Chloroplast DNA sequence from a miocene Magnolia species

Summer-Wet Hydrologic Cycle during the Middle Miocene of the United States: New Evidence from Fossil Fungi

Hydrologic reconstructions from North America are largely unknown for the Middle Miocene. Examination of fungal palynomorph assemblages coupled with traditional plant-based palynology permits delineation of local, as opposed to regional, climate signals and provides a baseline for study of ancient fungas. Here, the Fungi in a Warmer World project presents paleoecology and paleoclimatology of 351 fungal morphotypes from 3 sites in the United States: the Clarkia Konservat-Lagerstätte site (Idaho), the Alum Bluff site (Florida), and the Bouie River site (Mississippi). Of these, 83 fungi are identified as extant taxa and 41 are newly reported from the Miocene. Combining new plant-based paleoclimatic reconstructions with funga-based paleoclimate reconstructions, we demonstrate cooling and hydrologic changes from the Miocene climate optimum to the Serravallian. In the southeastern United States, this is comparable to that reconstructed with pollen and paleobotany alone. In the northwestern United States, cooling is greater than indicated by other reconstructions and hydrology shifts seasonally, from no dry season to a dry summer season. Our results demonstrate the utility of fossil fungi as paleoecologic and paleoclimatic proxies and that warmer than modern geological time intervals do not match the "wet gets wetter, dry gets drier" paradigm. Instead, both plants and fungi show an invigorated hydrological cycle across mid-latitude North America.

Environmental fate and behaviour of antibiotic resistance genes and small interference RNAs released from genetically modified crops

Rising global populations have amplified food scarcity across the world and ushered in the development of genetically modified (GM) crops to overcome these challenges. Cultivation of major crops such as corn and soy has favoured GM crops over conventional varieties to meet crop production and resilience needs. Modern GM crops containing small interference RNA molecules and antibiotic resistance genes have become increasingly common in the United States. However, the use of these crops remains controversial due to the uncertainty regarding the unintended release of its genetic material into the environment and possible downstream effects on human and environmental health. DNA or RNA transgenes may be exuded from crop tissues during cultivation or released during plant decomposition and adsorbed by soil. This can contribute to the persistence and bioavailability in soil or water environment and possible uptake by soil microbial communities and further passing of this information to neighbouring bacteria, disrupting microbial ecosystem services such as nutrient cycling and soil fertility. In this review, transgene mechanisms of action, uses in crops, and knowledge regarding their environmental fate and impact to microbes are evaluated. This aims to encapsulate the current knowledge and promote further research regarding unintended effects transgenes may cause.

Fingerprints of climatic changes through the late Cenozoic in southern Asian flora: Magnolia section Michelia (Magnoliaceae)

BACKGROUND AND AIMS

Ongoing global warming is a challenge for humankind. A series of drastic climatic changes have been proven to have occurred throughout the Cenozoic based on a variety of geological evidence, which helps to better understand our planet's future climate. Notably, extant biomes have recorded drastic environmental shifts. The climate in southern Asia, which hosts high biodiversity, is deeply impacted by the Asian monsoon. The origins and evolutionary dynamics of biomes occurring between the tropics and sub-tropics in southern Asia have probably been deeply impacted by climatic changes; however, these aspects remain poorly studied. We tested whether the evolutionary dynamics of the above biomes have recorded the drastic, late Cenozoic environmental shifts, by focusing on Magnolia section Michelia of the family Magnoliaceae.

METHODS

We established a fine time-calibrated phylogeny of M. section Michelia based on complete plastid genomes and inferred its ancestral ranges. Finally, we estimated the evolutionary dynamics of this section through time, determining its diversification rate and the dispersal events that occurred between tropical and sub-tropical areas.

KEY RESULTS

The tropical origin of M. section Michelia was dated to the late Oligocene; however, the diversification of its core group (i.e. M. section Michelia subsection Michelia) has occurred mainly from the late Miocene onward. Two key evolutionary shifts (dated approx. 8 and approx. 3 million years ago, respectively) were identified, each of them probably in response to drastic climatic changes.

