Genetics and Genomics Commons^™

Acoustic Telemetry Provides Insights For Improving Conservation And Management At A Spawning Aggregation Site Of The Endangered Nassau Grouper (Epinephelus Striatus), Richard S. Nemeth, Elizabeth Kadison, Jonathan Jossart, Mahmood Shivji, Bradley Wetherbee, Jordan Matley

Biology Faculty Articles

Nassau grouper (Epinephelus striatus, Serranidae) were one of the most important fishery species in the Caribbean, but are now listed as critically endangered. Population collapse in most places occurred primarily by fishers targeting their spawning aggregation sites, where thousands of fish gathered during full moon periods from December to April. Identifying management options for protecting this vulnerable period is crucial for their survival. In the US Virgin Islands, we tagged 24 Nassau grouper with acoustic transmitters at a fish spawning aggregation (FSA) site called the Grammanik Bank, a 1.5 km2, marine protected area (MPA) closed each year from …

Genomes Of Endangered Great Hammerhead And Shortfin Mako Sharks Reveal Historic Population Declines And High Levels Of Inbreeding In Great Hammerhead, Michael J. Stanhope, Kristina M. Ceres, Qi Sun, Minghui Wang, Jordan D. Zehr, Nicholas J. Marra, Aryn P. Wilder, Cheng Zou, Andrea M. Bernard, Paulina D. Pavinski Bitar, Mitchell G. Lokey, Mahmood Shivji

Biology Faculty Articles

Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and 1 Mbp. Both these sharks experienced precipitous declines in …

Genetic Population Dynamics Of The Critically Endangered Scalloped Hammerhead Shark (Sphyrna Lewini) In The Eastern Tropical Pacific, Sydney P. Harned, Andrea Bernard, Pelayo Salinas-De-Leon, Marissa Mehlrose, Jenifer Suarez, Yolani Robles, Sandra Bessudo Lion, Felipe Ladino, Andrés López Garo, Ilena Zanella, Kevin A. Feldheim, Mahmood Shivji

Biology Faculty Articles

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young-of-year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure suggesting that scalloped hammerheads in this ETP region comprise a single …

A Decade Of Gigascience: A Perspective On Conservation Genetics, Stephen James O'Brien

Biology Faculty Articles

Wide interest in species conservation is young. To many it began early in 1903 when Teddy Roosevelt and John Muir set up a camp under the Grizzly Giant in the Mariposa Grove of California's Yosemite Valley. Over three days they decided to broaden the US National Park footprint across the USA. Conservationists were inspired in the coming decades by the writings of wildlife conservation pioneers—Osa Johnson (I Married Adventure), Karen Blixen (Out of Africa) and Rachel Carson (The Silent Spring). Countless crusaders developed a passion for preserving dwindling species in those early days, yet …

Three Complete Mitochondrial Genomes Of Shortfin Mako Sharks, Isurus Oxyrinchus, From The Atlantic And Pacific Oceans, Marissa Mehlrose, Andrea Bernard, Kimberly A. Finnegan, Lauren E. Krausfeldt, Jose V. Lopez, Mahmood Shivji

Biology Faculty Articles

We present complete mitogenome sequences of three shortfin mako sharks (Isurus oxyrinchus) sampled from the western Pacific, and eastern and western Atlantic oceans. Mitogenome sequence lengths ranged between 16,699 bp and 16,702 bp, and all three mitogenomes contained one non-coding control region, two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. Comparative assessment of five mitogenomes from globally distributed shortfin makos (the current three and two previously published mitogenomes) yielded 98.4% identity, with the protein-coding genes ATP8, ATP6, and ND5 as the most variable regions (sequence identities of 96.4%, 96.5%, and 97.6%, respectively). These mitogenome sequences contribute resources …

The Earth Biogenome Project 2020: Starting The Clock, Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Katharine B. Baker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica Dipalma, Richard Durbin, Thankgod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kjetill Sigurd Jakobson, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin-Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O'Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, Guojie Zhang

Biology Faculty Articles

No abstract provided.

