Proboscidean DNA from Museum and Fossil Specimens: An Assessment of Ancient DNA Extraction and Amplification Techniques

Applications of reliable DNA extraction and amplification techniques to postmortem samples are critical to ancient DNA research. Commonly used methods for isolating DNA from ancient material were tested and compared using both soft tissue and bones from fossil and contemporary museum proboscideans. DNAs isolated using three principal methods served as templates in subsequent PCR amplifications, and the PCR products were directly sequenced. Authentication of the ancient origin of obtained nucleotide sequences was established by demonstrating reproducibility under a blind testing system and by phylogenetic analysis. Our results indicate that ancient samples may respond differently to extraction buffers or purification procedures, and no single method was universally successful. A CTAB buffer method, modified from plant DNA extraction protocols, was found to have the highest success rate. Nested PCR was shown to be a reliable approach to amplify ancient DNA templates that failed in primary amplification.     

New fossil anthropoids from the middle Miocene of East Africa and their bearing on the origin of the oreopithecidae

Recent paleontological collections at the middle Miocene locality of Maboko Island in Kenya, dated at 15-16 million years, have yielded numerous new specimens belonging to at least five species of fossil anthropoids. The most common species of ape at the site, a medium-sized primate with a very distinctive dental morphology, clearly represents a previously undescribed taxon. When compared with other Miocene anthropoids from East Africa, it has its closest affinities with the poorly known species Rangwapithecus vancouveringi from the early Miocene locality of Rusinga Island. The species from Maboko Island is described here as belonging to a new genus of fossil anthropoid, to which "Rangwapithecus" vancouveringi is also referred. The new genus has a highly distinctive suite of derived characters of its molars and premolars, which it shares with Oreopithecus bambolii from the late Miocene of Europe. These synapomorphies indicate a close phyletic relationship between the East African species and Oreopithecus and form the basis for the inclusion of these taxa in a single family, the Oreopithecidae Schwalbe, 1915. In many respects, however, the East African forms are more conservative than Oreopithecus, and in a general sense they can be regarded as an intermediate grade between Oreopithecus and the more generalized early Miocene catarrhines, the proconsuloids. There is, therefore, good fossil evidence to indicate that the origins of the Oreopithecidae can be traced back to the early Miocene of Africa.     

Amplification of bacterial genomic DNA by the polymerase chain reaction and direct sequencing after asymmetric amplification: application to the study of periplasmic permeases.

The polymerase chain reaction (PCR) has been used to amplify DNA fragments by using eucaryotic genomic DNA as a template. We show that bacterial genomic DNA can be used as a template for PCR amplification. We demonstrate that DNA fragments at least as large as 4,400 base pairs can be amplified with fidelity and that the amplified DNA can be used as a substrate for most operations involving DNA. We discuss problems inherent in the direct sequencing of the amplified product, one of the important exploitations of this methodology. We have solved the problems by developing an "asymmetric amplification" method in which one of the oligonucleotide primers is used in limiting amounts, thus allowing the accumulation of single-stranded copies of only one of the DNA strands. As an illustration of the use of PCR in bacteria, we have amplified, sequenced, and subcloned several DNA fragments carrying mutations in genes of the histidine permease operon. These mutations are part of a preliminary approach to studying protein-protein interactions in transport, and their nature is discussed.     

The thermal history of human fossils and the likelihood of successful DNA amplification

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.     

Mid-Tertiary elapid snakes (Squamata, Colubroidea) from Riversleigh, northern Australia: early steps in a continent-wide adaptive radiation