CONCLUSION

Here, we inferred the underlying evolutionary dynamics of biomes in southern Asia, which probably reflect late Cenozoic climatic changes. The occurrence of modern Asian monsoons was probably fundamental for the origin of M. section Michelia; moreover, the occurrence of asymmetric dispersal events between the tropics and sub-tropics hint at an adaptation strategy of M. section Michelia to global cooling, in agreement with the tropical conservatism hypothesis.

The evolutionary history of the Caribbean magnolias (Magnoliaceae): Testing species delimitations and biogeographical hypotheses using molecular data

The Caribbean islands provide an ideal setting for studying biodiversity, given their complex geological and environmental history, and their historical and current geographical proximity to the American mainland. Magnolia, a flagship tree genus that has 15 endemic and threatened taxa (12 species and 3 subspecies) on the Caribbean islands, offers an excellent case study to empirically test Caribbean biogeographical hypotheses. We constructed phylogenetic hypotheses to: (1) reveal their evolutionary history, (2) test the current largely morphology-based classification and assess species limits, and (3) investigate major biogeographic hypotheses proposed for the region. Nuclear and chloroplast DNA sequence data of all 15 Caribbean Magnolia taxa are included, supplemented by a selection of American mainland species, and species representing most major clades of the Magnoliaceae family. We constructed phylogenetic hypotheses in a time-calibrated Bayesian framework, supplemented with haplotype network analyses and ancestral range estimations. Genetic synapomorphies in the studied markers confirm the species limits of 14 out of 15 morphologically recognizable Caribbean Magnolia taxa. There is evidence for four colonization events of Magnolia into the Caribbean from the American mainland, which most likely occurred by overwater dispersal, given age estimates of maximum 16 mya for their presence on the Caribbean islands.

Phylogeny and time scale of diversification in the fossil-rich sunfishes and black basses (Teleostei: Percomorpha: Centrarchidae)

Species of the North American freshwater fish lineage Centrarchidae are apex predators in their habitats and are among the world's most popular sport fishes. Centrarchids boast a rich fossil record that extends from the latest Eocene to the Pleistocene. To investigate the phylogeny and timing of diversification of Centrarchidae, we deploy a dataset of DNA sequences of 16 nuclear genes sampled from nearly all of the recognized and undescribed species. We also utilize previously published morphological datasets to assess the phylogenetic placement of one of the oldest known centrarchid fossils, †Plioplarchus whitei. A Bayesian multispecies coalescent species tree analysis provides insight on relationships that evaded resolution in earlier studies, such as the relationships of Acantharchus pomotis, the resolution of a clade consisting of species previously synonymized under the Spotted Bass, Micropterus punctulatus, and a clade of recently described species previously considered populations of the Redeye Bass, Micropterus coosae. This new molecular phylogeny and the inclusion of †P. whitei and other centrarchid fossils in the tip-dated fossilized birth-death analysis results in a new hypothesis of the timing of diversification in Centrarchidae that contextualizes the ages of centrarchid fossils to the timing of speciation among the extant species. In addition to providing new temporal perspectives on the diversification of freshwater fishes in North America, this study may close of the chapter of centrarchid phylogeny inferred using Sanger-sequenced genes, as the use of genomic-scale datasets becomes mainstream in the phylogenetics of fishes.

Ancient Plant Genomics in Archaeology, Herbaria, and the Environment

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.

Quaternary DNA: A Multidisciplinary Research Field

The purpose of this Milankovitch review is to explain the significance of Quaternary DNA studies and the importance of the recent methodological advances that have enabled the study of late Quaternary remains in more detail, and the testing of new assumptions in evolutionary biology and phylogeography to reconstruct the past. The topic is wide, and this review is not intended to be an exhaustive account of all the aDNA work performed in the last three decades on late-Quaternary remains. Instead, it is a selection of relevant studies aimed at illustrating how aDNA has been used to reconstruct not only environments of the past, but also the history of many species including our own.

