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2. Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation

Author

Frugone, María José, Cole, Theresa L., López, María Eugenia, Clucas, Gemma, Matos-Maraví, Pável, Lois, Nicolás A., Pistorius, Pierre, Bonadonna, Francesco, Trathan, Phil, Polanowski, Andrea, Wienecke, Barbara, Raya-Rey, Andrea, Pütz, Klemens, Steinfurth, Antje, Bi, Ke, Wang-Claypool, Cynthia Y., Waters, Jonathan M., Bowie, Rauri C. K., Poulin, Elie, and Vianna, Juliana A.

Published
2021

4. Comparative Genomics Supports Ecologically Induced Selection as a Putative Driver of Banded Penguin Diversification.

Author

León, Fabiola, Pizarro, Eduardo, Noll, Daly, Pertierra, Luis R, Parker, Patricia, Espinaze, Marcela P A, Luna-Jorquera, Guillermo, Simeone, Alejandro, Frere, Esteban, Dantas, Gisele P M, Cristofari, Robin, Cornejo, Omar E, Bowie, Rauri C K, and Vianna, Juliana A

Subjects
GENETIC drift, COLONIES (Biology), GENE families, COMPARATIVE genomics, ECOLOGICAL niche
Abstract

The relative importance of genetic drift and local adaptation in facilitating speciation remains unclear. This is particularly true for seabirds, which can disperse over large geographic distances, providing opportunities for intermittent gene flow among distant colonies that span the temperature and salinity gradients of the oceans. Here, we delve into the genomic basis of adaptation and speciation of banded penguins, Galápagos (Spheniscus mendiculus), Humboldt (Spheniscus humboldti), Magellanic (Spheniscus magellanicus), and African penguins (Spheniscus demersus), by analyzing 114 genomes from the main 16 breeding colonies. We aim to identify the molecular mechanism and genomic adaptive traits that have facilitated their diversifications. Through positive selection and gene family expansion analyses, we identified candidate genes that may be related to reproductive isolation processes mediated by ecological thermal niche divergence. We recover signals of positive selection on key loci associated with spermatogenesis, especially during the recent peripatric divergence of the Galápagos penguin from the Humboldt penguin. High temperatures in tropical habitats may have favored selection on loci associated with spermatogenesis to maintain sperm viability, leading to reproductive isolation among young species. Our results suggest that genome-wide selection on loci associated with molecular pathways that underpin thermoregulation, osmoregulation, hypoxia, and social behavior appears to have been crucial in local adaptation of banded penguins. Overall, these results contribute to our understanding of how the complexity of biotic, but especially abiotic, factors, along with the high dispersal capabilities of these marine species, may promote both neutral and adaptive lineage divergence even in the presence of gene flow. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Mito-nuclear discordance across a recent contact zone for California voles

Author

Lin, Dana, Bi, Ke, Conroy, Christopher J, Lacey, Eileen A, Schraiber, Joshua G, and Bowie, Rauri C. K

Subjects
BRII recipient: Lin
Abstract

To examine the processes that maintain genetic diversity among closely related taxa, we investigated the dynamics of introgression across a contact zone between two lineages of California voles (Microtus californicus). We tested the prediction that introgression of nuclear loci would be greater than that for mitochondrial loci, assuming ongoing gene flow across the contact zone. We also predicted that genomic markers would show a mosaic pattern of differentiation across this zone, consistent with genomes that are semi‐permeable. Using mitochondrial cytochrome b sequences and genome‐wide loci developed via ddRAD‐seq, we analyzed genetic variation for 10 vole populations distributed along the central California coast; this transect included populations from within the distributions of both parental lineages as well as the putative contact zone. Our analyses revealed that (1) the two lineages examined are relatively young, having diverged ca. 8.5–54 kya, (2) voles from the contact zone in Santa Barbara County did not include F1 or early generation backcrossed individuals, and (3) there appeared to be little to no recurrent gene flow across the contact zone. Introgression patterns for mitochondrial and nuclear markers were not concordant; only mitochondrial markers revealed evidence of introgression, putatively due to historical hybridization. These differences in genetic signatures are intriguing given that the contact zone occurs in a region of continuous vole habitat, with no evidence of past or present physical barriers. Future studies that examine specific isolating mechanisms, such as microhabitat use and mate choice, will facilitate our understanding of how genetic boundaries are maintained in this system.

Published
2018

7. Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

Author

Benham, Phred M, primary, Cicero, Carla, additional, Escalona, Merly, additional, Beraut, Eric, additional, Fairbairn, Colin, additional, Marimuthu, Mohan P A, additional, Nguyen, Oanh, additional, Sahasrabudhe, Ruta, additional, King, Benjamin L, additional, Thomas, W Kelley, additional, Kovach, Adrienne I, additional, Nachman, Michael W, additional, and Bowie, Rauri C K, additional

Published
2024
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8. Genome-wide analyses reveal drivers of penguin diversification

Author

Vianna, Juliana A., Fernandes, Flávia A. N., Frugone, María José, Figueiró, Henrique V., Pertierra, Luis R., Noll, Daly, Bi, Ke, Wang-Claypool, Cynthia Y., Lowther, Andrew, Parker, Patricia, Le Bohec, Celine, Bonadonna, Francesco, Wienecke, Barbara, Pistorius, Pierre, Steinfurth, Antje, Burridge, Christopher P., Dantas, Gisele P. M., Poulin, Elie, Simison, W. Brian, Henderson, Jim, Eizirik, Eduardo, Nery, Mariana F., and Bowie, Rauri C. K.