Vertebral and cranial remains of elapid snakes have been collected from fossil assemblages at Riversleigh, north-west Queensland, Australia; most are Miocene but one may be late Oligocene and another as young as Pliocene. The oldest specimen (probably the oldest elapid yet known anywhere) is a vertebra that can be referred provisionally to the extant taxon Laticauda (Hydrophiinae, sensu Slowinski and Keogh, 2000), implying that the basal divergences among Australasian hydrophiine lineages had occurred by the early Miocene, in contrast to most previous estimates for the age of this geographically isolated adaptive radiation. Associated vertebrae and jaw elements from a Late Miocene deposit are described as Incongruelaps iteratus nov. gen. et sp., which has a unique combination of unusual derived characters otherwise found separately in several extant hydrophiine taxa that are only distantly related. Associated vertebrae from other sites, and two parietals from a possibly Pliocene deposit, suggest the presence of several other taxa distinct from extant forms, but the amount of material (and knowledge of variation in extant taxa) is currently insufficient to diagnose these forms. The Tertiary elapids of Riversleigh thus appear to be relatively diverse taxonomically, but low in abundance and, with one exception, not referable to extant taxa below the level of Hydrophiinae. This implies that the present diversity of hydrophiine elapids (31 recognized terrestrial genera, and approximately 16 marine) represents the result of substantial extinction as well as the “cone of increasing diversity” that could be inferred from phylogenetic studies on extant forms.     

Sequencing PCR DNA amplified directly from a bacterial colony

We show that PCR product asymmetrically amplified directly from a bacterial colony can be sequenced to yield results as good as those obtained when purified template DNA is used for the PCR amplification step. With either template, greater than 300 nucleotides can be read from a typical sequencing reaction. Taq DNA polymerase was used for both the PCR amplification and sequencing reactions.     

Genotyping and haplotyping of polymorphisms directly from genomic DNA via coupled amplification and sequencing (CAS).

Coupled amplification and sequencing (CAS) allows a segment of DNA to be sequenced directly from genomic DNA. An initial PCR amplification stage selects and amplifies the target. During a subsequent stage both strands of the target segment are sequenced simultaneously and amplified further. We show that CAS can readily identify variant base pairs. Genotyping of a population for known sequence variation can be achieved simply and directly from genomic DNA of each organism by performing CAS only for the variant bases. The procedure supercedes development and optimization of alternative typing assays based on oligonucleotide hybridization or ligation. In addition, we show that competitive oligonucleotide priming with allelic primers can be readily performed in concert with the second stage of CAS. The combination of techniques allows sequencing of a single chromosome from a heterozygous genomic sample and direct haplotyping of the polymorphism at the priming site with any others encompassed within the amplified segment.     

A comprehensive phylogeny of extinct and extant Rhizomyinae (Rodentia): evidence for multiple intercontinental dispersals

The subfamily Rhizomyinae is known from the Late Oligocene up to the present. Today this group comprises six species, which live in southern Asia and eastern Africa. Despite the current moderate diversity of the rhizomyines, they had a greater diversification and wider distribution in the past: from Asia, their land of origin, to Africa, which they entered during the Early Miocene. So far 33 fossil species can be referred to this group. A cladistic analysis involving fossil and living species has been carried out. Prokanisamys spp. turned out to be the most basal taxa of the ingroup. This analysis calls into question the monophyly of several genera, and allows the proposal of a phylogenetic definition of the tribes Tachyoryctini and Rhizomyini. It also provides information about the origin of the African rhizomyines and allows inferring multiple dispersal phenomena from Asia to Africa in Early and Late Miocene times.     

