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1. A Novel Terabit Grid-of-Beam Optical Wireless Multi-User Access Network With Beam Clustering

Author

Kazemi, Hossein, Sarbazi, Elham, Crisp, Michael, El-Gorashi, Taisir E. H., Elmirghani, Jaafar M. H., Penty, Richard V., White, Ian H., Safari, Majid, and Haas, Harald

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

In this paper, we put forward a proof of concept for sixth generation (6G) Terabit infrared (IR) laser-based indoor optical wireless networks. We propose a novel double-tier access point (AP) architecture based on an array of arrays of vertical cavity surface emitting lasers (VCSELs) to provide a seamless grid-of-beam coverage with multi-Gb/s per beam. We present systematic design and thorough analytical modeling of the AP architecture, which are then applied to downlink system modeling using non-imaging angle diversity receivers (ADRs). We propose static beam clustering with coordinated multi-beam joint transmission (CoMB-JT) for network interference management and devise various clustering strategies to address inter-beam interference (IBI) and inter-cluster interference (ICI). Non-orthogonal multiple access (NOMA) and orthogonal frequency division multiple access (OFDMA) schemes are also adopted to handle intra-cluster interference, and the resulting signal-to-interference-plus-noise ratio (SINR) and achievable data rate are derived. The network performance is studied in terms of spatial distributions and statistics of the downlink SINR and data rate through extensive computer simulations. The results demonstrate that data rates up to 15 Gb/s are achieved within the coverage area and a properly devised clustering strikes a balance between the sum rate and fairness depending on the number of users., Comment: 15 pages, 13 figures, 1 table

Published
2024

2. Design and Optimisation of High-Speed Receivers for 6G Optical Wireless Networks

Author

Sarbazi, Elham, Kazemi, Hossein, Crisp, Michael, El-Gorashi, Taisir, Elmirghani, Jaafar, Penty, Richard, White, Ian, Safari, Majid, and Haas, Harald

Subjects
Computer Science - Information Theory, Electrical Engineering and Systems Science - Signal Processing
Abstract

To achieve multi-Gb/s data rates in 6G optical wireless access networks based on narrow infrared (IR) laser beams, a high-speed receiver with two key specifications is needed: a sufficiently large aperture to collect the required optical power and a wide field of view (FOV) to avoid strict alignment issues. This paper puts forward the systematic design and optimisation of multi-tier non-imaging angle diversity receivers (ADRs) composed of compound parabolic concentrators (CPCs) coupled with photodiode (PD) arrays for laser-based optical wireless communication (OWC) links. Design tradeoffs include the gain-FOV tradeoff for each receiver element and the area-bandwidth tradeoff for each PD array. The rate maximisation is formulated as a non-convex optimisation problem under the constraints on the minimum required FOV and the overall ADR dimensions to find optimum configuration of the receiver bandwidth and FOV, and a low-complexity optimal solution is proposed. The ADR performance is studied using computer simulations and insightful design guidelines are provided through various numerical examples. An efficient technique is also proposed to reduce the ADR dimensions based on CPC length truncation. It is shown that a compact ADR with a height of $\leq0.5$ cm and an effective area of $\leq0.5$ cm$^2$ reaches a data rate of $12$ Gb/s with a half-angle FOV of $30^\circ$ over a $3$ m link distance.

