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Ancient DNA enables researchers to study the genetics of populations in the past; despite difficulties in its extraction, aDNA reveals that evolution is even more complex than we had imagined.
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... of the decay that occurs with time, there is a limit to how far back aDNA can gaze (Box 1). “Your ideal preservation conditions are something that falls under ice, freezes instantly, and stays frozen until you get it,” says Cooper. “As soon as we get up to 2 million [years ago] we can’t get anything to work, and that’s even under deep-frozen conditions.” But within the past 60,000 years, there are several major evolutionary events that are worth studying—including a glacial maximum around 18,000 years ago, the invasion of the New World by humans about 12,000 years ago, and a global mass extinction about 11,000 years ago. These relatively recent events should be a good model for working out how similar events affected genetic diversity throughout evolutionary history. Cooper’s latest work has analysed DNA from over 400 bison fossils from Beringia—the frozen wastes between eastern Siberia and the Canadian Northwest Territories [3]. “What we’ve done is carbon-date a shitload of bison and get DNA out of them.” It’s the largest aDNA study to date, he says (Figure 1). The icy conditions mean that good quality mitochondrial DNA could be extracted from most of the specimens. The bison could also be dated accurately. This allowed Cooper and his colleagues to trace the changes in the bison genetic diversity from 150,000 years ago to the present. It was even possible to predict the effective population size throughout this period of bison evolution. “Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population’s genetic diversity began to decline dramatically,” they note. This fi nding challenges some common assumptions. It has been argued that modern bison are descended from Beringian bison, but Cooper’s data suggest otherwise. “All modern bison belong to a clade distinct from Beringian bison,” he and his colleagues report. Furthermore, the dramatic decline in the numbers of bison occurs long before humans arrive on the scene, scuppering the idea that hunting pressure was primarily responsible for the demise of the bison. As the glacial maximum approached 18,000 years ago, the cooler, dryer conditions were probably responsible for the downturn in the bison population, argues Cooper. “Climate change is giving the animals an absolute whacking,” he concludes. A similar analysis of brown bear DNA excavated from permafrost and cave deposits in the Arctic is also challenging conventional evolutionary wisdom [4]. Being able to get both a radiocarbon date and some DNA from a specimen pins a particular genetic sequence to a particular moment in time. These data suggest that genetically and geographically distinct groups of bear have replaced each other relatively often during the last 60,000 years. Regional extinctions and replacements seem to be tied to climate change and competition with the much larger short-faced bears, the authors argue (Figure 2). Recent analysis of aDNA from Haast’s eagle has also thrown up a surprising result. This New Zealand giant had a wingspan of up to three metres and a weight of around 14 kilograms, says Michael Bunce, an anthropologist at MacMaster University in Ontario, Canada. Analysis of aDNA from 2,000-year-old specimens indicates that this extinct creature is closely related to the little eagle from Australia and New Guinea, which typically weighs less than one kilogram. The common ancestor of these two eagles lived as recently as 1 million years ago, he and his colleagues estimate [5]. “It means an eagle arrived in New Zealand and increased in (A) Maize cob from the Ocampo Caves in Mexico dated to 3,890 years before the present. aDNA can reveal the selection of traits during early maize domestication that cannot be observed in the fossil record. (B) Examples of modern maize. (Images: [A] Svante Pääbo, Max Planck Institute, [B] Keith Weller, USDA Agriculture Research Service) weight by 10–15 times over this period,” says Bunce. “Such rapid size change is unprecedented in terrestrial vertebrates.” In addition to illuminating these natural events, the study of aDNA can also show changes in the frequency of key genes that occurred during the domestication of crops and animals. For example, aDNA from samples of early maize reveals when certain desirable traits appeared [6]. “It’s the fi rst study of ancient DNA that looks at phenotype,” says Svante Pääbo, an evolutionary anthropologist at the Max Planck Institute in Leipzig, Germany. “One can actually look at specifi c genes that early humans selected during domestication of an important crop.” Pääbo’s analysis suggests that the alleles typical of contemporary maize were already present in Mexican maize 4,400 years ago, so just a couple of thousand years after its initial domestication from the wild grass teosinte (Figure 3). “Quite early on, properties were selected that were not only the structure of the plant but also the biochemistry,” he says. aDNA is also being used to decipher human origins. Mitochondrial DNA from Neanderthals looks quite different from the mitochondrial DNA of early modern humans [7]. This lends support to the hypothesis that modern humans have a “single African origin” rather than the alternative hypothesis of “multiregional evolution”, where the ancestors of modern humans bred with Neanderthals. aDNA could also, in principle, be used to shed light on the evolutionary position of the 18,000-year-old “hobbit” recently unearthed on the Indonesian island of Flores [8]. Both Cooper and Pääbo have offered to have a go at isolating DNA from ...