Published
2020

9. Cryptic speciation in gentoo penguins is driven by geographic isolation and regional marine conditions : Unforeseen vulnerabilities to global change

Author

Pertierra, Luis R., Segovia, Nicolás I., Noll, Daly, Martinez, Pablo A., Pliscoff, Patricio, Barbosa, Andrés, Aragón, Pedro, Rey, Andrea Raya, Pistorius, Pierre, Trathan, Phil, Polanowski, Andrea, Bonadonna, Francesco, Le Bohec, Céline, Bi, Ke, Wang-Claypool, Cynthia Y., González-Acuña, Daniel, Dantas, Gisele P. M., Bowie, Rauri C. K., Poulin, Elie, and Vianna, Juliana A.

Published
2020

11. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes

Author

Hanna, Zachary R, Henderson, James B, Wall, Jeffrey D, Emerling, Christopher A, Fuchs, Jerome, Runckel, Charles, Mindell, David P, Bowie, Rauri C. K, DeRisi, Joseph L, and Dumbacher, John P

Subjects
BRII recipient: Hanna
Abstract

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106nt. We calculated the genome-wide fixation index (F ST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.

Published
2017

12. A phylogeny-informed characterisation of global tetrapod traits addresses data gaps and biases.

Author

Moura, Mario R., Ceron, Karoline, Guedes, Jhonny J. M., Chen-Zhao, Rosana, Sica, Yanina V., Hart, Julie, Dorman, Wendy, Portmann, Julia M., González-del-Pliego, Pamela, Ranipeta, Ajay, Catenazzi, Alessandro, Werneck, Fernanda P., Toledo, Luís Felipe, Upham, Nathan S., Tonini, João F. R., Colston, Timothy J., Guralnick, Robert, Bowie, Rauri C. K., Pyron, R. Alexander, and Jetz, Walter

Subjects
AMPHIBIANS, GLOBAL modeling systems, MISSING data (Statistics), ECOSYSTEMS, BODY size, DATABASES, TETRAPODS
Abstract

Tetrapods (amphibians, reptiles, birds, and mammals) are model systems for global biodiversity science, but continuing data gaps, limited data standardisation, and ongoing flux in taxonomic nomenclature constrain integrative research on this group and potentially cause biased inference. We combined and harmonised taxonomic, spatial, phylogenetic, and attribute data with phylogeny-based multiple imputation to provide a comprehensive data resource (TetrapodTraits 1.0.0) that includes values, predictions, and sources for body size, activity time, micro- and macrohabitat, ecosystem, threat status, biogeography, insularity, environmental preferences, and human influence, for all 33,281 tetrapod species covered in recent fully sampled phylogenies. We assess gaps and biases across taxa and space, finding that shared data missing in attribute values increased with taxon-level completeness and richness across clades. Prediction of missing attribute values using multiple imputation revealed substantial changes in estimated macroecological patterns. These results highlight biases incurred by nonrandom missingness and strategies to best address them. While there is an obvious need for further data collection and updates, our phylogeny-informed database of tetrapod traits can support a more comprehensive representation of tetrapod species and their attributes in ecology, evolution, and conservation research. Tetrapods are model systems for global biodiversity science, but continuing data gaps and limited data standardization potentially introduce biases. TetrapodTraits is a database of 33,281 tetrapod species, integrating taxonomic, spatial, phylogenetic and attribute data through phylogeny-based multiple imputation. [ABSTRACT FROM AUTHOR]

Published
2024
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18. A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris

Author

Kozak, Krzysztof M, primary, Escalona, Merly, additional, Chumchim, Noravit, additional, Fairbairn, Colin, additional, Marimuthu, Mohan P A, additional, Nguyen, Oanh, additional, Sahasrabudhe, Ruta, additional, Seligmann, William, additional, Conroy, Chris, additional, Patton, James L, additional, Bowie, Rauri C K, additional, and Nachman, Michael W, additional

Published
2023
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20. De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica

Author

DeRaad, Devon A, primary, Escalona, Merly, additional, Benham, Phred, additional, Marimuthu, Mohan P A, additional, Sahasrabudhe, Ruta M, additional, Nguyen, Oanh, additional, Chumchim, Noravit, additional, Beraut, Eric, additional, Fairbairn, Colin W, additional, Seligmann, William, additional, Bowie, Rauri C K, additional, Cicero, Carla, additional, McCormack, John E, additional, and Wayne, Robert K, additional

Published
2023
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22. A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.

