Nature, Год журнала: 2024, Номер 636(8042), С. 296 - 298
Опубликована: Дек. 10, 2024
DNA recovered from ancient remains is transforming our understanding of organisms and ecosystems tens, thousands even millions years ago – but the growing volume data must be better preserved.
Язык: Английский
Molecular Biology and Evolution, Год журнала: 2025, Номер 42(4)
Опубликована: Апрель 1, 2025
Abstract The genomic study of specimens dating to the Early and Middle Pleistocene (EP MP), a period spanning from 2.6 million years ago (Ma) 126 thousand (ka), has potential elucidate evolutionary processes that shaped present-day biodiversity. Obtaining data this is challenging, but mitochondrial DNA, given its higher abundance compared nuclear could play an important role understand at time scale. In study, we report 34 new mitogenomes, including two EP nine MP mammoth (Mammuthus spp.) Siberia North America analyze them jointly with >200 publicly available mitogenomes reconstruct transect mitogenome diversity throughout last years. We find our fall outside all Late (LP) mammoths, while those derived mammoths are basal LP Clades 2 3, supporting ancient Siberian origin these lineages. contrast, geographical Clade 1 remains unresolved. With deep-time observe diversification events across clades appear consistent previously hypothesized demographic changes. Furthermore, improve upon existing methodology for molecular clock >50 ka, demonstrating need be individually dated avoid biases in their age estimates. Both analytical improvements presented here highlight importance discover long-lost genetic diversity, enabling better assessments histories.
Язык: Английский
Процитировано
0
Опубликована: Янв. 1, 2025
Язык: Английский
Процитировано
0
Trends in Ecology & Evolution, Год журнала: 2025, Номер unknown
Опубликована: Май 1, 2025
Язык: Английский
Процитировано
0
Advanced Science, Год журнала: 2025, Номер unknown
Опубликована: Май 19, 2025
Abstract Nucleic acid‐based cryptographic approaches are an innovative emerging field for information process. However, the poor reproducibility and interference from bioenvironment of existing decryption led to different binary translation according fixed threshold defined by “Sender”, which seriously affects authenticity during message communication. Here, a programmed DNA constitutional dynamic network (CDN)‐derived adaptive is shown, difference value two groups output patterns CDN. Under external stimuli, generated patterns, avoids contrary slight on under threshold. Importantly, there self‐calibrating in each group total concentration constituents CDN system constant, greatly eliminates data error. The accompanied computational simulation, can predict at states. used control orthogonal cascaded nanoparticle‐based molecular amplifiers expand volume transmitting message, as well allow accurate specific sensing DNA. Various state‐of‐the‐art representation demonstrated coding decoding types messages.
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июль 1, 2024
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding features this animal class that other terrestrial vertebrates. The need for genomic resources is more urgent than ever due to increasing threats group. are one most imperiled taxonomic groups, with approximately 41% species threatened extinction habitat loss, changes in land use patterns, disease, climate change, synergistic effects. Amphibian have provided better ontogenetic diversity, tissue regeneration, life history reproductive modes, antipredator strategies, resilience adaptive responses. They also serve as essential models studying broad traits, such evolutionary genome expansions contractions, they exhibit widest range sizes among all taxa possess multiple mechanisms genetic sex determination. Despite these features, sequencing amphibians has significantly lagged behind vertebrates, primarily challenges assembling large, repeat-rich genomes relative lack societal support. emergence long-read technologies, combined advanced molecular computational techniques improve scaffolding reduce workloads, now making it possible address some challenges. To promote accelerate production research international coordination collaboration, we launched Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) early 2023. This burgeoning community already 282 members from 41 countries. AGC aims leverage capabilities its advance bridge implementation gap biologists, bioinformaticians, conservation practitioners. Here evaluate state field genomics, highlight previous studies, present overcome, call on communities unite part enable "leap" next level.
