Processes in the formation of ancient world systems

Thomas C. Patterson is Professor of Anthropology and History at Temple University, Philadelphia.     

New evidence for ancient cultivation ofCanna edulis in Peru

Preserved rhizomes ofCanna edulis from 5 archaeological sites in the Casma Valley of Peru are illustrated and described. These were identified by their extant surface features and by their starch grains, which are different from those of any other known flowering plant species. Based on radiocarbon assays, these specimens range in date from 2250–295 B.C. Materials used for comparative purposes in this study included a collection of edible canna from the Peruvian archaeological site of Pachacamac and a modern-day specimen. A theory on the place of origin and time of domestication of this species is given in the conclusions of this paper.     

Palaeontology in a molecular world: the search for authentic ancient DNA

The survival of ancient DNA in specimens up to several thousands of years old is established. However, there have been several claims concerning the recovery of geologically ancient DNA from fossil material many millions of years old. The authenticity of these fossil DNA sequences is questionable on theoretical and empirical grounds, and the existence of authentic geologically ancient DNA remains to be proven.     

Evidence for S. cerevisiae fermentation in ancient wine

Saccharomyces cerevisiae is the principal yeast used in modern fermentation processes, including winemaking, breadmaking, and brewing. From residue present inside one of the earliest known wine jars from Egypt, we have extracted, amplified, and sequenced ribosomal DNA from S. cerevisiae. These results indicate that this organism was probably responsible for wine fermentation by at least 3150 B.C. This inference has major implications for the evolution of bread and beer yeasts, since it suggests that S. cerevisiae yeast, which occurs naturally on the surface bloom of grapes, was also used as an inoculum to ferment cereal products.     

Evidence of recombination in putative ancient asexuals

Ancient asexuals have been considered to be a contradiction of the basic tenets of evolutionary theory. Barred from rearranging genetic variation by recombination, their reduced number of gene arrangements is thought to hamper their response to changing environments. For the same reason, it should be difficult for them to avoid the build-up of deleterious mutations. Several groups of taxonomically diverse organisms are thought to be ancient asexuals, although clear evidence for or against the existence of recombination events is scarce. Several methods have recently been developed for predicting recombination events by analyzing aligned sequences of a given region of DNA that all originate from one species. The methods are based on phylogenetic, substitution, and compatibility analyses. Here we present the results of analyses of sequence data from different loci studied in several groups of evolutionarily distant species that are considered to be ancient asexuals, using seven different types of analysis. The groups of organisms were the arbuscular mycorrhizal fungi (Glomales), Darwinula stevensoni (Darwinuloidea crustacean ostracods) and the bdelloid rotifers (Bdelloidea), which are thought to have been asexual for the last 400, 25-100, and 35-40 Myr, respectively. The seven different analytical methods evaluated the evolutionary relationships among haplotypes, and these methods had previously been shown to be reliable for predicting the occurrence of recombination events. Despite the different degree of genetic variation among the different groups of organisms, at least some evidence for recombination was found in all species groups. In particular, predictions of recombination events in the arbuscular mycorrhizal fungi were frequent. Predictions of recombination were also found for sequence data that have previously been used to infer the absence of recombination in bdelloid rotifers. Although our results have to be taken with some caution because they could signal very ancient recombination events or possibly other genetic variation of nonrecombinant origin, they suggest that some cryptic recombination events may exist in these organisms.     

Evidence in favour of ancient octaploidy in the vertebrate genome

Vertebrate genomes are larger than invertebrates and show evidence of extensive gene duplication, including many collinear chromosomal segments. On the basis of this intra-genomic synteny, it has been proposed that two rounds of whole genome duplication (octaploidy) occurred early in the vertebrate lineage. Recently, this early vertebrate octaploidy has been challenged on the basis of gene trees. We report new linkage groups encompassing the matrilin (MATN), syndecan (SDC), Eyes Absent (EYA), HCK kinase and SRC kinase paralogous gene quartets. In contrast to other studies, the sequence trees are weakly supportive of ancient octaploidy. It is concluded that there is no strong evidence against the octaploidy, provided that consecutive genome duplication was rapid.     

Insect cell culture media for cultivation of new world Leishmania

Monophasic insect cell culture media were evaluated for suitability in the propagation of strains of Leishmania brasiliensis, L. mexicana and L. enriettii. Amastigotes were inoculated into Grace's, Schneider's and Mitsuhashi-Maramorosch's Media containing antibiotics and varying concentrations of fetal calf serum. After 4–7 days incubation at 27°C, promastigote yields exceeded 1 × 10⁸/rr.l in some instances in contrast to yields of approximately 2 × 10⁷/ml in blood-based media. Optimal concentrations of fetal calf serum were determined to be 15% or more for most of the strains tested.     

