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3. Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Author

André, Mathilde, Brucato, Nicolas, Hudjasov, Georgi, Pankratov, Vasili, Yermakovich, Danat, Montinaro, Francesco, Kreevan, Rita, Kariwiga, Jason, Muke, John, Boland, Anne, Deleuze, Jean-François, Meyer, Vincent, Evans, Nicholas, Cox, Murray P., Leavesley, Matthew, Dannemann, Michael, Org, Tõnis, Metspalu, Mait, Mondal, Mayukh, and Ricaut, François-Xavier

Published
2024
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5. A single fungal strain was the unexpected cause of a mass aspergillosis outbreak in the world’s largest and only flightless parrot

Author

Winter, David J, Weir, Bevan S, Glare, Travis, Rhodes, Johanna, Perrott, John, Fisher, Matthew C, Stajich, Jason E, Consortium, Kākāpō Aspergillosis Research, Digby, Andrew, Dearden, Peter K, and Cox, Murray P

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Emerging Infectious Diseases, Rare Diseases, Infection, Kākāpō Aspergillosis Research Consortium, Animals, Microbiology parasite, Parasitology
Abstract

Kākāpō are a critically endangered species of parrots restricted to a few islands off the coast of New Zealand. Kākāpō are very closely monitored, especially during nesting seasons. In 2019, during a highly successful nesting season, an outbreak of aspergillosis affected 21 individuals and led to the deaths of 9, leaving a population of only 211 kākāpō. In monitoring this outbreak, cultures of aspergillus were grown, and genome sequenced. These sequences demonstrate that, very unusually for an aspergillus outbreak, a single strain of aspergillus caused the outbreak. This strain was found on two islands, but only one had an outbreak of aspergillosis; indicating that the strain was necessary, but not sufficient, to cause disease. Our analysis provides an understanding of the 2019 outbreak and provides potential ways to manage such events in the future.

Published
2022

7. Species-wide genomics of kākāpō provides tools to accelerate recovery

Author

Guhlin, Joseph, Le Lec, Marissa F., Wold, Jana, Koot, Emily, Winter, David, Biggs, Patrick J., Galla, Stephanie J., Urban, Lara, Foster, Yasmin, Cox, Murray P., Digby, Andrew, Uddstrom, Lydia R., Eason, Daryl, Vercoe, Deidre, Davis, Tāne, Howard, Jason T., Jarvis, Erich D., Robertson, Fiona E., Robertson, Bruce C., Gemmell, Neil J., Steeves, Tammy E., Santure, Anna W., and Dearden, Peter K.

Published
2023
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8. Collective action is needed to build a more just science system

Author

Rayne, Aisling, Arahanga-Doyle, Hitaua, Cox, Bethany, Cox, Murray P., Febria, Catherine M., Galla, Stephanie J., Hendy, Shaun C., Locke, Kirsten, Matheson, Anna, Pawlik, Aleksandra, Roa, Tom, Sharp, Emma L., Walker, Leilani A., Watene, Krushil, Wehi, Priscilla M., and Steeves, Tammy E.

Published
2023
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12. The GenomeAsia 100K Project enables genetic discoveries across Asia