Author

Kozak, Krzysztof M, Escalona, Merly, Chumchim, Noravit, Fairbairn, Colin, Marimuthu, Mohan P A, Nguyen, Oanh, Sahasrabudhe, Ruta, Seligmann, William, Conroy, Chris, Patton, James L, Bowie, Rauri C K, and Nachman, Michael W

Subjects
MICE, GENETIC variation, PHYSIOLOGICAL adaptation, ARID regions, GENOMICS
Abstract

The little pocket mouse, Perognathus longimembris , and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus , reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa. [ABSTRACT FROM AUTHOR]

Published
2024
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25. A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats

Author

Kakhki, Niloofar Alaei, Schweizer, Manuel, Lutgen, Dave, Bowie, Rauri C. K., Shirihai, Hadoram, Suh, Alexander, Schielzeth, Holger, Burri, Reto, Kakhki, Niloofar Alaei, Schweizer, Manuel, Lutgen, Dave, Bowie, Rauri C. K., Shirihai, Hadoram, Suh, Alexander, Schielzeth, Holger, and Burri, Reto

Abstract

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.

Published
2023
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26. Climate Cycles, Habitat Stability, and Lineage Diversification in an African Biodiversity Hotspot

Author

Bowie, Rauri C. K., Monahan, William B., Fjeldså, Jon, Bowie, Rauri C. K., Monahan, William B., and Fjeldså, Jon

Abstract

The Eastern Arc Mountains of Tanzania and Kenya, a montane archipelago of 13 uplifted fault blocks (sky islands) isolated by lowland arid savanna, are a center of exceptional biological endemism. Under the influence of humid winds from the Indian Ocean, forests and associated species may have persisted in this region since the final uplift of these blocks in the late Miocene. Today, these mountains are inhabited by a remarkable diversity of bird species. To better understand the evolutionary processes behind this diversity, we combined molecular phylogenetic studies of East African montane birds with paleoclimate modeling of its montane forests. Across its largest lowland barrier, the 125 km between the Usambara and Nguru/Nguu Mountains, 10 of the 14 bird lineages exhibited a phylogeographic break. Using Bayesian methods, we established that at least three periods of forest contraction and expansion affected the diversification of Eastern Arc birds. Habitat distribution models suggest that lower-elevation hills may have acted as stepping-stones connecting isolated highlands to allow for the dispersal of montane forest-dependent species across them. Periods of vicariance during paleoclimatic cycles extending back through the Last Glacial Maximum would have then isolated these populations within the highlands they had reached. The broad distribution of neoendemic species across the mountains of East Africa provides evidence of climate cycling as a driver of lineage diversification. The high incidence of narrow-range endemism of paleoendemic species on the Usambara, Uluguru, and Udzungwa Mountains of this region is harder to explain. Our paleoclimate models retrodicted the persistence of montane forest during climate cycles on several Eastern Arc sky islands but not on the Southern Tanzania Volcanic Highlands. Consistent with recent theoretical work, different rates of local extinction rather than increased rates of lineage diversification may explain the pattern of ex, The Eastern Arc Mountains of Tanzania and Kenya, a montane archipelago of 13 uplifted fault blocks (sky islands) isolated by lowland arid savanna, are a center of exceptional biological endemism. Under the influence of humid winds from the Indian Ocean, forests and associated species may have persisted in this region since the final uplift of these blocks in the late Miocene. Today, these mountains are inhabited by a remarkable diversity of bird species. To better understand the evolutionary processes behind this diversity, we combined molecular phylogenetic studies of East African montane birds with paleoclimate modeling of its montane forests. Across its largest lowland barrier, the 125 km between the Usambara and Nguru/Nguu Mountains, 10 of the 14 bird lineages exhibited a phylogeographic break. Using Bayesian methods, we established that at least three periods of forest contraction and expansion affected the diversification of Eastern Arc birds. Habitat distribution models suggest that lower-elevation hills may have acted as stepping-stones connecting isolated highlands to allow for the dispersal of montane forest-dependent species across them. Periods of vicariance during paleoclimatic cycles extending back through the Last Glacial Maximum would have then isolated these populations within the highlands they had reached. The broad distribution of neoendemic species across the mountains of East Africa provides evidence of climate cycling as a driver of lineage diversification. The high incidence of narrow-range endemism of paleoendemic species on the Usambara, Uluguru, and Udzungwa Mountains of this region is harder to explain. Our paleoclimate models retrodicted the persistence of montane forest during climate cycles on several Eastern Arc sky islands but not on the Southern Tanzania Volcanic Highlands. Consistent with recent theoretical work, different rates of local extinction rather than increased rates of lineage diversification may explain the pattern of