Published
2022

3. AusTraits, a curated plant trait database for the Australian flora

Author

Falster, Daniel, Gallagher, Rachael, Wenk, Elizabeth H, Wright, Ian J, Indiarto, Dony, Andrew, Samuel C, Baxter, Caitlan, Lawson, James, Allen, Stuart, Fuchs, Anne, Monro, Anna, Kar, Fonti, Adams, Mark A, Ahrens, Collin W, Alfonzetti, Matthew, Angevin, Tara, Apgaua, Deborah MG, Arndt, Stefan, Atkin, Owen K, Atkinson, Joe, Auld, Tony, Baker, Andrew, von Balthazar, Maria, Bean, Anthony, Blackman, Chris J, Bloomfield, Keith, Bowman, David MJS, Bragg, Jason, Brodribb, Timothy J, Buckton, Genevieve, Burrows, Geoff, Caldwell, Elizabeth, Camac, James, Carpenter, Raymond, Catford, Jane A, Cawthray, Gregory R, Cernusak, Lucas A, Chandler, Gregory, Chapman, Alex R, Cheal, David, Cheesman, Alexander W, Chen, Si-Chong, Choat, Brendan, Clinton, Brook, Clode, Peta L, Coleman, Helen, Cornwell, William K, Cosgrove, Meredith, Crisp, Michael, Cross, Erika, Crous, Kristine Y, Cunningham, Saul, Curran, Timothy, Curtis, Ellen, Daws, Matthew I, DeGabriel, Jane L, Denton, Matthew D, Dong, Ning, Du, Pengzhen, Duan, Honglang, Duncan, David H, Duncan, Richard P, Duretto, Marco, Dwyer, John M, Edwards, Cheryl, Esperon-Rodriguez, Manuel, Evans, John R, Everingham, Susan E, Farrell, Claire, Firn, Jennifer, Fonseca, Carlos Roberto, French, Ben J, Frood, Doug, Funk, Jennifer L, Geange, Sonya R, Ghannoum, Oula, Gleason, Sean M, Gosper, Carl R, Gray, Emma, Groom, Philip K, Grootemaat, Saskia, Gross, Caroline, Guerin, Greg, Guja, Lydia, Hahs, Amy K, Harrison, Matthew Tom, Hayes, Patrick E, Henery, Martin, Hochuli, Dieter, Howell, Jocelyn, Huang, Guomin, Hughes, Lesley, Huisman, John, Ilic, Jugoslav, Jagdish, Ashika, Jin, Daniel, Jordan, Gregory, Jurado, Enrique, Kanowski, John, and Kasel, Sabine

Subjects
Plant Biology, Biological Sciences, Ecology, Australia, Databases, Factual, Phenotype, Plant Physiological Phenomena, Plants
Abstract

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

Published
2021

15. Design and Optimization of High-Speed Receivers for 6G Optical Wireless Networks

Author

Sarbazi, Elham, Kazemi, Hossein, Crisp, Michael, El-Gorashi, Taisir, Elmirghani, Jaafar, Penty, Richard V., White, Ian H., Safari, Majid, and Haas, Harald

Abstract

To achieve multi-Gb/s data rates in 6G optical wireless access networks based on narrow infrared (IR) laser beams, a high-speed receiver with two key specifications is needed: a sufficiently large aperture to collect the required optical power and a wide field-of-view (FOV) to avoid strict alignment issues. This paper puts forward the systematic design and optimisation of multi-tier non-imaging angle diversity receivers (ADRs) composed of compound parabolic concentrators (CPCs) coupled with photodiode (PD) arrays for laser-based optical wireless communication (OWC) links. Design tradeoffs include the gain-FOV tradeoff for each receiver element and the area-bandwidth tradeoff for each PD array. The rate maximisation is formulated as a non-convex optimisation problem under the constraints on the minimum required FOV and the overall ADR dimensions to find the optimum configuration of the receiver bandwidth and FOV, and a low-complexity optimal solution is proposed. The ADR performance is studied using computer simulations and insightful design guidelines are provided through various numerical examples. An efficient technique is also proposed to reduce the ADR dimensions based on CPC length truncation. It is shown that a compact ADR with a height of $\leq 0.5$ cm and an effective area of $\leq 0.5$ cm2 reaches a data rate of 12 Gb/s with a half-angle FOV of 30° over a 3 m link distance.

Published
2024
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16. A Disconnect between Staff and Student Perceptions of Learning: An ACELL Educational Analysis of the First Year Undergraduate Chemistry Experiment 'Investigating Sugar Using a Home Made Polarimeter'

Author

Crisp, Michael G., Kable, Scott H., Read, Justin R., and Buntine, Mark A.

Abstract

This paper describes an educational analysis of a first year university chemistry practical called "Investigating sugar using a home made polarimeter". The analysis follows the formalism of the Advancing Chemistry by Enhancing Learning in the Laboratory (ACELL) project, which includes a statement of education objectives, and an analysis of the student learning experience. The practical requires students to accurately prepare solutions of known concentrations of a common consumer chemical (sucrose), and then investigate the interaction between these solutions and plane-polarised light. The instrument used is a "home built" polarimeter which students assemble, allowing them to recognise that scientific apparatus need not be mysterious in its operation or construction. Student feedback data were conducted using the ACELL Student Learning Experience (ASLE) instrument. Analysis of the data shows that overwhelmingly students rate the experiment as "worthwhile" or better. However, many also rate the experiment as "boring" or "uninteresting". By contrast, staff and student feedback at an ACELL experiential workshop rated the experiment very highly in terms of the "interest" criterion. In this contribution we discuss this alignment of staff and student perceptions of various elements, including "interest" and explore the correlation with the overall laboratory experience. (Contains 3 figures and 3 tables.)