Enamel thickness,microstructure and development in Afropithecus turkanensis

Afropithecus turkanensis, a 17-17.5 million year old large-bodied hominoid from Kenya, has previously been reported to be the oldest known thick-enamelled Miocene ape. Most investigations of enamel thickness in Miocene apes have been limited to opportunistic or destructive studies of small samples. Recently, more comprehensive studies of enamel thickness and microstructure in Proconsul, Lufengpithecus, and Dryopithecus, as well as extant apes and fossil humans, have provided information on rates and patterns of dental development, including crown formation time, and have begun to provide a comparative context for interpretation of the evolution of these characters throughout the past 20 million years of hominoid evolution. In this study, enamel thickness and aspects of the enamel microstructure in two A. turkanensis second molars were quantified and provide insight into rates of enamel apposition, numbers of cells actively secreting enamel, and the time required to form regions of the crown. The average value for relative enamel thickness in the two molars is 21.4, which is a lower value than a previous analysis of this species, but which is still relatively thick compared to extant apes. This value is similar to those of several Miocene hominoids, a fossil hominid, and modern humans. Certain aspects of the enamel microstructure are similar to Proconsul nyanzae, Dryopithecus laietanus, Lufengpithecus lufengensis, Graecopithecus freybergi and Pongo pygmaeus, while other features differ from extant and fossil hominoids. Crown formation times for the two teeth are 2.4-2.6 years and 2.9-3.1 years respectively. These times are similar to a number of extant and fossil hominoids, some of which appear to show additional developmental similarities, including thick enamel. Although thick enamel may be formed through several developmental pathways, most Miocene hominoids and fossil hominids with relatively thick enamel are characterized by a relatively long period of cuspal enamel formation and a rapid rate of enamel secretion throughout the whole cusp, but a shorter total crown formation time than thinner-enamelled extant apes.     

Morphology of the hallucial phalanges in extant anthropoids and fossil hominoids

Pedal phalanges of living anthropoids and several Miocene fossil hominoid taxa were studied to reveal functional adaptations of living anthropoid feet and to infer positional behavior of fossil hominoids. Among the examined living anthropoids, Pan has a very developed (long and robust) hallux. Proconsul and Nacholapithecus, a large hominoid from Nachola, northern Kenya, display a moderately long hallux like Alouatta and Cebus, suggesting the well-developed capability of a hallux-assisted power grip. Allometric analyses revealed that the Miocene hominoids examined (mainly from East Africa) as a whole displayed a different scaling pattern about the width of the proximal articular surface of the hallucial terminal phalanx from that of living anthropoids. Larger-sized hominoids display a wider articular surface than comparable-sized living anthropoids while smaller-sized fossil hominoids do the reverse. Such a difference was less marked for the height of the articular surface. These results may suggest that positional adaptations of Miocene hominoids are not merely resultants of a common body size function that is observed in living anthropods. The wide articular surface of fossil hominoid hallucial terminal phalanges suggests an adaptation for vertical climbing and clinging, in which the hallux is kept perpendicularly to the long axis of the vertical support.     

The phylogenetic affinities of Otavipithecus namibiensis

The middle Miocene hominoid Otavipithecus namibiensis is the first and most complete fossil ape from sub-equatorial Africa and represents a significant addition to the taxonomically sparse African middle Miocene hominoid fossil record. The Otavipithecus hypodigm comprises the holotype mandible, which presents a unique mosaic of dental and gnathic characters, and several attributed cranial and postcranial elements which resemble the stem hominoid Proconsul. Contrary to initial hopes that this discovery would provide new insights into hominoid morphological diversity and phylogenetic relationships, a variety of conflicting phylogenetic hypotheses have been advanced suggesting ties to virtually every major large-bodied hominoid group (Conroy et al., 1992; Andrews, 1992 a; Conroy, 1994; Pickford et al., 1994; Begun, 1994 a). Cladistic analysis of a matrix of 22 qualitative and ten quantitative characters of the mandible and mandibular dentition found no support for a close phylogenetic relationship between Otavipithecus and either the African ape or great ape clades, or with any of the Eurasian fossil hominoids with which it has previously been compared. A close relationship between Otavipithecus and Kenyapithecus cannot be ruled out, but is deemed unlikely on the basis both of morphological comparisons and the absence of support within a cladistic framework. The present analysis indicates that Otavipithecus is most closely related to Afropithecus, as previously suggested by Andrews (1992 a) among others. Due to lack of statistical support for this result, a conservative interpretation, that these taxa represented related but divergent lineages of a late early Miocene hominoid radiation, is currently favored. Findings are consistent with the allocation of Otavipithecus to Andrews' (1992 a) tribe Afropithecini which represents the sister group to Kenyapithecus and the extant ape clade.     

Fossil avian eggshell preserves ancient DNA

Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.     