Physiological and molecular genetic studies on two elicitors for improving the tolerance of six Egyptian soybean cultivars to cotton leaf worm

Cotton leaf worm (Spodoptera littoralis) is considered one of the most destructive agricultural pests in Egypt. Six soybean cultivars (Giza-21, Giza-22, Giza-35, Giza-82, Giza-83 and Giza-111) were grown under natural infection with cotton leaf worm. The effect of two elicitors, methyl jasmonate and sodium nitroprusside on enhancing the ability of susceptible cultivars to tolerate (Spodoptera littoralis) was studied. Giza-35 and Giza-111 showed tolerance performance under natural infection compared to Giza-22 and Giza-82 as sensitive ones, while Giza-83 and Giza-21 showed moderate tolerance. Both treatments positively affected seed yield and its components and fatty acid composition. Extracted fatty acids showed variable changes in treated plants compared with the untreated controls. Plants treated with the two elicitors showed an increase in Linoleic acid and Linolenic acid fatty acids and decrease in Palmitic acid and Palmitolic acid content. Treatment with methyl jasmonate was found to be more effective than sodium nitroprusside and enhanced resistance of the susceptible cultivars. Eight IRAP and iPBS retrotransposon-based markers were used to detect genetic differences among studied soybean cultivars and to develop molecular genetic markers for cotton leaf worm infestation. The technique successfully identified soybean genotypes in addition to nineteen molecular markers related to soybean tolerance.

Extending the scope of Darwin's 'abominable mystery': integrative approaches to understanding angiosperm origins and species richness

Background and aims

Angiosperms are the most species-rich group of land plants, but their origins and fast and intense diversification still require an explanation.

Scope

Extending research scopes can broaden theoretical frameworks and lines of evidence that can lead to solving this 'abominable mystery'. Solutions lie in understanding evolutionary trends across taxa and throughout the Phanerozoic, and integration between hypotheses and ideas that are derived from multiple disciplines.

Key Findings

Descriptions of evolutionary chronologies should integrate between molecular phylogenies, descriptive palaeontology and palaeoecology. New molecular chronologies open new avenues of research of possible Palaeozoic angiosperm ancestors and how they evolved during as many as 200Myr until the emergence of true angiosperms. The idea that 'biodiversity creates biodiversity' requires evidence from past and present ecologies, with changes in herbivory and resource availability throughout the Phanerozoic appearing to be particularly promising.

Conclusions

Promoting our understanding of angiosperm origins and diversification in particular, and the evolution of biodiversity in general, requires more profound understanding of the ecological past through integrating taxonomic, temporal and ecological scopes.

Biodiversity in targeted metabolomics analysis of filamentous fungal pathogens by 1H NMR-based studies

The taxonomical classification among fungi kingdom in the last decades was evolved. In this work the targeted metabolomics study based on 1H NMR spectroscopy combined with chemometrics tools was reported to be useful for differentiation of three model of fungal strains, which represent various genus of Ascomycota (Aspergillus pallidofulvus, Fusarium oxysporum, Geotrichum candidum) were selected in order to perform metabolomics studies. Each tested species, revealed specific metabolic profile of primary endo-metabolites. The species of A. pallidofulvus is represented by the highest concentration of glycerol, glucitol and Unk5. While, F. oxysporum species is characterised by increased level of propylene glycol, ethanol, 4-aminobutyrate, succinate, xylose, Unk1 and Unk4. In G. candidum, 3-methyl-2-oxovalerate, glutamate, pyruvate, glutamine and citrate were elevated. Additionally, a detailed analysis of metabolic changes among A. pallidofulvus, F. oxysporum and G. candidum showed that A. pallidofulvus seems to be the most pathogenic fungi. The obtained results demonstrated that targeted metabolomics analysis could be utilized in the future as a supporting taxonomical tool for currently methods.

