Dr Alana Alexander

2025

Journal - Research Article

McGrath, N., le Roux, J., Whibley, A., Alexander, A., Oliphant Stewart, R., Johnstone, M., … Silander, O. K. (2025). A high-quality Oxford Nanopore assembly of the hourglass dolphin (Lagenorhynchus cruciger) genome. Genes Genomes Genetics. Advance online publication. doi: 10.1093/g3journal/jkaf044

2024

Journal - Research Article

Bennington, S. M., Bourke, S. D., Wilkinson, S. P., Englebert, N., Bond, D. M., Jeunen, G.-J., Dawson, S., Slooten, E., Dillingham, P. W., Rayment, W. J., & Alexander, A. (2024). New insights into the population structure of Hector's dolphin (Cephalorhynchus hectori) revealed using environmental DNA. Environmental DNA, 6, e70024. doi: 10.1002/edn3.70024

Bond, D. M., Veale, A., Alexander, A., & Hore, T. A. (2024). Coat colour in marsupials: Genetic variants at the ASIP locus determine grey and black fur of the brushtail possum. Royal Society Open Science, 11(7), 240806. doi: 10.1098/rsos.240806

Baca, S. M., Gustafson, G. T., DeRaad, D. A., Alexander, A., Hime, P. M., & Short, A. E. Z. (2024). A shallow-scale phylogenomics approach reveals repeated patterns of diversification among sympatric lineages of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae). Systematic Entomology. Advance online publication. doi: 10.1111/syen.12643

Clark, A. C., Edison, R., Esvelt, K., Kamau, S., Dutoit, L., Champer, J., … Alexander, A., & Gemmell, N. J. (2024). A framework for identifying fertility gene targets for mammalian pest control. Molecular Ecology Resources, 24(2), e13901. doi: 10.1111/1755-0998.13901

Journal - Research Other

Romas, S. C., Kinziger, A. P., & Alexander, A. (2024). Hīkina te mānuka: Advancing Indigenous leadership in molecular ecology. Molecular Ecology Resources, e14049. Advance online publication. doi: 10.1111/1755-0998.14049

Urban, L., Santure, A. W., Uddstrom, L., Digby, A., Vercoe, D., Eason, D., … Kākāpō Recovery Team, including Thompson, T., Weinzweig, N., Whittaker, M., and also Wylie, M. J., … Le Lec, M. F., Guhlin, J., … Alexander, A., Fuentes-Cross, P., Dearden, P. K., Gemmell, N. J., Azeem, F., Weyland, M., Schwefel, H. G. L., … Morales, H. E. (2024). The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator. PLoS Biology, 22(9), e3002755. doi: 10.1371/journal.pbio.3002755

Conference Contribution - Published proceedings: Abstract

Aranui, A., Tromp, M., White, S., Greig, K., Alexander, A., Baker, C. S., … Warinner, C. (2024). Ika moana, ika whenua. Proceedings of the New Zealand Archaeological Association (NZAA) Annual Conference. (pp. 6). Retrieved from https://nzarchaeology.org

2023

Journal - Research Article

Bond, D. M., Ortega-Recalde, O., Laird, M. K., Hayakawa, T., Richardson, K. S., Reese, F. C. B., Kyle, B., McIsaac-Williams, B. E., Robertson, B. C., van Heezik, Y., Adams, A. L., … Gemmell, N. J., Alexander, A., & Hore, T. A. (2023). The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Nature Communications, 14, 6364. doi: 10.1038/s41467-023-41784-8

Foote, A. D., Alexander, A., Ballance, L. T., Constantine, R., Vernazzani Muñoz, B. G., Guinet, C., … Morin, P. A. (2023). “Type D” killer whale genomes reveal long-term small population size and low genetic diversity. Journal of Heredity, 114, 94-109. doi: 10.1093/jhered/esac070

Shakya, S. B., Alexander, A., Lim, H. C., Manthey, J. D., Prawiradilaga, D., Chan, K. O., … Moyle, R. G. (2023). Demographic history of a complex polymorphism in populations of the oriental dwarf kingfisher, Ceyx erithaca/rufidorsa of Southeast Asia. Ibis. Advance online publication. doi: 10.1111/ibi.13207

Bentley, B. P., Carrasco-Valenzuela, T., Ramos, E. K. S., Pawar, H., Arantes, L. S., Alexander, A., … Gemmell, N. J., … Komoroske, L. M. (2023). Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. PNAS, 120(7), e2201076120. doi: 10.1073/pnas.2201076120

