scholarly journals Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

2015 ◽  
Vol 370 (1660) ◽  
pp. 20130374 ◽  
Author(s):  
Federico Sánchez-Quinto ◽  
Carles Lalueza-Fox
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Complete Mitochondrial Genome ◽  
Modern Human ◽  
Small Population ◽  
High Coverage ◽  
Spatial And Temporal Scales ◽  
Hybridization Capture ◽  
Sequencing Technologies

Nearly two decades since the first retrieval of Neanderthal DNA, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a Neanderthal and a Denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the Neanderthal lineage. This genomic information, coupled with diversity exome data from several Neanderthal specimens is shedding new light on evolutionary processes such as the genetic basis of Neanderthal and modern human-specific adaptations—including morphological and behavioural traits—as well as the extent and nature of the admixture events between them. An emerging picture is that Neanderthals had a long-term small population size, lived in small and isolated groups and probably practised inbreeding at times. Deleterious genetic effects associated with these demographic factors could have played a role in their extinction. The analysis of DNA from further remains making use of new large-scale hybridization-capture-based methods as well as of new approaches to discriminate contaminant DNA sequences will provide genetic information in spatial and temporal scales that could help clarify the Neanderthal's—and our very own—evolutionary history.

scholarly journals Identifying global synchronies in marine zooplankton populations: issues and opportunities

2004 ◽  
Vol 61 (4) ◽  
pp. 445-456 ◽  
Author(s):  
R.Ian Perry ◽  
Harold P Batchelder ◽  
David L Mackas ◽  
Sanae Chiba ◽  
Edward Durbin ◽  
...  
Keyword(s):  
Large Scale ◽  
International Comparisons ◽  
Data Access ◽  
Ecosystem Change ◽  
Data Sets ◽  
Time Lags ◽  
Structural Constraints ◽  
Spatial And Temporal Scales ◽  
Marine Zooplankton

Abstract Analyses of the influences of climate variability on local zooplankton populations and those within ocean basins are relatively recent (past 5–10 years). What is lacking are comparisons of zooplankton population variability among the world's oceans, in contrast to such global comparisons of fish populations. This article examines the key questions, capabilities, and impediments for global comparisons of zooplankton populations using long-term (>10 year) data sets. The key question is whether global synchronies in zooplankton populations exist. If yes, then (i) to what extent are they driven by “bottom-up” (productivity) or “top-down” (predation) forcing; (ii) are they initiated by persistent forcing or by episodic events whose effects propagate through the system with different time-lags; and (iii) what proportion of the biological variance is caused directly by physical forcing and what proportion might be caused by non-linear instabilities in the biological dynamics (e.g. through trophodynamic links)? The capabilities are improving quickly that will enable global comparisons of zooplankton populations. Several long-term sampling programmes and data sets exist in many ocean basins, and the data are becoming more available. In addition, there has been a major philosophical change recently that now recognizes the value of continuing long-term zooplankton observation programmes. Understanding of life-history characteristics and the ecosystem roles of zooplankton are also improving. A first and critical step in exploring possible synchrony among zooplankton from geographically diverse regions is to recognize the limitations of the various data sets. There exist several impediments that must be surmounted before global comparisons of zooplankton populations can be realized. Methodological issues concerned with the diverse spatial and temporal scales of “monitored” planktonic populations are one example. Other problems include data access issues, structural constraints regarding funding of international comparisons, and lack of understanding by decision-makers of the value of zooplankton as indicators of ecosystem change. We provide recommendations for alleviating some of these impediments, and suggest a need for an easily understood example of global synchrony in zooplankton populations and the relation of those signals to large-scale climate drivers.

scholarly journals CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase

2020 ◽  
Author(s):  
Yang Young Lu ◽  
Jiaxing Bai ◽  
Yiwen Wang ◽  
Ying Wang ◽  
Fengzhu Sun
Keyword(s):  
Dna Sequences ◽  
Sequence Comparison ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Practical Interest ◽  
Supplementary Information ◽  
Computationally Efficient ◽  
Sequencing Technologies ◽  
Alignment Free

AbstractMotivationRapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based on k-mer frequencies offers a computationally efficient solution, yet in practice, the k-mer frequency vectors for large k of practical interest lead to excessive memory and storage consumption.ResultsWe report CRAFT, a general genomic/metagenomic search engine to learn compact representations of sequences and perform fast comparison between DNA sequences. Specifically, given genome or high throughput sequencing (HTS) data as input, CRAFT maps the data into a much smaller embedding space and locates the best matching genome in the archived massive sequence repositories. With 102 – 104-fold reduction of storage space, CRAFT performs fast query for gigabytes of data within seconds or minutes, achieving comparable performance as six state-of-the-art alignment-free measures.AvailabilityCRAFT offers a user-friendly graphical user interface with one-click installation on Windows and Linux operating systems, freely available at https://github.com/jiaxingbai/[email protected]; [email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Re-evaluating inheritance in genome evolution: widespread transfer of LINEs between species