[aDNA Research From a Historical Perspective]

aDNA studies are a cooperative field of research with a broad range of applications including evolutionary biology, genetics, anthropology and archaeology. Scientists are using ancient molecules as source material for historical questions. Colleagues from the humanities are observing this with both interest and concern because aDNA research is affecting academic identities and both concepts of history and historiography. aDNA research developed in a way that can be described as a Hype Cycle (Chackie Fenn). Technological triggers such as Sanger Sequencing and the Polymerase Chain Reaction kicked off a multitude of experiments with ancient DNA during the 1980s and 1990s. Geneticists, microbiologists, anthropologists and many more euphorically joined a "molecule hunt". aDNA was promoted as a time machine. Media attention was enormous. As experiments and implementations began to fail and contamination was discovered to be a tremendous problem, media interest waned and many labs lost their interest. Some turned their disillusionment into systematic research into methodology and painstakingly established lab routines. The authenticity problem was first addressed by control oriented measures but later approached from a more cognitive theoretical perspective as the pitfalls and limits of aDNA became clearer. By the end of the 2000s the field reached its current plateau of productivity. Cross-disciplinary debates, conflicts and collaborations are increasing critical reflection among all participants. Historians should consider joining the field in a kind of critical friendship to both make the most of its possibilities and give an input from a constructivist perspective.

Toward high-resolution population genomics using archaeological samples

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 this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.

Chloroplast genomes: diversity, evolution, and applications in genetic engineering

Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.

Microwave-assisted digestion combined with silica-based spin column for DNA isolation from human bones

A protocol for the extraction of DNA from ancient skeletal material was developed. Bone specimen samples (powder or slice), buffer, pretreatment, and extraction methodologies were compared to investigate the best conditions yielding the highest concentration of DNA. The degree of extract contamination by polymerase chain reaction (PCR) inhibitors was compared as well. Pretreatment was carried out using agitation in an incubator shaker and microwave digestion. Subsequently, DNA from bones was isolated by the classical organic phenol-chloroform extraction and silica-based spin columns. Decalcification buffer for total demineralization was required as well as lysis buffer for cell lysis to obtain DNA, whereas microwave-assisted digestion proved to be very rapid, with an incubation time of 2min instead of 24h at an incubator shaker without using lysis buffer. The correction of isolated DNA was detected using real-time PCR with melt curve analysis, which was 82.8±0.2°C for highly repetitive α-satellite gene region specific for human chromosome 17 (locus D17Z1). Consequently, microwave-based DNA digestion followed by silica column yielded a high-purity DNA with a concentration of 19.40ng/μl and proved to be a superior alternative to the phenol-chloroform method, presenting an environmentally friendly and efficient technique for DNA extraction.

Re-inventing ancient human DNA

For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next- or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research.

Biomolecular Archaeology

Ancient biomolecules including DNA, proteins, and lipids are often preserved in archaeological skeletons or artifacts such as potsherds from cooking vessels. Techniques for analyzing these molecules have improved dramatically in recent years, though challenges remain in ensuring that results are authentic and not confused by the presence of contaminating modern biomolecules. Ancient DNA (aDNA) can be used to identify the sex, kinship relationships, and population affinities of human skeletons, and also to detect the presence of disease-causing organisms such as the plague and tuberculosis bacteria. Stable isotope ratios in collagen and other skeletal proteins enable past diets to be studied, and similar work with lipids from potsherds have revealed that dairying in Europe began 2,000 years earlier than previously thought. Biomolecular archaeology has therefore developed into a mature discipline that is making a significant contribution to different aspects of our understanding of the human past.

Ancient DNA damage

Under favorable conditions DNA can survive for thousands of years in the remains of dead organisms. The DNA extracted from such remains is invariably degraded to a small average size by processes that at least partly involve depurination. It also contains large amounts of deaminated cytosine residues that are accumulated toward the ends of the molecules, as well as several other lesions that are less well characterized.

