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16. The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Published
2023
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17. A revision of the higher latitude periwinkle species Laevilitorina caliginosa sensu lato.

Author

Rosenfeld, Sebastián, Segovia, Nicolás I, Maturana, Claudia S, Aldea, Cristián, Saucède, Thomas, Brickle, Paul, Spencer, Hamish G, Poulin, Elie, and González-Wevar, Claudio A

Subjects
MOLECULAR phylogeny, BAYESIAN analysis, BIOGEOGRAPHY, VICARIANCE, GENETIC speciation
Abstract

The marine gastropod genus Laevilitorina is exclusive to the Southern Hemisphere, with 21 species from southern South America, Antarctica, Australia, New Zealand, and sub-Antarctic Islands. We present a comprehensive revision of Laevilitorina , using molecular and morphological analyses, to address formally the interspecific divergences within the nominal taxon Laevilitorina caliginosa s.l. We confirm the validity of L. caliginosa and Laevilitorina venusta , and we demonstrate that specimens from the Strait of Magellan and Hornos Island constitute four new species here described: Laevilitorina magellanica sp. nov. Laevilitorina pepita sp. nov. Laevilitorina fueguina sp. nov. and Laevilitorina hicana sp. nov. All six species are clearly distinguishable genetically, morphologically, and through radular tooth shape and configurations. Laevilitorina venusta is broadly distributed across the Antarctic Peninsula, South Georgia, and sub-Antarctic Islands (Marion, Crozet, Kerguelen, and Macquarie), whereas L. caliginosa s.s. appears geographically restricted to Cape Horn, the Falkland/Malvinas Islands, and South Georgia. The identification of populations from Macquarie Island as L. caliginosa is dubious; we suggest that these records are likely to pertain to L. venusta. This detailed revision of Laevilitorina , whereby hidden diversity was detected, significantly enriches our knowledge of the evolutionary history of this group. [ABSTRACT FROM AUTHOR]

Published
2024
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24. The radiation of Austral teals (Aves: Anseriformes) and the evolution of flightlessness.

Author

Rosinger, Hanna S, Kardailsky, Olga, Kennedy, Martyn, Spencer, Hamish G, Steiner, Florian M, Schlick-Steiner, Birgit C, Rawlence, Nicolas J, and Knapp, Michael

Subjects
MIOCENE Epoch, MALLARD, ISLANDS, PHYLOGENY, RADIATION
Abstract

The origin and evolution in the Southern Hemisphere of the Austral teals, consisting of the grey-teal and brown-teal species complexes, remains poorly understood owing to limited molecular data. With the group containing multiple independent examples of flight loss, understanding the evolutionary history of the group is of significant interest for functional genomic studies into the evolution of flightlessness. Here, we present the first whole-mitogenome-based phylogeny of the Austral teals. We show that the group diverged from a common ancestor with mallards in the late Miocene and soon after radiated into the brown-teal and grey-teal lineages, in addition to the widely distributed pintails and green-winged teals. The brown-teal species complex, which includes the volant brown teal, the flight-impaired, sub-Antarctic Auckland Island teal, and the flightless, Chatham Island and sub-Antarctic Campbell Island teals, radiated within the past 0.9–1.8 Myr. The divergence of the extinct Chatham Island teal and the colonization of the Auckland and Campbell Islands occurred from mainland New Zealand. Morphological changes towards flightlessness are also present in the volant brown teal on mainland New Zealand, suggesting that this group was on the pathway to flightlessness, a trend that accelerated in some insular island lineages. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Both high and low dispersal? Apparently contradictory genetic patterns in the Antarctic littorinid gastropod Laevilacunaria antarctica

Author

González-Wevar, Claudio A., primary, Poveda, Yarleth, additional, Segovia, Nicolás I., additional, Rosenfeld, Sebastián, additional, Maturana, Claudia S., additional, Jeldres, Vanessa, additional, Schmider-Martínez, Andreas, additional, Gérard, Karin, additional, Spencer, Hamish G., additional, and Poulin, Elie, additional

Published
2024
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32. Report of bilateral gynandromorphy in a Green Honeycreeper (Chlorophanes spiza) from Colombia.

Author

Murillo, John, Campbell-Thompson, Edwin, Bishop, Thomas F., Beck, Caroline W., and Spencer, Hamish G.