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... can actually look at specifi c genes that early humans selected during domestication of an important crop." Pääbo's analysis suggests that the alleles typical of contemporary maize were already present in Mexican maize 4,400 years ago, so just a couple of thousand years after its initial domestication from the wild grass teosinte (Figure 3). "Quite early on, properties were selected that were not only the structure of the plant but also the biochemistry," he says. ...
Similar publications
Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will allow more complex and fine-scale inferences about population history than ever before; however, new methods are needed to test complex hypothe...
Citations
... The age of origin of the taxa is given by the 95% highest posterior density intervals (HPD) for the stem group (when it diverged from its sister lineage). The time range between LOWE and MMCO demarcated by the grey rectangle highlights the period of inferred increase in diversification of Eucerinae as suggested by the plot of lineages through time (LTT) depicted in Figure 4. Palaeo-maps on the bottom (Blakey, 2008) In recent decades, several efforts were conducted to improve the placement of fossil taxa in the tree of life, including the obtention of molecular data from fossil specimens (Hofreiter et al., 2001;Nicholls, 2005). Additionally, analytical approaches integrating fossil temporal and morphological information while estimating the phylogeny and divergence times became available, using a tip-dating approach (Ronquist et al., 2012;Zhang et al., 2016). ...
Aim
An antitropical pattern is characterized by the occurrence of closely related taxa south and north of the tropics but absent or uncommonly represented closer to the equator, in contrast to most taxa, which tend to have their highest diversity in the tropical regions. We investigate the antitropical distribution of eucerine bees with the aim of contributing to the characterization and understanding of this pattern.
Location
All continents except Antarctica and Australia.
Taxon
Eucerine bees (Hymenoptera: Apidae: Eucerinae).
Methods
We carried out phylogenomic dating under two different clock models and used multiple strategies to vary matrix composition, evaluating the overlapping of divergence times estimated across models using Bhattacharyya coefficients. Lastly, we reconstructed the biogeographic history of eucerine bees using a Bayesian implementation of the DEC model.
Results
Eucerinae is estimated to have started diversifying during the Palaeocene, with all its tribes originating during the Palaeocene/Eocene transition in southern South America. At least two range expansions happened into North America before the full closure of the Isthmus of Panama. We show that divergence between closely related groups with disjunct distributions would have happened in periods when the climate favoured the expansion of open habitats and became isolated when the forests were re‐established.
Main conclusions
We describe the early diversification of eucerine bees, revealing an intimate association with southern South America. Events of range evolution of Eucerinae were likely affected by periods of global cooling and aridification, and palaeoclimatic and vegetational conditions probably have been more relevant to the formation of the antitropical distribution of Eucerinae than the consolidation of the Isthmus of Panama connecting the Americas. We also demonstrate that most uncertainty in divergence time estimation is not due to the amount of molecular data being used, but more likely other factors like fossil calibrations and violations of clock models.
... Approximately 10% of the alleles found in the 1920-1930 Cumbrian samples are not found in any other population, including the 1970-1990 Cumbrian material, their loss probably being due to one or more bottlenecks in the intervening period. Comparable comparisons of historic and current levels of genetic diversity are rare, probably due to the challenges of working with ancient DNA (Nicholls 2005;Bi et al. 2013;Burrell et al. 2015). However a similar loss of genetic diversity and of particular alleles between historic and present populations has been documented in the African lion (Panthera leo) in the Kavango-Zambezi conservation area (Dures et al. 2019). ...