Corre, P. H. C., Alexander, A., Daniel, B. K., & Wibowo, E. (2023). Job prospects and career pathways for human anatomy graduates from the University of Otago: Implications for student support and professional development. Anatomical Sciences Education, 16, 582-599. doi: 10.1002/ase.2243

Conference Contribution - Verbal presentation and other Conference outputs

Clark, A. C., Messer, P. W., Alexander, A., & Gemmell, N. J. (2023, August-September). Exploring outcomes of genetic pest control in multi-species models. Verbal presentation at the He taonga tuku iho: Queenstown Molecular Biology (QMB) Bioprotection Aotearoa Satellite, Queenstown, New Zealand.

Alvarez-Costes, S., Baker, C. S., Constantine, R., Carroll, E., Dutoit, L., Ferreira, S., … Gemmell, N., Gillum, J., … Rayment, W., … Urban, L., & Alexander, A. (2023, August). Reference genomes, genome-wide heterozygosity, and historical demography of Hector's (Cephalorhynchus hectori hectori) and Māui (Cephalorhynchus hectori maui) dolphins. Verbal presentation at the Queenstown Molecular Biology (QMB) Genomics Satellite, Queenstown, New Zealand.

Alexander, A. (2023, July). Haepapa, hapa and hollandaise. Verbal presentation at the Third Ira Rangahau Māori Symposium, Dunedin, New Zealand.

2022

Journal - Research Article

Alexander, A., Robbins, M. B., Holmes, J., Moyle, R. G., & Peterson, A. T. (2022). Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change. Molecular Ecology, 31, 6634-6648. doi: 10.1111/mec.16727

Palmer, E., Alexander, A., Liggins, L., Guerra, M., Bury, S. J., Hendriks, H., … Peters, K. J. (2022). A piece of the puzzle: Analyses of recent strandings and historical records reveal new genetic and ecological insights on New Zealand sperm whales. Marine Ecology Progress Series, 690, 201-217. Retrieved from https://www.int-res.com/abstracts/meps/v690/p201-217/

Albertson, G. R., Alexander, A., Archer, F. I., Caballero, S., Martien, K. K., Hemery, L. G., … Baker, C. S. (2022). Worldwide phylogeography of rough-toothed dolphins (Steno bredanensis) provides evidence for subspecies delimitation. Marine Mammal Science, 38, 1371-1397. doi: 10.1111/mms.12933

Pearman, W. S., Urban, L., & Alexander, A. (2022). Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data. Molecular Ecology Resources, 22, 2599-2613. doi: 10.1111/1755-0998.13646

Girardet, J., Sarano, F., Richard, G., Tixier, P., Guinet, C., Alexander, A., … Jung, J.-L. (2022). Long distance runners in the marine realm: New insights into genetic diversity, kin relationships and social fidelity of Indian Ocean male sperm whales. Frontiers in Marine Science, 9, 815684. doi: 10.3389/fmars.2022.815684

Miller, A. K., Timoshevskaya, N., Smith, J. J., Gillum, J., Sharif, S., Clarke, S., … Gemmell, N. J., & Alexander, A. (2022). Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis). Journal of Heredity, 113, 380-397. doi: 10.1093/jhered/esac014

Conference Contribution - Published proceedings: Abstract

Alexander, A. (2022). Pātai about parāoa: Molecular ecology of sperm whales. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Conference Contribution - Poster Presentation (not in published proceedings)

Miller, A. K., Baker, C., Kitson, J., Gillum, J., Sharif, S., Clarke, … Gemmell, N. J., & Alexander, A. (2022, August-September). Population genomics of New Zealand pouched lamprey (kanakana: Geotria australis). Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Vallender, M., Dodds, K., Symonds, J. E., Gabrielson, R., Alexander, A., Walker, S. P., Gemmell, N. J., & Clarke, S. (2022, August). A big data, population genetics approach of low depth genotype-by-sequencing (GBS) to inform stock management of wild Chinook salmon (Oncorhynchus tshawytscha). Verbal presentation at the Applied Genetics/Genomics in Breeding Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.

