32 results on '"Cole, Theresa L."'
Search Results
2. Genomic insights into the secondary aquatic transition of penguins
- Author
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Cole, Theresa L., Zhou, Chengran, Fang, Miaoquan, Pan, Hailin, Ksepka, Daniel T., Fiddaman, Steven R., Emerling, Christopher A., Thomas, Daniel B., Bi, Xupeng, Fang, Qi, Ellegaard, Martin R., Feng, Shaohong, Smith, Adrian L., Heath, Tracy A., Tennyson, Alan J. D., Borboroglu, Pablo García, Wood, Jamie R., Hadden, Peter W., Grosser, Stefanie, Bost, Charles-André, Cherel, Yves, Mattern, Thomas, Hart, Tom, Sinding, Mikkel-Holger S., Shepherd, Lara D., Phillips, Richard A., Quillfeldt, Petra, Masello, Juan F., Bouzat, Juan L., Ryan, Peter G., Thompson, David R., Ellenberg, Ursula, Dann, Peter, Miller, Gary, Dee Boersma, P., Zhao, Ruoping, Gilbert, M. Thomas P., Yang, Huanming, Zhang, De-Xing, and Zhang, Guojie
- Published
- 2022
- Full Text
- View/download PDF
3. Receding ice drove parallel expansions in Southern Ocean penguins
- Author
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Cole, Theresa L., Dutoit, Ludovic, Dussex, Nicolas, Hart, Tom, Alexander, Alana, Younger, Jane L., Clucas, Gemma V., Frugone, María José, Cherel, Yves, Cuthbert, Richard, Ellenberg, Ursula, Fiddaman, Steven R., Hiscock, Johanna, Houston, David, Jouventin, Pierre, Mattern, Thomas, Miller, Gary, Miskelly, Colin, Nolan, Paul, Polito, Michael J., Quillfeldt, Petra, Ryan, Peter G., Smith, Adrian, Tennyson, Alan J. D., Thompsona, David, Wieneckeb, Barbara, Viannac, Juliana A., and Waters, Jonathan M.
- Published
- 2019
4. Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey
- Author
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Seersholm, Frederik V., Cole, Theresa L., Grealy, Alicia, Rawlence, Nicolas J., Greig, Karen, Knapp, Michael, Stat, Michael, Hansen, Anders J., Easton, Luke J., Shepherd, Lara, Tennyson, Alan J. D., Scofield, R. Paul, Walter, Richard, and Bunce, Michael
- Published
- 2018
5. Independent evolution of intermediate bill widths in a seabird clade
- Author
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Masello, Juan F., Ryan, Peter G., Shepherd, Lara D., Quillfeldt, Petra, Cherel, Yves, Tennyson, Alan J. D., Alderman, Rachael, Calderón, Luciano, Cole, Theresa L., Cuthbert, Richard J., Dilley, Ben J., Massaro, Melanie, Miskelly, Colin M., Navarro, Joan, Phillips, Richard A., Weimerskirch, Henri, Moodley, Yoshan, Masello, Juan F., Ryan, Peter G., Shepherd, Lara D., Quillfeldt, Petra, Cherel, Yves, Tennyson, Alan J. D., Alderman, Rachael, Calderón, Luciano, Cole, Theresa L., Cuthbert, Richard J., Dilley, Ben J., Massaro, Melanie, Miskelly, Colin M., Navarro, Joan, Phillips, Richard A., Weimerskirch, Henri, and Moodley, Yoshan
- Abstract
Interspecific introgression can occur between species that evolve rapidly within an adaptive radiation. Pachyptila petrels differ in bill size and are characterised by incomplete reproductive isolation, leading to interspecific gene flow. Salvin's prion (Pachyptila salvini), whose bill width is intermediate between broad-billed (P. vittata) and Antarctic (P. desolata) prions, evolved through homoploid hybrid speciation. MacGillivray's prion (P. macgillivrayi), known from a single population on St Paul (Indian Ocean), has a bill width intermediate between salvini and vittata and could also be the product of interspecies introgression or hybrid speciation. Recently, another prion population phenotypically similar to macgillivrayi was discovered on Gough (Atlantic Ocean), where it breeds 3 months later than vittata. The similarity in bill width between the medium-billed birds on Gough and macgillivrayi suggest that they could be closely related. In this study, we used genetic and morphological data to infer the phylogenetic position and evolutionary history of P. macgillivrayi and the Gough medium-billed prion relative other Pachyptila taxa, to determine whether species with medium bill widths evolved through common ancestry or convergence. We found that Gough medium-billed prions belong to the same evolutionary lineage as macgillivrayi, representing a new population of MacGillivray's prion that originated through a colonisation event from St Paul. We show that macgillivrayi's medium bill width evolved through divergence (genetic drift) and independently from that of salvini, which evolved through hybridisation (gene flow). This represents the independent convergence towards a similarly medium-billed phenotype. The newly discovered MacGillivray's prion population on Gough is of utmost conservation relevance, as the relict macgillivrayi population in the Indian Ocean is very small.