The Marsh Fritillary butterfly (Euphydryas aurinia) is a Eurasian species which has suffered significant reductions in occurrence and abundance over the past century, particularly across the western side of its range, due to agricultural intensification and habitat loss. This loss has been particularly severe in the UK with extensive localised extinctions. Following sympathetic management, reintroduction was undertaken at four Cumbria (northern UK) sites in 2007 with stock from a captive admixture population descended from Cumbrian and Scottish founders. Annual population monitoring of the reintroductions was undertaken. Nine years post-reintroduction, the level of population genetic variation was assessed using microsatellites. Variation in historical Cumbrian samples was determined using museum samples and Scottish samples from current populations were assayed to characterise natural population variation. Half of the Scottish sites also served as indicators of the alleles present in the founder populations. The genetic contribution of the founder populations allied to population size data allowed patterns of genetic variation to be modelled. Alleles from Cumbrian and Scottish founders are present in the reintroduced populations. The four sites have levels of variation akin to natural populations and exhibit differentiation as predicted by statistical modelling and comparable with natural populations. This suggests that reintroduction following captive breeding can produce self-sustaining populations with natural levels of genetic diversity. These populations appear to be undergoing the same evolutionary dynamics with bottlenecks and drift as natural populations.
Implications for insect conservation
Reintroduction of captive bred individuals is a viable strategy for producing populations with natural levels of genetic diversity and evolutionary dynamics. Hybridisation of populations on the brink of extinction with those thriving can preserve some of the genetic distinctiveness of the declining population.
... Since DNA is a very stable molecule, it survives several years. This DNA is called extracellular DNA (eDNA) [73]. Many studies have confirmed the presence of eDNA in biofilm matrix. ...
Oral cavity is an ecologically complex environment and hosts a diverse microbial community. Most of these organisms are commensals, however, on occasion, some have the potential to become pathogenic causing damage to the human host. Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. Most bacteria in the environment do not exist in free-living state but are found as complex matrix enclosed aggregates known as biofilms. There has been research interest in microbial biofilms because of their importance in industrial and biomedical settings. Bacteria respond to environmental cues to fine-tune the transition from planktonic growth to biofilm by directing gene expression changes favorable for sessile community establishment. Meta-approaches have been used to identify complex microbial associations within human oral cavity leading to important insights. Comparative gene expression analysis using deep sequencing of RNA and metagenomics studies done under varying conditions have been successfully used in understanding and identifying possible triggers of pathogenicity and biofilm formation in oral commensals.
... When an organism dies, the DNA and RNA can be released from the cells during lysis (Hebsgaard, Phillips, & Willerslev, 2005;Jakubovics, Shields, Rajarajan, & Burgess, 2013;Nicholls, 2005). ...
DNA and RNA detected in soil using molecular techniques may originate from a living or dead organism. It is therefore of interest to know how long the DNA and RNA from a decaying organism can persist in soil, and how environmental conditions such as soil temperature, moisture, and microbial populations impact on the survival time. This study determined the difference between the persistence of Phytophthora cinnamomi mRNA and DNA in different soil types. DNA and RNA were extracted from P. cinnamomi and 10 ng/250 mg of soil was applied to five different soil types that were
either air-dried or maintained at 70% field capacity. The persistence of DNA at 20°C was tested after intervals of 0, 3, 7, 14, 90, 241, and 378 days, and for RNA at 0, 1, 3, and 7 days using qPCR and RT-qPCR techniques, respectively. Persistence was longer in dry than moist soil, P. cinnamomi DNA could be readily detected in dry soil conditions for up to 90 days and was found at extremely low levels at 241 and 378 days. RNA was detected only on day 1, except for dry river sand, and moist sandy loam in which it persisted for 3 days; it was not detected after seven days. These results confirm that RNA degrades very quickly, making it a valuable tool for determining the presence of viable Phytophthora in soil. In contrast, DNA can be remarkably stable in
some environments, and positive results could be obtained even after the death of the organism for a year or more prior to the test. For diagnostics, the use of an RNAbased test avoids the possibility of such false positive results. In the context of the research project, this study is relevant to determining how long viable Phytophthora
remains in soil after the eradication protocols have been instigated. In a broader context, the persistence of DNA is relevant to any study using environmental DNA for diagnostics or for metabarcoding when undertaking community ecology or microbiome studies. These results are relevant for studies using detection of P. cinnamomi nucleic acids in soils for purposes of diagnostics, ecological research, or projects on
eradication.