甜菜碱增强长片段PCR的扩增

聚合酶链式反应(PCR)作为一项非常成熟的技术可以用于基因组序列的扩增。普通的PCR技术只适合于短片段DNA的扩增,一般在6kb以下。对于6kb至十几kb甚至几十kb以上的DNA片段的扩增就非常困难。通过添加不同化学物质,发现甜菜碱对长片段PCR的扩增有非常有效的增强作用。通过对玉米总DNA以及质粒DNA的扩增,发现1mol／L到2．5mol／L甜菜碱对改进PCR扩增效果明显。通过添加甜菜碱,可以从玉米基因组中扩增出9kb以上的单拷贝片段,从质粒中扩增出16kb以上片段。经过试验,发现不同GC含量的引物需要使用不同浓度的甜菜碱。甜菜碱可以减少甚至消除长片段PCR中的非特异性扩增。同时,我们发现其它的添加物,如DMSO,甘油,甲酰胺对长片段PCR的作用不明显。     

Stickleback fishes: Bridging the gap between population biology and paleobiology

Integration of evolutionary mechanisms and phylogeny requires study of phenotypes that change in the fossil record and continue to evolve in extant populations. Pelvic reduction in the three-spined stickle-back has evolved rapidly in a Miocene fossil assemblage and in numerous extant isolated lake populations throughout its distribution. Although pelvic reduction is caused by selection, expression of reduced pelvic phenotypes is constrained by development and other factors. However, lineages with pelvis reduction rapidly go extinct while lineages that retain the fully formed pelvic girdle tend to persist. Existence of pelvic reduction since the Miocene has depended on an equilibrium between divergence and extinction. The phylogenetic topology resulting from this process differs greatly from the conventional view of evolutionary history, and could only be recognized by analysis of both extant populations and fossil material. If this phylogenetic topology is common, it may help to account for the different perceptions that population biologists and paleobiologists have of evolutionary tempo.     

Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations

We sequenced 2167 base pairs (bp) of mitochondrial DNA cytochrome b and 16S, and 1390 bp of nuclear genes BRCA1 and ApoB in shrews taxa (Eulipotyphla, family Soricidae). The aim was to study the relationships at higher taxonomic levels within this family, and in particular the position of difficult clades such as Anourosorex and Myosorex. The data confirmed two monophyletic subfamilies, Soricinae and Crocidurinae. In the former, the tribes Anourosoricini, Blarinini, Nectogalini, Notiosoricini, and Soricini were supported. The latter was formed by the tribes Myosoricini and Crocidurini. The genus Suncus appeared to be paraphyletic and included Sylvisorex. We further suggest a biogeographical hypothesis, which shows that North America was colonized by three independent lineages of Soricinae during middle Miocene. Our hypothesis is congruent with the first fossil records for these taxa. Using molecular dating, the first exchanges between Africa and Eurasia occurred during the middle Miocene. The last one took place in the Late Miocene, with the dispersion of the genus Crocidura through the old world.     

A succession of Miocene rodent assemblages from fissure fillings in southern France: palaeoenvironmental interpretation and comparison with Spain

An Early to Late Miocene sequence of rodent assemblages from southern France has been quantitatively studied. The resulting pattern seems very similar to a contemporary sequence from central Spain (Calatayud–Teruel Basin). The fossil mammal-bearing localities are of different types: mainly karst infills in France and localities situated in sedimentary basins in Spain. In order to interpret the fossil record, a comparison has been made between southern France faunas of similar age but collected in karst infills and in basin deposits. There seems to be no difference between the two kinds of faunas and thus there is no indication that karst infills systematically give a picture of drier and more open environments. Both types of localities may give a similar relative abundance of taxa and when differences exist they can be attributed to local conditions. The comparison between southern France and the Calatayud–Teruel Basin (central Spain) shows that: (1) similar trends occurred in the two areas; (2) differences between spectra were more important during the late Early Miocene than during the Middle Miocene; (3) the shift between the late Early Miocene and the Middle Miocene environments in southern France does not seem to be correlated with a general drop in temperatures as inferred from the analysis of central Spain faunas.     