Standards Recommendations For The Earth Biogenome Project, Mara K. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques-Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katherine J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose V. Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Françoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards

Biology Faculty Articles

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. …

Why Sequence All Eukaryotes?, Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A.M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin

Biology Faculty Articles

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes—about 2 million species—should be sequenced to high quality to produce a …

Commentary: Unbiasing Genome-Based Analyses Of Selection: An Example Using Iconic Shark Species, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Vincent P. Richards, Stephen J. O'Brien, Agostinho Antunes, Mahmood S. Shivji

Biology Faculty Articles

No abstract provided.

Genome-Wide Association Study Identifies New Loci Associated With Risk Of Hbv Infection And Disease Progression, Zheng Zeng, Liu Hankui, Xu Huifang, Lu Haiying, Yu Yanyan, Xu Xiaoyuan, Yu Min, Zhang Tao, Tian Xiulan, Xi Hongli, Guan Liping, Zhang Jianguo, Stephen James O'Brien

Biology Faculty Articles

Background: Recent studies have identified susceptibility genes of HBV clearance, chronic hepatitis B, liver cirrhosis, hepatocellular carcinoma, and showed the host genetic factors play an important role in these HBV-related outcomes.

Results: In order to discover new susceptibility genes for HBV-related outcomes, we conducted a genome-wide association study in 1031 Chinese participants, including 275 HBV clearance subjects, 92 asymptomatic persistence infection carriers (ASPI), 93 chronic hepatitis B patients (CHB), 188 HBV-related decompensated cirrhosis patients (DC), 214 HBV-related hepatocellular carcinoma patients (HCC) and 169 healthy controls (HC). In the case-control study, we observed novel locus significantly associated with CHB …

Genomic Adaptations And Evolutionary History Of The Extinct Scimitar-Toothed Cat, Homotherium Latidens, Ross Barnett, Michael V. Westbury, Marcela Sandoval-Velasco, Filipe Garrett Vieira, Sungwon Jeon, Grant Zazula, Michael D. Martin, Simon Y.W. Ho, Niklas Mather, Shyam Gopalakrishnan, Jazmín Ramos-Madrigal, Marc De Manuel, M. Lisandra Zepeda-Mendoza, Agostinho Antunes, Aldo Carmona Baez, Binia De Cahsan, Greger Larson, Stephen J. O'Brien, Eduardo Eizirik, Warren E. Johnson, Klaus Peter Koepfli, Andreas Wilting, Jörns Fickel, Love Dalén, Eline D. Lorenzen, Tomas Marques-Bonet, Anders J. Hansen, Guojie Zhang, Jong Bhak

Biology Faculty Articles

Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1–4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6–8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread …

Ultracontinuous Single Haplotype Genome Assemblies For The Domestic Cat (Felis Catus) And Asian Leopard Cat (Prionailurus Bengalensis), Kevin R. Bredemeyer, Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody E. Roelke-Parker, Stephen James O'Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy

Biology Faculty Articles

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the …

Karyotype Evolution In 10 Pinniped Species: Variability Of Heterochromatin Versus High Conservatism Of Euchromatin As Revealed By Comparative Molecular Cytogenetics, Violetta R. Beklemisheva, Polina L. Perelman, Natalya A. Lemskaya, Anastasiya A. Proskuryakova, Natalya A. Serdyukova, Vladimir N. Burkanov, Maksim B. Gorshunov, Oliver A. Ryder, Mary Thompson, Gina Lento, Stephen James O'Brien, Alexander S. Graphodatsky

Biology Faculty Articles

Pinnipedia karyotype evolution was studied here using human, domestic dog, and stone marten whole-chromosome painting probes to obtain comparative chromosome maps among species of Odobenidae (Odobenus rosmarus), Phocidae (Phoca vitulina, Phoca largha, Phoca hispida, Pusa sibirica, Erignathus barbatus), and Otariidae (Eumetopias jubatus, Callorhinus ursinus, Phocarctos hookeri, and Arctocephalus forsteri). Structural and functional chromosomal features were assessed with telomere repeat and ribosomal-DNA probes and by CBG (C-bands revealed by barium hydroxide treatment followed by Giemsa staining) and CDAG (Chromomycin A3-DAPI after G-banding) methods. We demonstrated diversity of heterochromatin among pinniped karyotypes in terms of localization, …