2017 ◽  
Author(s):  
Atma M. Ivancevic ◽  
R. Daniel Kortschak ◽  
Terry Bertozzi ◽  
David L. Adelson
Keyword(s):  
Genome Evolution ◽  
Dna Sequences ◽  
Large Scale ◽  
Mobile Dna ◽  
Long Term Effects ◽  
New Host ◽  
Transfer Event ◽  
Blood Sucking ◽  
Foreign Dna

Transposable elements (TEs) are mobile DNA sequences, colloquially known as ‘jumping genes’ because of their ability to replicate to new genomic locations. Given a vector of transfer (e.g. tick or virus), TEs can jump further: between organisms or species in a process known as horizontal transfer (HT). Here we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient HT events. Using a 503-genome dataset, we identify multiple ancient L1 HT events in eukaryotes and provide evidence that L1s infiltrated the mammalian lineage after the monotreme-therian split. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new potential blood-sucking parasite vectors and occurrences in new lineages (e.g. bats, frog). Given that these TEs make up nearly half of the genome sequence in today’s mammals, our results provide the first evidence that HT can have drastic and long-term effects on the new host genomes. This revolutionizes our perception of genome evolution to consider external factors, such as the natural introduction of foreign DNA. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be the first of many large-scale phylogenomic analyses exploring the role of HT in genome evolution.Significance statementLINE-1 (L1) elements occupy about half of most mammalian genomes (1), and they are believed to be strictly vertically inherited (2). Mutagenic L1 insertions are thought to account for approximately 1 of every 1000 random, disease-causing insertions in humans (4-7). Our research indicates that the very presence of L1s in humans, and other therian mammals, is due to an ancient transfer event – which has drastic implications for our perception of genome evolution. Using a machina analyses over 503 genomes, we trace the origins of L1 and BovB retrotransposons across the tree of life, and provide evidence of their long-term impact on eukaryotic evolution.

scholarly journals Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

2017 ◽  
Author(s):  
Raúl Amado Cattáneo ◽  
Luis Diambra ◽  
Andrés Norman McCarthy
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Low Frequency ◽  
Genomic Data ◽  
Data Sets ◽  
High Coverage ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Alignment Free ◽  
Chloroplast Phylogeny

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

scholarly journals Limits of long-term selection against Neandertal introgression

2019 ◽  
Vol 116 (5) ◽  
pp. 1639-1644 ◽  
Author(s):  
Martin Petr ◽  
Svante Pääbo ◽  
Janet Kelso ◽  
Benjamin Vernot
Keyword(s):  
Negative Selection ◽  
Modern Human ◽  
Model Parameters ◽  
Human Populations ◽  
Modern Humans ◽  
High Coverage ◽  
Protein Coding ◽  
The Past ◽  
Wide Range

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.

scholarly journals Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

2017 ◽  
Author(s):  
Raúl Amado Cattáneo ◽  
Luis Diambra ◽  
Andrés Norman McCarthy
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Low Frequency ◽  
Genomic Data ◽  
Data Sets ◽  
High Coverage ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Alignment Free ◽  
Chloroplast Phylogeny

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

Abating pocket gophers (Thomomys spp.) to regenerate forests in clearcuts

1999 ◽  
Vol 26 (1) ◽  
pp. 59-65 ◽  
Author(s):  
K. SHAWN SMALLWOOD
Keyword(s):  
Forest Regeneration ◽  
Large Scale ◽  
Environmental Damage ◽  
Pocket Gophers ◽  
Conifer Seedlings ◽  
Spatial And Temporal Scales ◽  
Population Responses ◽  
Thomomys Bottae ◽  
Surrounding Landscape

Pocket gophers have long suppressed forest regeneration in clearcuts in western North America, despite the application of intensive and costly, large-scale abatement practices, which also kill non-target wildlife and may increase soil erosion. At four national forests in northern California, gophers (Thomomys bottae and T. monticola) on 50 clearcuts were baited with a 0.5% strychnine concentration on wheat or oat groats, which were presented as loose grains or in 1 × 2 cm paraffin pellets for added durability. The various baits and baiting regimes usually reduced gopher abundance by 50-100% within one month. However, gopher populations recovered too quickly to protect seedlings planted for forest regeneration, especially on plots baited with a mechanical burrow-builder. In some plots where abatement was most successful initially, gopher densities increased to levels exceeding those in control plots by 7-13 months later. As gopher populations recovered following abatement, active burrows first appeared at the plot peripheries and advanced toward the plot centres, suggesting that abated territorial residents were replaced by immigrants dispersing from the surrounding landscape.Whereas conventional abatement practices can reduce gopher abundance in clearcuts, the small spatial and temporal scales of application encourage reinvasion of vacated ecological space. These population responses defeat the goal of forest management by increasing gopher density in clearcuts; at the same time the conifer seedlings are vulnerable to gopher predation. Predation of conifer seedlings might be reduced by not abating gophers or by using alternative harvest regimes. These alternative strategies would avoid creating the conditions under which gophers contribute to slowing forest regeneration following timber harvests, and they would avoid the widespread and possibly long-term environmental damage caused by applying acute poisons and by using the burrow-builder.