Published
2023

27. Specimen collection is essential for modern science

Author

Nachman, Michael W., Beckman, Elizabeth J., Bowie, Rauri C. K., Cicero, Carla, Conroy, Chris J., Dudley, Robert, Hayes, Tyrone B., Koo, Michelle S., Lacey, Eileen A., Martin, Christopher H., McGuire, Jimmy A., Patton, James L., Spencer, Carol L., Tarvin, Rebecca D., Wake, Marvalee H., Wang, Ian J., Achmadi, Anang, Álvarez-Castañeda, Sergio Ticul, Andersen, Michael J., Arroyave, Jairo, Austin, Christopher C., Barker, F. Keith, Barrow, Lisa N., Barrowclough, George F., Bates, John, Bauer, Aaron M., Bell, Kayce C., Bell, Rayna C., Bronson, Allison W., Brown, Rafe M., Burbrink, Frank T., Burns, Kevin J., Cadena, Carlos Daniel, Cannatella, David C., Castoe, Todd A., Chakrabarty, Prosanta, Colella, Jocelyn P., Cook, Joseph A., Cracraft, Joel L., Davis, Drew R., Rabosky, Alison R. Davis, D'Elía, Guillermo, Dumbacher, John P., Dunnum, Jonathan L., Edwards, Scott V., Esselstyn, Jacob A., Faivovich, Julián, Fjeldså, Jon, Flores-Villela, Oscar A., Ford, Kassandra, Fuchs, Jérôme, Fujita, Matthew K., Good, Jeffrey M., Greenbaum, Eli, Greene, Harry W., Hackett, Shannon, Hamidy, Amir, Hanken, James, Haryoko, Tri, Hawkins, Melissa T.R., Heaney, Lawrence R., Hillis, David M., Hollingsworth, Bradford D., Hornsby, Angela D., Hosner, Peter A., Irham, Mohammad, Jansa, Sharon, Jiménez, Rosa Alicia, Joseph, Leo, Kirchman, Jeremy J., LaDuc, Travis J., Leaché, Adam D., Lessa, Enrique P., López-Fernández, Hernán, Mason, Nicholas A., McCormack, John E., McMahan, Caleb D., Moyle, Robert G., Ojeda, Ricardo A., Olson, Link E., Onn, Chan Kin, Parenti, Lynne R., Parra-Olea, Gabriela, Patterson, Bruce D., Pauly, Gregory B., Pavan, Silvia E., Peterson, A. Townsend, Poe, Steven, Rabosky, Daniel L., Raxworthy, Christopher J., Reddy, Sushma, Rico-Guevara, Alejandro, Riyanto, Awal, Rocha, Luiz A., Ron, Santiago R., Rovito, Sean M., Rowe, Kevin C., Rowley, Jodi, Ruane, Sara, Salazar-Valenzuela, David, Shultz, Allison J., Sidlauskas, Brian, Sikes, Derek S., Simmons, Nancy B., Stiassny, Melanie L. J., Streicher, Jeffrey W., Stuart, Bryan L., Summers, Adam P., Tavera, Jose, Teta, Pablo, Thompson, Cody W., Timm, Robert M., Torres-Carvajal, Omar, Voelker, Gary, Voss, Robert S., Winker, Kevin, Witt, Christopher, Wommack, Elizabeth A., Zink, Robert M., Nachman, Michael W., Beckman, Elizabeth J., Bowie, Rauri C. K., Cicero, Carla, Conroy, Chris J., Dudley, Robert, Hayes, Tyrone B., Koo, Michelle S., Lacey, Eileen A., Martin, Christopher H., McGuire, Jimmy A., Patton, James L., Spencer, Carol L., Tarvin, Rebecca D., Wake, Marvalee H., Wang, Ian J., Achmadi, Anang, Álvarez-Castañeda, Sergio Ticul, Andersen, Michael J., Arroyave, Jairo, Austin, Christopher C., Barker, F. Keith, Barrow, Lisa N., Barrowclough, George F., Bates, John, Bauer, Aaron M., Bell, Kayce C., Bell, Rayna C., Bronson, Allison W., Brown, Rafe M., Burbrink, Frank T., Burns, Kevin J., Cadena, Carlos Daniel, Cannatella, David C., Castoe, Todd A., Chakrabarty, Prosanta, Colella, Jocelyn P., Cook, Joseph A., Cracraft, Joel L., Davis, Drew R., Rabosky, Alison R. Davis, D'Elía, Guillermo, Dumbacher, John P., Dunnum, Jonathan L., Edwards, Scott V., Esselstyn, Jacob A., Faivovich, Julián, Fjeldså, Jon, Flores-Villela, Oscar A., Ford, Kassandra, Fuchs, Jérôme, Fujita, Matthew K., Good, Jeffrey M., Greenbaum, Eli, Greene, Harry W., Hackett, Shannon, Hamidy, Amir, Hanken, James, Haryoko, Tri, Hawkins, Melissa T.R., Heaney, Lawrence R., Hillis, David M., Hollingsworth, Bradford D., Hornsby, Angela D., Hosner, Peter A., Irham, Mohammad, Jansa, Sharon, Jiménez, Rosa Alicia, Joseph, Leo, Kirchman, Jeremy J., LaDuc, Travis J., Leaché, Adam D., Lessa, Enrique P., López-Fernández, Hernán, Mason, Nicholas A., McCormack, John E., McMahan, Caleb D., Moyle, Robert G., Ojeda, Ricardo A., Olson, Link E., Onn, Chan Kin, Parenti, Lynne R., Parra-Olea, Gabriela, Patterson, Bruce D., Pauly, Gregory B., Pavan, Silvia E., Peterson, A. Townsend, Poe, Steven, Rabosky, Daniel L., Raxworthy, Christopher J., Reddy, Sushma, Rico-Guevara, Alejandro, Riyanto, Awal, Rocha, Luiz A., Ron, Santiago R., Rovito, Sean M., Rowe, Kevin C., Rowley, Jodi, Ruane, Sara, Salazar-Valenzuela, David, Shultz, Allison J., Sidlauskas, Brian, Sikes, Derek S., Simmons, Nancy B., Stiassny, Melanie L. J., Streicher, Jeffrey W., Stuart, Bryan L., Summers, Adam P., Tavera, Jose, Teta, Pablo, Thompson, Cody W., Timm, Robert M., Torres-Carvajal, Omar, Voelker, Gary, Voss, Robert S., Winker, Kevin, Witt, Christopher, Wommack, Elizabeth A., and Zink, Robert M.

