| 1. |
- Balint, Miklos, et al.
(författare)
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Environmental DNA time series in ecology
- 2018
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Ingår i: Trends in Ecology & Evolution. - London : Elsevier. - 0169-5347 .- 1872-8383. ; 33:12, s. 945-957
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Forskningsöversikt (refereegranskat)abstract
- Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.
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| 2. |
- Bálint, Miklós, et al.
(författare)
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Millions of reads, thousands of taxa : microbial community structure and associations analyzed via marker genes
- 2016
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Ingår i: FEMS Microbiology Reviews. - : Oxford University Press (OUP). - 0168-6445 .- 1574-6976. ; 40:5, s. 686-700
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Tidskriftsartikel (refereegranskat)abstract
- With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.
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| 3. |
- Danev, Danyo, 1973-, et al.
(författare)
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Multiple Access Adder Channel
- 2007
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Ingår i: Multiple Access Channels - Theory and Practice. - Amsterdam : IOS Press. - 9781586037284 - 1586037285 ; , s. 26-53
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- While multiple-access communication dates back to systems invented in the 1870's to transmit simultaneous data through a single wire, the foundation of the discipline now known as 'multiuser information theory' was laid in 1961, when Claude E. Shannon published his paper on two-way channels. Since then, multiuser information theory has been an extremely active research area, and has seen a large number of fundamental contributions, covering, besides the two-way channel studied in, multiple access, interference, broadcast, and wiretap channels. However, several key canonical problems have defied many efforts. This book brings together leading experts working in the fields of information theory, coding theory, multiple user communications, discrete mathematics, etc., who survey recent and general results on multiple-access channels (rate regions, rate splitting, etc.), and give an overview of the problems of current CDMA solutions (fading channels, multi-user detection, multiple-antenna systems, iterative joint decoding, OFDMA, etc.). This publication consist of three parts. The first part includes chapters devoted to the information-theoretical aspects of multiple-access communication. In the second part, multiple-access techniques are discussed and the third part of this volume covers coding techniques
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| 4. |
- Formenti, Giulio, et al.
(författare)
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The era of reference genomes in conservation genomics
- 2022
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Ingår i: Trends in Ecology & Evolution. - : Elsevier. - 0169-5347 .- 1872-8383. ; 37:3, s. 197-202
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
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| 5. |
- Lewin, Harris A., et al.
(författare)
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The Earth BioGenome Project 2020 : Starting the clock
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Magyari, Eniko K., et al.
(författare)
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Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 66-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site. Results: We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact. Conclusion: Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect. This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species.
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| 7. |
- Theissinger, Kathrin, et al.
(författare)
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How genomics can help biodiversity conservation
- 2023
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Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 39:7, s. 545-559
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Forskningsöversikt (refereegranskat)abstract
- The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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