Identification of DNA-PK in the arthropods. Evidence for the ancient ancestry of vertebrate non-homologous end-joining

Cellular life depends upon the preservation and transmission of genetic material. Double stranded DNA breaks (DSBs) cause catastrophic gene loss in cell division and must be promptly and accurately repaired. In eukaryotes DSBs may be repaired by either non-homologous end-joining (NHEJ), single strand annealing or homologous recombination (HR). Vertebrate NHEJ has been shown to depend upon the DNA-dependent protein kinase (DNA-PK) consisting of the phosphatidylinositol 3 (PI 3)-kinase like (PIKK) catalytic sub-unit (DNA-PKcs) and the DNA targeting factor Ku. Our analysis of recently completed genomes found several novel PIKKs in Anopheles gambiae and Drosophila melanogaster including a novel mosquito DNA-PKcs orthologue, the first non-vertebrate DNA-PKcs described to date. We also detected a DNA-PKcs fragment in the high quality EST set of Apis mellifera ligustica (honey bee) suggesting that DNA-PK is a far older and more important eukaryotic complex than previously thought.     

Inferring ancient Agave cultivation practices from contemporary genetic patterns

Several Agave species have played an important ethnobotanical role since prehistory in Mesoamerica and semiarid areas to the north, including central Arizona. We examined genetic variation in relict Agave parryi populations northeast of the Mogollon Rim in Arizona, remnants from anthropogenic manipulation over 600 years ago. We used both allozymes and microsatellites to compare genetic variability and structure in anthropogenically manipulated populations with putative wild populations, to assess whether they were actively cultivated or the result of inadvertent manipulation, and to determine probable source locations for anthropogenic populations. Wild populations were more genetically diverse than anthropogenic populations, with greater expected heterozygosity, polymorphic loci, effective number of alleles and allelic richness. Anthropogenic populations exhibited many traits indicative of past active cultivation: fixed heterozygosity for several loci in all populations (nonexistent in wild populations); fewer multilocus genotypes, which differed by fewer alleles; and greater differentiation among populations than was characteristic of wild populations. Furthermore, manipulated populations date from a period when changes in the cultural context may have favoured active cultivation near dwellings. Patterns of genetic similarity among populations suggest a complex anthropogenic history. Anthropogenic populations were not simply derived from the closest wild A. parryi stock; instead they evidently came from more distant, often more diverse, wild populations, perhaps obtained through trade networks in existence at the time of cultivation.     

Tracking the history of grapevine cultivation in Georgia by combining geometric morphometrics and ancient DNA

Vegetation History and Archaeobotany - The Near East and the Caucasus are commonly regarded as the original domestication centres of Vitis vinifera (grapevine), and the region continues to be home...     

Three genetically divergent lineages of the Oryx in eastern Africa: Evidence for an ancient introgressive hybridization

Phylogeographic and population genetic studies using sequence information are frequently used to infer species boundaries and history; and to assess hybridization and population level processes. In this study, partial mitochondrial DNA (mtDNA) control region (423 bp) and cytochrome b sequences (666 bp) of Oryx beisa sampled from five isolated localities in its entire current range in Africa were analyzed to investigate the extent of genetic variation and differentiation between populations. We observed high nucleotide diversity at the control region in the total sample (6.3%) but within populations, it varied considerably ranging from 1.6% to 8.1%. Population pairwise genetic differentiation was generally significantly high (ranging from F _ST = 0.15, P<0.01 to F _ST = 0.54, P<0.001). In the total sample, 29 and 12 haplotypes were observed in the control region and the cytochrome b data sets respectively. For both data sets, the haplotypes cluster into three distinct clades (sequence divergence ranged from 6.0%–12.9% to 0.8%–1.0% for the control region and cytochrome b sequences, respectively) that do not correspond to sampling locations. Two of these clades are found in the same localities (Samburu and Marsabit), which represent the O.beisa beisa subspecies, whereas the last clade represents the fringe-eared oryx (O. beisa callotis). We interpret these findings in terms of an ancient hybridization and introgression between two formerly isolated taxa of Oryx beisa.     

The emergence of molecular machines as a prerequisite of the ancient RNA world evolution

The problem of the start of biological evolution in the ancient RNA world is considered. It is postulated that the appearance of catalytic RNAs — ribozymes — via spontaneous cis- and trans-rearrangements of polyribonucleotides in primordial Darwin ponds should not have been sufficient for the start of evolution, until a new class of functional RNA, namely energy-dependent molecular machines, arose. The proposed hypothesis is that the simplest and primary type of molecular machines could be nucleoside triphosphate-dependent RNA-based helicases, which were capable of unwinding the stable double-helical RNAs inevitably formed during RNA syntheses on complementary templates. Thereupon, unwinding RNA polymerases could appear as a result of association or fusion of helicases and polyribonucleotide-polymerizing ribozymes. The latter event provided the mechanism of RNA replication using the double-helical RNAs as a communal genofond (gene pool) of a Darwin pond, and thus initiated the fast evolution of the ancient RNA world.     

Evidence of ancient DNA reveals the first European lineage in Iron Age Central China

Various studies on ancient DNA have attempted to reconstruct population movement in Asia, with much interest focused on determining the arrival of European lineages in ancient East Asia. Here, we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China, and Taiyuan may be the easternmost location of the discovered remains of European lineage in ancient China.     