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

Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10(-6) per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R(2) = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.

Ancient DNA studies: new perspectives on old samples

In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.

Capillary electrophoresis of human mtDNA control region sequences from highly degraded samples using short mtDNA amplicons

The forensic applications of mtDNA sequencing center primarily on samples that are either highly degraded or contain little or no nuclear DNA, since the testing of these sample types is often unsuccessful with more widely used nuclear STR profiling assays. In these cases, sequence data from the noncoding mtDNA control region are targeted due to its high variability. However, the ease of authentic DNA recovery and the strategy used for recovery depend strictly on the quality of the sample. In this chapter, we will cover mitochondrial DNA sequencing procedures for short mtDNA amplicons which range in size from 100 to 350 bp. Generally speaking, amplicons of this size are required only for the most degraded specimens, and the protocols described here have been specifically developed for recalcitrant human skeletal remains encountered during the course of a large-scale missing persons' identification effort. DNA templates from these types of specimens tend to exhibit various forms of intrastrand damage that, in turn, manifest as artifacts in the sequence data. Because these artifacts are not generally observed among sequence data from pristine templates, we address the particular data idiosyncrasies that warrant additional scrutiny. Although this chapter will primarily highlight this particular application, the basic experimental parameters and data considerations should easily extend to other applications and/or sample types. The protocols described here have been deliberately designed to produce raw sequence electropherograms and final mtDNA profiles that adhere to the strictest forensic guidelines in terms of overall data quality.

Palaeontological evidence of membrane relationship in step-by-step membrane fusion

Studies on membrane fusion in living cells indicate that initiation of membrane fusion is a transient and hard to capture process. Despite previous research, membrane behaviour at this point is still poorly understood. Recent palaeobotanical research has revealed snapshots of membrane fusion in a 15-million-year-old fossil pinaceous cone. To reveal the membrane behaviour during the fusion, we conducted more observations on the same fossil material. Several discernible steps of membrane fusion have been fixed naturally and observed in the fossil material. This observation provides transmission electron microscope (TEM) images of the transient intermediate stage and clearly shows the relationship between membranes. Observing such a transient phenomenon in fossil material implies that the fixing was most likely accomplished quickly by a natural process. The mechanism behind this phenomenon is clearly worthy of further enquiry.

Evidence of a genomic biomarker in normal human epithelial mammary cell line, MCF-10A, that is absent in the human breast cancer cell line, MCF-7

This study investigated the use of DNA amplification fingerprinting (DAF) to identify biomarkers useful in the elucidating genetic factors that lead to carcinogenesis. The DNA amplification fingerprinting (DAF) technique was used to generate fingerprint profiles of a normal human mammary epithelial cell line (MCF-10A) and a human breast cancer cell line (MCF-7). When compared with one another, a polymorphic biomarker gene (262 base pairs (bps)) was identified in MCF-10A but was not present in MCF-7. This gene was cloned from the genomic DNA of the MCF-10A cell line, and subjected to Genbank database analysis. The analysis of the nucleotide sequence polymorphic marker (Genbank account: AC079630) shows that this biomarker has 100% homology with the nucleotide sequence of human chromosome 12 BAC RP11-476D10 (bps 19612-19353). The nucleotide sequence was used for possible protein translation product and the result obtained indicated that the gene codes for hypothetical protein XF2620. In order to evaluate the effects that the 262 bps biomarker would have on the morphology of MCF-7 cells, it was transfected into MCF-7 cells. There were observable changes in the morphology of the transfected cells. These changes included an increase in cell elongation and a decrease in cell aggregation.

Ancient mitogenomics

The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.

