4.7 Article

Ancient DNA is preserved in fish fossils from tropical lake sediments

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Anthropology

Ancient DNA sequence quality is independent of fish bone weight

Lane M. Atmore et al.

Summary: This study evaluates the capacity of retrieving ancient DNA from small archaeological remains and finds no significant relationship between bone weight and DNA extraction success, content, or complexity. The results suggest that even minute bones can yield positive results, expanding the range of specimens suitable for aDNA analysis.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2023)

Article Geography, Physical

A chronologically reliable record of 17,000 years of biomass burning in the Lake Victoria area

Yunuen Temoltzin-Loranca et al.

Summary: This study provides insights into the fire regime changes and long-term vegetation dynamics in Lake Victoria over the past 17,000 years by using 14C dating of sediment cores. The results suggest that climate and vegetation play significant roles in shaping the fire regime, which can inform ecosystem management and conservation strategies.

QUATERNARY SCIENCE REVIEWS (2023)

Article Multidisciplinary Sciences

A continuous fish fossil record reveals key insights into adaptive radiation

Nare Ngoepe et al.

Summary: Adaptive radiations play a crucial role in generating biodiversity, but the relative importance of species' ecological versatility and arrival order in determining which lineage radiates is still unclear. Through analyzing the fossil record of cichlid fishes in Lake Victoria, it was found that their ecological versatility was key to their persistence in new habitats, suggesting that it played a major role in adaptive radiation.

NATURE (2023)

Article Multidisciplinary Sciences

A continuous fish fossil record reveals key insights into adaptive radiation

Nare Ngoepe et al.

Summary: This study presents a continuous fossil record showing how haplochromine cichlids came to dominate the fish fauna of Lake Victoria in Africa.

NATURE (2023)

Review Ecology

An integrative paleolimnological approach for studying evolutionary processes

Maria Cuenca-Cambronero et al.

Summary: The field of paleolimnology has made significant progress in reconstructing past environmental conditions of aquatic ecosystems based on sediment records. Advances in molecular technologies have further enhanced the understanding of evolutionary processes and species diversification over long timescales. Integrative use of paleolimnological, paleogenetic, and molecular approaches provides important insights into ecological and evolutionary responses of species and communities to environmental change.

TRENDS IN ECOLOGY & EVOLUTION (2022)

Review Ecology

Ancient and historical DNA in conservation policy

Evelyn L. Jensen et al.

Summary: Genetic diversity, including ancient and historical DNA, plays a crucial role in biodiversity conservation. However, it has not been adequately incorporated into conservation policies and regulations. Utilizing genetic information from ancient and historical specimens can help resolve key conservation issues and assist countries in meeting their obligations under the Convention on Biological Diversity (CBD).

TRENDS IN ECOLOGY & EVOLUTION (2022)

Article Multidisciplinary Sciences

Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics

Lane M. Atmore et al.

Summary: This study evaluates the past impacts of humans on the marine environment by studying the long-term population dynamics of Baltic herring. The research demonstrates the joint impact of climate change and human exploitation on marine species and highlights the role of historical ecology in conservation and management policies.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species

Tabitha Blackwell et al.

Summary: In this study, newly discovered evolutionarily significant populations of Korogwe tilapia from southern Tanzania are threatened by hybridization with invasive Nile tilapia. Genetic analysis shows distinct differences between southern and northern populations of O. korogwe, with evidence of hybrids in southern lakes. This highlights the need for conservation interventions to protect these unique genetic resources.

MOLECULAR ECOLOGY (2021)

Article Biochemistry & Molecular Biology

Ancient and modern stickleback genomes reveal the demographic constraints on adaptation

Melanie Kirch et al.

Summary: The study used paleogenomics to compare ancient and modern stickleback populations, finding that modern lake populations have incomplete adaptation to freshwater, likely due to founder effects, drift, and selection reducing ancestral variation in the founder populations.

CURRENT BIOLOGY (2021)

Article Anthropology

The preservation of ancient DNA in archaeological fish bone

Giada Ferrari et al.