Bond, D. M., Ortega-Recalde, O. J., Laird, M. K., Richardson, K. S., Reese, F. C. B., Alexander, A. M., … Gemmell, N. J., & Hore, T. A. (2022, August-September). Long read sequencing and understanding the genome and biology of the New Zealand Brushtail Possum. Verbal presentation at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Commissioned Report for External Body

Forsdick, N. J., Adams, C. I. M., Alexander, A., Clark, A. C., Collier-Robinson, L., Cubrinovska, I., … Dowle, E. J., … Verry, A. J. F., … Steeves, T. E. (2022). Current applications and future promise of genetic/genomic data for conservation in an Aotearoa New Zealand context [Science for Conservation 337]. Commissioned by Department of Conservation (DOC). Wellington, New Zealand: Department of Conservation Te Papa Atawhai. 57p. Retrieved from https://www.doc.govt.nz/about-us/science-publications/series/science-for-conservation

2021

Journal - Research Article

Foote, A. D., Hooper, R., Alexander, A., Baird, R. W., Baker, C. S., Ballance, L., … Morin, P. A. (2021). Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Molecular Ecology, 30, 6162-6177. doi: 10.1111/mec.16137

Baca, S. M., Gustafson, G. T., Alexander, A. M., Gough, H. M., & Toussaint, E. F. A. (2021). Integrative phylogenomics reveals a Permian origin of Adephaga beetles. Systematic Entomology, 46, 968-990. doi: 10.1111/syen.12506

Miller, A. K., Baker, C., Kitson, J. C., Yick, J. L., Manquel, P. E. I., Alexander, A., & Gemmell, N. J. (2021). The Southern Hemisphere lampreys (Geotriidae and Mordaciidae). Reviews in Fish Biology & Fisheries, 31, 201-232. doi: 10.1007/s11160-021-09639-x

Conference Contribution - Published proceedings: Abstract

Miller, A. K., Baker, C., Kitson, J., Gillum, J., Sharif, S., Clarke, S., Gemmell, N. J., & Alexander, A. (2021). Getting to know your shy neighbour: Population genomics of kanakana/piharau. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Bond, D. M., Ortega-Recalde, O. J., Laird, M. K., Richardson, K. S., Reese, F. C. B., Alexander, A. M., Adams, A. L., van Heezik, Y., Robertson, B. C., The Vertebrate Genomes Project, Gemmell, N. J., & Hore, T. A. (2021). Sequencing the genome of the New Zealand brushtail possum: A platform for biological discovery and pest control. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Conference Contribution - Verbal presentation and other Conference outputs

Vallender, M., Dodds, K., Alexander, A., Gabriellsson, R., Symonds, J., Clarke, S., & Gemmell, N. (2021, February). Demographic inference for wild New Zealand chinook salmon (Oncorhynchus tshawytscha) populations using genotype-free estimation of allele frequency spectra. Verbal presentation at the Quantitative Genetics Symposium, Dunedin, New Zealand.

Pearman, W., Urban, L., & Alexander, A. (2021, February). Hardy-Weinberg filtering and population stratification choice shapes population genomic inferences. Verbal presentation at the Quantitative Genetics Symposium, Dunedin, New Zealand.

2020

Journal - Research Article

Gustafson, G. T., Baca, S. M., Alexander, A. M., & Short, A. E. Z. (2020). Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance. Systematic Entomology, 45, 552-570. doi: 10.1111/syen.12413

Journal - Research Other

Morin, P. A., Alexander, A., Blaxter, M., Caballero, S., Fedrigo, O., Fontaine, M. C., … Jarvis, E. D. (2020). Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species. Marine Mammal Science, 36, 1356-1366. doi: 10.1111/mms.12721

Alexander, A., & Dutoit, L. (2020). Roe deer on ice: Selection despite limited effective population size through the Pleistocene. Molecular Ecology, 29, 2765-2767. doi: 10.1111/mec.15511

2019

Journal - Research Article

Cole, T. L., Dutoit, L., Dussex, N., Hart, T., Alexander, A., Younger, J. L., … Ellenberg, U., … Mattern, T., … Waters, J. M. (2019). Receding ice drove parallel expansions in Southern Ocean penguins. PNAS, 116(52), 26690-26696. doi: 10.1073/pnas.1904048116

Gustafson, G. T., Alexander, A., Sproul, J. S., Pflug, J. M., Maddison, D. R., & Short, A. E. Z. (2019). Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization. Ecology & Evolution, 9(12), 6933-6948. doi: 10.1002/ece3.5260

Dobelmann, J., Alexander, A., Baty, J. W., Gemmell, N. J., Gruber, M. A. M., Quinn, O., … Lester, P. J. (2019). The association between mitochondrial genetic variation and reduced colony fitness in an invasive wasp. Molecular Ecology, 28, 3324-3338. doi: 10.1111/mec.15159