- Published
- 2022
6. Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors
- Author
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Fiddaman, Steven R., Vinkler, Michal, Spiro, Simon G., Levy, Hila, Emerling, Christopher A., Boyd, Amy C., Dimopoulos, Evangelos A., Vianna, Juliana A., Cole, Theresa L., Pan, Hailin, Fang, Miaoquan, Zhang, Guojie, Hart, Tom, Frantz, Laurent A. F., Smith, Adrian L., Fiddaman, Steven R., Vinkler, Michal, Spiro, Simon G., Levy, Hila, Emerling, Christopher A., Boyd, Amy C., Dimopoulos, Evangelos A., Vianna, Juliana A., Cole, Theresa L., Pan, Hailin, Fang, Miaoquan, Zhang, Guojie, Hart, Tom, Frantz, Laurent A. F., and Smith, Adrian L.
- Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
- Published
- 2022
7. Independent evolution of intermediate bill widths in a seabird clade
- Author
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Agencia Estatal de Investigación (España), German Research Foundation, Department of Environmental Affairs (South Africa), Royal Society of New Zealand, Masello, Juan F., Ryan, Peter G., Shepherd, Lara D., Quillfeldt, Petra, Cherel, Yves, Tennyson, Alan J.D., Alderman, Rachael, Calderón, Luciano, Cole, Theresa L., Cuthbert, Richard, Dilley, Ben J., Massaro, Melanie, Miskelly, Colin M., Navarro, Joan, Phillips, Richard A., Weimerskirch, Henri, Moodley, Yoshan, Agencia Estatal de Investigación (España), German Research Foundation, Department of Environmental Affairs (South Africa), Royal Society of New Zealand, Masello, Juan F., Ryan, Peter G., Shepherd, Lara D., Quillfeldt, Petra, Cherel, Yves, Tennyson, Alan J.D., Alderman, Rachael, Calderón, Luciano, Cole, Theresa L., Cuthbert, Richard, Dilley, Ben J., Massaro, Melanie, Miskelly, Colin M., Navarro, Joan, Phillips, Richard A., Weimerskirch, Henri, and Moodley, Yoshan
- Abstract
Interspecific introgression can occur between species that evolve rapidly within an adaptive radiation. Pachyptila petrels differ in bill size and are characterised by incomplete reproductive isolation, leading to interspecific gene flow. Salvin’s prion (Pachyptila salvini), whose bill width is intermediate between broad-billed (P. vittata) and Antarctic (P. desolata) prions, evolved through homoploid hybrid speciation. MacGillivray’s prion (P. macgillivrayi), known from a single population on St Paul (Indian Ocean), has a bill width intermediate between salvini and vittata and could also be the product of interspecies introgression or hybrid speciation. Recently, another prion population phenotypically similar to macgillivrayi was discovered on Gough (Atlantic Ocean), where it breeds 3 months later than vittata. The similarity in bill width between the medium-billed birds on Gough and macgillivrayi suggest that they could be closely related. In this study, we used genetic and morphological data to infer the phylogenetic position and evolutionary history of P. macgillivrayi and the Gough medium-billed prion relative other Pachyptila taxa, to determine whether species with medium bill widths evolved through common ancestry or convergence. We found that Gough medium-billed prions belong to the same evolutionary lineage as macgillivrayi, representing a new population of MacGillivray’s prion that originated through a colonisation event from St Paul. We show that macgillivrayi’s medium bill width evolved through divergence (genetic drift) and independently from that of salvini, which evolved through hybridisation (gene flow). This represents the independent convergence towards a similarly medium-billed phenotype. The newly discovered MacGillivray’s prion population on Gough is of utmost conservation relevance, as the relict macgillivrayi population in the Indian Ocean is very small
- Published
- 2022
8. Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors
- Author
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Fiddaman, Steven R, primary, Vinkler, Michal, additional, Spiro, Simon G, additional, Levy, Hila, additional, Emerling, Christopher A, additional, Boyd, Amy C, additional, Dimopoulos, Evangelos A, additional, Vianna, Juliana A, additional, Cole, Theresa L, additional, Pan, Hailin, additional, Fang, Miaoquan, additional, Zhang, Guojie, additional, Hart, Tom, additional, Frantz, Laurent A F, additional, and Smith, Adrian L, additional
- Published
- 2021
- Full Text
- View/download PDF
9. Front Cover
- Author
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Frugone, María José, primary, Cole, Theresa L., additional, López, María Eugenia, additional, Clucas, Gemma, additional, Matos‐Maraví, Pável, additional, Lois, Nicolás A., additional, Pistorius, Pierre, additional, Bonadonna, Francesco, additional, Trathan, Phil, additional, Polanowski, Andrea, additional, Wienecke, Barbara, additional, Raya‐Rey, Andrea, additional, Pütz, Klemens, additional, Steinfurth, Antje, additional, Bi, Ke, additional, Wang‐Claypool, Cynthia Y., additional, Waters, Jonathan M., additional, Bowie, Rauri C. K., additional, Poulin, Elie, additional, and Vianna, Juliana A., additional
- Published
- 2021
- Full Text
- View/download PDF
10. Ancient DNA from bulk bone reveals past genetic diversity of vertebrate fauna on Kangaroo Island, Australia
- Author
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Seersholm, Frederik V., Grealy, Alicia, McDowell, Matthew, Cole, Theresa L., Arnold, Lee J, Prideaux, Gavin, Bunce, Michael, Seersholm, Frederik V., Grealy, Alicia, McDowell, Matthew, Cole, Theresa L., Arnold, Lee J, Prideaux, Gavin, and Bunce, Michael
- Abstract
It is indisputable that much of Australia's modern biodiversity decline was triggered by European settlement. However, the driver(s) of pre-European extinctions and extirpations are more challenging to identify, particularly on islands where animals are faced with the additional pressures imposed by isolation. Kangaroo Island, South Australia, has been identified as a potential haven for the reintroduction of endangered animals, but the genetic relationship between reintroduction candidates on the mainland and their extinct relatives on Kangaroo Island is poorly understood. Here, we present a late Pleistocene to mid-Holocene genetic record from Kangaroo Island based on bulk bone metabarcoding of two thousand bone fragments excavated from Kelly Hill Cave. We detect 33 species of bird, reptile, fish and mammal and report additional intra-specific genetic diversity in Kangaroo Island's now extinct population of spotted-tailed quoll. Furthermore, we provide genetic evidence that the Eastern grey kangaroo formerly inhabited Kangaroo Island. Taken together, these data establish a more complete baseline of local biodiversity against which reintroduction programmes and bushfire recovery measures can be evaluated, which is more important than ever in light of the recent fires that devastated much of Kangaroo Island's flora and fauna.