Published
2011
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19. Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades

Author

The Legume Phylogeny Working Group, Bruneau, Anne, Doyle, Jeff J., Herendeen, Patrick, Hughes, Colin, Kenicer, Greg, Lewis, Gwilym, Mackinder, Barbara, Pennington, R. Toby, Sanderson, Michael J., Wojciechowski, Martin F., Boatwright, Stephen, Brown, Gillian, Cardoso, Domingos, Crisp, Michael, Egan, Ashley, Fortunato, Renée H., Hawkins, Julie, Kajita, Tadashi, Klitgaard, Bente, Koenen, Erik, Lavin, Matt, Luckow, Melissa, Marazzi, Brigitte, McMahon, Michelle M., Miller, Joseph T., Murphy, Daniel J., Ohashi, Hiroyoshi, de Queiroz, Luciano P., Rico, Lourdes, Särkinen, Tiina, Schrire, Brian, Simon, Marcelo F., Souza, Elvia R., Steele, Kelly, Torke, Benjamin M., Wieringa, Jan J., and van Wyk, Ben-Erik

Published
2013

30. Advanced Modeling of Surface Waves on Twisted Pair Cables: Surface Wave Stopbands

Author

Schaich, Tobias, primary, Dinc, Ergin, additional, Molnar, Daniel, additional, Drolia, Mayank, additional, Bukhari, Syed, additional, Aziz, Ahmed, additional, Toledano, Ilana, additional, Morsman, Trevor, additional, Burton, Fraser, additional, Crisp, Michael, additional, de Lera Acedo, Eloy, additional, Rawi, Anas Al, additional, Penty, Richard, additional, and Payne, Mike, additional

Published
2022
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39. Phylogenetic biome conservatism on a global scale

Author

Crisp, Michael D., Arroyo, Mary T. K., Cook, Lyn G., Gandolfo, Maria A., Jordan, Gregory J., McGlone, Matt S., Weston, Peter H., Westoby, Mark, Wilf, Peter, and Linder, H. Peter

Subjects
Influence, Research, Climate change -- Influence -- Research, Conservatism -- Influence -- Research, Phylogeny -- Research, Biomes -- Research, Climatic changes -- Influence -- Research
Abstract

In recent years, the extent to which species retain ancestral ecological traits and environmental distributions ('niche conservatism') has been debated (11,13-15). Whether ecology is evolutionarily labile or conserved appears to [...], How and why organisms are distributed as they are has long intrigued evolutionary biologists (1-4). The tendency for species to retain their ancestral ecology has been demonstrated in distributions on local and regional scales (5-7), but the extent of ecological conservatism over tens of millions of years and across continents has not been assessed (8-13). Here we show that biome stasis at speciation has outweighed biome shifts by a ratio of more than 25:1, by inferring ancestral biomes for an ecologically diverse sample of more than 11,000 plant species from around the Southern Hemisphere. Stasis was also prevalent in transocean colonizations. Availability of a suitable biome could have substantially influenced which lineages establish on more than one landmass, in addition to the influence of the rarity of the dispersal events themselves. Conversely, the taxonomic composition of biomes has probably been strongly influenced by the rarity of species' transitions between biomes. This study has implications for the future because if clades have inherently limited capacity to shift biomes (13), then their evolutionary potential could be strongly compromised by biome contraction as climate changes.

Published
2009

40. Dinuclear organoplatinum(II) complexes containing N-methylbenzamide

Author

Crisp, Michael G. and Rendina, Louis M.

