4.8 Article

Genomics of adaptive evolution in the woolly mammoth

Related references

Note: Only part of the references are listed.
Review Cell Biology

The Role of TP53 in Adaptation and Evolution

Konstantinos Voskarides et al.

Summary: The TP53 gene is crucial in cancer formation and is considered the most important tumor suppressor gene. It functions as a transcription factor and is involved in various cellular processes. TP53 is also associated with fertility, aging, longevity, and environmental adaptation. Studies have shown that TP53 mutations are beneficial for animals living in specific environments, and multiple copies of TP53 in elephants may explain their low cancer incidence. This review provides an in-depth analysis of TP53's role in adaptation across different levels.

CELLS (2023)

Letter Reproductive Biology

Recurrent pregnancy loss in mice lacking the X-linked Ccnb3 gene

Jessica Y. Chotiner et al.

BIOLOGY OF REPRODUCTION (2022)

Article Multidisciplinary Sciences

Placental genomics mediates genetic associations with complex health traits and disease

Arjun Bhattacharya et al.

Summary: The placenta plays a vital role in the Developmental Origins of Health and Disease (DOHaD) hypothesis, but its study has been historically neglected. In this research, we investigate placental genetrait associations (GTAs) for 40 traits across different stages of life. By analyzing placental multi-omics data, we identify 248 GTAs, mainly related to neonatal and metabolic traits, and enriched in cell growth and immunological pathways. We find that genetic effects mediated by placental gene expression significantly contribute to early-life traits, but not later-in-life traits. We also discover hypotheses for distal regulation of GTAs through distal genetic variants.

NATURE COMMUNICATIONS (2022)

Article Multidisciplinary Sciences

Mice with a deficiency in Peroxisomal Membrane Protein 4 (PXMP4) display mild changes in hepatic lipid metabolism

Maaike Blankestijn et al.

Summary: The study of a Pxmp4 knockout mouse model suggests that PXMP4 is not critical for overall peroxisome function but may have a role in the metabolism of (ether)lipids.

SCIENTIFIC REPORTS (2022)

Article Genetics & Heredity

Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA

Marianne Dehasque et al.

Summary: This study presents a new silica column-based extraction protocol for retrieving endogenous DNA from ancient specimens. The efficiency of different optimizations, including bleach wash, predigestion, column selection, and uracil-treatment, were systematically tested. The results indicate that bleach wash combined with predigestion did not significantly increase sequencing efficiency, MinElute columns were more efficient for ancient DNA extractions than QIAquick columns, and uracil treatments were effective in removing DNA damage even at lower concentrations.

GENES (2022)

Article Biochemical Research Methods

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Verena E. Kutschera et al.

Summary: The study presents a flexible, scalable, and modular pipeline for comparing patterns of genomic erosion in samples from different time periods. The pipeline utilizes state-of-the-art bioinformatics tools to process whole-genome re-sequencing data from ancient/historical and modern samples, and produces comparable estimates of genomic erosion indices.

BMC BIOINFORMATICS (2022)

Article Biotechnology & Applied Microbiology

Gene network analysis reveals candidate genes related with the hair follicle development in sheep

Junmin He et al.

Summary: This study identified differentially expressed genes during the development of hair follicles in Merino sheep and identified key genes affecting hair follicle morphogenesis through network analysis. These findings are important for understanding fleece evolution in animals and provide a theoretical basis for breeding fine wool sheep.

BMC GENOMICS (2022)

Article Multidisciplinary Sciences

Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome

Tom van der Valk et al.

Summary: Woolly mammoths had genetic adaptations, including deletions and indels, that contributed to their unique phenotypic adaptations for surviving in the Arctic environment.

ISCIENCE (2022)

Article Geography, Physical

Mammoth evolution in the late Middle Pleistocene: The Mammuthus trogontherii-primigenius transition in Europe

Adrian M. Lister

Summary: This study examines the transition from the steppe mammoth to the woolly mammoth in Europe during the late Middle Pleistocene. Through a metrical study of molariform teeth from various locations, the study traces the morphological trend and finds that the transition occurred around the MIS 7/6 boundary. The study also highlights the importance of considering size change and using bivariate analysis when studying metric variables.

QUATERNARY SCIENCE REVIEWS (2022)

Article Cell Biology

Genome-Wide Expression Profiling and Networking Reveals an Imperative Role of IMF-Associated Novel CircRNAs as ceRNA in Pigs

Salsabeel Yousuf et al.