- Published
- 2021
11. A new extinct species of Polynesian sandpiper (Charadriiformes: Scolopacidae: Prosobonia) from Henderson Island, Pitcairn Group, and the phylogenetic relationships of Prosobonia
- Author
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De Pietri, Vanesa L., Worthy, Trevor H., Scofield, R. Paul, Cole, Theresa L., Wood, Jamie R., Mitchell, Kieren J., Cibois, Alice, Jansen, Justin J. F. J., Cooper, Alan J., Feng, Shaohong, Chen, Wanjun, Tennyson, Alan Jd, Wragg, Graham M., De Pietri, Vanesa L., Worthy, Trevor H., Scofield, R. Paul, Cole, Theresa L., Wood, Jamie R., Mitchell, Kieren J., Cibois, Alice, Jansen, Justin J. F. J., Cooper, Alan J., Feng, Shaohong, Chen, Wanjun, Tennyson, Alan Jd, and Wragg, Graham M.
- Abstract
We describe a new species of Polynesian sandpiper from Henderson Island, Prosobonia sauli sp. nov., based on multiple Holocene fossil bones collected during the Sir Peter Scott Commemorative Expedition to the Pitcairn Islands (1991-92). Prosobonia sauli is the only species of Prosobonia to be described from bone accumulations and extends the record of known extinct Polynesian sandpipers to four. It is readily differentiated from the extant Tuamotu Sandpiper P. parvirostris in several features of the legs and bill, implying ecological adaptations to different environments. The geographically nearest Prosobonia populations to Henderson Island were found on Mangareva, where it is now extinct. A previous record of a species of Prosobonia from Tubuai, Austral Islands, is here shown to belong to the Sanderling Calidris alba. Our analyses of newly sequenced genetic data, which include the mitochondrial genomes of P. parvirostris and the extinct Tahiti Sandpiper P. leucoptera, confidently resolve the position of Prosobonia as sister-taxon to turnstones and calidrine sandpipers. We present a hypothesis for the timing of divergence between species of Prosobonia and other scolopacid lineages. Our results further provide a framework to interpret the evolution of sedentary lineages within the normally highly migratory Scolopacidae.
- Published
- 2021
12. Mid-Holocene coprolites from southern New Zealand provide new insights into the diet and ecology of the extinct little bush moa (Anomalopteryx didiformis)
- Author
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Wood, Jamie R., Vermeulen, Melanie J., Bolstridge, Nicola, Briden, Shar, Cole, Theresa L., Rivera-Perez, Jessica, Shepherd, Lara D., Rawlence, Nicolas J., Wilmshurst, Janet M., Wood, Jamie R., Vermeulen, Melanie J., Bolstridge, Nicola, Briden, Shar, Cole, Theresa L., Rivera-Perez, Jessica, Shepherd, Lara D., Rawlence, Nicolas J., and Wilmshurst, Janet M.
- Abstract
Knowledge about the diets of New Zealand's extinct moa (Aves: Dinornithiformes) is heavily biased towards just three species (Dinornis robustus, Megalapteryx didinus and Pachyornis elephantopus), which represent about 90% of all identified coprolites and gizzard content samples. By comparison, the diets of the other six moa species are poorly known. Here, we report the discovery of a new coprolite deposit attributed to little bush moa (Anomalopteryx didiformis) based on DNA barcoding and former moa species distributions. The deposit is the southernmost site from which moa coprolites have been recovered and just the second to contain mid-Holocene specimens. Moreover, the deposit provides the longest known temporal span (∼2200 years) of moa coprolites within a stratigraphic context. Pollen and plant DNA from the coprolites, as well as associated plant macrofossils, indicate that the deposit spans a period when the forest canopy was transitioning from Podocarpaceae to silver beech (Lophozonia menziesii) dominance about 6800–4600 years ago. Our analysis of coprolite content supports the current hypothesis that little bush moa browsed trees and shrubs within the forest understorey, but provides new evidence that ferns were also an important part of their diet. Based on this finding, we suggest that moa might once have played a previously unrecognised role in the dispersal of ground fern spores throughout New Zealand forests.