Author

Wall, Jeffrey D, Stawiski, Eric W, Ratan, Aakrosh, Kim, Hie Lim, Kim, Changhoon, Gupta, Ravi, Suryamohan, Kushal, Gusareva, Elena S, Purbojati, Rikky Wenang, Bhangale, Tushar, Stepanov, Vadim, Kharkov, Vladimir, Schroeder, Markus S, Ramprasad, Vedam, Tom, Jennifer, Durinck, Steffen, Bei, Qixin, Li, Jiani, Guillory, Joseph, Phalke, Sameer, Basu, Analabha, Stinson, Jeremy, Nair, Sandhya, Malaichamy, Sivasankar, Biswas, Nidhan K, Chambers, John C, Cheng, Keith C, George, Joyner T, Khor, Seik Soon, Kim, Jong-Il, Cho, Belong, Menon, Ramesh, Sattibabu, Thiramsetti, Bassi, Akshi, Deshmukh, Manjari, Verma, Anjali, Gopalan, Vivek, Shin, Jong-Yeon, Pratapneni, Mahesh, Santhosh, Sam, Tokunaga, Katsushi, Md-Zain, Badrul M, Chan, Kok Gan, Parani, Madasamy, Natarajan, Purushothaman, Hauser, Michael, Allingham, R Rand, Santiago-Turla, Cecilia, Ghosh, Arkasubhra, Gadde, Santosh Gopi Krishna, Fuchsberger, Christian, Forer, Lukas, Schoenherr, Sebastian, Sudoyo, Herawati, Lansing, J Stephen, Friedlaender, Jonathan, Koki, George, Cox, Murray P, Hammer, Michael, Karafet, Tatiana, Ang, Khai C, Mehdi, Syed Q, Radha, Venkatesan, Mohan, Viswanathan, Majumder, Partha P, Seshagiri, Somasekar, Seo, Jeong-Sun, Schuster, Stephan C, and Peterson, Andrew S

Subjects
Human Genome, Genetics, Biotechnology, Alleles, Asian People, Datasets as Topic, Genome, Human, Genome-Wide Association Study, Genotype, Humans, GenomeAsia100K Consortium, General Science & Technology
Abstract

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world's population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.

Published
2019

17. Supporting Graduate Student Instructors in Calculus

Author

Reinholz, Daniel L., Cox, Murray, and Croke, Ryan

Abstract

This paper focuses on the use of the teaching method Peer-Assisted Reflection (PAR) to help graduate student instructors (GSIs) develop as teachers. PAR engages students in analyzing the work of their peers and providing feedback to promote their abilities of communication, collaboration, and persistence. The goals of the PAR activity were taken as goals for instruction generally, and used to support the GSIs to develop student-centered pedagogies. This report provides in-depth case studies of two of four GSIs involved in implementing PAR in their introductory calculus recitation sections. Two of the GSIs showed considerable changes in practices and beliefs, while the others showed little growth.

Published
2015

19. Impact of the COVID-19 pandemic on health-care use among patients with cancer in England, UK: a comprehensive phase-by-phase time-series analysis across attendance types for 38 cancers

Author

Tan, Yen Yi, Chang, Wai Hoong, Katsoulis, Michail, Denaxas, Spiros, King, Kayla C, Cox, Murray P, Davie, Charles, Balloux, Francois, and Lai, Alvina G

Abstract

The COVID-19 pandemic resulted in the widespread disruption of cancer health provision services across the entirety of the cancer care pathway in the UK, from screening to treatment. The potential long-term health implications, including increased mortality for individuals who missed diagnoses or appointments, are concerning. However, the precise impact of lockdown policies on national cancer health service provision across diagnostic groups is understudied. We aimed to systematically evaluate changes in patterns of attendance for groups of individuals diagnosed with cancer, including the changes in attendance volume and consultation rates, stratified by both time-based exposures and by patient-based exposures and to better understand the impact of such changes on cancer-specific mortality.

Published
2024
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21. High Frequency Haplotypes are Expected Events, not Historical Figures

Author

Guillot, Elsa G. and Cox, Murray P.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Cultural transmission of reproductive success states that successful men have more children and pass this raised fecundity to their offspring. Balaresque and colleagues found high frequency haplotypes in a Central Asian Y chromosome dataset, which they attribute to cultural transmission of reproductive success by prominent historical men, including Genghis Khan. Using coalescent simulation, we show that these high frequency haplotypes are consistent with a neutral model, where they commonly appear simply by chance. Hence, explanations invoking cultural transmission of reproductive success are statistically unnecessary., Comment: 8 pages, 1 figure, reply letter