Summary: This study investigates the interaction between non-coding RNAs and mRNAs in intramuscular fat deposition and explores the potential pathogenic role of competing endogenous RNA (ceRNA) in IMF tissues. The study identifies key circRNAs and their associated miRNA-mRNA networks, which are involved in lipid metabolism, fat deposition, and meat quality. The findings provide insights into the underlying molecular mechanisms of adipocyte differentiation and IMF deposition, and can contribute to improving meat quality and treating lipid metabolic syndromes.

CELLS (2022)

Article Ophthalmology

Multimodal Retinal Imaging Findings in Two Cousins With VCAN-Related Vitreoretinopathy or Wagner Disease

M. Margarita Parra et al.

Summary: Wagner disease is a rare, non-syndromic vitreoretinopathy that can lead to retinal problems, and its clinical phenotype shows variability.

OPHTHALMIC SURGERY LASERS & IMAGING RETINA (2022)

Article Dermatology

High-resolution single-cell transcriptomics reveals heterogeneity of self-renewing hair follicle stem cells

Gopal Chovatiya et al.

Summary: This study investigates the molecular heterogeneity of hair follicle stem cells (HFSCs) using high-resolution single-cell RNA sequencing and identifies five major populations distinguished by known markers associated with the bulge and outer root sheath (ORS). Lineage trajectory analysis predicts prospective differentiation paths of cellular states within these populations. Gene set enrichment analysis reveals potential distinct functions of different subpopulations within the bulge and ORS, shedding light on communication and nutrient transfer mechanisms within the hair follicle.

EXPERIMENTAL DERMATOLOGY (2021)

Article Biochemistry & Molecular Biology

Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology

Judith A. Blake et al.

Summary: The Mouse Genome Database serves as a community model organism knowledge base for laboratory mice, providing authoritative biological reference data related to mouse genes, gene functions, phenotypes, and mouse models of human disease. It follows official guidelines for gene, allele, and mouse strain nomenclature and curates information from biomedical literature and datasets contributed by investigators. Major enhancements have been made to content and interfaces at MGD, including improvements in the Multi Genome Viewer, inclusion of more mouse strains, and integration of extensive data about mouse strain variants.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Million-year-old DNA sheds light on the genomic history of mammoths

Tom van der Valk et al.

Summary: This study reveals the presence of two distinct mammoth lineages in eastern Siberia during the Early Pleistocene, with one lineage giving rise to the woolly mammoth and another representing an unrecognized lineage ancestral to the first mammoths to colonize North America. Additionally, the study shows that the Columbian mammoth of North America can trace its ancestry back to a hybridization event between these two lineages during the Middle Pleistocene, with roughly equal admixture proportions. Moreover, the majority of protein-coding changes associated with cold adaptation in woolly mammoths were found to be present as early as one million years ago.

NATURE (2021)

Article Multidisciplinary Sciences

Ivory poaching and the rapid evolution of tusklessness in African elephants

Shane C. Campbell-Staton et al.

Summary: The study found that ivory poaching during the Mozambican Civil War had strong selective pressure on the evolution of African savanna elephants in Gorongosa National Park, resulting in the emergence of tuskless elephants. Genome scans identified two candidate genes (AMELX and MEP1a) related to elephant tooth development, with one gene, AMELX, associated with human tooth growth.

SCIENCE (2021)

Review Oncology

Advances in the DNA methylation hydroxylase TET1

Wenzheng Liu et al.

Summary: TET1 is a crucial demethylation protein, playing important roles in maintaining genomic methylation homeostasis and pluripotency of stem cells. Its functions in different tumors are still under investigation.

BIOMARKER RESEARCH (2021)

Article Biochemistry & Molecular Biology

Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses

Marc Tollis et al.

Summary: Disease susceptibility and resistance are crucial for the conservation of endangered species like elephants. Research found that Asian elephants are more prone to tumors and malignancies compared to African elephants, and show higher susceptibility to tuberculosis and elephant endotheliotropic herpesvirus. Genetic regulation plays a significant role in the differential inflammatory response between Asian and African elephants, leading to increased susceptibility to infectious diseases and cancer in Asian elephants.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Review Neurosciences

Pain behavior in SCN9A (Nav1.7) and SCN10A (Nav1.8) mutant rodent models

Yaping Xue et al.

Summary: The review summarizes the findings from rodent models with Scn9a and Scn10a gene mutations, showing that loss-of-function or knockout of these genes decrease pain sensitivity, while certain mutations can lead to painful small fiber neuropathy. Future research on these mutations in preclinical models can provide insights into the impact of these mutations on pain.

NEUROSCIENCE LETTERS (2021)

Article Geography, Physical

Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

Marianne Dehasque et al.

Summary: This study combined radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. Mammoths disappeared on the eastern Siberian mainland before the Younger Dryas, but persisted in the northernmost parts of central and western Siberia until the early Holocene. Genetic results support the hypothesis that mammoths recolonized Wrangel Island from a central and/or west-Siberian population and lived there for about 6000 years before going extinct around 4000 years ago.