... One of the most noticeable changes in the aDNA structure is the deamination of nucleotides, which leads to substitutions of bases in the polymerase chain reaction (PCR) process: cytosine to uracil, 5-methylcytosine to thymine (both variants lead 1 3 to incorporation into the growing chain of thymine instead of cytosine), and, more rarely, adenine to hypoxanthine (causing inclusion of guanine instead of adenine) (Gilbert et al. 2003a, b;Hofreiter et al. 2001). Another very serious obstacle to studying aDNA is the contamination of ancient samples by the DNA of other organisms (Austin et al. 1997b;Gutierrez and Marin 1998;Nicholls 2005;Zischler et al. 1995). The vast majority of such samples contain exogenous DNA: ancient and modern saprotrophic bacteria, fungi, and modern human DNA caught in samples during archaeological excavations, transportation, and sample preparation in the lab. ...
In this study, we aimed to develop an approach for genetic material extraction and sample preparation of ancient DNA for next generation sequencing that minimizes intra-laboratory contamination. A special module system consisting of four sterile gloveboxes connected by antechambers, which maintain a high purity atmosphere and allow conducting all stages of sample preparation in an isolated clean environment, starting with the processing of archaeological material, was developed. Furthermore, a fast and cost-effective double-stranded library preparation protocol for massive parallel sequencing was developed using non-standard modified sequencing adaptors, which enabled obtaining a library of fragments from extremely low amounts of starting degraded material. Bioinformatics data processing showed that the distribution of substitution frequencies in a subset of reads, mapped to the human reference genome, completely coincides with the pattern of postmortem modifications expected when the double-stranded library preparation method is employed. This is a strong evidence for the endogenous origin of the sequenced fragments of the human genome. Thus, the results of ancient sample and negative control sample sequencing, indicated the absence of visible contamination during sample preparation procedure.
... En effet dans les biofilms karstiques les E. coli pourraient se maintenir en état de dormance, VNC ou sous forme de trace d'ADN. Bien que l'ADN soit une molécule stable qui peut rester intact pendant plusieurs années dans un environnement protégé(Hebsgaard et al. 2005;Nicholls 2005) nous montrons dans cette étude que son ADN ne semble pas s'y maintenir non plus, écartant l'hypothèse qu'elle persisterait sous forme viable non cultivable ou d'une disponibilité de son ADN pour des échanges génétiques horizontaux avec les bactéries du biofilm. Ces résultats suggèrent un décrochage des E. coli des biofilms qui pourrait être dû à des contraintes physiques sur les biofilms provoquées par les variations du débit intra-karstique comme cela a déjà été montré ...
Dans le but de caractériser les conditions environnementales, hydrologiques et d’usage des sols, menant à la contamination d’un système karstique cette étude combine hydrogéologie et microbiologie environnementale. Les chroniques de température et d’hydrologie (pluviométrie, turbidité, conductivité) de l’hydrosystème karstique de Norville (SO Karst) des 5 dernières années ont été analysées pour trouver une corrélation entre les conditions hydrologiques menant au ruissellement sur le bassin versant et la contamination par E. coli de l’hydrosystème (eau et biofilms). Quinze campagnes de prélèvement d’eau à l’entrée (la perte) et la sortie (la source) du système et de biofilms ont été réalisées. La relation entre l’abondance et la diversité génétique (distribution des phylogroupes) des populations de E. coli circulant dans l’hydrosystème et les conditions hydrologiques et d’usage des sols a été étudiée. Un indicateur de contamination des eaux par E. coli (IndiCE) basé sur l’enregistrement de la température et la pluviométrie et corrélé avec la contamination d’eau de surface et sous terraine par E. coli d’un hydrosystème karstique, simple d’utilisation est proposé. Le rôle de réservoir de pathogène des biofilms karstiques, responsable de contamination secondaire, a été étudié en suivant l’occurrence de E. coli et des intégrons de classe 1 dans des biofilms formés à la source de l’hydrosystème karstique de Norville.Il a été montré en chemostat la capacité de E. coli à former des biofilms sur la craie en condition oligotrophique. In situ E. coli et les integrons de classe 1 peuvent s’associer à des biofilms autochtones sous forme cultivable transitoirement. L’ensemble de ces travaux de thèse a permis de mieux comprendre la dynamique de la contamination par E. coli des hydrosystèmes karstiques, dans l’eau et les biofilms.