Summary: The majority of archaeological sites yield high levels of endogenous DNA, depending on excavation site and pre-extraction treatment. Balancing library preparation success and levels of endogenous DNA can be achieved through alternative extraction strategies.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2021)

Article Environmental Sciences

Paleoecological evidence for a multi-trophic regime shift in a perialpine lake (Lake Joux, Switzerland)

Marie-Eve Monchamp et al.

Summary: Freshwater ecosystems are facing new and increasing threats from human activities. This study used paleoecological records to track ecological transitions over decadal to millennial timescales, identifying a regime shift in Lake Joux triggered by rapid cultural eutrophication in the 1950s. Despite decades of restoration efforts, the biotic communities in Lake Joux have not returned to their pre-disturbance composition due to other confounding factors such as climate warming.

ANTHROPOCENE (2021)

Article Ecology

Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

Lourdes Martinez-Garcia et al.

Summary: This study investigated the genetic diversity of ancient and modern Atlantic cod populations, finding little evidence of significant mitogenomic changes over time. The results suggest that historical events and gene flow play a key role in shaping the mitogenomic variation in Atlantic cod, while anthropogenic pressures such as commercial fisheries have minimal impact on genetic diversity.

FRONTIERS IN ECOLOGY AND EVOLUTION (2021)

Article Evolutionary Biology

Unlocking the potential of ancient fish DNA in the genomic era

Tom Oosting et al.

EVOLUTIONARY APPLICATIONS (2019)

Article Multidisciplinary Sciences

Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains

Albina Hulda Palsdottir et al.

ROYAL SOCIETY OPEN SCIENCE (2019)

Article Geography, Physical

Diagenesis of archaeological bone and tooth

Christopher Kendall et al.

PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY (2018)

Article Biology

Arrival order and release from competition does not explain why haplochromine cichlids radiated in Lake Victoria

Moritz Muschick et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2018)

Article Multidisciplinary Sciences

Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation

Roseina Woods et al.

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

Article Evolutionary Biology

Evolutionary Patterns and Processes: Lessons from Ancient DNA

Michela Leonardi et al.

SYSTEMATIC BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase

Marie-Theres Gansauge et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

A new model for ancient DNA decay based on paleogenomic meta-analysis

Logan Kistler et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biology

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum

Christian Kehlmaier et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Article Multidisciplinary Sciences

Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Gemma G. R. Murray et al.

SCIENCE (2017)

Article Multidisciplinary Sciences

Ancient hybridization fuels rapid cichlid fish adaptive radiations

Joana I. Meier et al.

NATURE COMMUNICATIONS (2017)

Article Multidisciplinary Sciences

Climate warming reduces fish production and benthic habitat in Lake Tanganyika, one of the most biodiverse freshwater ecosystems

Andrew S. Cohen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Biochemical Research Methods

Reducing microbial and human contamination in DNA extractions from ancient bones and teeth

Petra Korlevic et al.

BIOTECHNIQUES (2015)

Article Multidisciplinary Sciences

Biology in the Anthropocene: Challenges and insights from young fossil records

Susan M. Kidwell

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Editorial Material Multidisciplinary Sciences

BREAKING A TROPICAL TABOO

Lizzie Wade

SCIENCE (2015)

Review Ecology

Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene

Courtney A. Hofman et al.

TRENDS IN ECOLOGY & EVOLUTION (2015)

Article Anthropology

Methodological strategies to assess the degree of bone preservation for ancient DNA studies

Gabriele Scorrano et al.

ANNALS OF HUMAN BIOLOGY (2015)

Review Biochemistry & Molecular Biology

The future of ancient DNA: Technical advances and conceptual shifts

Michael Hofreiter et al.

BIOESSAYS (2015)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biology

Ancient DNA and the tropics: a rodent's tale

Tania A. Gutierrez-Garcia et al.