Язык: Английский
Процитировано
3
Elsevier eBooks, Год журнала: 2024, Номер unknown, С. 673 - 690
Опубликована: Фев. 24, 2024
Язык: Английский
Процитировано
2
Quaternary Science Reviews, Год журнала: 2024, Номер 331, С. 108650 - 108650
Опубликована: Апрель 11, 2024
Climate seasonality critically influences the functioning and dynamics of ecosystems in continental areas. The ecological importance winter temperatures on high-latitude vegetation changes has recently been argued to be largely overlooked comparison summer temperatures. Oymyakon region from eastern Siberia, with its strong continentality extremely cold winters moderately warm summers, is ideally suited study response past seasonal temperature based long time-series. However, few paleorecords are available this area. history regional glacial activity potential plant refugia since Marine Isotope Stage (MIS) 3 not well understood. Here, we present geochemical DNA metabarcoding records retrieved a sediment core Lake Ulu region, which provides detailed information glacier over last 43 cal. ka BP. Our results suggest that fluctuations were primarily driven by insolation, was likely initiated retreat during MIS 3. catchment experienced multiple advance/retreat cycles until Last Glacial Maximum, glaciers fully retreated 20 In addition, tundra-steppe landscape dominated Dryas, Papaver, Saliceae, Anthemideae occupied for most time began collapse around 19 BP following expansion trees shrubs such as Larix, Betula, Alnus, Vaccinium. Postglacial assemblages exhibit high sensitivity variations, minimal impact This can explained dominance insolation amplitude, extreme continentality, extended growing season, genetic adaptation cold. Notably, our ancient record show earliest postglacial larch Siberia (around 18.6 BP), related presence local refugia. implies may one sources recolonization more research should implemented provide insights into migration, better predict future scenarios Siberian forests.
Язык: Английский
Процитировано
1
Trends in Microbiology, Год журнала: 2024, Номер unknown
Опубликована: Окт. 1, 2024
In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges opportunities for studying ancient environmental microbiomes (AEMs). a field currently reliant on several assumptions, discuss theoretical empirical feasibility recovering microbial nucleic acids (NAs) from permafrost varying degrees antiquity. We also summarize contamination control best practices highlight considerations latest approaches, including shotgun metagenomics, downstream bioinformatic authentication approaches. review adoption existing software provide an overview more recently published programs, reference to their suitability AEM studies. Finally, outstanding likely future directions research.
Язык: Английский
Процитировано
1
BMC Genomics, Год журнала: 2024, Номер 25(1)
Опубликована: Ноя. 1, 2024
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding features this animal class that other terrestrial vertebrates. The need for genomic resources is more urgent than ever due to increasing threats group. are one most imperiled taxonomic groups, with approximately 41% species threatened extinction habitat loss, changes in land use patterns, disease, climate change, synergistic effects. Amphibian have provided better ontogenetic diversity, tissue regeneration, life history reproductive modes, anti-predator strategies, resilience adaptive responses. They also serve as essential models studying broad traits, such evolutionary genome expansions contractions, they exhibit widest range sizes among all taxa possess multiple mechanisms genetic sex determination. Despite these features, sequencing amphibians has significantly lagged behind vertebrates, primarily challenges assembling large, repeat-rich genomes relative lack societal support. emergence long-read technologies, combined advanced molecular computational techniques improve scaffolding reduce workloads, now making it possible address some challenges. To promote accelerate production research international coordination collaboration, we launched Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) early 2023. This burgeoning community already 282 members from 41 countries. AGC aims leverage capabilities its advance bridge implementation gap biologists, bioinformaticians, conservation practitioners. Here evaluate state field genomics, highlight previous studies, present overcome, call on communities unite part enable "leap" next level.
Язык: Английский
Процитировано
1
Palaeogeography Palaeoclimatology Palaeoecology, Год журнала: 2024, Номер 640, С. 112090 - 112090
Опубликована: Фев. 13, 2024
Antarctica is one of the most susceptible regions to climate change on Earth. Rising ocean temperatures, glacier melting, and disruptions marine ecosystems make this polar region a focus research ecosystem transformation associated with ongoing change. Within Antarctic ecosystem, diatoms, key group phytoplankton at base food web, play crucial role in maintaining balance functioning. Conventionally, fossil diatom assemblages have been investigated sediment records reconstruct paleoenvironmental conditions understand patterns Antarctica. Recently, application ancient DNA techniques sediments (sedimentary DNA, sedaDNA) has provided new insights into community responses environmental over geological time scales. One benefit sedaDNA analysis that technique can detect fragile species do not preserve well are thus difficult study via traditional microscopy techniques. In paper, we review importance diatoms as indicators change, novel use assist reconstruction, challenges promises using approach . We propose Fragilariopsis cylindrus, an extant species, ideal model organism adaptation changing due its ecological success through availability whole-genome information for species. Novel genetic obtainable from F. other will help us better predict evolutionary adaptive dynamics important primary producers climatically vulnerable region.
Язык: Английский
Процитировано
0