... In a laboratory context, this has ranged from the lack of experimental controls and reporting, to a 'sensible approach' with good, stringent cleaning protocols, or the assessment of equipment for the presence of starch (Barton & Torrence 2015). However, it has been suggested that decontamination protocols applied to laboratory work represent 'symptomatic treatment' only (Hebsgaard et al. 2005), which indicates the possibility that contamination of archaeological specimens in the field may be more extensive than realized (Nicholls 2005). ...
No agreement on what constitutes a safe and reproducible anticontamination protocol exists for ancient starch
research. Protocols applied to laboratory work may represent ‘symptomatic treatment’ only, as contamination of
archaeological materials in the field may be more extensive than realized. This paper is the first systematic study on the impact that modern starches from surface and buried soils, windborne dispersal, human motion, excavation techniques and toolkits, and field attire has on archaeological sample quality. The study area is Olduvai Gorge, Tanzania. We identify seven starch types (discrete granules, n = 788) that embody the starch contamination landscape for the region. This study also demonstrates the various diagenetic changes that buried starch granules undergo in a short time, such as cavitation, fissuring, disruption and gelatinization. There are significant differences in morphotype class representation between the topsoil starches and those collected deeper below ground at excavated sites. Diagenetically transformed granules from underground storage organs dominate in soils, while native starches from cereal endosperm (Panicoideae and Triticeae) abound above ground in airborne samples. Furthermore, we illustrate how lithic samples excavated under standard field conditions can be contaminated, and that when a sample is compromised during excavation, it may be impossible to distinguish between target and introduced starches, especially when granules are identical or morphologically similar. The paper provides field recommendations to control false positives.
... Early researchers did not consider or were unaware that there are major problems resulting from contamination of archaeological samples with modern DNA. It has been argued that aDNA has "come of age" (Nicholls 2005) partly because we now have standard protocols and requirements for aDNA laboratories and research. Despite this fact, papers that do not meet these standard requirements are still being published, and unfortunately, they are being published in archaeological and anthropological journals. ...
... 103 In addition to these examples, several other aDNA projects have been impeded by contamination of ancient samples. 98,[103][104][105][106] To prevent contamination, the experiment must be properly managed, including special requirements for sample collection, sterilization of the working area, DNA authentication, and independent reproducibility. 97,107 These protocols are constantly being refined and improved. ...
The term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In
... Sampling is of enduring importance in systematics (e.g., Lecointre and Philippe,'93;Graybeal,'98;Hillis,'98;Rannala et al.,'98) because the inclusion of intermediate morphologies or genotypes helps avoid a broad set of systematic biases, including the above-mentioned long-branch attraction (Gauthier et al.,'88b;Donoghue et al.,'89). However, whereas paleontologists at least have the potential to sample all of life, despite massive taphonomic filters (Benton et al., 2000), molecular systematists can only sample extant taxa, or at best newly extinct taxa (Nicholls, 2005). This issue is compounded by the fact that extant taxa do not sample the Amniote tree at random, but rather as eight discrete clades (i.e., Aves, Crocodilia, Monotremata, Marsupialia, Placentalia, Squamata, Sphenodon, and Testudines) that diversified within the last 100 Ma and that are interconnected by lineages spanning many hundreds of millions of years (e.g., Wang et al., 2013). ...
The origin of turtles and their unusual body plan has fascinated scientists for the last two centuries. Over the course of the last decades, a broad sample of molecular analyses have favored a sister group relationship of turtles with archosaurs, but recent studies reveal that this signal may be the result of systematic biases affecting molecular approaches, in particular sampling, non-randomly distributed rate heterogeneity among taxa, and the use, and the use of concatenated data sets. Morphological studies, by contrast, disfavor archosaurian relationships for turtles, but the proposed alternative topologies are poorly supported as well. The recently revived paleontological hypothesis that the Middle Permian Eunotosaurus africanus is an intermediate stem turtle is now robustly supported by numerous characters that were previously thought to be unique to turtles and that are now shown to have originated over the course of tens of millions of years unrelated to the origin of the turtle shell. Although E. africanus does not solve the placement of turtles within Amniota, it successfully extends the stem lineage of turtles to the Permian and helps resolve some questions associated with the origin of turtles, in particular the non-composite origin of the shell, the slow origin of the shell, and the terrestrial setting for the origin of turtles. J. Exp. Zool. (Mol. Dev. Evol.) 9999B: 1-13, 2015. © 2015 Wiley Periodicals, Inc.
© 2015 Wiley Periodicals, Inc.
