’s Terrestrial Ecosystems Research Network (www.tern.org.au) – an Australian research infrastructure facility established under the National Collaborative Research Infrastructure Strategy and Education Infrastructure Fund–Super Science Initiative through the Department of Industry, Innovation, Science, Research and Tertiary Education.
Methods
Field collection
1
Leaf tissue was collected over the summer 2012-13, with additional sampling at Mt. Stirling and Mt. Howitt in October 2013. For each species, a minimum of 30 ~1 gram samples of fresh growth was collected within an area of approximately 100 m2, specifically avoiding adjacent individuals to reduce the possibility of sampling closely related individuals. This is particularly important for prostrate spreading species such as Pimelea alpina, where clonal/spreading individuals can be difficult to distinguish. GPS coordinates were logged at each site within. Individual samples with unique identifiers were preserved in paper coffee filters and desiccated with silica gel.
DNA extraction and genotyping
2
For each species at each location 30 mg leaf of tissue were weighed out and sent to the Australian Genome Research Facility Ltd (AGRF) Plant Genomics Centre, Adelaide. Extraction was performed as per the NucleoSpin® 96 Plant II protocol (Machery-Nagel Inc., Düren, KO, GER). DNA quantitation was performed as per the QuantiFluor® dsDNA System (Promega Inc,, Madison, NY, USA).
Genotyping By Sequencing (GBS) was chosen for the study. GBS facilitates genotyping across populations for tens of thousands to hundreds of thousands of anonymous genetic markers (Elshire et al. 2011; Thudi et al. 2012; Lu et al. 2013).
Due to financial limitations of the project and the number samples sequenced, samples were pooled at the population level for each species. Anderson et al. (2014) recently outlined potential issues associated with pooling samples for molecular ecology, in light of this, stringent DNA quantifications and standardisation steps, coupled with stringent SNP filtering criteria were implemented.
For each species ten individual DNA extractions from each site were pooled to a total of 500 ng. Subsequently volumes were standardised by evaporating the samples with a CentriVap® Centrifugal Concentrator (Labcono, Kansas City, MO, USA) at 45ºC for two hours, and re-suspending in nuclease-free water. A 0.75 ng/µl concentration of a PstI barcode adapter working stock was aliquoted at 3 µl per sample. Samples were digested with 0.2 µl of PstI-HF® (New England BioLabs, Ipswich, MA, USA) enzyme at 37ºC for two hours. The samples were then purified using a MinElute® PCR purification kit (QIAGEN, Redwood City, CA, USA). A volume of 20 µl of T4 DNA ligase (Bioline, Taunton, MA, USA) was used to ligate the PstI adaptors, incubated at 16ºC for two hours and 80ºC for 80 minutes. PCR amplification was performed on 10 µl of purified post-ligation product with 25 µl of MyTaq™ HS Red Mix (Bioline, Taunton, MA, USA) and 1 µl at 10 µM each of Illumina Dual Index Sequencing Primers 1 & 2 (Illumina Inc., San Diego, CA, USA). PCR conditions were; 72º for 5 min and 95º for 1 min, followed by; 95º for 30 s, 65º for 30 s, 72º for 30 s for 24 cycles, followed by; 72º 5 min.
Quantitation, quality checking and size fractionation was performed on a MCE®-202 MultiNA with a DNA-1000 kit (Shimadzu, Kyoto), see appendix 2 for virtual gel captures.
Libraries were subsequently pooled equimolar into single 0.6 µl microcentrifuge tube and sequenced on a single HiSeq™ 2000 lane at the Australian National University Biomolecular Resource Facility.
References
Anderson EC, Skaug HJ, Barshis DJ (2014) Next‐generation sequencing for molecular ecology: a caveat regarding pooled samples. Molecular ecology, 23, 502–512.
Elshire RJ, Glaubitz JC, Sun Q et al. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species (L Orban, Ed,). PLoS ONE, 6, e19379.
Lu F, Lipka AE, Glaubitz J et al. (2013) Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol. PLoS Genet, 9, e1003215.
Thudi M, Li Y, Jackson SA, May GD, Varshney RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Briefings in Functional Genomics, 11, 3–11.
Genotyping By Sequencing (GBS) was chosen for the study. GBS facilitates genotyping across populations for tens of thousands to hundreds of thousands of anonymous genetic markers (Elshire et al. 2011; Thudi et al. 2012; Lu et al. 2013).
Due to financial limitations of the project and the number samples sequenced, samples were pooled at the population level for each species. Anderson et al. (2014) recently outlined potential issues associated with pooling samples for molecular ecology, in light of this, stringent DNA quantifications and standardisation steps, coupled with stringent SNP filtering criteria were implemented.