Urine As A High-Quality Source Of Host Genomic Dna From Wild Populations, Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone

Biology Faculty Articles

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that …

Genome-Wide Sequence Analyses Of Ethnic Populations Across Russia, Daria V. Zhernakova, Vladimir Brukhin, Sergey Malov, Taras K. Oleksyk, Klaus Peter Koepfli, Anna Zhuk, Pavel Dobrynin, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Anna Gorbunova, Ekaterina Chernyaeva, Andrey Shevchenko, Sofia Kolchanova, Alexei Komissarov, Serguei Simonov, Alexey Antonik, Anton Logachev, Dmitrii E. Polev, Olga A. Pavlova, Andrey S. Glotov, Vladimir Ulantsev, Ekaterina Noskova, Tatyana K. Davydova, Tatyana M. Sivtseva

Biology Faculty Articles

The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show …

Characterization Of The Microbiome And Bioluminescent Symbionts Across Life Stages Of Ceratioid Anglerfishes Of The Gulf Of Mexico, Lindsay L. Freed, Cole Easson, Lydia Baker, D. Fenolio, Tracey Sutton, Yasmin Khan, Patricia Blackwelder, Tory Hendry, Jose Lopez

Biology Faculty Articles

The interdependence of diverse organisms through symbiosis reaches even the deepest parts of the oceans. As part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity, we profiled the bacterial communities (‘microbiomes’) and luminous symbionts of 36 specimens of adult and larval deep-sea anglerfishes of the suborder Ceratioidei using 16S rDNA. Transmission Electron Microscopy was used to characterize the location of symbionts in adult light organs (esca). Whole larval microbiomes, and adult skin and gut microbiomes, were dominated by bacteria in the genera Moritella and Pseudoalteromonas genera. 16S rDNA sequencing results from adult fishes corroborate …

Precision Nomenclature For The New Genomics, Harris A. Lewin, Jennifer A. Marshall Graves, Oliver A. Ryder, Alexander S. Graphodatsky, Stephen James O'Brien

Biology Faculty Articles

The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images …

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji

Biology Faculty Articles

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …

Integrated Analysis Of Competing Endogenous Rna Network Revealing Potential Prognostic Biomarkers Of Hepatocellular Carcinoma, Xiwen Liao, Xiangkun Wang, Ketuan Huang, Chuangye Han, Jianlong Deng, Tingdong Yu, Chengkun Yang, Rui Huang, Xiaoguang Liu, Long Yu, Guangzhi Zhu, Hao Su, Wei Qin, Xianmin Zeng, Bowen Han, Quanfa Han, Zhengqian Liu, Xin Zhou, Yizhen Gong, Zhengtao Liu, Jianlv Huang, Cheryl A. Winkler, Stephen J. O'Brien, Xinping Ye, Tao Peng

Biology Faculty Articles

Objective: The goal of our study is to identify a competing endogenous RNA (ceRNA) network using dysregulated RNAs between HCC tumors and the adjacent normal liver tissues from The Cancer Genome Atlas (TCGA) datasets, and to investigate underlying prognostic indicators in hepatocellular carcinoma (HCC) patients. Methods: All of the RNA- and miRNA-sequencing datasets of HCC were obtained from TCGA, and dysregulated RNAs between HCC tumors and the adjacent normal liver tissues were investigated by DESeq and edgeR algorithm. Survival analysis was used to confirm underlying prognostic indicators. Results: In the present study, we constructed a ceRNA network based on 16 …

Red Fox Genome Assembly Identifies Genomic Regions Associated With Tame And Aggressive Behaviours, Anna V. Kukekova, Jennifer L. Johnson, Xueyan Xiang, Shaohong Feng, Shiping Liu, Halie M. Rando, Anastasiya V. Kharlamova, Yury Herbeck, Natalya A. Serdyukova, Zijun Xiong, Violetta Beklemischeva, Klaus Peter Koepfli, Rimma G. Gulevich, Anastasiya V. Vladimirova, Jessica P. Hekman, Polina L. Perelman, Aleksander S. Graphodatsky, Stephen J. O’Brien, Xu Wang, Andrew G. Clark, Gregory M. Acland, Lyudmila N. Trut, Guojie Zhang