Biochemical and genomic characterization of terpene synthases in Magnolia grandiflora

Magnolia grandiflora (Southern Magnolia) is a primitive evergreen tree that has attracted attention because of its horticultural distinctiveness, the wealth of natural products associated with it, and its evolutionary position as a basal angiosperm. Three cDNAs corresponding to terpene synthase (TPS) genes expressed in young leaves were isolated, and the corresponding enzymes were functionally characterized in vitro. Recombinant Mg25 converted farnesyl diphosphate (C(15)) predominantly to beta-cubebene, while Mg17 converted geranyl diphosphate (C(5)) to alpha-terpineol. Efforts to functionally characterize Mg11 were unsuccessful. Transcript levels for all three genes were prominent in young leaf tissue and significantly elevated for Mg25 and Mg11 messenger RNAs in stamens. A putative amino-terminal signal peptide of Mg17 targeted the reporter green fluorescent protein to both chloroplasts and mitochondria when transiently expressed in epidermal cells of Nicotiana tabacum leaves. Phylogenetic analyses indicated that Mg25 and Mg11 belonged to the angiosperm sesquiterpene synthase subclass TPS-a, while Mg17 aligned more closely to the angiosperm monoterpene synthase subclass TPS-b. Unexpectedly, the intron-exon organizations for the three Magnolia TPS genes were different from one another and from other well-characterized TPS gene sets. The Mg17 gene consists of six introns arranged in a manner similar to many other angiosperm sesquiterpene synthases, but Mg11 contains only four introns, and Mg25 has only a single intron located near the 5' terminus of the gene. Our results suggest that the structural diversity observed in the Magnolia TPS genes could have occurred either by a rapid loss of introns from a common ancestor TPS gene or by a gain of introns into an intron-deficient progenote TPS gene.

Paleontological evidence for membrane fusion between a unit membrane and a half-unit membrane

Membrane fusion is of fundamental importance for many biological processes and has been a topic of intensive research in past decades with several models being proposed for it. Fossils had previously not been considered relevant to studies on membrane fusion. But here two different membrane fusion patterns are reported in the same well-preserved fossil plant from the Miocene (15-20 million years old) at Clarkia, Idaho, US. Scanning electron microscope, transmission electron microscope, and traditional studies reveal the vesicles in various states (even transient semi-fusion) of membrane fusion, and thus shed new light on their membrane structure and fusion during exocytoses. The new evidence suggests that vesicles in plant cells may have not only a unit membrane but also a half-unit membrane, and that a previously overlooked membrane fusion pattern exists in plant cells. This unexpected result from an unexpected material not only marks the first evidence of on-going physiological activities in fossil plants, but also raises questions on membrane fusion in recent plants.

[Biological evolution and ancient DNA]

Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.

Isolation and analysis of DNA from archaeological, clinical, and natural history specimens

The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. Novel methods exist for the isolation, purification, and analysis of aDNA because these DNA templates are likely to be damaged, fragmented and?or associated with non-nucleic acid material. However, contamination of ancient specimens and DNA extracts with modern DNA is more widespread than is generally acknowledged and remains a significant problem in aDNA analysis. Studies of human aDNA are uniquely sensitive to contamination due to the continual presence of potential contamination sources. Meticulous authentication of results and careful selection of polymorphic markers capable of distinguishing between aDNA and probable DNA contaminants are critical to a successful aDNA study.

Cloning and characterization of hoxH genes from Arthrospira and Spirulina and application in phylogenetic study

Partial hoxH genes of 2 cyanobacterial genera, including 5 strains of Arthrospira and 2 strains of Spirulina, were cloned and characterized. This gene encodes the large subunit of nickel-iron hydrogenase. The results showed that these genes comprised 1349 nucleotides in Arthrospira and 1343 nucleotides in Spirulina, respectively. The GC contents of hoxH were 45.7% to 47.3% in Arthrospira and up to 50.4% to 50.9% in Spirulina. The hoxH gene was demonstrated to be single copy by Southern analysis, and its transcription was verified by reverse transcriptase polymerase chain reaction in Arthrospira platensis FACHB341. The similarities of nucleotide sequences among the 5 strains of Arthrospira ranged from 95.7% to 99.8%, which are higher than those between Arthrospira and Spirulina (72.9-77.0%). However, similarity between the 2 Spirulina strains was only 72.5%, slightly lower than that between the 2 genera. A phylogenetic tree based on hoxH was constructed. All 5 strains of Arthrospira formed a monophyletic clade, which was highly supported by bootstrap value, while the 2 strains of Spirulina were separated into 2 different clades.