Published
2023

34. Supplemental Figure 1 from Hummingbird ingestion of low-concentration ethanol within artificial nectar

Author

Choi, Julia, Lee, Lilianne, Maro, Aleksey, Corl, Ammon, McGuire, Jimmy A., Bowie, Rauri C. K., and Dudley, Robert

Abstract

Rates of either nectar consumption (in g/h; open circles) or total ethanol consumption (in mg/h; closed circles) by individual hummingbirds for all binary choice trials between two solutions of varying ethanol concentrations, as indicated on the abscissa. No ethanol consumption is indicated for the [0%–0%] trial as it was presumed to be absent in these solutions. For values of rates of ethanol consumption, individual bird identities (i.e., #1, 2, or 3) are indicated next to the data points.

Published
2023
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37. Natural history collections as a resource for conservation genomics: Understanding the past to preserve the future.

Author

Benham, Phred M and Bowie, Rauri C K

Subjects
*NATURAL history, *GENOMICS, *COLLECTIONS, *DNA sequencing, *BIODIVERSITY conservation
Abstract

To avoid the worst outcomes of the current biodiversity crisis we need a deep understanding of population responses to human-induced ecological change. Rapidly expanding access to genomic resources for nonmodel taxa promises to play a unique role in meeting this goal. In particular, the increasing feasibility of sequencing DNA from historical specimens enables direct measures of population responses to the past century of anthropogenic change that will inform management strategies and refine projections of species responses to future environmental change. In this review, we discuss the methods that can be used to generate genome-scale data from the hundreds of millions of specimens housed in natural history collections around the world. We then highlight recent studies that utilize genomic data from specimens to address questions of fundamental importance to biodiversity conservation. Finally, we emphasize how traditional motivations of museum collectors, such as studies of geographic variation and community-wide inventories, provide unique opportunities for broad scale comparisons of genomic responses to anthropogenic change across time. We conclude that as sequencing technologies become increasingly accessible and more researchers take advantage of this resource, the importance of collections to the conservation of biodiversity will continue to grow. [ABSTRACT FROM AUTHOR]

Published
2023
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39. A set of principles and practical suggestions for equitable fieldwork in biology

Author

Ramírez-Castañeda, Valeria, primary, Westeen, Erin P., additional, Frederick, Jeffrey, additional, Amini, Sina, additional, Wait, Daniel R., additional, Achmadi, Anang S., additional, Andayani, Noviar, additional, Arida, Evy, additional, Arifin, Umilaela, additional, Bernal, Moisés A., additional, Bonaccorso, Elisa, additional, Bonachita Sanguila, Marites, additional, Brown, Rafe M., additional, Che, Jing, additional, Condori, F. Peter, additional, Hartiningtias, Diny, additional, Hiller, Anna E., additional, Iskandar, Djoko T., additional, Jiménez, Rosa Alicia, additional, Khelifa, Rassim, additional, Márquez, Roberto, additional, Martínez-Fonseca, José G., additional, Parra, Juan L., additional, Peñalba, Joshua V., additional, Pinto-García, Lina, additional, Razafindratsima, Onja H., additional, Ron, Santiago R., additional, Souza, Sara, additional, Supriatna, Jatna, additional, Bowie, Rauri C. K., additional, Cicero, Carla, additional, McGuire, Jimmy A., additional, and Tarvin, Rebecca D., additional

Published
2022
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43. AVONET:morphological, ecological and geographical data for all birds