FOSSIL BLOOD DROPLETS IN MIOCENE DOMINICAN AMBER YIELD CLUES TO SPEED AND DIRECTION OF RESIN SECRETION

Abstract:  Two spiders (Filistatidae) in Miocene Dominican Republic amber, one newly identified and only the second known fossil of this family, have autospasized legs (detached at a predetermined locus of weakness when restrained by a non-self-induced source) at the patella-tibia joint. In both specimens, droplets of haemolymph (blood) are preserved exiting the patellae. The autospasized legs and the presence of haemolymph suggests that both spiders were engulfed in rapid-flowing resin seeps of relatively low viscosity, rather than having wandered onto a sticky exudate, becoming stuck and then covered by a subsequent resin flow. These are the first reported incidences of such fossilized blood droplets, the shape, size and position of which provide clues to preservational taphonomy, an understanding of which is necessary for reliable conclusions concerning fossil communities and ecosystems. In addition, haemolymph droplets may serve as reservoirs for fossil DNA.     

New fossil leaves and fruits of Lauraceae from the Middle Miocene of Fujian,southeastern China differentiated using a cluster analysis

The fossil record of Lauraceae can be traced back to the Early Cretaceous of eastern Asia based on fossil flowers. Here, we refer a number of new occurrences of leaf and fruit fossils of Lauraceae from the Middle Miocene of Zhangpu, Fujian, China, to seven species. These data provide evidence supporting the fact that a diverse subtropical, or tropical, Lauraceae-dominated evergreen forest surrounded this region 15 million years ago (Mya). The Lauraceae fossils presented in this paper provide evidence for the evolution of this group as well as new materials that enable the study of the Fujian Province Neogene flora. The fossils described in this paper fill in the gaps in studies about Lauraceae pollen in the Middle Miocene from Fotan, Fujian, China. In addition, these fossils also enrich the Middle Miocene fossil records of Lauraceae in eastern Asia, especially improving the study of the macrostructures and reproductive organs of fossil Lauraceae from southern China. The similarity between fossil and modern fruits shows that during the Middle Miocene the fruit morphological of Lauraceae have changed very little. We also identify families where the fossils we report belong to their closest relatives and can be used to reconstruct the paleoenvironment of Fujian in the Middle Miocene.     

Hominoid phalanges from the middle Miocene site of Paşalar, Turkey

Eleven proximal and ten intermediate partial or complete hominoid phalanges have been recovered from the middle Miocene site of Pa?alar in Turkey. Based on species representation at Pa?alar, it is likely that most or all of the phalanges belong to Griphopithecus alpani rather than Kenyapithecus kizili, but both species may be represented. All of the complete or nearly complete phalanges appear to be manual, so comparisons to extant and other fossil primate species were limited to manual phalanges. Comparisons were made to extant hominoid and cercopithecoid primate genera expressing a variety of positional repertoires and varying degrees of arboreality and terrestriality. The comparisons consisted of a series of bivariate indices derived from previous publications on Miocene catarrhine phalangeal morphology. The proximal phalanges have dorsally expanded proximal articular surfaces, which is characteristic of cercopithecoids and most other Miocene hominoids, and indicates that the predominant positional behaviors involved pronograde quadrupedalism. Among the extant primates, many of the proximal and intermediate phalangeal indices clearly distinguish more habitually terrestrial taxa from those that are predominantly arboreal, and especially from taxa that commonly engage in suspensory activities. For nearly every index, the values of the Pa?alar phalanges occupy an intermediate position-most similar to values for Pan and, to a lesser extent, Macaca-indicating a generalized morphology and probably the use of both arboreal and terrestrial substrates. At least some terrestrial activity is also compatible with reconstructions of the Pa?alar habitat. Most proximal and intermediate phalanges of other middle and late Miocene hominoids have similar index values to those of the Pa?alar specimens, revealing broadly similar manual phalangeal morphology among many Miocene hominoids.