Subjects
Organometallic compounds -- Chemical properties, Platinum compounds -- Chemical properties, Chemistry, Chemical properties, Properties
Abstract

The preparation and characterization of cationic, dinuclear complexes of the type trans-[Pt[([PPh.sub.3]).sub.2] (σ-[C.sub.6][H.sub.4]NHMe) -μ-L-Pt[([PPh.sub.3].sub.2] (σ-[C.sub.6][H.sub.4]NHMe)][(OTf).sub.2] (L = 4,4'-bipyridine, 4,7-phenanthroline, 4,4'-dipyrazolylmethane, and 1,1?-diphenyl-4,4'-dipyrazolylmethane; OTf = trifluoromethanesulfonate (triflate)) containing two [C.sup.3]-N-methylbenzamide ligands are described. The key structural feature of the cationic complexes is the presence of two convergent amide groups that may allow for charge-assisted, H-bonding interactions in solution with suitable heteroaromatic guest molecules such as nucleobases. Key words: organoplatinum(II) complex, organometallic host, dinuclear complex, N-methylbenzamide. On decrit la preparation et la caracterisation de complexes cationiques dinucleaires du type trans-[Pt[([PPh.sub.3]).sub.2] (σ-[C.sub.6][H.sub.4]NHMe)-μ-L-Pt[([PPh.sub.3].sub.2] (σ-[C.sub.6][H.sub.4]NHMe)][(OTf).sub.2] [L= 4,4?-bipyridine; 4,7-phenanthroline; 4,4?-dipyrazolylmethane; et 1,1'-diphenyl-4,4'-dipyrazolylmethane; OTf = trifluoromethanesulfonate (triflate)] contenant deux ligands [C.sup.3]-N-methylbenzamide. La caracteristique structurale cle des complexes cationiques est la presence de deux groupes amides convergents qui, en solution, peuvent favoriser des interactions de liaisons hydrogenes assistees par des charges avec des molecules hotes heteroaromatiques appropriees, telles des nucleobases. Mots-cles : complexe organique du platine(II), hote organometallique, complexe dinucleaire, N-methylbenzamide. [Traduit par la Redaction], Introduction There is great interest in the study of synthetic receptors for the selective binding of nucleobases (1, 2), owing to their many important functional roles in biological systems, e.g., [...]