Journal - Research Other

Al-Jiab, R. A., Gillum, J., Alexander, A., Tompkins, D. M., Phillips, C. B., Dearden, P. K., & Gemmell, N. J. (2019). The complete mitogenome sequence of the agricultural pest, clover root weevil: The key to its own demise? [Mitogenome announcement]. Mitochondrial DNA Part B, 4(1), 878-879. doi: 10.1080/23802359.2018.1561218

Conference Contribution - Published proceedings: Abstract

Cole, T., Dutoit, L., Dussex, N., Hart, T., Alexander, A., Frugone, M. J., … Ellenberg, U., … Mattern, T., … Waters, J. (2019). Receding ice drove rapid expansions in eight Southern Ocean penguins. Proceedings of the Genetics Society of Australasia (GSA) Conference. Retrieved from https://event.crowdcompass.com/gsa2019

McCartney, A., Guhlin, J., Alexander, A., Santure, A., Chagne, D., & Buckley, T. (2019). Genome assembly strategies for endemic New Zealand species. Proceedings of the Genetics Society of Australasia (GSA) Conference. Retrieved from https://event.crowdcompass.com/gsa2019

Cole, T. L., Dutoit, L., Dussex, N., Hart, T., Alexander, A., Frugone, M. J., … Ellenberg, U., … Mattern, T., … Waters, J. M. (2019). Contrasting demographic histories between widespread and endemic penguin taxa. Proceedings of the 10th International Penguin Conference (IPC10). (pp. 39-40). Retrieved from https://www.penguin-conference.com

Conference Contribution - Verbal presentation and other Conference outputs

Alexander, A., Constantine, R., Roe, W., Baker, C. S., Heimeier, D., Hamner, R. M., … Jeunen, G.-J., & Gemmell, N. (2019, August-September). Hologenomics for conservation: A first test of utility using New Zealand's endemic Māui and Hector's dolphins. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

McCartney, A., Guhlin, J., Alexander, A., Santure, A., Chagne, D., & Buckley, T. (2019, August-September). Genome assembly strategies for endemic New Zealand species. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2018

Journal - Research Article

Heimeier, D., Alexander, A., Hamner, R. M., Pichler, F., & Baker, C. S. (2018). The influence of selection on MHC DQA and DQB haplotypes in the endemic New Zealand Hector's and Māui Dolphins. Journal of Heredity, 109(7), 744-756. doi: 10.1093/jhered/esy050

Morin, P. A., Foote, A. D., Baker, C. S., Hancock-Hanser, B. L., Kaschner, K., Mate, B. R., … Alexander, A. (2018). Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses. Molecular Ecology, 27(11), 2604-2619. doi: 10.1111/mec.14698

Conference Contribution - Poster Presentation (not in published proceedings)

Alexander, A., Robbins, M., Holmes, J., Moyle, R., & Peterson, A. T. (2018, August). Movement of genes, song, and morphology across the black-capped/Carolina chickadee hybrid zone in Missouri. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Alexander, A. (2018, November). Differential movement of song, morphology, and genes across the black-capped/Carolina chickadee hybrid zone in Missouri. Verbal presentation at the MapNet meeting, Dunedin, New Zealand.

2017

Journal - Research Article

Warren, W. C., Kuderna, L., Alexander, A., Catchen, J., Pérez-Silva, J. G., López-Otín, C., … Wise, Sr, J. P. (2017). The novel evolution of the sperm whale genome. Genome Biology & Evolution, 9(12), 3260-3264. doi: 10.1093/gbe/evx187

Baca, S. M., Alexander, A., Gustafson, G. T., & Short, A. E. Z. (2017). Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’. Systematic Entomology, 42(4), 786-795. doi: 10.1111/syen.12244

Chan, K. O., Alexander, A. M., Grismer, L. L., Su, Y.-C., Grismer, J. L., Quah, E. S. H., & Brown, R. M. (2017). Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs. Molecular Ecology, 26(20), 5435-5450. doi: 10.1111/mec.14296

Campbell, L. P., & Alexander, A. M. (2017). Landscape genetics of Aedes mcintoshi (Diptera: Culicidae), an important vector of rift valley fever virus in Northeastern Kenya. Journal of Medical Entomology, 54(5), 1258-1265. doi: 10.1093/jme/tjx072

Alexander, A. M., Su, Y.-C., Oliveros, C. H., Olson, K. V., Travers, S. L., & Brown, R. M. (2017). Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs. Evolution, 71(2), 475-488. doi: 10.1111/evo.13133

Conference Contribution - Verbal presentation and other Conference outputs

Alexander, A., Su, Y.-C., Oliveros, C., Olson, K., Travers, S., & Brown, R. (2017, June). Mito-nuclear discordance: Distinguishing between contemporary hybridization, ILS and introgression. Invited presentation at the Joint Annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN), Portland, USA.