- Published
- 2021
13. Vertical distribution of prokaryotes communities and predicted metabolic pathways in New Zealand wetlands, and potential for environmental DNA indicators of wetland condition
- Author
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Wood, Jamie R., Burge, Olivia R., Bolstridge, Nic, Bonner, Karen, Clarkson, Beverley, Cole, Theresa L., Davis, Carina, Fergus, Alex, King, Perēri, McKeown, Michelle M., Morse, Chris, Richardson, Sarah J., Robertson, Hugh, Wilmshurst, Janet M., Wood, Jamie R., Burge, Olivia R., Bolstridge, Nic, Bonner, Karen, Clarkson, Beverley, Cole, Theresa L., Davis, Carina, Fergus, Alex, King, Perēri, McKeown, Michelle M., Morse, Chris, Richardson, Sarah J., Robertson, Hugh, and Wilmshurst, Janet M.
- Abstract
Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of biodiversity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health.
- Published
- 2021
14. Vertical distribution of prokaryotes communities and predicted metabolic pathways in New Zealand wetlands, and potential for environmental DNA indicators of wetland condition
- Author
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Wood, Jamie R., primary, Burge, Olivia R., additional, Bolstridge, Nic, additional, Bonner, Karen, additional, Clarkson, Beverley, additional, Cole, Theresa L., additional, Davis, Carina, additional, Fergus, Alex, additional, King, Perēri, additional, McKeown, Michelle M., additional, Morse, Chris, additional, Richardson, Sarah J., additional, Robertson, Hugh, additional, and Wilmshurst, Janet M., additional
- Published
- 2021
- Full Text
- View/download PDF
15. Latitudinal, sex and inter-specific differences in mercury and other trace metal concentrations in Adélie and Emperor penguins in the Ross Sea, Antarctica
- Author
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Pilcher, Natalie, Gaw, Sally, Eisert, Regina, Horton, Travis W., Gormley, Andrew M., Cole, Theresa L., Lyver, Phil O.B., Pilcher, Natalie, Gaw, Sally, Eisert, Regina, Horton, Travis W., Gormley, Andrew M., Cole, Theresa L., and Lyver, Phil O.B.
- Abstract
We sought to determine mercury (Hg) and other trace metal concentrations in Adélie (Pygoscelis adeliae) and emperor penguin (Aptenodytes forsteri) breast feathers from the Ross Sea, Antarctica, and relate those concentrations to the trophic position and the habitats in which each of these species forage. Adélie penguin feathers from the southern Ross Sea colonies were higher in Hg than those sampled further north in the Ross Sea, potentially due to greater exposure to local sources, such as volcanism. Female Adélie penguins had lower feather total Hg concentrations than males. This may reflect female penguin's capacity to eliminate Hg through the egg development and laying process, or the larger and/or older prey items that male birds can consume, reflected by their higher trophic position. Emperor penguins have higher Hg concentrations than Adélie penguins which is also partially explained by Adélie penguins feeding at lower trophic levels than emperor penguins.
- Published
- 2020
16. Cole, Theresa L.
- Author
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Cole, Theresa L. and Cole, Theresa L.
- Published
- 2020
17. Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors.
- Author
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Fiddaman, Steven R, Vinkler, Michal, Spiro, Simon G, Levy, Hila, Emerling, Christopher A, Boyd, Amy C, Dimopoulos, Evangelos A, Vianna, Juliana A, Cole, Theresa L, Pan, Hailin, Fang, Miaoquan, Zhang, Guojie, Hart, Tom, Frantz, Laurent A F, and Smith, Adrian L
- Subjects
IMMUNOGENETICS ,PSEUDOGENES ,WILDLIFE diseases ,IMMUNOLOGY ,HAPLOTYPES - Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B , TLR4 , and TLR5. Intriguingly, TLR15 , which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp. but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus , which is responsible for significant mortality in wild and captive bird populations. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
18. Correction to: High-coverage genomes to elucidate the evolution of penguins
- Author
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Pan, Hailin, primary, Cole, Theresa L, primary, Bi, Xupeng, primary, Fang, Miaoquan, primary, Zhou, Chengran, primary, Yang, Zhengtao, primary, Ksepka, Daniel T, primary, Hart, Tom, primary, Bouzat, Juan L, primary, Argilla, Lisa S, primary, Bertelsen, Mads F, primary, Boersma, P Dee, primary, Bost, Charles-Andre, primary, Cherel, Yves, primary, Dann, Peter, primary, Fiddaman, Steven R, primary, Howard, Pauline, primary, Labuschagne, Kim, primary, Mattern, Thomas, primary, Miller, Gary, primary, Parker, Patricia, primary, Phillips, Richard A, primary, Quillfeldt, Petra, primary, Ryan, Peter G, primary, Taylor, Helen, primary, Thompson, David R, primary, Young, Melanie J, primary, Ellegaard, Martin R, primary, Gilbert, M Thomas P, primary, Sinding, Mikkel-Holger S, primary, Pacheco, George, primary, Shepherd, Lara D, primary, Tennyson, Alan J D, primary, Grosser, Stefanie, primary, Kay, Emily, primary, Nupen, Lisa J, primary, Ellenberg, Ursula, primary, Houston, David M, primary, Reeve, Andrew Hart, primary, Johnson, Kathryn, primary, Masello, Juan F, primary, Stracke, Thomas, primary, McKinlay, Bruce, primary, Garc´ıa Borboroglu, Pablo, primary, Zhang, De-Xing, primary, and Zhang, Guojie, primary