Published
2009

42. AusTraits – a curated plant trait database for the Australian flora

Author

Falster, Daniel ; https://orcid.org/0000-0002-9814-092X, Gallagher, Rachael, Wenk, Elizabeth, Wright, Ian, Indiarto, Dony ; https://orcid.org/0000-0001-9546-8201, Baxter, Caitlan, Andrew, Samuel C, Lawson, James, Allen, Stuart, Fuchs, Anne, Adams, Mark A, Ahrens, Collin W ; https://orcid.org/0000-0002-0614-9928, Alfonzetti, Matthew, Angevin, Tara, Atkin, Owen K, Auld, Tony ; https://orcid.org/0000-0002-8766-2829, Baker, Andrew, Bean, Anthony, Blackman, Chris J, Bloomfield, Keith, Bowman, David, Bragg, Jason ; https://orcid.org/0000-0002-7621-7295, Brodribb, Timothy J, Buckton, Genevieve, Burrows, Geoff, Caldwell, Elizabeth, Camac, James, Carpenter, Raymond, Catford, Jane A, Cawthray, Gregory R, Cernusak, Lucas A, Chandler, Gregory, Chapman, Alex R, Cheal, David, Cheesman, Alexander W, Chen, Si-Chong, Choat, Brendan, Clinton, Brook, Clode, Peta, Coleman, Helen, Cornwell, William K ; https://orcid.org/0000-0003-4080-4073, Cosgrove, Meredith, Crisp, Michael, Cross, Erika, Crous, Kristine Y, Cunningham, Saul, Curtis, Ellen, Daws, Matthew I, DeGabriel, Jane L, Denton, Matthew D, Dong, Ning, Duan, Honglang, Duncan, David H, Duncan, Richard P, Duretto, Marco, Dwyer, John M, Edwards, Cheryl, Esperon-Rodriguez, Manuel, Evans, John R, Everingham, Susan E, Firn, Jennifer, Fonseca, Carlos Roberto, French, Ben J, Frood, Doug, Funk, Jennifer L, Geange, Sonya R, Ghannoum, Oula ; https://orcid.org/0000-0002-1341-0741, Gleason, Sean M, Gosper, Carl R, Gray, Emma, Groom, Philip K, Gross, Caroline, Guerin, Greg, Guja, Lydia, Hahs, Amy K, Harrison, Matthew Tom, Hayes, Patrick E, Henery, Martin, Hochuli, Dieter, Howell, Jocelyn, Huang, Guomin, Hughes, Lesley, Huisman, John, Ilic, Jugoslav, Jagdish, Ashika, Jin, Daniel, Jordan, Gregory, Jurado, Enrique, Kasel, Sabine, Kellermann, Jürgen, Kohout, Michele, Kooyman, Robert M, Kotowska, Martyna M, Lai, Hao Ran, Laliberté, Etienne, Lambers, Hans, Lamont, Byron B, Lanfear, Robert, van Langevelde, Frank, Laughlin, Daniel C, Laugier-Kitchener, Bree-Anne, Lehmann, Caroline ER, Leigh, Andrea, Leishman, Michelle R, Lenz, Tanja, Lepschi, Brendan, Lewis, James D, Lim, Felix, Liu, Udayangani, Lord, Janice, Lusk, Christopher H, Macinnis-Ng, Cate, McPherson, Hannah, Manea, Anthony, Mayfield, Margaret, McCarthy, James K, Meers, Trevor, van der Merwe, Marlien, Metcalfe, Daniel, Milberg, Per, Mokany, Karel, Moles, Angela T ; https://orcid.org/0000-0003-2041-7762, Moore, Ben D, Moore, Nicholas, Morgan, John W, Morris, William, Muir, Annette, Munroe, Samantha, Nicholson, Áine, Nicolle, Dean, Nicotra, Adrienne B, Niinemets, Ülo, North, Tom, O’Reilly-Nugent, Andrew, O’Sullivan, Odhran S, Oberle, Brad, Onoda, Yusuke, Ooi, Mark KJ ; https://orcid.org/0000-0002-3046-0417, Osborne, Colin P, Paczkowska, Grazyna, Pekin, Burak, Pereira, Caio Guilherme, Pickering, Catherine, Pickup, Melinda, Pollock, Laura J, Poot, Pieter, Powell, Jeff R, Power, Sally A, Prentice, Iain Colin, Prior, Lynda, Prober, Suzanne M, Read, Jennifer, Reynolds, Victoria, Richards, Anna E, Richardson, Ben, Roderick, Michael L, Rosell, Julieta A, Rossetto, Maurizio, Rye, Barbara, Rymer, Paul D, Sams, Michael A, Sanson, Gordon, Schmidt, Susanne, Schulze, Ernst-Detlef, Sendall, Kerrie, Sinclair, Steve, Smith, Benjamin, Smith, Renee, Soper, Fiona, Sparrow, Ben, Standish, Rachel, Staples, Timothy L, Taseski, Guy, Thomas, Freya, Tissue, David T, Tjoelker, Mark G, Tng, David Yue Phin, Tomlinson, Kyle, Turner, Neil C, Veneklaas, Erik, Venn, Susanna, Vesk, Peter, Vlasveld, Carolyn, Vorontsova, Maria S, Warren, Charles, Weerasinghe, Lasantha K, Westoby, Mark, White, Matthew, Williams, Nicholas, Wills, Jarrah, Wilson, Peter