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6 results on '"Sarah K. Brown"'

1. Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography

Author

Zachary T. Lounsberry, Steven R. Fain, Benjamin N. Sacks, Sarah K. Brown, Kristopher Kluepfel, Halie M. Rando, and Anna V. Kukekova

Subjects
Male, 0106 biological sciences, 0301 basic medicine, Mitochondrial DNA, lcsh:QH426-470, Pleistocene, Vulpes, Vulpes fulva, Foxes, Single-nucleotide polymorphism, Y chromosome, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, parasitic diseases, Genetics, Animals, Polymorphism, Genetics (clinical), Phylogenetic tree, Ecotype, biology, target capture, Sequence Analysis, DNA, DNA, Single Nucleotide, vulpes, biology.organism_classification, lcsh:Genetics, Phylogeography, 030104 developmental biology, Evolutionary biology, V. vulpes, Sequence Analysis, geographic locations
Abstract

The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes, and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (∼100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

Published
2021
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2. Distinguishing between northern salt marsh and western harvest mice

Author

Patty Q. Finfrock, Laureen Barthman-Thompson, Laura Patterson, Francis X. Villablanca, Sarah K. Brown, Sarah Estrella, and Diego Sustaita

Subjects
0106 biological sciences, geography, geography.geographical_feature_category, Ecology, biology, Reithrodontomys, biology.organism_classification, Logistic regression, 010603 evolutionary biology, 01 natural sciences, 010601 ecology, Agronomy, Discriminant function analysis, Salt marsh, General Earth and Planetary Sciences, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, General Environmental Science
Published
2018
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3. Conservation implications for dingoes from the maternal and paternal genome: Multiple populations, dog introgression, and demography

Author

J. William O. Ballard, Benjamin N. Sacks, Kylie M. Cairns, and Sarah K. Brown

Subjects
0106 biological sciences, 0301 basic medicine, demography, Life on Land, Human Y-chromosome DNA haplogroup, Biogeography, Population, population expansion, Introgression, mitochondrial DNA, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, biology.animal, 14. Life underwater, dingoes, education, hybridization, Ecology, Evolution, Behavior and Systematics, biogeography, Nature and Landscape Conservation, Apex predator, Original Research, Evolutionary Biology, education.field_of_study, Ecology, Y chromosome, mtDNA, Australia, conservation, 15. Life on land, 030104 developmental biology, Threatened species, Biological dispersal, Dingo
Abstract

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.

Published
2017

4. Ecological Insights from Ancient <scp>DNA</scp>

Author

Jessica L. Blois and Sarah K. Brown

Subjects
0106 biological sciences, 0301 basic medicine, education.field_of_study, Extinction, Ecology, Population size, fungi, Population, food and beverages, Climate change, Biology, 010603 evolutionary biology, 01 natural sciences, humanities, Natural (archaeology), 03 medical and health sciences, 030104 developmental biology, Ancient DNA, Habitat, sense organs, Adaptation, skin and connective tissue diseases, education
Abstract

Species have been shaped by past environmental conditions. Ancient remnants of species (bones, teeth, coprolites, pollen, shed cells, etc.) with preserved DNA (deoxyribonucleic acid) can reveal responses to past environmental changes through genetic information in the form of ancient DNA. Here we review the uses of ancient DNA to gain insights into ecological and evolutionary processes by investigating: (1) how climate has affected population dynamics through time, (2) how species react differently to climate change, (3) what triggers extinction for some species, (4) the detection of genomic adaptation to the environment and (5) how ancient DNA can be used to reconstruct past environmental conditions/habitats. The details that we can glean from past responses to climate change will provide information on how we can expect species to respond to future climate change. Key Concepts Ancient DNA (aDNA) can be utilised to infer how species reacted to past ecological changes. Populations are dynamic and respond to past climate change in many ways; through population size change, altered distributions and migrations. In combination with environmental data, ancient DNA is helping to elucidate what drove some species to extinction. Species have adapted to past climates. Ancient DNA, primarily through candidate gene searches, has revealed the genes behind these adaptations. Indirect methods of sampling soil for ancient DNA has aided in reconstructing past habitats. Ancient DNA can decipher how species responded to past natural climate change. This information can be used to aid in conservation. Keywords: ancient DNA; demography; adaptation; climate change; extinction