Evidence that rice and other cereals are ancient aneuploids

Detailed analyses of the genomes of several model organisms revealed that large-scale gene or even entire-genome duplications have played prominent roles in the evolutionary history of many eukaryotes. Recently, strong evidence has been presented that the genomic structure of the dicotyledonous model plant species Arabidopsis is the result of multiple rounds of entire-genome duplications. Here, we analyze the genome of the monocotyledonous model plant species rice, for which a draft of the genomic sequence was published recently. We show that a substantial fraction of all rice genes ( approximately 15%) are found in duplicated segments. Dating of these block duplications, their nonuniform distribution over the different rice chromosomes, and comparison with the duplication history of Arabidopsis suggest that rice is not an ancient polyploid, as suggested previously, but an ancient aneuploid that has experienced the duplication of one-or a large part of one-chromosome in its evolutionary past, approximately 70 million years ago. This date predates the divergence of most of the cereals, and relative dating by phylogenetic analysis shows that this duplication event is shared by most if not all of them.     

News from an ancient world: two novel astacin metalloproteases from the horseshoe crab

In this work, we report the cloning, heterologous expression, and characterization of two novel astacin proteases from the chelicerate Limulus polyphemus (horseshoe crab), designated as LAST (Limulus astacin) and LAST_MAM (Limulus astacin containing a MAM domain), respectively. The expression pattern showed ubiquitous occurrence of LAST_MAM, while LAST was predominantly restricted to the eyes and brain, indicating a function in the nervous system. Both enzymes contain the characteristic metzincin-type zinc-binding region and Met turn. While LAST is made up only of the typical prodomain and astacin-like protease domain, LAST_MAM contains an additional MAM (meprin A5 protein tyrosine phosphatase μ) domain, which so far only has been found in few astacins such as the vertebrate meprin Hydra and squid enzymes, and in a number of other extracellular proteins such as A5 protein and tyrosine phosphatase μ. These gave rise to the designation MAM for this protein module. MAM domains have been shown to be responsible for protein oligomerization in meprin proteases and tyrosine phosphatase μ. Since the horseshoe crab has kept its body plan for almost half a billion years, it is therefore a privileged organism for the study of protease evolution. In this context, we could show by phylogenetic analysis that this protease is not related to the other MAM-domain-containing astacins indicating different evolutionary origins of these proteins. Moreover, we clearly demonstrated the divergent evolvement of the MAM module itself, and not only with regard to proteases. However, there are some unique functional features that are not shared by other members of this protein family. For example, LAST_MAM is the only astacin protease known so far that is active in its zymogen form, indicating that the presence of the N-terminal propeptide does not prevent proteolytic activity.     

Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths

Although the iconic mammoth of the Late Pleistocene, the woolly mammoth (Mammuthus primigenius), has traditionally been regarded as the end point of a single anagenetically evolving lineage, recent paleontological and molecular studies have shown that successive allopatric speciation events must have occurred within Pleistocene Mammuthus in Asia, with subsequent expansion and hybridization between nominal taxa [1, 2]. However, the role of North American mammoth populations in these events has not been adequately explored from an ancient-DNA standpoint. To undertake this task, we analyzed mtDNA from a large data set consisting of mammoth samples from across Holarctica (n = 160) and representing most of radiocarbon time. Our evidence shows that, during the terminal Pleistocene, haplotypes originating in and characteristic of New World populations replaced or succeeded those endemic to Asia and western Beringia. Also, during the Last Glacial Maximum, mammoth populations do not appear to have suffered an overall decline in diversity, despite differing responses on either side of the Bering land bridge. In summary, the "Out-of-America" hypothesis holds that the dispersal of North American woolly mammoths into other parts of Holarctica created major phylogeographic structuring within Mammuthus primigenius populations, shaping the last phase of their evolutionary history before their demise.     

Papio cynocephalus endogenous retrovirus among old world monkeys: evidence for coevolution and ancient cross-species transmissions

To study the evolutionary history of Papio cynocephalus endogenous retrovirus (PcEV), we analyzed the distribution and genetic characteristics of PcEV among 17 different species of primates. The viral pol-env and long terminal repeat and untranslated region (LTR-UTR) sequences could be recovered from all Old World species of the papionin tribe, which includes baboons, macaques, geladas, and mangabeys, but not from the New World monkeys and hominoids we tested. The Old World genera Cercopithecus and Miopithecus hosted either a PcEV variant with an incomplete genome or a virus with substantial mismatches in the LTR-UTR. A complete PcEV was found in the genome of Colobus guereza-but not in Colobus badius-with a copy number of 44 to 61 per diploid genome, comparable to that seen in papionins, and with a sequence most closely related to a virus of the papionin tribe. Analysis of evolutionary distances among PcEV sequences for synonymous and nonsynonymous sites indicated that purifying selection was operational during PcEV evolution. Phylogenetic analysis suggested that possibly two subtypes of PcEV entered the germ line of a common ancestor of the papionins and subsequently coevolved with their hosts. One strain of PcEV was apparently transmitted from a papionin ancestor to an ancestor of the central African lowland C. guereza.