G, Yates, Colin, Zanne, Amy E, Ziemińska, Kasia, Falster, Daniel ; https://orcid.org/0000-0002-9814-092X, Gallagher, Rachael, Wenk, Elizabeth, Wright, Ian, Indiarto, Dony ; https://orcid.org/0000-0001-9546-8201, Baxter, Caitlan, Andrew, Samuel C, Lawson, James, Allen, Stuart, Fuchs, Anne, Adams, Mark A, Ahrens, Collin W ; https://orcid.org/0000-0002-0614-9928, Alfonzetti, Matthew, Angevin, Tara, Atkin, Owen K, Auld, Tony ; https://orcid.org/0000-0002-8766-2829, Baker, Andrew, Bean, Anthony, Blackman, Chris J, Bloomfield, Keith, Bowman, David, Bragg, Jason ; https://orcid.org/0000-0002-7621-7295, Brodribb, Timothy J, Buckton, Genevieve, Burrows, Geoff, Caldwell, Elizabeth, Camac, James, Carpenter, Raymond, Catford, Jane A, Cawthray, Gregory R, Cernusak, Lucas A, Chandler, Gregory, Chapman, Alex R, Cheal, David, Cheesman, Alexander W, Chen, Si-Chong, Choat, Brendan, Clinton, Brook, Clode, Peta, Coleman, Helen, Cornwell, William K ; https://orcid.org/0000-0003-4080-4073, Cosgrove, Meredith, Crisp, Michael, Cross, Erika, Crous, Kristine Y, Cunningham, Saul, Curtis, Ellen, Daws, Matthew I, DeGabriel, Jane L, Denton, Matthew D, Dong, Ning, Duan, Honglang, Duncan, David H, Duncan, Richard P, Duretto, Marco, Dwyer, John M, Edwards, Cheryl, Esperon-Rodriguez, Manuel, Evans, John R, Everingham, Susan E, Firn, Jennifer, Fonseca, Carlos Roberto, French, Ben J, Frood, Doug, Funk, Jennifer L, Geange, Sonya R, Ghannoum, Oula ; https://orcid.org/0000-0002-1341-0741, Gleason, Sean M, Gosper, Carl R, Gray, Emma, Groom, Philip K, Gross, Caroline, Guerin, Greg, Guja, Lydia, Hahs, Amy K, Harrison, Matthew Tom, Hayes, Patrick E, Henery, Martin, Hochuli, Dieter, Howell, Jocelyn, Huang, Guomin, Hughes, Lesley, Huisman, John, Ilic, Jugoslav, Jagdish, Ashika, Jin, Daniel, Jordan, Gregory, Jurado, Enrique, Kasel, Sabine, Kellermann, Jürgen, Kohout, Michele, Kooyman, Robert M, Kotowska, Martyna M, Lai, Hao Ran, Laliberté, Etienne, Lambers, Hans, Lamont, Byron B, Lanfear, Robert, van Langevelde, Frank, Laughlin, Daniel C, Laugier-Kitchener, Bree-Anne, Lehmann, Caroline ER, Leigh, Andrea, Leishman, Michelle R, Lenz, Tanja, Lepschi, Brendan, Lewis, James D, Lim, Felix, Liu, Udayangani, Lord, Janice, Lusk, Christopher H, Macinnis-Ng, Cate, McPherson, Hannah, Manea, Anthony, Mayfield, Margaret, McCarthy, James K, Meers, Trevor, van der Merwe, Marlien, Metcalfe, Daniel, Milberg, Per, Mokany, Karel, Moles, Angela T ; https://orcid.org/0000-0003-2041-7762, Moore, Ben D, Moore, Nicholas, Morgan, John W, Morris, William, Muir, Annette, Munroe, Samantha, Nicholson, Áine, Nicolle, Dean, Nicotra, Adrienne B, Niinemets, Ülo, North, Tom, O’Reilly-Nugent, Andrew, O’Sullivan, Odhran S, Oberle, Brad, Onoda, Yusuke, Ooi, Mark KJ ; https://orcid.org/0000-0002-3046-0417, Osborne, Colin P, Paczkowska, Grazyna, Pekin, Burak, Pereira, Caio Guilherme, Pickering, Catherine, Pickup, Melinda, Pollock, Laura J, Poot, Pieter, Powell, Jeff R, Power, Sally A, Prentice, Iain Colin, Prior, Lynda, Prober, Suzanne M, Read, Jennifer, Reynolds, Victoria, Richards, Anna E, Richardson, Ben, Roderick, Michael L, Rosell, Julieta A, Rossetto, Maurizio, Rye, Barbara, Rymer, Paul D, Sams, Michael A, Sanson, Gordon, Schmidt, Susanne, Schulze, Ernst-Detlef, Sendall, Kerrie, Sinclair, Steve, Smith, Benjamin, Smith, Renee, Soper, Fiona, Sparrow, Ben, Standish, Rachel, Staples, Timothy L, Taseski, Guy, Thomas, Freya, Tissue, David T, Tjoelker, Mark G, Tng, David Yue Phin, Tomlinson, Kyle, Turner, Neil C, Veneklaas, Erik, Venn, Susanna, Vesk, Peter, Vlasveld, Carolyn, Vorontsova, Maria S, Warren, Charles, Weerasinghe, Lasantha K, Westoby, Mark, White, Matthew, Williams, Nicholas, Wills, Jarrah, Wilson, Peter G, Yates, Colin, Zanne, Amy E, and Ziemińska, Kasia

