Yolanda Fernández-Jalvo

Freshly excavated fossil bones are best for amplification of ancient DNA.

Despite the enormous potential of analyses of ancient DNA for phylogeographic studies of past populations, the impact these analyses, most of which are performed with fossil samples from natural history museum collections, has been limited to some extent by the inefficient recovery of ancient genetic material. Here we show that the standard storage conditions and/or treatments of fossil bones in these collections can be detrimental to DNA survival. Using a quantitative paleogenetic analysis of 247 herbivore fossil bones up to 50,000 years old and originating from 60 different archeological and paleontological contexts, we demonstrate that freshly excavated and nontreated unwashed bones contain six times more DNA and yield twice as many authentic DNA sequences as bones treated with standard procedures. This effect was even more pronounced with bones from one Neolithic site, where only freshly excavated bones yielded results. Finally, we compared the DNA content in the fossil bones of one animal, a ≈3,200-year-old aurochs, excavated in two separate seasons 57 years apart. Whereas the washed museum-stored fossil bones did not permit any DNA amplification, all recently excavated bones yielded authentic aurochs sequences. We established that during the 57 years when the aurochs bones were stored in a collection, at least as much amplifiable DNA was lost as during the previous 3,200 years of burial. This result calls for a revision of the postexcavation treatment of fossil bones to better preserve the genetic heritage of past life forms.

Diagenetical changes in Pleistocene small mammal bones from Olduvai Bed I

Abstract Fossil bones of small mammals from two levels at Olduvai Bed I (Tanzania) were analysed for a range of elements using electron microprobe techniques. Comparison of the fossil samples is made with those of recent samples collected from close to the Natron alkaline lake (Tanzania). Values for the elements Na, Sr, Ba are significantly higher, and S lower in the fossil samples relative to the recent samples. In addition, concentrations of the rare earth elements reach exceptionally high concentration levels (i.e. > 6 wt.%) in one of the sites, whereas these elements are not detected in the recent samples. The high concentrations of these elements in the fossil samples are clearly a result of diagenetic alteration, although the effects of digestion are likely to have had some influence on the processes involved in the incorporation of elements during fossilisation. Statistical analyses show there are significant differences in the chemical compositions of fossil bones from two levels in Bed I. Observed changes in the rare earth element patterns, in particular the Ce anomaly, suggest that relative differences in the redox potentials of the burial and depositional environments existed at the two levels. Fluctuations in the size and extent of the palaeolake are considered to be the likely cause of these differences.

The Atapuerca sites and the ibeas hominids

The Atapuerca railway Trench and Ibeas sites near Burgos, Spain, are cave fillings that include a series of deposits ranging from below the Matuyama/Bruhnes reversal up to the end of Middle Pleistocene. The lowest fossil-bearing bed in the Trench contains an assemblage of large and small Mammals includingMimomys savini, Pitymys gregaloides, Pliomys episcopalis, Crocuta crocuta, Dama sp. and Megacerini; the uppermost assemblage includesCanis lupus, Lynx spelaea, Panthera (Leo) fossilis, Felis sylvestris, Equus caballus steinbeimensis, E.c. germanicus, Pitymys subterraneus, Microtus arvalis agrestis, Pliomys lenki, and alsoPanthera toscana, Dicerorbinus hemitoechus, Bison schoetensacki, which are equally present in the lowest level. The biostratigraphic correlation and dates of the sites are briefly discussed, as are the paleoclimatic interpretation of the Trench sequences. Stone artifacts are found in several layers; the earliest occurrences correspond to the upper beds containingMimomys savini. A set of preserved human occupation floors has been excavated in the top fossil-bearing beds. The stone-tool assemblages of the upper levels are of upper-medial Acheulean to Charentian tradition. The rich bone breccia SH, in the Cueva Mayor-Cueva del Silo, Ibeas de Juarros, is a derived deposit, due to a mud flow that dispersed and carried the skeletons of many carnivores and humans. The taxa represented are:Ursus deningeri (largely dominant),Panthera (Leo) fossilis, Vulpes vulpes, Homo sapiens var. Several traits of both mandibular and cranial remains are summarized. Preliminary attempts at dating suggest that the Ibeas fossil man is older than the Last Interglacial, or oxygen-isotope stage 5.