Geologically ancient DNA: fact or artefact?

Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.

Ancient DNA

In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

Ancient plant DNA: review and prospects

Ancient DNA has received much attention since the mid-1980s, when the first sequence of an extinct animal species was recovered from a museum specimen. Since then, the majority of ancient DNA studies have focused predominantly on animal species, while studies in plant palaeogenetics have been rather limited, with the notable exception of cultivated species found in archaeological sites. Here, we outline the recent developments in the analysis of plant ancient DNA. We emphasize the trend from species identification to population-level investigation and highlight the potential and the difficulties in this field, related to DNA preservation and to risks of contamination. Further efforts towards the analysis of ancient DNA from the abundant store of fossil plant remains should provide new research opportunities in palaeoecology and phylogeography. In particular, intraspecific variation should be considered not only in cultivated plants but also in wild taxa if palaeogenetics is to become a fully emancipated field of plant research.

Genetic Analyses from Ancient DNA

About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.

DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae)

We report a partial ndhF sequence (1528 bp) of Magnolia latahensis and a partial rbcL sequence (699 bp) of Persea pseudocarolinensis from the Clarkia fossil beds of Idaho, USA (Miocene; 17-20 million years [my] BP). The ndhF sequence from M. latahensis was identical to those of extant M. grandiflora, M. schiediana, M. guatemalensis, and M. tamaulipana. Parsimony analysis of the ndhF sequence of M. latahensis and previously reported ndhF sequences for Magnoliaceae placed M. latahensis within Magnolia as a member of the Theorhodon clade. This result is reasonable considering that: (1) the morphology of M. latahensis is very similar to that of extant M. grandiflora, and (2) a recent molecular phylogenetic study of Magnoliaceae showed that the maximum sequence divergence of ndhF among extant species is very low (1.05% in subfamily Magnolioideae) compared with other angiosperm families. We reanalyzed the previously reported rbcL sequence of M. latahensis with sequences for all major lineages of extant Magnoliales and Laurales. This sequence is sister to Liriodendron, rather than grouped with a close relative of M. grandiflora as predicted by morphology and the results of the ndhF analysis, possibly due to a few erroneous base calls in the sequences. The rbcL sequence of P. pseudocarolinensis differed from rbcL of extant Persea species by 3-6 nucleotides and from rbcL of extant Sassafras albidum by two nucleotides. Phylogenetic analyses of rbcL sequences for all major lineages of Magnoliales and Laurales placed the fossil P. pseudocarolinensis within Lauraceae and as sister to S. albidum. These results reinforce the suggestion that Clarkia and other similar sites hold untapped potential for molecular analysis of fossils.

Coevolution of viruses with hosts and vectors and possible paleontology

The coevolution of viruses with their hosts and vectors depends on the evolution of the hosts and vectors coupled with factors involved in virus evolution. The long-term perspective involves the origin of life forms, the evolution of host and vector (especially arthropods) kingdoms and families, and changes in biological diversity induced mainly by the last five great extinctions. In the medium term, the diversification of hosts and vectors is important, and in the short term, recent events, especially humans, have had a great impact on virus coevolution. As there are few, if any, examples of conventional fossils of viruses, evidence for their evolution related to host and vector evolution is being found from other sources, especially virus-induced cellular structures and recent developments in molecular biology. Recognizing these other sources is becoming important for paleontologists gaining an understanding of the influence that viruses have had on the development of higher organisms.