BIOLOGY LETTERS (2014)

Article Biodiversity Conservation

Use of Ancient Sedimentary DNA as a Novel Conservation Tool for High-Altitude Tropical Biodiversity

Sanne Boessenkool et al.

CONSERVATION BIOLOGY (2014)

Article Multidisciplinary Sciences

Fifty thousand years of Arctic vegetation and megafaunal diet

Eske Willerslev et al.

NATURE (2014)

Article Multidisciplinary Sciences

The genomic substrate for adaptive radiation in African cichlid fish

David Brawand et al.

NATURE (2014)

Article Multidisciplinary Sciences

Recent Warming of Lake Kivu

Sergei Katsev et al.

PLOS ONE (2014)

Article Biochemical Research Methods

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Hakon Jonsson et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

Marie-Theres Gansauge et al.

NATURE PROTOCOLS (2013)

Article Geochemistry & Geophysics

INTCAL13 AND MARINE13 RADIOCARBON AGE CALIBRATION CURVES 0-50,000 YEARS CAL BP

Paula J. Reimer et al.

RADIOCARBON (2013)

Article Cell Biology

Ancient DNA Damage

Jesse Dabney et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2013)

Article Multidisciplinary Sciences

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

Paul Brotherton et al.

NATURE COMMUNICATIONS (2013)

Article Anatomy & Morphology

DNA in ancient bone - Where is it located and how should we extract it?

Paula F. Campos et al.

ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER (2012)

Article Biochemistry & Molecular Biology

Convergent Evolution within an Adaptive Radiation of Cichlid Fishes

Moritz Muschick et al.

CURRENT BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Martin Kircher et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

Susanna Sawyer et al.

PLOS ONE (2012)

Article Biology

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

Morten E. Allentoft et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012)

Article Geography, Physical

Fish fossils as paleo-indicators of ichthyofauna composition and climatic change in Lake Malawi, Africa

Peter N. Reinthal et al.

PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY (2011)

Article Geography, Physical

High-resolution 14C dating of a 25,000-year lake-sediment record from equatorial East Africa

Maarten Blaauw et al.

QUATERNARY SCIENCE REVIEWS (2011)

Review Ecology

Conservation paleobiology: putting the dead to work

Gregory P. Dietl et al.

TRENDS IN ECOLOGY & EVOLUTION (2011)

Article Biochemical Research Methods

Fast and accurate long-read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Geography, Physical

Methods and code for 'classical' age-modelling of radiocarbon sequences

Maarten Blaauw

QUATERNARY GEOCHRONOLOGY (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts

Christine E. King et al.

BIOTECHNIQUES (2009)

Article Multidisciplinary Sciences

Half-precessional dynamics of monsoon rainfall near the East African Equator

Dirk Verschuren et al.

NATURE (2009)

Article Biology

Is amino acid racemization a useful tool for screening for ancient DNA in bone?

Matthew J. Collins et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2009)

Article Paleontology

Environment and excavation: Pre-lab impacts on ancient DNA analyses

Ruth Bollongino et al.

COMPTES RENDUS PALEVOL (2008)

Article Multidisciplinary Sciences

Freshly excavated fossil bones are best for amplification of ancient DNA

Melanie Pruvost et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biology

Invasion of an asexual American water flea clone throughout Africa and rapid displacement of a native sibling species

Joachim Mergeay et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)

Article Multidisciplinary Sciences

Out of the tropics: Evolutionary dynamics of the latitudinal diversity gradient

David Jablonski et al.

SCIENCE (2006)

Review Biology

African cichlid fish: a model system in adaptive radiation research

Ole Seehausen

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)

Article Biochemical Research Methods

A fast and symmetric DUST implementation to mask low-complexity DNA sequences

Aleksandr Morgulis et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2006)

Review Biotechnology & Applied Microbiology

Damage and repair of ancient DNA

D Mitchell et al.

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS (2005)

Article Limnology

A novel chemical method to quantify fish debris in marine sediments

SJ Schenau et al.

LIMNOLOGY AND OCEANOGRAPHY (2000)