For each species ten individual DNA extractions from each site were pooled to a total of 500 ng. Subsequently volumes were standardised by evaporating the samples with a CentriVap® Centrifugal Concentrator (Labcono, Kansas City, MO, USA) at 45ºC for two hours, and re-suspending in nuclease-free water. A 0.75 ng/µl concentration of a PstI barcode adapter working stock was aliquoted at 3 µl per sample. Samples were digested with 0.2 µl of PstI-HF® (New England BioLabs, Ipswich, MA, USA) enzyme at 37ºC for two hours. The samples were then purified using a MinElute® PCR purification kit (QIAGEN, Redwood City, CA, USA). A volume of 20 µl of T4 DNA ligase (Bioline, Taunton, MA, USA) was used to ligate the PstI adaptors, incubated at 16ºC for two hours and 80ºC for 80 minutes. PCR amplification was performed on 10 µl of purified post-ligation product with 25 µl of MyTaq™ HS Red Mix (Bioline, Taunton, MA, USA) and 1 µl at 10 µM each of Illumina Dual Index Sequencing Primers 1 & 2 (Illumina Inc., San Diego, CA, USA). PCR conditions were; 72º for 5 min and 95º for 1 min, followed by; 95º for 30 s, 65º for 30 s, 72º for 30 s for 24 cycles, followed by; 72º 5 min.
Quantitation, quality checking and size fractionation was performed on a MCE®-202 MultiNA with a DNA-1000 kit (Shimadzu, Kyoto), see appendix 2 for virtual gel captures.
Libraries were subsequently pooled equimolar into single 0.6 µl microcentrifuge tube and sequenced on a single HiSeq™ 2000 lane at the Australian National University Biomolecular Resource Facility.
References
Anderson EC, Skaug HJ, Barshis DJ (2014) Next‐generation sequencing for molecular ecology: a caveat regarding pooled samples. Molecular ecology, 23, 502–512.
Elshire RJ, Glaubitz JC, Sun Q et al. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species (L Orban, Ed,). PLoS ONE, 6, e19379.
Lu F, Lipka AE, Glaubitz J et al. (2013) Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol. PLoS Genet, 9, e1003215.
Thudi M, Li Y, Jackson SA, May GD, Varshney RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Briefings in Functional Genomics, 11, 3–11.
File Descriptions
vltm_phylgenomics_2012-2013_p333t553.pdf
Proxy data (Honours thesis resulting from data collected).
Contact Email
belln@unimelb.edu.au;
ary@unimelb.edu.au;
r.woodward@unsw.edu.au;
chwahren@gmail.com;
james.camac@gmail.com;
j.morgan@latrobe.edu.au
Contact Address
University of Melbourne
Bio21 Institute
Departments of Genetics and Zoology
Melbourne, VIC, 3010
Australia
Contact Phone Number
+61 3 8344 2282;
+61 2 9585 6051;
+61 3 9479 2226;
+61 3 9479 1230;
+61 428 810 214
Principal Investigator
Ary Hoffman
Supervisors
Ary Hoffman
Collaborators
Nick Bell;
John Morgan;
Adam Miller;
Renee Woodward
Fields of Research
0604 - Genetics
Keywords
GCMD:Earth Science > Biosphere > Vegetation;
LTERN Monitoring Theme:Climate change;
LTERN Monitoring Theme:Genetics;
keyword:Climate change;
Cryptic speciation;
keyword:Evidence based conservation;
keyword:Life-history traits;
keyword:Next-generation sequencing;
keyword:Phylogenetics;
keyword:Refugia;
keyword:Victorian alps;
Victorian Alpine;
Long Term Monitoring - Community Changes;
Multi-taxa Phylogenomic Data
Type of Research Activity
Strategic basic research
Date Coverage
2013
2012
Geospatial Location
Victorian Alpine Summit, South-east Highlands, Victoria, Australia
text
northlimit = -36.73575; southlimit = -37.49639; westlimit = 146.41728; eastLimit = 147.40598
iso19139dcmiBox
Date of data creation
2018-10-22
Year of data publication
2018
Creator(s) for Citation
Hoffman
Ary
Williams
Dick
Wahren
Henrick
Camac
James
Morgan
John
Papst
Warwick
Publisher for Citation
Long Term Ecological Research Network (LTERN), ANU Data Commons, The Australian National University
Publications
10.1111/jbi.13120
Bell, N., Griffin, P. C., Hoffmann, A. A., & Miller, A.D. (2018). Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics. Journal of Biogeography, 45, 177–189, https://doi.org/10.1111/jbi.13120
Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics.
purl
Other Related Identifiers
MorphoId:ltern7.118;
PackageId:333
Access Rights
Please contact the data owner (Nick Bell) directly for the raw data.
Access Rights Type
Open
Rights held in and over the data
Creative Commons Licence CC-BY-4_0 is assigned to this data. Details of the licence can be found at http://creativecommons.org.au/licences.
Licence Type
CC-BY - Attribution (Version 4)
Licence
LTERN Deed: 7
Date of execution: 2016-10-10
Retention Period
Indefinitely
Data Management Plan
No
Status: Published
Published to:
Published to:
- Australian National University
- Australian National Data Service
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- hasAssociationWith:
Victorian Alpine Plot Network: Victoria's Bogong High Plains and other high plains and mountain summits data packages, 1940-2018 [anudc:5556] - hasAssociationWith:
[anudc:5611] - hasAssociationWith:
Dr John Morgan [anudc:5596] - hasAssociationWith:
Ary Hoffmann [anudc:5563] - hasAssociationWith:
Adam Miller [anudc:5560]