- Published
- 2020
- Full Text
- View/download PDF
19. High-coverage genomes to elucidate the evolution of penguins
- Author
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Pan, Hailin, Cole, Theresa L., Bi, Xupeng, Fang, Miaoquan, Zhou, Chengran, Yang, Zhengtao, Hart, Tom, Bouzat, Juan L., Argilla, Lisa S., Bertelsen, Mads F., Boersma, P. Dee, Bost, Charles-André, Cherel, Yves, Dann, Peter, Fiddaman, Steven R., Howard, Pauline, Labuschagne, Kim, Mattern, Thomas, Miller, Gary, Parker, Patricia, Phillips, Richard A., Quillfeldt, Petra, Ryan, Peter G., Taylor, Helen, Thompson, David R., Young, Melanie J., Ellegaard, Martin R., Gilbert, M. Thomas P., Mikkel-Holger, S. Sinding, Pacheco, George, Shepherd, Lara D., Tennyson, Alan J.D., Grosser, Stefanie, Kay, Emily, Nupen, Lisa j., Ellenberg, Ursula, Houston, David M., Reeve, Andrew Hart, Johnson, Kathryn, Masello, Juan F., Stracke, Thomas, McKinlay, Bruce, Zhang, De Xing, Zhang, Guojie, Pan, Hailin, Cole, Theresa L., Bi, Xupeng, Fang, Miaoquan, Zhou, Chengran, Yang, Zhengtao, Hart, Tom, Bouzat, Juan L., Argilla, Lisa S., Bertelsen, Mads F., Boersma, P. Dee, Bost, Charles-André, Cherel, Yves, Dann, Peter, Fiddaman, Steven R., Howard, Pauline, Labuschagne, Kim, Mattern, Thomas, Miller, Gary, Parker, Patricia, Phillips, Richard A., Quillfeldt, Petra, Ryan, Peter G., Taylor, Helen, Thompson, David R., Young, Melanie J., Ellegaard, Martin R., Gilbert, M. Thomas P., Mikkel-Holger, S. Sinding, Pacheco, George, Shepherd, Lara D., Tennyson, Alan J.D., Grosser, Stefanie, Kay, Emily, Nupen, Lisa j., Ellenberg, Ursula, Houston, David M., Reeve, Andrew Hart, Johnson, Kathryn, Masello, Juan F., Stracke, Thomas, McKinlay, Bruce, Zhang, De Xing, and Zhang, Guojie
- Abstract
Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes.
- Published
- 2019
20. More than the eye can see: Genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean.
- Author
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Frugone, María José, López, María Eugenia, Segovia, Nicolás I., Cole, Theresa L., Lowther, Andrew, Pistorius, Pierre, Dantas, Gisele P.M., Petry, Maria Virginia, Bonadonna, Francesco, Trathan, Phil, Polanowski, Andrea, Wienecke, Barbara, Bi, Ke, Wang-Claypool, Cynthia Y., Waters, Jonathan M., Bowie, Rauri C.K., Poulin, Elie, Vianna, Juliana A., Frugone, María José, López, María Eugenia, Segovia, Nicolás I., Cole, Theresa L., Lowther, Andrew, Pistorius, Pierre, Dantas, Gisele P.M., Petry, Maria Virginia, Bonadonna, Francesco, Trathan, Phil, Polanowski, Andrea, Wienecke, Barbara, Bi, Ke, Wang-Claypool, Cynthia Y., Waters, Jonathan M., Bowie, Rauri C.K., Poulin, Elie, and Vianna, Juliana A.
- Abstract
The study of systematics in wide-ranging seabirds can be challenging due to the vast geographic scales involved, as well as the possible discordance between molecular, morphological and behavioral data. In the Southern Ocean, macaroni penguins (Eudyptes chrysolophus) are distributed over a circumpolar range including populations in Antarctic and sub-Antarctic areas. Macquarie Island, in its relative isolation, is home to a closely related endemic taxon — the royal penguin (Eudyptes schlegeli), which is distinguishable from E. chrysolophus mainly by facial coloration. Although these sister taxa are widely accepted as representing distinct species based on morphological grounds, the extent of their genome-wide differentiation remains uncertain. In this study, we use genome-wide Single Nucleotide Polymorphisms to test genetic differentiation between these geographically isolated taxa and evaluate the main drivers of population structure among breeding colonies of macaroni/royal penguins. Genetic similarity observed between macaroni and royal penguins suggests they constitute a single evolutionary unit. Nevertheless, royal penguins exhibited a tendency to cluster only with macaroni individuals from Kerguelen Island, suggesting that dispersal occurs mainly between these neighboring colonies. A stepping stone model of differentiation of macaroni/royal populations was further supported by a strong pattern of isolation by distance detected across its whole distribution range, possibly driven by large geographic distances between colonies as well as natal philopatry. However, we also detected intraspecific genomic differentiation between Antarctic and sub-Antarctic populations of macaroni penguins, highlighting the role of environmental factors together with geographic distance in the processes of genetic differentiation between Antarctic and sub-Antarctic waters.