Published
2015

24. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Subjects
Human Genome, Biotechnology, Genetics, Generic health relevance, Africa, Animals, Asia, Datasets as Topic, Estonia, Europe, Fossils, Gene Flow, Genetics, Population, Genome, Human, Genomics, Heterozygote, History, Ancient, Human Migration, Humans, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Population Dynamics, Racial Groups, General Science & Technology
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

Published
2016

25. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M., Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jérôme, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jønsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, André E. R., Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O., Székely, Tamás, Liu, Yang, Campana, Michael G., Corvelo, André, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Milá, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Ángela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie

Published
2020
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26. Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry.

Author

de Wit, Pierre JGM, van der Burgt, Ate, Ökmen, Bilal, Stergiopoulos, Ioannis, Abd-Elsalam, Kamel A, Aerts, Andrea L, Bahkali, Ali H, Beenen, Henriek G, Chettri, Pranav, Cox, Murray P, Datema, Erwin, de Vries, Ronald P, Dhillon, Braham, Ganley, Austen R, Griffiths, Scott A, Guo, Yanan, Hamelin, Richard C, Henrissat, Bernard, Kabir, M Shahjahan, Jashni, Mansoor Karimi, Kema, Gert, Klaubauf, Sylvia, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Mehrabi, Rahim, Ohm, Robin A, Owen, Timothy J, Salamov, Asaf, Schwelm, Arne, Schijlen, Elio, Sun, Hui, van den Burg, Harrold A, van Ham, Roeland CHJ, Zhang, Shuguang, Goodwin, Stephen B, Grigoriev, Igor V, Collemare, Jérôme, and Bradshaw, Rosie E

Subjects
Developmental Biology, Genetics
Published
2015

27. An informatics consult approach for generating clinical evidence for treatment decisions

Author

Lai, Alvina G., Chang, Wai Hoong, Parisinos, Constantinos A., Katsoulis, Michail, Blackburn, Ruth M., Shah, Anoop D., Nguyen, Vincent, Denaxas, Spiros, Davey Smith, George, Gaunt, Tom R., Nirantharakumar, Krishnarajah, Cox, Murray P., Forde, Donall, Asselbergs, Folkert W., Harris, Steve, Richardson, Sylvia, Sofat, Reecha, Dobson, Richard J. B., Hingorani, Aroon, Patel, Riyaz, Sterne, Jonathan, Banerjee, Amitava, Denniston, Alastair K., Ball, Simon, Sebire, Neil J., Shah, Nigam H., Foster, Graham R., Williams, Bryan, and Hemingway, Harry

Published
2021
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28. Papuan mitochondrial genomes and the settlement of Sahul

Author

Pedro, Nicole, Brucato, Nicolas, Fernandes, Veronica, André, Mathilde, Saag, Lauri, Pomat, William, Besse, Céline, Boland, Anne, Deleuze, Jean-François, Clarkson, Chris, Sudoyo, Herawati, Metspalu, Mait, Stoneking, Mark, Cox, Murray P., Leavesley, Matthew, Pereira, Luisa, and Ricaut, François-Xavier