Author

Tobias, Joseph A., Sheard, Catherine, Pigot, Alex L., Devenish, Adam J. M., Yang, Jingyi, Sayol, Ferran, Neate-Clegg, Montague H. C., Alioravainen, Nico, Weeks, Thomas L., Barber, Robert A., Walkden, Patrick A., MacGregor, Hannah E. A., Jones, Samuel E. I., Vincent, Claire, Phillips, Anna G., Marples, Nicola M., Montaño-Centellas, Flavia A., Leandro-Silva, Victor, Claramunt, Santiago, Darski, Bianca, Freeman, Benjamin G., Bregman, Tom P., Cooney, Christopher R., Hughes, Emma C., Capp, Elliot J. R., Varley, Zoë K., Friedman, Nicholas R., Korntheuer, Heiko, Corrales-Vargas, Andrea, Trisos, Christopher H., Weeks, Brian C., Hanz, Dagmar M., Töpfer, Till, Bravo, Gustavo A., Remeš, Vladimír, Nowak, Larissa, Carneiro, Lincoln S., Moncada R., Amilkar J., Matysioková, Beata, Baldassarre, Daniel T., Martínez-Salinas, Alejandra, Wolfe, Jared D., Chapman, Philip M., Daly, Benjamin G., Sorensen, Marjorie C., Neu, Alexander, Ford, Michael A., Mayhew, Rebekah J., Fabio Silveira, Luis, Kelly, David J., Annorbah, Nathaniel N. D., Pollock, Henry S., Grabowska-Zhang, Ada M., McEntee, Jay P., Carlos T. Gonzalez, Juan, Meneses, Camila G., Muñoz, Marcia C., Powell, Luke L., Jamie, Gabriel A., Matthews, Thomas J., Johnson, Oscar, Brito, Guilherme R. R., Zyskowski, Kristof, Crates, Ross, Harvey, Michael G., Jurado Zevallos, Maura, Hosner, Peter A., Bradfer-Lawrence, Tom, Maley, James M., Stiles, F. Gary, Lima, Hevana S., Provost, Kaiya L., Chibesa, Moses, Mashao, Mmatjie, Howard, Jeffrey T., Mlamba, Edson, Chua, Marcus A. H., Li, Bicheng, Gómez, M. Isabel, García, Natalia C., Päckert, Martin, Fuchs, Jérôme, Ali, Jarome R., Derryberry, Elizabeth P., Carlson, Monica L., Urriza, Rolly C., Brzeski, Kristin E., Prawiradilaga, Dewi M., Rayner, Matt J., Miller, Eliot T., Bowie, Rauri C. K., Lafontaine, René Marie, Scofield, R. Paul, Lou, Yingqiang, Somarathna, Lankani, Lepage, Denis, Illif, Marshall, Neuschulz, Eike Lena, Templin, Mathias, Dehling, D. Matthias, Cooper, Jacob C., Pauwels, Olivier S. G., Analuddin, Kangkuso, Fjeldså, Jon, Seddon, Nathalie, Sweet, Paul R., DeClerck, Fabrice A. J., Naka, Luciano N., Brawn, Jeffrey D., Aleixo, Alexandre, Böhning-Gaese, Katrin, Rahbek, Carsten, Fritz, Susanne A., Thomas, Gavin H., Schleuning, Matthias, Tobias, Joseph A., Sheard, Catherine, Pigot, Alex L., Devenish, Adam J. M., Yang, Jingyi, Sayol, Ferran, Neate-Clegg, Montague H. C., Alioravainen, Nico, Weeks, Thomas L., Barber, Robert A., Walkden, Patrick A., MacGregor, Hannah E. A., Jones, Samuel E. I., Vincent, Claire, Phillips, Anna G., Marples, Nicola M., Montaño-Centellas, Flavia A., Leandro-Silva, Victor, Claramunt, Santiago, Darski, Bianca, Freeman, Benjamin G., Bregman, Tom P., Cooney, Christopher R., Hughes, Emma C., Capp, Elliot J. R., Varley, Zoë K., Friedman, Nicholas R., Korntheuer, Heiko, Corrales-Vargas, Andrea, Trisos, Christopher H., Weeks, Brian C., Hanz, Dagmar M., Töpfer, Till, Bravo, Gustavo A., Remeš, Vladimír, Nowak, Larissa, Carneiro, Lincoln S., Moncada R., Amilkar J., Matysioková, Beata, Baldassarre, Daniel T., Martínez-Salinas, Alejandra, Wolfe, Jared D., Chapman, Philip M., Daly, Benjamin G., Sorensen, Marjorie C., Neu, Alexander, Ford, Michael A., Mayhew, Rebekah J., Fabio Silveira, Luis, Kelly, David J., Annorbah, Nathaniel N. D., Pollock, Henry S., Grabowska-Zhang, Ada M., McEntee, Jay P., Carlos T. Gonzalez, Juan, Meneses, Camila G., Muñoz, Marcia C., Powell, Luke L., Jamie, Gabriel A., Matthews, Thomas J., Johnson, Oscar, Brito, Guilherme R. R., Zyskowski, Kristof, Crates, Ross, Harvey, Michael G., Jurado Zevallos, Maura, Hosner, Peter A., Bradfer-Lawrence, Tom, Maley, James M., Stiles, F. Gary, Lima, Hevana S., Provost, Kaiya L., Chibesa, Moses, Mashao, Mmatjie, Howard, Jeffrey T., Mlamba, Edson, Chua, Marcus A. H., Li, Bicheng, Gómez, M. Isabel, García, Natalia C., Päckert, Martin, Fuchs, Jérôme, Ali, Jarome R., Derryberry, Elizabeth P., Carlson, Monica L., Urriza, Rolly C., Brzeski, Kristin E., Prawiradilaga, Dewi M., Rayner, Matt J., Miller, Eliot T., Bowie, Rauri C. K., Lafontaine, René Marie, Scofield, R. Paul, Lou, Yingqiang, Somarathna, Lankani, Lepage, Denis, Illif, Marshall, Neuschulz, Eike Lena, Templin, Mathias, Dehling, D. Matthias, Cooper, Jacob C., Pauwels, Olivier S. G., Analuddin, Kangkuso, Fjeldså, Jon, Seddon, Nathalie, Sweet, Paul R., DeClerck, Fabrice A. J., Naka, Luciano N., Brawn, Jeffrey D., Aleixo, Alexandre, Böhning-Gaese, Katrin, Rahbek, Carsten, Fritz, Susanne A., Thomas, Gavin H., and Schleuning, Matthias