- Published
- 2019
21. Additive traits lead to feeding advantage and reproductive isolation, promoting homoploid hybrid speciation
- Author
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Masello, Juan F., Quillfeldt, Petra, Sandoval-Castellanos, Edson, Alderman, Rachael, Calderón, Luciano, Cherel, Yves, Cole, Theresa L., Cuthbert, Richard J., Marin, Manuel, Massaro, Melanie, Navarro, Joan, Phillips, Richard A., Ryan, Peter G., Shepherd, Lara D., Suazo, Cristián G., Weimerskirch, Henri, Moodley, Yoshan, Russo, Claudia, Masello, Juan F., Quillfeldt, Petra, Sandoval-Castellanos, Edson, Alderman, Rachael, Calderón, Luciano, Cherel, Yves, Cole, Theresa L., Cuthbert, Richard J., Marin, Manuel, Massaro, Melanie, Navarro, Joan, Phillips, Richard A., Ryan, Peter G., Shepherd, Lara D., Suazo, Cristián G., Weimerskirch, Henri, Moodley, Yoshan, and Russo, Claudia
- Abstract
Speciation through homoploid hybridization (HHS) is considered extremely rare in animals. This is mainly because the establishment of reproductive isolation as a product of hybridization is uncommon. Additionally, many traits are underpinned by polygeny and/or incomplete dominance, where the hybrid phenotype is an additive blend of parental characteristics. Phenotypically intermediate hybrids are usually at a fitness disadvantage compared to parental species and tend to vanish through backcrossing with parental population(s). It is therefore unknown whether the additive nature of hybrid traits in itself could lead successfully to HHS. Using a multi-marker genetic data set and a meta-analysis of diet and morphology, we investigated a potential case of HHS in the prions (Pachyptila spp.), seabirds distinguished by their bills, prey choice and timing of breeding. Using approximate Bayesian computation, we show that the medium-billed Salvin’s prion (P. salvini) could be a hybrid between the narrow-billed Antarctic prion (P. desolata) and broad-billed prion (P. vittata). Remarkably, P. salvini’s intermediate bill width has given it a feeding advantage with respect to the other Pachyptila species, allowing it to consume a broader range of prey, potentially increasing its fitness. Available metadata showed that P. salvini is also intermediate in breeding phenology and, with no overlap in breeding times, it is effectively reproductively isolated from either parental species through allochrony. These results provide evidence for a case of HHS in nature, and show for the first time that additivity of divergent parental traits alone can lead directly to increased hybrid fitness and reproductive isolation.
- Published
- 2019
22. Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation
- Author
-
Cole, Theresa L., Ksepka, Daniel T., Mitchell, Kieren J, Tennyson, Alan J. D., Thomas, Daniel B., Pan, Hailin, Zhang, Guojie, Rawlence, Nicolas J., Wood, Jamie R., Bover, Pere, Bouzat, Juan L., Cooper, Alan, Fiddaman, Steven R., Hart, Tom, Miller, Gary, Ryan, Peter G., Shepherd, Lara D., Wilmshurst, Janet M., Waters, Jonathan M., Cole, Theresa L., Ksepka, Daniel T., Mitchell, Kieren J, Tennyson, Alan J. D., Thomas, Daniel B., Pan, Hailin, Zhang, Guojie, Rawlence, Nicolas J., Wood, Jamie R., Bover, Pere, Bouzat, Juan L., Cooper, Alan, Fiddaman, Steven R., Hart, Tom, Miller, Gary, Ryan, Peter G., Shepherd, Lara D., Wilmshurst, Janet M., and Waters, Jonathan M.
- Abstract
The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos.