Published
2020
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29. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin, Monika, Saag, Lauri, Vicente, Mário, Sayres, Melissa A Wilson, Järve, Mari, Talas, Ulvi Gerst, Rootsi, Siiri, Ilumäe, Anne-Mai, Mägi, Reedik, Mitt, Mario, Pagani, Luca, Puurand, Tarmo, Faltyskova, Zuzana, Clemente, Florian, Cardona, Alexia, Metspalu, Ene, Sahakyan, Hovhannes, Yunusbayev, Bayazit, Hudjashov, Georgi, DeGiorgio, Michael, Loogväli, Eva-Liis, Eichstaedt, Christina, Eelmets, Mikk, Chaubey, Gyaneshwer, Tambets, Kristiina, Litvinov, Sergei, Mormina, Maru, Xue, Yali, Ayub, Qasim, Zoraqi, Grigor, Korneliussen, Thorfinn Sand, Akhatova, Farida, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Ricaut, François-Xavier, Kusuma, Pradiptajati, Razafindrazaka, Harilanto, Pierron, Denis, Cox, Murray P, Sultana, Gazi Nurun Nahar, Willerslev, Rane, Muller, Craig, Westaway, Michael, Lambert, David, Skaro, Vedrana, Kovačevic´, Lejla, Turdikulova, Shahlo, Dalimova, Dilbar, Khusainova, Rita, Trofimova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Lichman, Daria V, Isakova, Jainagul, Pocheshkhova, Elvira, Sabitov, Zhaxylyk, Barashkov, Nikolay A, Nymadawa, Pagbajabyn, Mihailov, Evelin, Seng, Joseph Wee Tien, Evseeva, Irina, Migliano, Andrea Bamberg, Abdullah, Syafiq, Andriadze, George, Primorac, Dragan, Atramentova, Lubov, Utevska, Olga, Yepiskoposyan, Levon, Marjanovic´, Damir, Kushniarevich, Alena, Behar, Doron M, Gilissen, Christian, Vissers, Lisenka, Veltman, Joris A, Balanovska, Elena, Derenko, Miroslava, Malyarchuk, Boris, Metspalu, Andres, Fedorova, Sardana, Eriksson, Anders, Manica, Andrea, Mendez, Fernando L, Karafet, Tatiana M, Veeramah, Krishna R, Bradman, Neil, Hammer, Michael F, Osipova, Ludmila P, Balanovsky, Oleg, Khusnutdinova, Elza K, Johnsen, Knut, Remm, Maido, Thomas, Mark G, Tyler-Smith, Chris, Underhill, Peter A, Willerslev, Eske, Nielsen, Rasmus, Metspalu, Mait, Villems, Richard, and Kivisild, Toomas

Subjects
Biological Sciences, Genetics, Human Genome, Base Sequence, Chromosomes, Human, Y, DNA, Mitochondrial, Evolution, Molecular, Genetic Variation, Genetics, Population, Haplotypes, Humans, Male, Models, Genetic, Phylogeny, Racial Groups, Sequence Analysis, DNA, Medical and Health Sciences, Bioinformatics
Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

30. Semi-automatic selection of summary statistics for ABC model choice

Author

Prangle, Dennis, Fearnhead, Paul, Cox, Murray P., Biggs, Patrick J., and French, Nigel P.

Subjects
Statistics - Computation, Statistics - Applications
Abstract

A central statistical goal is to choose between alternative explanatory models of data. In many modern applications, such as population genetics, it is not possible to apply standard methods based on evaluating the likelihood functions of the models, as these are numerically intractable. Approximate Bayesian computation (ABC) is a commonly used alternative for such situations. ABC simulates data x for many parameter values under each model, which is compared to the observed data xobs. More weight is placed on models under which S(x) is close to S(xobs), where S maps data to a vector of summary statistics. Previous work has shown the choice of S is crucial to the efficiency and accuracy of ABC. This paper provides a method to select good summary statistics for model choice. It uses a preliminary step, simulating many x values from all models and fitting regressions to this with the model as response. The resulting model weight estimators are used as S in an ABC analysis. Theoretical results are given to justify this as approximating low dimensional sufficient statistics. A substantive application is presented: choosing between competing coalescent models of demographic growth for Campylobacter jejuni in New Zealand using multi-locus sequence typing data.

