All Outputs (19)

Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific (2017)
Journal Article
Payacan, C., Moncada, X., Rojas, G., Clarke, A., Chung, K. F., Allaby, R., …Seelenfreund, A. (2017). Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific. Annals of Botany, 120(3), 387-404. https://doi.org/10.1093/aob/mcx062

© The Author 2017. Background and Aims Paper mulberry or Broussonetia papyrifera (L.) L'Her. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-h... Read More about Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific.

Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication (2015)
Journal Article
Kistler, L., Newsom, L. A., Ryan, T. M., Clarke, A. C., Smith, B. D., & Perry, G. H. (2015). Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication. Proceedings of the National Academy of Sciences, 112(49), 15107-15112. https://doi.org/10.1073/pnas.1516109112

The genus Cucurbita (squashes, pumpkins, gourds) contains numerous domesticated lineages with ancient New World origins. It was broadly distributed in the past but has declined to the point that several of the crops' progenitor species are scarce or... Read More about Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication.

Are current ecological restoration practices capturing natural levels of genetic diversity? A New Zealand case study using AFLP and ISSR data from mahoe (Melicytus ramiflorus) (2015)
Journal Article
Stevens, M. I., Clarke, A. C., Clarkson, F. M., Goshorn, M., & Gemmill, C. E. (2015). Are current ecological restoration practices capturing natural levels of genetic diversity? A New Zealand case study using AFLP and ISSR data from mahoe (Melicytus ramiflorus). New Zealand Journal of Ecology, 39(2), 190-197

© New Zealand Ecological Society. Sourcing plant species of local provenance (eco-sourcing) has become standard practice in plantcommunity restoration projects. Along with established ecological restoration practices, knowledge of genetic variation i... Read More about Are current ecological restoration practices capturing natural levels of genetic diversity? A New Zealand case study using AFLP and ISSR data from mahoe (Melicytus ramiflorus).

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops (2015)
Journal Article
Allaby, R. G., Gutaker, R., Clarke, A. C., Pearson, N., Ware, R., Palmer, S. A., …Smith, O. (2015). Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philosophical Transactions B: Biological Sciences, 370(1660), https://doi.org/10.1098/rstb.2013.0377

© 2014 The Author(s) Published by the Royal Society. All rights reserved. Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex proce... Read More about Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops.

Archaeogenomic insights into the adaptation of plants to the human environment: Pushing plant-hominin co-evolution back to the Pliocene (2015)
Journal Article
Allaby, R. G., Kistler, L., Gutaker, R. M., Ware, R., Kitchen, J. L., Smith, O., & Clarke, A. C. (2015). Archaeogenomic insights into the adaptation of plants to the human environment: Pushing plant-hominin co-evolution back to the Pliocene. Journal of Human Evolution, 79, 150-157. https://doi.org/10.1016/j.jhevol.2014.10.014

© 2014 The Authors. The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for... Read More about Archaeogenomic insights into the adaptation of plants to the human environment: Pushing plant-hominin co-evolution back to the Pliocene.

From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes (2014)
Journal Article
Clarke, A. C., Prost, S., Stanton, J. L., White, W. T. J., Kaplan, M. E., Matisoo-Smith, E. A., & The Genographic Consortium. (2014). From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics, 15(1), Article 68. https://doi.org/10.1186/1471-2164-15-68

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete m... Read More about From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.

DNA and Pacific Commensal Models: Applications, Construction, Limitations, and Future Prospects (2013)
Journal Article
Storey, A. A., Clarke, A. C., Ladefoged, T., Robins, J., & Matisoo-Smith, E. (2013). DNA and Pacific Commensal Models: Applications, Construction, Limitations, and Future Prospects. Journal of Island and Coastal Archaeology, 8(1), 37-65. https://doi.org/10.1080/15564894.2012.761299

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganis... Read More about DNA and Pacific Commensal Models: Applications, Construction, Limitations, and Future Prospects.

Ethnobiology: The missing link in ecology and evolution (2012)
Journal Article
Saslis-Lagoudakis, C. H., & Clarke, A. C. (2013). Ethnobiology: The missing link in ecology and evolution. Trends in Ecology and Evolution, 28(2), 67-68. https://doi.org/10.1016/j.tree.2012.10.017

Evolutionary biologists and ecologists increasingly appreciate the value of local knowledge of human communities for research into the past, present, and future of biodiversity. However, there are often significant problems accessing and interpreting... Read More about Ethnobiology: The missing link in ecology and evolution.

Setting the stage – Building and working in an ancient DNA laboratory (2011)
Journal Article
Knapp, M., Clarke, A. C., Horsburgh, K. A., & Matisoo-Smith, E. A. (2012). Setting the stage – Building and working in an ancient DNA laboratory. Annals of Anatomy, 194(1), 3-6. https://doi.org/10.1016/j.aanat.2011.03.008

With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can cont... Read More about Setting the stage – Building and working in an ancient DNA laboratory.

Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system (2010)
Journal Article
Stolting, K. N., Clarke, A. C., Meudt, H. M., Blankenhorn, W. U., & Wilson, A. B. (2011). Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system. Molecular Ecology Resources, 11(3), 494-502. https://doi.org/10.1111/j.1755-0998.2010.02957.x

The amplified fragment length polymorphism (AFLP) technique is a widely used multi-purpose DNA fingerprinting tool. The ability to size-separate fluorescently labelled AFLP fragments on a capillary electrophoresis instrument has provided a means for... Read More about Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system.

Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: anthropological, botanical and genetic considerations (2010)
Journal Article
Seelenfreund, D., Clarke, A., Oyanedel, N., Piña, R., Lobos, S., Matisoo-Smith, E., & Seelenfreund, A. (2010). Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: anthropological, botanical and genetic considerations. New Zealand Journal of Botany, 48(3-4), 231-247. https://doi.org/10.1080/0028825X.2010.520323

Paper mulberry (Broussonetia papyrifera (L.) Vent.) was one of the most widely distributed crop species in prehistoric Oceania, occurring from continental East Asia to the Polynesian islands. Its broad distribution is largely due to human-mediated di... Read More about Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: anthropological, botanical and genetic considerations.

Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers (2008)
Journal Article
McCallum, J., Thomson, S., Pither-Joyce, M., Kenel, F., Clarke, A., & Havey, M. J. (2008). Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. Journal of the American Society for Horticultural Science, 133(6), 810-818. https://doi.org/10.21273/jashs.133.6.810

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (... Read More about Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers.

Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution (2008)
Journal Article
Holland, B. R., Clarke, A. C., & Meudt, H. M. (2008). Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution. Systematic Biology, 57(3), 347-366. https://doi.org/10.1080/10635150802044037

The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary electrophoresis now allow very precise estimates of DNA... Read More about Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution.

Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species (2008)
Journal Article
Michel, C., Hicks, B. J., Stölting, K. N., Clarke, A. C., Stevens, M. I., Tana, R., …van den Heuvel, M. R. (2008). Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species. BMC Evolutionary Biology, 8(1), Article 49. https://doi.org/10.1186/1471-2148-8-49

Background. Many postglacial lakes contain fish species with distinct ecomorphs. Similar evolutionary scenarios might be acting on evolutionarily young fish communities in lakes of remote islands. One process that drives diversification in island fre... Read More about Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species.

Monitoring the Effects of Pulp and Paper Effluent Is Restricted in Genetically Distinct Populations of Common Bully (Gobiomorphuscotidianus) (2007)
Journal Article
van den Heuvel, M. R., Michel, C., Stevens, M. I., Clarke, A. C., Stölting, K. N., Hicks, B. J., & Tremblay, L. A. (2007). Monitoring the Effects of Pulp and Paper Effluent Is Restricted in Genetically Distinct Populations of Common Bully (Gobiomorphuscotidianus). Environmental Science and Technology, 41(7), 2602-2608. https://doi.org/10.1021/es061922q

The common bully (Gobiomorphuscotidianus), a small-bodied New Zealand native fish species, was used to monitor population impacts of multiple effluents in the Tarawera River, New Zealand. In an initial survey, the absence of reproductive development... Read More about Monitoring the Effects of Pulp and Paper Effluent Is Restricted in Genetically Distinct Populations of Common Bully (Gobiomorphuscotidianus).

Almost Forgotten or Latest Practice? AFLP applications, analyses and advances (2007)
Journal Article
Meudt, H. M., & Clarke, A. C. (2007). Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science, 12(3), 106-117. https://doi.org/10.1016/j.tplants.2007.02.001

Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR mark... Read More about Almost Forgotten or Latest Practice? AFLP applications, analyses and advances.

Genetic mapping of a major gene affecting onion bulb fructan content (2006)
Journal Article
McCallum, J., Clarke, A., Pither-Joyce, M., Shaw, M., Butler, R., Brash, D., …Havey, M. J. (2006). Genetic mapping of a major gene affecting onion bulb fructan content. TAG Theoretical and Applied Genetics, 112(5), 958-967. https://doi.org/10.1007/s00122-005-0199-5

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these car... Read More about Genetic mapping of a major gene affecting onion bulb fructan content.

Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria) (2006)
Journal Article
Clarke, A. C., Burtenshaw, M. K., McLenachan, P. A., Erickson, D. L., & Penny, D. (2006). Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria). Molecular Biology and Evolution, 23(5), 893-900. https://doi.org/10.1093/molbev/msj092

The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from thi... Read More about Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria).

An Asian origin for a 10,000-year-old domesticated plant in the Americas (2005)
Journal Article
Erickson, D. L., Smith, B. D., Clarke, A. C., Sandweiss, D. H., & Tuross, N. (2005). An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proceedings of the National Academy of Sciences, 102(51), 18315-18320. https://doi.org/10.1073/pnas.0509279102

New genetic and archaeological approaches have substantially improved our understanding of the transition to agriculture, a major turning point in human history that began 10,000–5,000 years ago with the independent domestication of plants and animal... Read More about An Asian origin for a 10,000-year-old domesticated plant in the Americas.