- Published
- 2019
23. Additive Traits Lead to Feeding Advantage and Reproductive Isolation, Promoting Homoploid Hybrid Speciation
- Author
-
Institut Polaire Français, Terres Australes et Antarctiques Francaises, Mohamed bin Zayed Species Conservation Fund, Brian Mason Scientific and Technical Trust, German Research Foundation, Natural Environment Research Council (UK), Masello, Juan F., Quillfeldt, Petra, Sandoval-Castellanos, Edson, Alderman, Rachael, Calderón, Luciano, Cherel, Yves, Cole, Theresa L., Cuthbert, Richard, Marin, Manuel, Massaro, Melanie, Navarro, Joan, Phillips, Richard A., Ryan, Peter G., Shepherd, Lara D., Suazo, Cristián G., Weimerskirch, Henri, Moodley, Yoshan, Institut Polaire Français, Terres Australes et Antarctiques Francaises, Mohamed bin Zayed Species Conservation Fund, Brian Mason Scientific and Technical Trust, German Research Foundation, Natural Environment Research Council (UK), Masello, Juan F., Quillfeldt, Petra, Sandoval-Castellanos, Edson, Alderman, Rachael, Calderón, Luciano, Cherel, Yves, Cole, Theresa L., Cuthbert, Richard, Marin, Manuel, Massaro, Melanie, Navarro, Joan, Phillips, Richard A., Ryan, Peter G., Shepherd, Lara D., Suazo, Cristián G., Weimerskirch, Henri, and Moodley, Yoshan
- Abstract
Speciation through homoploid hybridization (HHS) is considered extremely rare in animals. This is mainly because the establishment of reproductive isolation as a product of hybridization is uncommon. Additionally, many traits are underpinned by polygeny and/or incomplete dominance, where the hybrid phenotype is an additive blend of parental characteristics. Phenotypically intermediate hybrids are usually at a fitness disadvantage compared with parental species and tend to vanish through backcrossing with parental population(s). It is therefore unknown whether the additive nature of hybrid traits in itself could lead successfully to HHS. Using a multi-marker genetic data set and a meta-analysis of diet and morphology, we investigated a potential case of HHS in the prions (Pachyptila spp.), seabirds distinguished by their bills, prey choice, and timing of breeding. Using approximate Bayesian computation, we show that the medium-billed Salvin’s prion (Pachyptila salvini) could be a hybrid between the narrow-billed Antarctic prion (Pachyptila desolata) and broad-billed prion (Pachyptila vittata). Remarkably, P. salvini’s intermediate bill width has given it a feeding advantage with respect to the other Pachyptila species, allowing it to consume a broader range of prey, potentially increasing its fitness. Available metadata showed that P. salvini is also intermediate in breeding phenology and, with no overlap in breeding times, it is effectively reproductively isolated from either parental species through allochrony. These results provide evidence for a case of HHS in nature, and show for the first time that additivity of divergent parental traits alone can lead directly to increased hybrid fitness and reproductive isolation
- Published
- 2019
24. High-coverage genomes to elucidate the evolution of penguins
- Author
-
Pan, Hailin, primary, Cole, Theresa L, primary, Bi, Xupeng, primary, Fang, Miaoquan, primary, Zhou, Chengran, primary, Yang, Zhengtao, primary, Ksepka, Daniel T, primary, Hart, Tom, primary, Bouzat, Juan L, primary, Argilla, Lisa S, primary, Bertelsen, Mads F, primary, Boersma, P Dee, primary, Bost, Charles-André, primary, Cherel, Yves, primary, Dann, Peter, primary, Fiddaman, Steven R, primary, Howard, Pauline, primary, Labuschagne, Kim, primary, Mattern, Thomas, primary, Miller, Gary, primary, Parker, Patricia, primary, Phillips, Richard A, primary, Quillfeldt, Petra, primary, Ryan, Peter G, primary, Taylor, Helen, primary, Thompson, David R, primary, Young, Melanie J, primary, Ellegaard, Martin R, primary, Gilbert, M Thomas P, primary, Sinding, Mikkel-Holger S, primary, Pacheco, George, primary, Shepherd, Lara D, primary, Tennyson, Alan J D, primary, Grosser, Stefanie, primary, Kay, Emily, primary, Nupen, Lisa J, primary, Ellenberg, Ursula, primary, Houston, David M, primary, Reeve, Andrew Hart, primary, Johnson, Kathryn, primary, Masello, Juan F, primary, Stracke, Thomas, primary, McKinlay, Bruce, primary, Borboroglu, Pablo García, primary, Zhang, De-Xing, primary, and Zhang, Guojie, primary
- Published
- 2019
- Full Text
- View/download PDF
25. Additive Traits Lead to Feeding Advantage and Reproductive Isolation, Promoting Homoploid Hybrid Speciation
- Author
-
Masello, Juan F, primary, Quillfeldt, Petra, additional, Sandoval-Castellanos, Edson, additional, Alderman, Rachael, additional, Calderón, Luciano, additional, Cherel, Yves, additional, Cole, Theresa L, additional, Cuthbert, Richard J, additional, Marin, Manuel, additional, Massaro, Melanie, additional, Navarro, Joan, additional, Phillips, Richard A, additional, Ryan, Peter G, additional, Shepherd, Lara D, additional, Suazo, Cristián G, additional, Weimerskirch, Henri, additional, and Moodley, Yoshan, additional
- Published
- 2019
- Full Text
- View/download PDF
26. Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation
- Author
-
Cole, Theresa L, primary, Ksepka, Daniel T, primary, Mitchell, Kieren J, primary, Tennyson, Alan J D, primary, Thomas, Daniel B, primary, Pan, Hailin, primary, Zhang, Guojie, primary, Rawlence, Nicolas J, primary, Wood, Jamie R, primary, Bover, Pere, primary, Bouzat, Juan L, primary, Cooper, Alan, primary, Fiddaman, Steven R, primary, Hart, Tom, primary, Miller, Gary, primary, Ryan, Peter G, primary, Shepherd, Lara D, primary, Wilmshurst, Janet M, primary, and Waters, Jonathan M, primary
- Published
- 2019
- Full Text
- View/download PDF
27. Evidence for breeding of Megadyptes penguins in the North Island at the time of human arrival
- Author
-
Rawlence, Nicolas J., primary, Tennyson, Alan J. D., additional, Cole, Theresa L., additional, Verry, Alexander J. F., additional, and Scofield, R. Paul, additional