2016

Journal - Research Article

Grismer, J. L., Schulte II, J. A., Alexander, A., Wagner, P., Travers, S. L., Buehler, M. D., … Brown, R. M. (2016). The Eurasian invasion: Phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards. BMC Evolutionary Biology, 16, 43. doi: 10.1186/s12862-016-0611-6

Alexander, A., Steel, D., Hoekzema, K., Mesnick, S. L., Engelhaupt, D., Kerr, I., … Baker, C. S. (2016). What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)? Molecular Ecology, 25(12), 2754-2772. doi: 10.1111/mec.13638

King, C., Alexander, A., Chubb, T., Cursons, R., Mackay, J., McCormick, H., … Veale, A., & Zhang, H. (2016). What can the geographic distribution of mtDNA haplotypes tell us about the invasion of New Zealand by house mice Mus musculus? Biological Invasions, 18, 1551-1565. doi: 10.1007/s10530-016-1100-y

Conference Contribution - Verbal presentation and other Conference outputs

Alexander, A., Manthey, J., Sheldon, F., & Moyle, R. (2016, June). One kingfisher, two kingfisher, red kingfisher, blue kingfisher: Using RADseq to describe the species status of the Oriental dwarf kingfisher. Verbal presentation at the Joint Annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN), Austin, USA.

2015

Conference Contribution - Verbal presentation and other Conference outputs

Alexander, A., Steel, D., Hoekzema, K., Mesnick, S., Engelhaupt, D., Kerr, I., … Baker, C. S. (2015, December). What drives the genetic structure in oceanic populations of the sperm whale (Physeter macrocephalus)? Verbal presentation at the 21st Biennial Conference of the Society for Marine Mammalogy, San Franscisco, USA.

2014

Journal - Research Article

Carroll, E. L., Rayment, W. J., Alexander, A. M., Baker, C. S., Patenaude, N. J., Steel, D., … Childerhouse, S. (2014). Reestablishment of former wintering grounds by New Zealand southern right whales. Marine Mammal Science, 30(1), 206-220. doi: 10.1111/mms.12031

Awarded Doctoral Degree

Alexander, A. (2014). The influence of social structure and molecular evolution on genetic diversity in the sperm whale (Physeter macrocephalus) (PhD). Oregon State University, Corvallis, OR. Retrieved from http://hdl.handle.net/1957/52554

2013

Journal - Research Article

MacKay, J. W. B., Alexander, A., Hauber, M. E., Murphy, E. C., & Clout, M. N. (2013). Does genetic variation among invasive house mice in New Zealand affect eradication success? New Zealand Journal of Ecology, 37(1), 18-25.

Alexander, A., Steel, D., Slikas, B., Hoekzema, K., Carraher, C., Parks, M., … Baker, C. S. (2013). Low diversity in the mitogenome of sperm whales revealed by Next-Generation Sequencing. Genome Biology & Evolution, 5(1), 113-129. doi: 10.1093/gbe/evs126

Other Research Output

Alexander, A. (2013, August). A bottleneck for Moby Dick? Patterns of genetic differentiation and diversity in the sperm whale. Oregon Institute of Marine Biology Seminar Series, Charleston, OR. [Invited Presentation].

2012

Journal - Research Article

Carroll, E. L., Childerhouse, S. J., Christie, M., Lavery, S., Patenaude, N., Alexander, A., … Baker, C. S. (2012). Paternity assignment and demographic closure in the New Zealand southern right whale. Molecular Ecology, 21(16), 3960-3973. doi: 10.1111/j.1365-294X.2012.05676.x

2011

Journal - Research Article

Carroll, E., Patenaude, N., Alexander, A., Steel, D., Harcourt, R., Childerhouse, S., … Baker, C. S. (2011). Population structure and individual movement of southern right whales around New Zealand and Australia. Marine Ecology Progress Series, 432, 257-268. doi: 10.3354/meps09145