Published
2013

34. Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity

Author

Zammit, Nathan W., Siggs, Owen M., Gray, Paul E., Horikawa, Keisuke, Langley, David B., Walters, Stacey N., Daley, Stephen R., Loetsch, Claudia, Warren, Joanna, Yap, Jin Yan, Cultrone, Daniele, Russell, Amanda, Malle, Elisabeth K., Villanueva, Jeanette E., Cowley, Mark J., Gayevskiy, Velimir, Dinger, Marcel E., Brink, Robert, Zahra, David, Chaudhri, Geeta, Karupiah, Gunasegaran, Whittle, Belinda, Roots, Carla, Bertram, Edward, Yamada, Michiko, Jeelall, Yogesh, Enders, Anselm, Clifton, Benjamin E., Mabbitt, Peter D., Jackson, Colin J., Watson, Susan R., Jenne, Craig N., Lanier, Lewis L., Wiltshire, Tim, Spitzer, Matthew H., Nolan, Garry P., Schmitz, Frank, Aderem, Alan, Porebski, Benjamin T., Buckle, Ashley M., Abbott, Derek W., Ziegler, John B., Craig, Maria E., Benitez-Aguirre, Paul, Teo, Juliana, Tangye, Stuart G., King, Cecile, Wong, Melanie, Cox, Murray P., Phung, Wilson, Tang, Jia, Sandoval, Wendy, Wertz, Ingrid E., Christ, Daniel, Goodnow, Christopher C., and Grey, Shane T.

Published
2019
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36. The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa.

Author

Eaton, Carla J, Cabrera, Ilva E, Servin, Jacqueline A, Wright, Sara J, Cox, Murray P, and Borkovich, Katherine A

Subjects
Cell Membrane, Cell Surface Extensions, Vacuoles, Neurospora crassa, Spores, Fungal, GTP-Binding Protein alpha Subunits, Guanine Nucleotide Exchange Factors, Fungal Proteins, Luminescent Proteins, Recombinant Fusion Proteins, Microscopy, Fluorescence, Signal Transduction, Amino Acid Sequence, Conserved Sequence, Protein Transport, Molecular Sequence Data, Gene Knockout Techniques, Time-Lapse Imaging, Microscopy, Fluorescence, Spores, Fungal, General Science & Technology
Abstract

Heterotrimeric G protein signaling is essential for normal hyphal growth in the filamentous fungus Neurospora crassa. We have previously demonstrated that the non-receptor guanine nucleotide exchange factor RIC8 acts upstream of the Gα proteins GNA-1 and GNA-3 to regulate hyphal extension. Here we demonstrate that regulation of hyphal extension results at least in part, from an important role in control of asexual spore (conidia) germination. Loss of GNA-3 leads to a drastic reduction in conidial germination, which is exacerbated in the absence of GNA-1. Mutation of RIC8 leads to a reduction in germination similar to that in the Δgna-1, Δgna-3 double mutant, suggesting that RIC8 regulates conidial germination through both GNA-1 and GNA-3. Support for a more significant role for GNA-3 is indicated by the observation that expression of a GTPase-deficient, constitutively active gna-3 allele in the Δric8 mutant leads to a significant increase in conidial germination. Localization of the three Gα proteins during conidial germination was probed through analysis of cells expressing fluorescently tagged proteins. Functional TagRFP fusions of each of the three Gα subunits were constructed through insertion of TagRFP in a conserved loop region of the Gα subunits. The results demonstrated that GNA-1 localizes to the plasma membrane and vacuoles, and also to septa throughout conidial germination. GNA-2 and GNA-3 localize to both the plasma membrane and vacuoles during early germination, but are then found in intracellular vacuoles later during hyphal outgrowth.

Published
2012

38. Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations.

Author

Cox, Murray P, Morales, David A, Woerner, August E, Sozanski, Jesse, Wall, Jeffrey D, and Hammer, Michael F

Subjects
Humans, Population Growth, Polymorphism, Genetic, Archaeology, Agriculture, Africa South of the Sahara, Polymorphism, Genetic, General Science & Technology
Abstract

BackgroundA major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?Methodology/principal findingsWe investigate the timing of human population expansion by performing a multilocus analysis of > or = 20 unlinked autosomal noncoding regions, each consisting of approximately 6 kilobases, resequenced in approximately 184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.Conclusions/significanceThe data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (approximately 41 thousand years ago, approximately 13-fold) than our food-producing populations (approximately 31 thousand years ago, approximately 7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.