Biology Faculty Articles

Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes …

Analytical “Bake-Off” Of Whole Genome Sequencing Quality For The Genome Russia Project Using A Small Cohort For Autoimmune Hepatitis, Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David L. Valle, Minzhong Tang, Emilia Shin, Kathleen B. Schwarz, Stephen James O'Brien

Biology Faculty Articles

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight …

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Biology Faculty Articles

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is …

The Complete Phylogeny Of Pangolins: Scaling Up Resources For The Molecular Tracing Of The Most Trafficked Mammals On Earth, Philippe Gaubert, Agostinho Antunes, Hao Meng, Lin Miao, Stéphane Peigné, Fabienne Justy, Flobert Njiokou, Sylvain Dufour, Emmanuel Danquah, Jayanthi Alahakoon, Erik Verheyen, William T. Stanley, Stephen J. O'Brien, Warren E. Johnson, Shu Jin Luo

Biology Faculty Articles

Pangolins, considered the most-traffcked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here, we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and 9 nuclear genes. We confrm deep divergence among Asian and African pangolins occurring not later than the Oligocene-Miocene boundary ca. 23 million years ago (Ma) (95% HPD = 18.7-27.2), limited fossil evidence suggesting dispersals from Europe. We recognize 3 genera including Manis (Asian pangolins), Smutsia (large African pangolins), and Phataginus …

Internal Validation Of Strmix™ – A Multi Laboratory Response To Pcast, Jo-Anne Bright, Rebecca Richards, Maarten Kruijver, Hannah Kelly, Catherine Mcgovern, Alan Magee, Andrew Mcwhorter, Anne Cieko, Brian Peck, Chase Baumgartner, Christina Buettner, Scott Mcwilliams, Claire Mckenna, Colin Gallacher, Ben Mallinder, Darren Wright, Deven Johnson, Dorothy Catella, Eugene Lien, Craig O'Connor, George Duncan, Jason Bundy, Jillian Echard, John Lowe, Joshua Stewart, Kathleen Corrado, Sheila Gentile, Marla Kaplan, Michelle Hassler, Naomi Mcdonald, Paul Hulme, Rachel H. Oefelein, Shawn Montpetit, Melissa Strong, Sarah Noel, Simon Malsom, Steven Myers, Susan Welti, Tamyra Moretti, Teresa Mcmahon, Thomas Grill, Tim Kalafut, Mary Margaret Greer-Ritzheimer, Vickie Beamer, Duncan A. Taylor, John S. Buckleton

Biology Faculty Articles

We report a large compilation of the internal validations of the probabilistic genotyping software STRmix™. Thirty one laboratories contributed data resulting in 2825 mixtures comprising three to six donors and a wide range of multiplex, equipment, mixture proportions and templates. Previously reported trends in the LR were confirmed including less discriminatory LRs occurring both for donors and non-donors at low template (for the donor in question) and at high contributor number. We were unable to isolate an effect of allelic sharing. Any apparent effect appears to be largely confounded with increased contributor number.

Marker Of Proliferation Ki-67 Expression Is Associated With Transforming Growth Factor Beta 1 And Can Predict The Prognosis Of Patients With Hepatic B Virus-Related Hepatocellular Carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, Tao Peng

Biology Faculty Articles

Hepatocellular carcinoma (HCC) is the most frequent malignancy of the liver. Transforming growth factor beta 1 (TGFB1) and marker of proliferation Ki-67 (MKI67) regulate cell proliferation, differentiation, and growth. The association between MKI67 and TGFB1 expression and its clinical implications in HCC remain unknown. Methods: Public databases were used to analyze TGFB1 and MKI67 expression in different pathologic grades/stages and tissue types of HCC. The association between MKI67 and TGFB1 expression was explored using pathway analysis and in a HepG2 cell line treated with TGFB1. Survival analysis was performed to evaluate the prognostic value of TGFB1 and MKI67 expression in …