Abstract

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

Published
2022

47. Cover Image: Volume 25 Number 3, March 2022

Author

Tobias, Joseph A., primary, Sheard, Catherine, additional, Pigot, Alex L., additional, Devenish, Adam J. M., additional, Yang, Jingyi, additional, Sayol, Ferran, additional, Neate‐Clegg, Montague H. C., additional, Alioravainen, Nico, additional, Weeks, Thomas L., additional, Barber, Robert A., additional, Walkden, Patrick A., additional, MacGregor, Hannah E. A., additional, Jones, Samuel E. I., additional, Vincent, Claire, additional, Phillips, Anna G., additional, Marples, Nicola M., additional, Montaño‐Centellas, Flavia A., additional, Leandro‐Silva, Victor, additional, Claramunt, Santiago, additional, Darski, Bianca, additional, Freeman, Benjamin G., additional, Bregman, Tom P., additional, Cooney, Christopher R., additional, Hughes, Emma C., additional, Capp, Elliot J. R., additional, Varley, Zoë K., additional, Friedman, Nicholas R., additional, Korntheuer, Heiko, additional, Corrales‐Vargas, Andrea, additional, Trisos, Christopher H., additional, Weeks, Brian C., additional, Hanz, Dagmar M., additional, Töpfer, Till, additional, Bravo, Gustavo A., additional, Remeš, Vladimír, additional, Nowak, Larissa, additional, Carneiro, Lincoln S., additional, Moncada R., Amilkar J., additional, Matysioková, Beata, additional, Baldassarre, Daniel T., additional, Martínez‐Salinas, Alejandra, additional, Wolfe, Jared D., additional, Chapman, Philip M., additional, Daly, Benjamin G., additional, Sorensen, Marjorie C., additional, Neu, Alexander, additional, Ford, Michael A., additional, Mayhew, Rebekah J., additional, Fabio Silveira, Luis, additional, Kelly, David J., additional, Annorbah, Nathaniel N. D., additional, Pollock, Henry S., additional, Grabowska‐Zhang, Ada M., additional, McEntee, Jay P., additional, Carlos T. Gonzalez, Juan, additional, Meneses, Camila G., additional, Muñoz, Marcia C., additional, Powell, Luke L., additional, Jamie, Gabriel A., additional, Matthews, Thomas J., additional, Johnson, Oscar, additional, Brito, Guilherme R. R., additional, Zyskowski, Kristof, additional, Crates, Ross, additional, Harvey, Michael G., additional, Jurado Zevallos, Maura, additional, Hosner, Peter A., additional, Bradfer‐Lawrence, Tom, additional, Maley, James M., additional, Stiles, F. Gary, additional, Lima, Hevana S., additional, Provost, Kaiya L., additional, Chibesa, Moses, additional, Mashao, Mmatjie, additional, Howard, Jeffrey T., additional, Mlamba, Edson, additional, Chua, Marcus A. H., additional, Li, Bicheng, additional, Gómez, M. Isabel, additional, García, Natalia C., additional, Päckert, Martin, additional, Fuchs, Jérôme, additional, Ali, Jarome R., additional, Derryberry, Elizabeth P., additional, Carlson, Monica L., additional, Urriza, Rolly C., additional, Brzeski, Kristin E., additional, Prawiradilaga, Dewi M., additional, Rayner, Matt J., additional, Miller, Eliot T., additional, Bowie, Rauri C. K., additional, Lafontaine, René‐Marie, additional, Scofield, R. Paul, additional, Lou, Yingqiang, additional, Somarathna, Lankani, additional, Lepage, Denis, additional, Illif, Marshall, additional, Neuschulz, Eike Lena, additional, Templin, Mathias, additional, Dehling, D. Matthias, additional, Cooper, Jacob C., additional, Pauwels, Olivier S. G., additional, Analuddin, Kangkuso, additional, Fjeldså, Jon, additional, Seddon, Nathalie, additional, Sweet, Paul R., additional, DeClerck, Fabrice A. J., additional, Naka, Luciano N., additional, Brawn, Jeffrey D., additional, Aleixo, Alexandre, additional, Böhning‐Gaese, Katrin, additional, Rahbek, Carsten, additional, Fritz, Susanne A., additional, Thomas, Gavin H., additional, and Schleuning, Matthias, additional