Published
2009

40. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

Author

Cox, Murray P, Woerner, August E, Wall, Jeffrey D, and Hammer, Michael F

Subjects
Biological Sciences, Genetics, Human Genome, Basic Behavioral and Social Science, Behavioral and Social Science, Base Sequence, Chromosomes, Human, X, Computer Simulation, DNA, Intergenic, Emigration and Immigration, Gene Flow, Genetics, Population, Geography, Humans, Models, Genetic, Population Density, Reproducibility of Results, Time Factors
Abstract

BackgroundDespite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions.ResultsHere, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM) model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at approximately 10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300-9,000) than non-African populations (300-3,300). We estimate mean rates of bidirectional gene flow at 4.8 x 10(-4)/generation. Bidirectional migration rates are approximately 5-fold higher among non-African populations (1.5 x 10(-3)) than among African populations (2.7 x 10(-4)). Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4).ConclusionWe conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

Published
2008

41. Sex-biased evolutionary forces shape genomic patterns of human diversity.

Author

Hammer, Michael F, Mendez, Fernando L, Cox, Murray P, Woerner, August E, and Wall, Jeffrey D

Subjects
Chromosomes, Human, Chromosomes, Human, X, Humans, Sequence Analysis, DNA, Genetics, Population, Population Density, Evolution, Molecular, Sex Characteristics, Mutation, Models, Genetic, Female, Male, Genetic Variation, Selection, Genetic, Chromosomes, Human, X, Evolution, Molecular, Genetics, Population, Models, Genetic, Selection, Sequence Analysis, DNA, Developmental Biology
Abstract

Comparisons of levels of variability on the autosomes and X chromosome can be used to test hypotheses about factors influencing patterns of genomic variation. While a tremendous amount of nucleotide sequence data from across the genome is now available for multiple human populations, there has been no systematic effort to examine relative levels of neutral polymorphism on the X chromosome versus autosomes. We analyzed approximately 210 kb of DNA sequencing data representing 40 independent noncoding regions on the autosomes and X chromosome from each of 90 humans from six geographically diverse populations. We correct for differences in mutation rates between males and females by considering the ratio of within-human diversity to human-orangutan divergence. We find that relative levels of genetic variation are higher than expected on the X chromosome in all six human populations. We test a number of alternative hypotheses to explain the excess polymorphism on the X chromosome, including models of background selection, changes in population size, and sex-specific migration in a structured population. While each of these processes may have a small effect on the relative ratio of X-linked to autosomal diversity, our results point to a systematic difference between the sexes in the variance in reproductive success; namely, the widespread effects of polygyny in human populations. We conclude that factors leading to a lower male versus female effective population size must be considered as important demographic variables in efforts to construct models of human demographic history and for understanding the forces shaping patterns of human genomic variability.

Published
2008

48. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M., Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jérôme, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jønsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, André E. R., Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O., Székely, Tamás, Liu, Yang, Campana, Michael G., Corvelo, André, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Milá, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Ángela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie

Published
2021
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49. Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Author

André, Mathilde, primary, Brucato, Nicolas, additional, Hudjasov, Georgi, additional, Pankratov, Vasili, additional, Yermakovich, Danat, additional, Kreevan, Rita, additional, Kariwiga, Jason, additional, Muke, John, additional, Boland, Anne, additional, Deleuze, Jean-François, additional, Meyer, Vincent, additional, Evans, Nicholas, additional, Cox, Murray P., additional, Leavesley, Matthew, additional, Dannemann, Michael, additional, Org, Tõnis, additional, Metspalu, Mait, additional, Mondal, Mayukh, additional, and Ricaut, François-Xavier, additional

Published
2022
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