QUATERNARY SCIENCE REVIEWS (2021)

Article Biochemistry & Molecular Biology

MEGA11 Molecular Evolutionary Genetics Analysis Version 11

Koichiro Tamura et al.

Summary: MEGA software, a mature tool for computational molecular evolution, has been enhanced with new additions for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. These additions include methods for estimating divergence times, confidence intervals, and new options for tagging sequences with spatiotemporal sampling information. The enhancements aim to improve user experience, result quality, and the pace of biological discovery.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Review Biochemistry & Molecular Biology

Deimination and Peptidylarginine Deiminases in Skin Physiology and Diseases

Marie-Claire Mechin et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Immunology

Siglec-14 Enhances NLRP3-Inflammasome Activation in Macrophages

Chih-Ming Tsai et al.

JOURNAL OF INNATE IMMUNITY (2020)

Review Ophthalmology

RP1L1 and inherited photoreceptor disease: A review

Nicole C. L. Noel et al.

SURVEY OF OPHTHALMOLOGY (2020)

Article Geochemistry & Geophysics

THE INTCAL20 NORTHERN HEMISPHERE RADIOCARBON AGE CALIBRATION CURVE (0-55 CAL KBP)

Paula J. Reimer et al.

RADIOCARBON (2020)

Review Cell Biology

Versican: A Dynamic Regulator of the Extracellular Matrix

Shamima Islam et al.

JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY (2020)

Article Multidisciplinary Sciences

TET1 is a beige adipocyte-selective epigenetic suppressor of thermogenesis

Sneha Damal Villivalam et al.

NATURE COMMUNICATIONS (2020)

Article Audiology & Speech-Language Pathology

Hearing loss and brain abnormalities due to pathogenic mutations in ADGRV1 gene: a case report

Flavio Faletra et al.

HEARING BALANCE AND COMMUNICATION (2020)

Article Multidisciplinary Sciences

Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus)

Zeshan Lin et al.

SCIENCE (2019)

Article Biochemistry & Molecular Biology

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas

Tom van der Valk et al.

CURRENT BIOLOGY (2019)

Article Endocrinology & Metabolism

Investigating the link of ACAD10 deficiency to type 2 diabetes mellitus

Kaitlyn Bloom et al.

JOURNAL OF INHERITED METABOLIC DISEASE (2018)

Review Cell & Tissue Engineering

Medical application of glycosaminoglycans: a review

Alexander Koewitsch et al.

JOURNAL OF TISSUE ENGINEERING AND REGENERATIVE MEDICINE (2018)

Article Gastroenterology & Hepatology

Genetic Variants Associated With Obesity and Insulin Resistance in Hispanic Boys With Nonalcoholic Fatty Liver Disease

John C. Rausch et al.

JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION (2018)

Article Multidisciplinary Sciences

A comprehensive genomic history of extinct and living elephants

Eleftheria Palkopoulou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Review Genetics & Heredity

Netherton Syndrome: A Genotype-Phenotype Review

Constantina A. Sarri et al.

MOLECULAR DIAGNOSIS & THERAPY (2017)

Article Genetics & Heredity

Excess of genomic defects in a woolly mammoth on Wrangel island

Rebekah L. Rogers et al.

PLOS GENETICS (2017)

Article Genetics & Heredity

Mutations in Three Genes Encoding Proteins Involved in Hair Shaft Formation Cause Uncombable Hair Syndrome

F. Buket U. Basmanav et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2016)

Review Biology

Adaptations to polar life in mammals and birds

Arnoldus Schytte Blix

JOURNAL OF EXPERIMENTAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

Eleftheria Palkopoulou et al.

CURRENT BIOLOGY (2015)

Article Developmental Biology

Expression of multiple formins in adult tissues and during developmental stages of mouse brain

Priyanka Dutta et al.

GENE EXPRESSION PATTERNS (2015)

Article Biochemistry & Molecular Biology

Exome sequencing reveals a nonsense mutation in TEX15 causing spermatogenic failure in a Turkish family

Ozlem Okutman et al.

HUMAN MOLECULAR GENETICS (2015)

Article Dentistry, Oral Surgery & Medicine

Genetic Association of ARHGAP21 Gene Variant with Mandibular Prognathism

L. Perillo et al.

JOURNAL OF DENTAL RESEARCH (2015)

Article Multidisciplinary Sciences

Evolution and dispersal of mammoths across the Northern Hemisphere

A. M. Lister et al.

SCIENCE (2015)

Article Multidisciplinary Sciences

Dissection of keratin network formation, turnover and reorganization in living murine embryos

Nicole Schwarz et al.