- Published
- 2018
- Full Text
- View/download PDF
28. The ancient DNA revolution: the latest era in unearthing New Zealand’s faunal history
- Author
-
Cole, Theresa L., primary and Wood, Jamie R., additional
- Published
- 2017
- Full Text
- View/download PDF
29. Evidence for breeding of Megadyptes penguins in the North Island at the time of human arrival.
- Author
-
Rawlence, Nicolas J., Tennyson, Alan J. D., Cole, Theresa L., Verry, Alexander J. F., and Scofield, R. Paul
- Subjects
MEGADYPTES ,BIRD breeding ,BIOLOGICAL extinction ,PALEONTOLOGY - Abstract
The arrival of humans in New Zealand around 750 years ago resulted in widespread faunal extinctions including the endemic Waitaha penguin (Megadyptes waitaha). Previously thought to have only bred on coastal South Island and Stewart Island, recent genetic reanalysis of prehistoric large penguin bones from the lower North Island indicates that the Waitaha penguin may have been a common resident. Here we synthesise previous studies and present new palaeontological and archaeological evidence to suggest that the Waitaha penguin was probably breeding in the lower North Island at the time of human arrival, and did not represent vagrant individuals from more southerly breeding colonies. The elimination of breeding Megadyptes from the North Island would add to the already significant avifaunal losses from New Zealand, of which the North Island suffered the greatest biodiversity loss after the arrival of humans. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
30. Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds
- Author
-
Moodley, Yoshan, Masello, Juan F., Cole, Theresa L., Calderon, Luciano, Munimanda, Gopi K., Thali, Marco R., Alderman, Rachael, Cuthbert, Richard J., Marin, Manuel, Massaro, Melanie, Navarro, Joan, Phillips, Richard A., Ryan, Peter G., Suazo, Cristián G., Cherel, Yves, Weimerskirch, Henri, Quillfeldt, Petra, Moodley, Yoshan, Masello, Juan F., Cole, Theresa L., Calderon, Luciano, Munimanda, Gopi K., Thali, Marco R., Alderman, Rachael, Cuthbert, Richard J., Marin, Manuel, Massaro, Melanie, Navarro, Joan, Phillips, Richard A., Ryan, Peter G., Suazo, Cristián G., Cherel, Yves, Weimerskirch, Henri, and Quillfeldt, Petra
- Abstract
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased non-amplification, or disruptions that may lead to decreased polymorphism in non-target species. Furthermore, high mutation rates and constraints on allele size may also lead, with evolutionary time, to an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of non-amplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly non-linear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa.
- Published
- 2015
31. The ancient DNA revolution: the latest era in unearthing New Zealand’s faunal history.
- Author
-
Cole, Theresa L. and Wood, Jamie R.
- Subjects
- *
NUCLEOTIDE sequence , *DNA analysis , *NUCLEIC acid isolation methods , *ANIMAL genetics , *PARASITES - Abstract
In the 25 years since the first DNA sequences were obtained from the extinct moa, ancient DNA analyses have significantly advanced our understanding of New Zealand's unique fauna. Here, we review how DNA extracted from ancient faunal remains has provided new insights into the evolutionary histories and phylogenetic relationships of New Zealand animals, and the impacts of human activities upon their populations. Moreover, we review how ancient DNA has played a key role in improving our ability to taxonomically identify fragmentary animal remains, determine biological function within extinct species, reconstruct past faunas and communities based on DNA preserved in sediments, resolve aspects of the ecology of extinct animals and characterising prehistoric parasite faunas. As ancient DNA analyses continue to become increasingly applied, and sequencing technologies continue to improve, the next 25 years promises to provide many more exciting new insights and discoveries about New Zealand's unique fauna. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
32. Evidence for breeding of Megadyptespenguins in the North Island at the time of human arrival
- Author
-
Rawlence, Nicolas J., Tennyson, Alan J. D., Cole, Theresa L., Verry, Alexander J. F., and Scofield, R. Paul
- Abstract
ABSTRACTThe arrival of humans in New Zealand around 750 years ago resulted in widespread faunal extinctions including the endemic Waitaha penguin (Megadyptes waitaha). Previously thought to have only bred on coastal South Island and Stewart Island, recent genetic reanalysis of prehistoric large penguin bones from the lower North Island indicates that the Waitaha penguin may have been a common resident. Here we synthesise previous studies and present new palaeontological and archaeological evidence to suggest that the Waitaha penguin was probably breeding in the lower North Island at the time of human arrival, and did not represent vagrant individuals from more southerly breeding colonies. The elimination of breeding Megadyptesfrom the North Island would add to the already significant avifaunal losses from New Zealand, of which the North Island suffered the greatest biodiversity loss after the arrival of humans.
- Published
- 2019
- Full Text
- View/download PDF
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