Published
2016
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5. The complete mitochondrial genome of the dusky-footed woodrat(Neotoma fuscipes) (Rodentia, Cricetidae)

Author

Sarah K. Brown and Jessica L. Blois

Subjects
0106 biological sciences, 0301 basic medicine, Mitochondrial DNA, Peromyscus, Rodent, Population, Zoology, Neotoma fuscipes, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Mitochondrial genome, Genus, biology.animal, Genetics, education, Molecular Biology, Mitogenome Announcement, education.field_of_study, biology, biology.organism_classification, cricetidae, Microtus fortis, 030104 developmental biology, Research Article, Cricetidae
Abstract

The dusky-footed woodrat (Neotoma fuscipes) is an endemic North American rodent belonging to the family Cricetidae. We present here the first complete mitogenome within the Neotoma genus. The mitogenome is 16,199 bp in length, and has a structure and gene organization similar to other rodent species (e.g. Mus musculus, Peromyscus maniculatus and Microtus fortis calamorum). The overall base composition is A (35.2%), C (25.5%), G (12.3%), T (27.0%), with a GC content of 37.8%, similar to other rodents. This mitogenome serves as a foundation for future phylogenetic, phylogeographic and population genetic studies.

Published
2016
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6. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009–30 November 2009

Author

Gen-Bo Xu, Yi Kyung Kim, Zhen Xia Sha, N. Sreejayan, Maria Domenica Moccia, B. W. Hou, Fuwen Wei, Shaoying Liu, Mi Sook Min, Radosavljević Ivan, William Stewart Grant, Peter Kaňuch, Hai Hui Ye, Monika Pfunder, Stefan Woltmann, Antonis Rokas, Z. Y. Feng, Susanne Gustafsson, Benjamin N. Sacks, Hang Lee, M. L. Xie, Eun Ha Shin, Xiao Jun Xu, Kevin A. Feldheim, Scott A. Taylor, Zlatko Šatović, Maria Gaillard, Martin Lascoux, Christopher A. Saski, Ryan P. Walter, Vicki L. Friesen, Junghwa An, Shao Jing Li, Gudasalamani Ravikanth, Arnaud Béchet, William D. Templin, Juan A. Galaraza, Qingui Cai, Yi Wang, Zac Grauvogel, Åsa Berggren, Kyung Seok Kim, Sang Gyu Kim, James A. Morris-Pocock, Brian R. Kreiser, Sung Kyoung Choi, K. N. Ganeshaiah, Branka Javornik, X. Y. Ding, L. Han, Sofia Hemmilä, Julia Geraci, Daniel D. Heath, Leonardo A. Gallo, J. Zhong, Kyung i.Kl Kim, Frank Cézilly, Zhengxin Sun, Marcelle Moore, Maren A. Klich, Kumara P. Mohana, Yong Fan, F. Zhang, Zlatko Liber, Xiaolin Liao, Yong Jin Won, Athena Lam, Giovanni G. Vendramin, Alex Widmer, Xiangjiang Zhan, Sarah K. Brown, Han Chan Park, Yong Tao, Ramesh Vasudeva, Y. H. Ma, Yajun Ma, D. L. Li, Jing Wu, Kelly Lasater, George K. Roderick, Ke Jian Wang, Anna Cassel-Lundhagen, Carolina Soliani, J. Derek Hogan, Jernej Jakše, Yun Sun Lee, Ye Seul Kwan, Song-Lin Chen, Xin Hui Luo, Sean D. Schoville, Michael William Bruford, Jeffrey Robert Guyon, John G. Gibbons, Lin Lin, R. Uma Shaanker, Sang In Kim, Federico Sebastiani, W. Y. Li, Gui Zhong Wang, Rémi Wattier, Wei Cheng, Paula Marchelli, Woo-Jin Kim, BK21 program for Veterinary Science, Seoul National University [Seoul] (SNU), Centre de recherche de la Tour du Valat, Department of Ecology, Swedish University of Agricultural Sciences (SLU), Canid Diversity and Conservation Laboratory, University of California, Biodiversity and Ecological Processes Group, Cardiff University, Caopo Nature Reserves, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture-Chinese Academy of Fishery Sciences, Alaska Department of Fish and Game, Jiangsu Provincal Key Laboratory for Biodiversity & Biotechnology, Nanjing Normal University (NNU), Department of Pathogen Biology and State Key Laboratory for Medical Immunology, Second Military Medical University, Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Department of Biology, Queen's University, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Unidad de Genética Ecológica y Mejoramiento Forestal, INTA EEA Bariloche, School of Ecology and Conservation, University of Agricultural Sciences, Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Department of Forestry and Environmental