Abstract

We introduce the AusTraits database - a compilation of measurements of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 375 traits across 29230 taxa from field campaigns, published literature, taxonomic monographs, and individual taxa descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological parameters (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual-, species- and genus-level observations coupled to, where available, contextual information on site properties. This data descriptor provides information on version 2.1.0 of AusTraits which contains data for 937243 trait-by-taxa combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data to increase our collective understanding of the Australian flora.

Published
2021

46. Turnover of southern cypresses in the post-Gondwanan world: extinction, transoceanic dispersal, adaptation and rediversification

Author

50325130, 50726809, Crisp, Michael D., Cook, Lyn G., Bowman, David M. J. S., Cosgrove, Meredith, Isagi, Yuji, Sakaguchi, Shota, 50325130, 50726809, Crisp, Michael D., Cook, Lyn G., Bowman, David M. J. S., Cosgrove, Meredith, Isagi, Yuji, and Sakaguchi, Shota

Abstract

Cupressaceae subfamily Callitroideae has been an important exemplar for vicariance biogeography, but its history is more than just disjunctions resulting from continental drift. We combine fossil and molecular data to better assess its extinction and, sometimes, rediversification after past global change. Key fossils were reassessed and their phylogenetic placement for calibration was determined using trait mapping and Bayes Factors. Five vicariance hypotheses were tested by comparing molecular divergence times with the timing of tectonic rifting. The role of adaptation to fire (serotiny) in its spread across a drying Australia was tested for Callitris. Our findings suggest that three transoceanic disjunctions within the Callitroideae probably arose from long‐distance dispersal. A signature of extinction, centred on the end‐Eocene global climatic chilling and drying, is evident in lineages‐through‐time plots and in the fossil record. Callitris, the most diverse extant callitroid genus, suffered extinctions but surviving lineages adapted and re‐radiated into dry, fire‐prone biomes that expanded in the Neogene. Serotiny, a key adaptation to fire, likely evolved in Callitris coincident with the biome shift. Both extinction and adaptive shifts have probably played major roles in this chronicle of turnover and renewal, but better understanding of biogeographical history requires improved taxonomy of fossils.

Published
2019

47. Identifying genetic markers for a range of phylogenetic utility–From species to family level

Author

Choi, Bokyung, Crisp, Michael, Cook, Lyn, Meusemann, Karen, Edwards, Robert D., Toon, A., Kulheim, Carsten, Choi, Bokyung, Crisp, Michael, Cook, Lyn, Meusemann, Karen, Edwards, Robert D., Toon, A., and Kulheim, Carsten

Abstract

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.

Published
2019

48. A dated molecular perspective of eucalypt taxonomy,evolution and diversification

Author

Thornhill, Andrew H., Crisp, Michael, Kulheim, Carsten, Lam, Kristy E., Nelson, Leigh, Yeates, David K., Miller, Joseph T., Thornhill, Andrew H., Crisp, Michael, Kulheim, Carsten, Lam, Kristy E., Nelson, Leigh, Yeates, David K., and Miller, Joseph T.

Abstract

The eucalypts, which include Eucalyptus, Angophora and Corymbia, are native to Australia and Malesia and include over 800 named species in a mixture of diverse and depauperate lineages. We assessed the fit of the eucalypt taxonomic classification to a phylogeny of 711 species scored for DNA sequences of plastid matK and psbA–trnH, as well as nuclear internal transcribed spacer and external transcribed spacer. Two broadly similar topologies emerge from both maximum likelihood and Bayesian analyses, showing Angophora nested within Corymbia, or Angophora sister to Corymbia. The position of certain species-poor groups on long branches fluctuated relative to the three major Eucalyptus subgenera, and positions of several closely related species within those subgenera were unstable and lacked statistical support. Most sections and series of Eucalyptus were not recovered as monophyletic. We calibrated these phylogenies against time, using penalised likelihood and constraints obtained from fossil ages. On the basis of these trees, most major eucalypt subgenera arose in the Late Eocene and Early Oligocene. All Eucalyptus clades with taxa occurring in south-eastern Australia have crown ages <20 million years. Several eucalypt clades display a strong present-day geographic disjunction, although these clades did not have strong phylogenetic statistical support. In particular, the estimated age of the separation between the eudesmids (Eucalyptus subgenus Eudesmia) and monocalypts (Eucalyptus subgenus Eucalyptus) was consistent with extensive inland water bodies in the Eocene. Bayesian analysis of macroevolutionary mixture rates of net species diversification accelerated in five sections of Eucalyptus subgenus Symphyomyrtus, all beginning 2–3 million years ago and associated with semi-arid habitats dominated by mallee and mallet growth forms, and with open woodlands and forests in eastern Australia. This is the first time that a calibrated molecular study has shown support for the

Published
2019

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