Climate and Climatological Variations in the Jornada Basin

2006 ◽  
Author(s):  
John Wainright
Keyword(s):  
Spatial Variability ◽  
Time Scales ◽  
Large Scale ◽  
Temporal Scales ◽  
Extreme Rainfall Events ◽  
Spatial And Temporal Scales ◽  
Circulation Patterns ◽  
Jornada Basin ◽  
Instrumental Records

The purpose of this chapter is to review the climatic data for the Jornada Basin over the period for which instrumental records exist. Over this time period, up to 83 years in the case of the Jornada Experimental Range (JER), we can deduce both the long-term mean characteristics and variability on a range of different spatial and temporal scales. Short-term variability is seen in individual rainstorms. Longer-term patterns are controlled spatially by factors such as large-scale circulation patterns and basin and regional orography and temporally by the large-scale fluctuations in atmospheric and oceanic circulation patterns. Variability can have significant impacts on the biogeography of a region (Neilson 1986) or its geomorphic processes (Cooke and Reeves 1976), which may set in motion a series of feedbacks, most important those referring to desertification (Schlesinger et al. 1990; Conley et al. 1992). Understanding the frequency and magnitude of such variability is therefore fundamental in explaining the observed landscape changes in areas such as the Jornada Basin. The patterns observed for different climatic variables within the available instrumental records for the Jornada Basin are defined in a hierarchical series of temporal scales, starting with the patterns that emerge from long-term average conditions and moving to seasonal and monthly, daily, and subdaily time scales. Two further analyses are made because of their potential importance to the hydrological and ecological characteristics of the basin, namely, the occurrence of extreme rainfall events and of longer-term changes. The effects of El Niño events in controlling the rainfall over decadal time scales will be addressed in particular. Spatial variability is an additional important concern, especially when characterizing dryland areas such as the Jornada Basin, where spatial variability tends to be high. The overall climate of the basin can be defined according to the Köppen classification as being cool and arid, belonging to the midlatitude desert zone (BWk). However, interannual variability is important, and occasionally, the annual conditions are more characteristic of the semiarid steppe (BSk) zone. The higher rainfall rates in the higher altitudes of the basin are also more characteristic of semiarid conditions.

PARALLEL ALGORITHMS FOR MAPPING SHORT DEGENERATE AND WEIGHTED DNA SEQUENCES TO A REFERENCE GENOME

2012 ◽  
Vol 23 (02) ◽  
pp. 249-259
Author(s):  
COSTAS S. ILIOPOULOS ◽  
MIRKA MILLER ◽  
SOLON P. PISSIS
Keyword(s):  
Parallel Algorithms ◽  
Dna Sequences ◽  
Message Passing ◽  
Large Scale ◽  
Reference Genome ◽  
Single Experiment ◽  
Sequencing Technologies ◽  
Mapping Process ◽  
Specific Position ◽  
Parallelism Model

One of the most ambitious trends in current biomedical research is the large-scale genomic sequencing of patients. Novel high-throughput (or next-generation) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences (reads) in a single experiment, and with a much lower cost than previously possible. Due to this massive amount of data, efficient algorithms for mapping these sequences to a reference genome are in great demand, and recently, there has been ample work for publishing such algorithms. One important feature of these algorithms is the support of multithreaded parallel computing in order to speedup the mapping process. In this paper, we design parallel algorithms, which make use of the message-passing parallelism model, to address this problem efficiently. The proposed algorithms also take into consideration the probability scores assigned to each base for occurring in a specific position of a sequence. In particular, we present parallel algorithms for mapping short degenerate and weighted DNA sequences to a reference genome.

scholarly journals The limits of long-term selection against Neandertal introgression

2018 ◽  
Author(s):  
Martin Petr ◽  
Svante Pääbo ◽  
Janet Kelso ◽  
Benjamin Vernot
Keyword(s):  
Negative Selection ◽  
Western Europe ◽  
Modern Human ◽  
Model Parameters ◽  
Modern Humans ◽  
High Coverage ◽  
The Past ◽  
Deleterious Alleles ◽  
Wide Range

AbstractSeveral studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans due to deleterious alleles that had accumulated in the Neandertals after they split from the modern human lineage. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45 thousand years. Here we show that this apparent decline is an artifact caused by gene flow between West Eurasians and Africans, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When applying a more robust statistic that takes advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Western Europe over the past 45 thousand years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters, and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular a depletion of Neandertal ancestry in conserved genomic regions that are likely to be of functional importance. Thus, we find that negative selection against Neandertal ancestry has not played as strong a role in recent human evolution as had previously been assumed.

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