Whole-Genome Analysis Of Mycobacterium Tuberculosis From Patients With Tuberculous Spondylitis, Russia, Ekaterina Chernyaeva, Mikhail Rotkevich, Ksenia Krasheninnikova, Andrey Yurchenko, Anna Vyazovaya, Igor Mokrousov, Natalia Solovieva, Viacheslav Zhuravlev, Piotr Yablonsky, Stephen J. O’Brien

Biology Faculty Articles

Whole-genome analysis of Mycobacterium tuberculosis isolates collected in Russia (N = 71) from patients with tuberculous spondylitis supports a detailed characterization of pathogen strain distributions and drug resistance phenotype, plus distinguished occurrence and association of known resistance mutations. We identify known and novel genome determinants related to bacterial virulence, patho-genicity, and drug resistance.

X Chromosome Evolution In Cetartiodactyla, Anastasiya A. Proskuryakova, Anastasia I. Kulemzina, Polina L. Perelman, Alexey I. Makunin, Denis M. Larkin, Marta Farre, Anna V. Kukekova, Jennifer Lynn Johnson, Natalya A. Lemskaya, Violetta R. Beklemisheva, M. Roelke-Parker, June Bellizzi, Oliver A. Ryder, Stephen James O'Brien, Alexander S. Graphodatsky

Biology Faculty Articles

The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern between species. It is hypothesized that this sex chromosome has undergone multiple rearrangements that changed the centromere position and the order of syntenic segments over the last 80 million years of Cetartiodactyla speciation. To investigate its evolution we have selected 26 evolutionarily conserved bacterial artificial chromosome (BAC) clones from the cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution BAC …

Aldehyde Dehydrogenase 1 (Aldh1) Isoform Expression And Potential Clinical Implications In Hepatocellular Carcinoma, Cheng Kun Yang, Xiang Kun Wang, Xi Wen Liao, Chuang Ye Han, Ting Dong Yu, Wei Qin, Guang Zhi Zhu, Hao Su, Long Yu, Xiao Guang Liu, Si Cong Lu, Zhi Wei Chen, Zhen Liu, Ke Tuan Huang, Zheng Tao Liu, Yu Liang, Jian Lu Huang, Kai Yin Xiao, Min Hao Peng, Cheryl Ann Winkle, Stephen J. O’Brien, Tao Peng

Biology Faculty Articles

Hepatocellular carcinoma (HCC) is one of the most prevalent and life-threatening malignancies worldwide. There are few diagnostic and prognostic biomarkers and druggable targets for HCC. Aldehyde dehydrogenase 1 (ALDH1) is a marker of stem cells in a variety of cancers, but the mRNA levels and prognostic value of ALDH1 isoforms in HCC patients remain unknown. In the present study, gene ontology annotation of the ALDH1 family was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID), and the gene pathway analsis was performed using GeneMANIA software. The initial prognostic value of ALDH1 expression in 360 HCC patients was …

The Human Microbiome: An Emerging Tool In Forensics, Jarrad T. Hampton-Marcell, Jose V. Lopez, Jack A. Gilbert

Biology Faculty Articles

No abstract provided.

Comparative Transcriptomics Of Elasmobranchs And Teleosts Highlight Important Processes In Adaptive Immunity And Regional Endothermy, Nicholas J. Marra, Vincent P. Richards, Angela Early, Steve M. Bogdanowicz, Paulina D. Pavinski Bitar, Michael J. Stanhope, Mahmood S. Shivji

Biology Faculty Articles

Background: Comparative genomic and/or transcriptomic analyses involving elasmobranchs remain limited, with genome level comparisons of the elasmobranch immune system to that of higher vertebrates, non-existent. This paper reports a comparative RNA-seq analysis of heart tissue from seven species, including four elasmobranchs and three teleosts, focusing on immunity, but concomitantly seeking to identify genetic similarities shared by the two lamnid sharks and the single billfish in our study, which could be linked to convergent evolution of regional endothermy.

Results: Across seven species, we identified an average of 10,877 Swiss-Prot annotated genes from an average of 32,474 open reading frames within each …