Subjects
FEATHERS, SEX determination, SEXUAL dimorphism
Abstract

We report recent sightings, substantiated by color photographs and a short video, of a bilateral gynandromoph of the Green Honeycreeper (Chlorophanes spiza) from Villamaría, in the department of Caldas, Colombia. The bird exhibited typical male plumage on its right side and female plumage on the left. It was present for at least 21 months, and its behavior largely matched that of other wild Green Honeycreepers, although it often waited until they were gone before feeding on fruit that was put out daily by the property owners. We provide a comprehensive list and review of previous records of passerine bilateral gynandromorphy, noting which sex’s plumage occurred on the left side. We observe that female plumage is possible on either side, supporting the double-fertilization model of bilateral gynandromorphy. RESUMEN. Reportamos avistamientos recientes, corroborados por fotografías a color y un video corto, de una ginandromorfía bilateral de Chlorophanes spiza en Villamaría, departamento de Caldas, Colombia. El ave presentaba un plumaje típico de macho en el lado derecho y de hembra en el izquierdo. Estuvo presente durante al menos 21 meses, y su comportamiento coincidía en gran medida con el de otros C. spiza silvestres, aunque a menudo esperaba a que se fueran para alimentarse de la fruta que los propietarios de la finca ponían a diario. Proporcionamos una lista exhaustiva y una revisión de los registros anteriores de ginandromorfía bilateral de paseriformes, señalando el plumaje de qué sexo se produjo en el lado izquierdo. Observamos que el plumaje femenino es posible en ambos lados, conclusión que apoya el modelo de doble fecundación de la ginandromorfía bilateral. [ABSTRACT FROM AUTHOR]

Published
2023
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39. Phylogeny of the microcormorants, with the description of a new genus.

Author

Kennedy, Martyn, Salis, Alexander T, Seneviratne, Sampath S, Rathnayake, Dilini, Nupen, Lisa J, Ryan, Peter G, Volponi, Stefano, Lubbe, Pascale, Rawlence, Nicolas J, and Spencer, Hamish G

Subjects
PHYLOGENY, CORMORANTS, CONSERVATISM, SPECIES
Abstract

The aptly named microcormorants (currently placed in the genus Microcarbo) form a morphologically diminutive and distinct clade sister to all other living cormorants and shags. However, the relationships within Microcarbo are largely speculative. Sequence data resolve these relationships unambiguously, with our phylogeny suggesting that the microcormorants separated from the other cormorants ~16 Mya and showing that the two African species [the reed (or long-tailed) cormorant, Microcarbo africanus , and the crowned cormorant, Microcarbo coronatus ] are closely related sister taxa, forming a clade that diverged from the other microcormorants ~12 Mya. The deep split between the African microcormorants and the others is considerably older than many well-recognized generic splits within the cormorants (e.g. Leucocarbo and Phalacrocorax). Thus, we suggest that the African microcormorants warrant their own genus, and we erect Afrocarbo , with type species Pelecanus africanus. Within the reduced Microcarbo , we estimate that the little pied cormorant (Microcarbo melanoleucos of Australasia) separated from the sister pair of the Javanese and pygmy cormorants (respectively, Microcarbo niger from south/southeast Asia and Microcarbo pygmaeus from Europe) ~9 Mya and that the latter two species split ~2 Mya. Given the age of these splits, the microcormorants appear to represent another example of morphological conservatism in the Suliformes. [ABSTRACT FROM AUTHOR]

Published
2023
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40. Additional file 13 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 13: Supplementary Table S11. Differentially expressed cytokine or cytokine related genes in infected avian endothelial cells.

Published
2023
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41. Additional file 4 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 4: Supplementary Table S2. BUSCO analysis of the final genomes.

Published
2023
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42. Additional file 5 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 5: Supplementary Table S3. CEGMA analysis of the final genomes.

Published
2023
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43. Additional file 7 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 7: Supplementary Table S5. List of genes known to affect plumage colour in birds.

Published
2023
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44. Additional file 2 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 2: Supplementary Table S1. Heterozygosity, QV and completeness values for swan genomes.

Published
2023
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45. Additional file 6 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 6: Supplementary Table S4. GO biological process annotation of inverted genes in the Mallard duck (relative to the black swan).

Published
2023
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46. Additional file 3 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 3: Online Methods.

Published
2023
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47. Additional file 8 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 8: Supplementary Table S6. Immune gene families are contractive in black swans compared to mute swans. The number of genes in each immune gene sub-family identified is given in each column for the corresponding species.

Published
2023
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48. Structured Populations and the Maintenance of Sex

Author

Whigham, Peter A., Dick, Grant, Wright, Alden, Spencer, Hamish G., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Vanneschi, Leonardo, editor, Bush, William S., editor, and Giacobini, Mario, editor

Published
2013
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50. Figure 3 from: Rosenfeld S, Maturana CS, Spencer HG, Convey P, Saucède T, Brickle P, Bahamonde F, Jossart Q, Poulin E, Gonzalez-Wevar C (2022) Complete distribution of the genus Laevilitorina (Littorinimorpha, Littorinidae) in the Southern Hemisphere: remarks and natural history. ZooKeys 1127: 61-77. https://doi.org/10.3897/zookeys.1127.91310

Author

Rosenfeld, Sebastián, primary, Maturana, Claudia S., additional, Spencer, Hamish G., additional, Convey, Peter, additional, Saucède, Thomas, additional, Brickle, Paul, additional, Bahamonde, Francisco, additional, Jossart, Quentin, additional, Poulin, Elie, additional, and Gonzalez-Wevar, Claudio, additional

Published
2022
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