Sciences, Department of Biological Sciences [Nashville], Vanderbilt University [Nashville], Program in Evolutionary Functional Genomics, Uppsala University, Auke Bay Laboratories (ABL), Alaska Fisheries Science Center (AFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Great Lakes Institute for Environmental Research, University of Windsor [Ca], Centre for Plant Biotechnology and Breeding, University of Ljubljana, Biotechnology Research Division, National Fisheries Research and Development Institute, Conservation Genome Resource Bank for Korean Wildlife (CGRB), USDA, Agence Régionale de la Santé (ARS), Department of Biological Sciences, University of Southern Mississippi (USM), Division of EcoScience, EWHA Womans University (EWHA), Department of Environmental Science, Policy, and Management [Berkeley] (ESPM), University of California [Berkeley], University of California-University of California, Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, State Key Laboratory of Marine Environmental Science (MEL), Division of Botany [Zagreb], Department of Biology [Zagreb], Faculty of Science [Zagreb], University of Zagreb-University of Zagreb-Faculty of Science [Zagreb], University of Zagreb-University of Zagreb, Sichuan Academy of Forestry, College of Aqua-life Science and Technology, Shanghai Ocean University, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institute of Integrative Biology (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Crop Physiology, Biological Sciences Department [Sacrameno], California State University [Sacramento], Ecogenics GmbH, Department of Population Health and Reproduction, Genomics Institute, Clemson University, Department of Seed Science and Technology [Zagreb], Faculty of Agriculture [Zagreb] (UNIZG), Laboratorio Genexpress, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Forest Biology and Tree Improvement, Instituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche (CNR), Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences [Beijing] (CAS), Department of Ecology and Evolutionary Biology, Tulane University, College of Marine Life Sciences [Qingdao], Ocean University of China (OUC), Seoul National University [Seoul], Swedish University of Agricultural Sciences, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Nanjing Normal University, Estacion Biologica Doñana, Auke Bay Laboratories ( ABL ), Alaska Fisheries Science Center ( AFSC ), NOAA National Marine Fisheries Service ( NMFS ), National Oceanic and Atmospheric Administration ( NOAA ) -National Oceanic and Atmospheric Administration ( NOAA ) -NOAA National Marine Fisheries Service ( NMFS ), National Oceanic and Atmospheric Administration ( NOAA ) -National Oceanic and Atmospheric Administration ( NOAA ), University of Windsor, Conservation Genome Resource Bank for Korean Wildlife ( CGRB ), Agence Régionale de la Santé ( ARS ), University of Southern Mississippi, EWHA Womans University ( EWHA ), Department of Environmental Science, Policy and Management, State Key Laboratory of Marine Environmental Science, Department of Botany, University of Zagreb, Consejo Nacional de Investigaciones Científicas y Técnicas ( CONICET ), Eidgenössische Technische Hochschule [Zürich] ( ETH Zürich ), Department of Seed Science and Technology, Università degli Studi di Firenze [Firenze], Consiglio Nazionale delle Ricerche ( CNR ), Chinese Academy of Sciences [Beijing] ( CAS ), College of Marine Life Sciences, and Ocean University of China

Subjects
0106 biological sciences, Colias interior, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, food, Botany, Genetics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Database, Salvia officinalis, biology.organism_classification, food.food, Dendrobium devonianum, Dendrobium loddigesii, Nothofagus obliqua, Sula nebouxii, Colias eurytheme, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, Aspergillus clavatus, computer, Biotechnology
Abstract

5 pages; International audience; This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.

Published
2010
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