Published
2022
Full Text
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48. AVONET: morphological, ecological and geographical data for all birds

Author

Tobias, Joseph A., primary, Sheard, Catherine, additional, Pigot, Alex L., additional, Devenish, Adam J. M., additional, Yang, Jingyi, additional, Sayol, Ferran, additional, Neate‐Clegg, Montague H. C., additional, Alioravainen, Nico, additional, Weeks, Thomas L., additional, Barber, Robert A., additional, Walkden, Patrick A., additional, MacGregor, Hannah E. A., additional, Jones, Samuel E. I., additional, Vincent, Claire, additional, Phillips, Anna G., additional, Marples, Nicola M., additional, Montaño‐Centellas, Flavia A., additional, Leandro‐Silva, Victor, additional, Claramunt, Santiago, additional, Darski, Bianca, additional, Freeman, Benjamin G., additional, Bregman, Tom P., additional, Cooney, Christopher R., additional, Hughes, Emma C., additional, Capp, Elliot J. R., additional, Varley, Zoë K., additional, Friedman, Nicholas R., additional, Korntheuer, Heiko, additional, Corrales‐Vargas, Andrea, additional, Trisos, Christopher H., additional, Weeks, Brian C., additional, Hanz, Dagmar M., additional, Töpfer, Till, additional, Bravo, Gustavo A., additional, Remeš, Vladimír, additional, Nowak, Larissa, additional, Carneiro, Lincoln S., additional, Moncada R., Amilkar J., additional, Matysioková, Beata, additional, Baldassarre, Daniel T., additional, Martínez‐Salinas, Alejandra, additional, Wolfe, Jared D., additional, Chapman, Philip M., additional, Daly, Benjamin G., additional, Sorensen, Marjorie C., additional, Neu, Alexander, additional, Ford, Michael A., additional, Mayhew, Rebekah J., additional, Fabio Silveira, Luis, additional, Kelly, David J., additional, Annorbah, Nathaniel N. D., additional, Pollock, Henry S., additional, Grabowska‐Zhang, Ada M., additional, McEntee, Jay P., additional, Carlos T. Gonzalez, Juan, additional, Meneses, Camila G., additional, Muñoz, Marcia C., additional, Powell, Luke L., additional, Jamie, Gabriel A., additional, Matthews, Thomas J., additional, Johnson, Oscar, additional, Brito, Guilherme R. R., additional, Zyskowski, Kristof, additional, Crates, Ross, additional, Harvey, Michael G., additional, Jurado Zevallos, Maura, additional, Hosner, Peter A., additional, Bradfer‐Lawrence, Tom, additional, Maley, James M., additional, Stiles, F. Gary, additional, Lima, Hevana S., additional, Provost, Kaiya L., additional, Chibesa, Moses, additional, Mashao, Mmatjie, additional, Howard, Jeffrey T., additional, Mlamba, Edson, additional, Chua, Marcus A. H., additional, Li, Bicheng, additional, Gómez, M. Isabel, additional, García, Natalia C., additional, Päckert, Martin, additional, Fuchs, Jérôme, additional, Ali, Jarome R., additional, Derryberry, Elizabeth P., additional, Carlson, Monica L., additional, Urriza, Rolly C., additional, Brzeski, Kristin E., additional, Prawiradilaga, Dewi M., additional, Rayner, Matt J., additional, Miller, Eliot T., additional, Bowie, Rauri C. K., additional, Lafontaine, René‐Marie, additional, Scofield, R. Paul, additional, Lou, Yingqiang, additional, Somarathna, Lankani, additional, Lepage, Denis, additional, Illif, Marshall, additional, Neuschulz, Eike Lena, additional, Templin, Mathias, additional, Dehling, D. Matthias, additional, Cooper, Jacob C., additional, Pauwels, Olivier S. G., additional, Analuddin, Kangkuso, additional, Fjeldså, Jon, additional, Seddon, Nathalie, additional, Sweet, Paul R., additional, DeClerck, Fabrice A. J., additional, Naka, Luciano N., additional, Brawn, Jeffrey D., additional, Aleixo, Alexandre, additional, Böhning‐Gaese, Katrin, additional, Rahbek, Carsten, additional, Fritz, Susanne A., additional, Thomas, Gavin H., additional, and Schleuning, Matthias, additional

Published
2022
Full Text
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