SCIENTIFIC REPORTS (2015)

Article Cell Biology

Expression of Human Skin-Specific Genes Defined by Transcriptomics and Antibody-Based Profiling

Per-Henrik D. Edqvist et al.

JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

ANGSD: Analysis of Next Generation Sequencing Data

Thorfinn Sand Korneliussen et al.

BMC BIOINFORMATICS (2014)

Review Cell Biology

To grow or not to grow: Hair morphogenesis and human genetic hair disorders

Olivier Duverger et al.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2014)

Article Multidisciplinary Sciences

PARP-14 Binds Specific DNA Sequences to Promote Th2 Cell Gene Expression

Jonathan P. Riley et al.

PLOS ONE (2013)

Review Cell Biology

Pleiotropic effects of coat colour-associated mutations in humans, mice and other mammals

Monika Reissmann et al.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2013)

Article Genetics & Heredity

Molecular evolution of immunoglobulin superfamily genes in primates

Hitoshi Ohtani et al.

IMMUNOGENETICS (2011)

Article Multidisciplinary Sciences

Inference of human population history from individual whole-genome sequences

Heng Li et al.

NATURE (2011)

Article Immunology

Unique activation status of peripheral blood mononuclear cells at acute phase of Kawasaki disease

K. Ikeda et al.

CLINICAL AND EXPERIMENTAL IMMUNOLOGY (2010)

Article Cell Biology

Increased basal insulin secretion in Pdzd2-deficient mice

S. W. Tsang et al.

MOLECULAR AND CELLULAR ENDOCRINOLOGY (2010)

Article Biochemistry & Molecular Biology

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

Adrian W. Briggs et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Piccolo and bassoon maintain synaptic vesicle clustering without directly participating in vesicle exocytosis

Konark Mukherjee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Ecology

Adaptation genomics: the next generation

Jessica Stapley et al.

TRENDS IN ECOLOGY & EVOLUTION (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Eran Eden et al.

BMC BIOINFORMATICS (2009)

Article Geochemistry & Geophysics

BAYESIAN ANALYSIS OF RADIOCARBON DATES

Christopher Bronk Ramsey

RADIOCARBON (2009)

Review Cell Biology

CD1d presentation of glycolipids

Anneliese O. Speak et al.

IMMUNOLOGY AND CELL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Rapid evolution by positive darwinian selection in t-cell antigen CD4 in primates

Zhengdong D. Zhang et al.

JOURNAL OF MOLECULAR EVOLUTION (2008)

Review Neurosciences

From chills to chilis: mechanisms for thermosensation and chemesthesis via thermoTRPs

Michael Bandell et al.

CURRENT OPINION IN NEUROBIOLOGY (2007)

Article Multidisciplinary Sciences

Sensory neuron sodium channel Nav1.8 is essential for pain at low temperatures

Katharina Zimmermann et al.

NATURE (2007)

Article Endocrinology & Metabolism

Fidgetin-like 1 gene inhibited by basic fibroblast growth factor regulates the proliferation and differentiation of osteoblasts

Su Jin Park et al.

JOURNAL OF BONE AND MINERAL RESEARCH (2007)

Review Biochemistry & Molecular Biology

Mechanisms of cold pain

Thomas Foulkes et al.

CHANNELS (2007)

Article Allergy

Loss-of-function variations within the filaggrin gene predispose for atopic dermatitis with allergic sensitizations

Stephan Weidinger et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2006)

Article Multidisciplinary Sciences

Architecture of mammalian fatty acid synthase at 4.5 Å resolution

T Maier et al.

SCIENCE (2006)

Article Multidisciplinary Sciences

Heat activation of TRPM5 underlies thermal sensitivity of sweet taste

K Talavera et al.

NATURE (2005)

Article Genetics & Heredity

A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size

J Bond et al.

NATURE GENETICS (2005)

Article Medicine, Research & Experimental

Hush puppy: A new mouse mutant with pinna, ossicle, and inner ear defects

H Pau et al.

LARYNGOSCOPE (2005)

Review Oncology

BRCA1 and BRCA2:: 1994 and beyond

SA Narod et al.

NATURE REVIEWS CANCER (2004)

Article Biochemistry & Molecular Biology

The Rapp-Hodgkin syndrome results from mutations of the TP63 gene

G Bougeard et al.

EUROPEAN JOURNAL OF HUMAN GENETICS (2003)

Article Biochemistry & Molecular Biology

SIFT: predicting amino acid changes that affect protein function

PC Ng et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Genetics & Heredity

The chicken CD4 gene has remained conserved in evolution

R Koskinen et al.

IMMUNOGENETICS (2002)