The Azokh Cave complex: Middle Pleistocene to Holocene human occupation in the Caucasus.

Azokh Cave is located near the village of the same name in the Nagorno-Karabagh region of the south-eastern part of the Lesser Caucasus (3937.09’ N and 4659.19’ E, 962 metres –a.s.l.). Azokh Cave and other relevant Acheulian sites in the Caucasus (Fig. 1) were described by Lioubine (2002). Together with Mousterian sites (Klein, 1969, 1999; Hoffecker and Cleghorn, 2000; Hoffecker, 2002; Stringer and Andrews, 2005) and sites producing evidence of the Middle-Late Palaeolithic transition (Joris and Adler 2008), the Caucasus region has provided evidence of continuous human settlement of the area throughout the Pleistocene. The geographical location of these sites indicates the persistence of a natural corridor that Lioubine (2002) named the ‘Caucasus isthmus’ and which we describe as the Trans-Caucasian corridor. Based on a geological survey of Quaternary deposits in collaboration with the Armenian Academy of Sciences (Ferna´ndez-Jalvo et al., 2004; King et al., 2003), we observe that the topography of the area has changed considerably due to tectonic compression and periglacial isostasy. This is in agreement with estimations by GPS studies (Mosar, 2006, Mosar et al., 2007) and ESR (Gru¨n et al., 1999) that establishedan uplift rate of12 to14 mm/year or 0.8–1.0 cm/year, respectively. The corridor has changed greatly since the middle Pleistocene, with uplift and erosion altering the landscape, but it is likely that passage through the Caucasian mountains has always been possible. The Trans-Caucasian corridor and other routes via Turkey and towards Asia (Bar-Yosef and Belfer-Cohen, 2001) were migration pathways during the Pleistocene. Fossil humans in the Caucasian area are scarce. The site of Dmanisi in Georgia yielded the earliest known Eurasian hominins (1.7 Ma, Gabunia et al., 2000; Rightmire et al., 2006; Martino´ n- Torres et al., 2008). Late surviving Neanderthals are present at several sites: Mezmaiskaya Cave, in the Northern Caucasus of Russia (30 ka, Skinner et al., 2005), provided remains of late surviving Neanderthals; a mandible of a 2–3 year old Neanderthal child was found at Barakay Cave (North Caucasus; Lubin et al., 2002). Two incisor fragments and one premolar from Kudaro I may be human (Lioubine, 2002). In this context, Azokh Cave fills an important temporal gap. Azokh Cave contains a nearly continuous stratigraphic section from >300 ka to the present, and mandible fragments of Homo heidelbergensis found at the site (Kasimova, 2001) represent the easternmost extent of this species. Here we review the finds of this long forgotten site and present results of our recent work.

Introduction and Rationale

I HAVE long wanted to write a book on venture capital but felt it was necessary to obtain sufficient experience before undertaking the task in order to be able to talk or, more accurately, write from strength. After over thirty years of practical experience, I believe that the time has come to put pen to paper before it is too late. In doing so, I realise that I am risking the wrath, albeit posthumously, of the Field Marshal who is supposed to have said ‘there is a book in everyone but that is where it should stay.’

Taphonomy and Site Formation of Azokh 1

This chapter aims to describe the complete scenario that existed during the Middle Pleistocene in Azokh Caves and the Lesser Caucasus area from the evidence provided by the fossil assemblages recovered from excavations between 2002 and 2009. In the case of Azokh 1, taphonomic studies are particularly relevant since there is no such information from the early phase of excavations (1960–1980), during which much of the sediment was removed. This study, based on the taphonomy of large mammals, has allowed us to distinguish two sources of the large mammal fauna. Cave bear remains accumulated as a result of hibernation, and some of the carcasses were butchered by hominins in situ. The other faunal remains, mainly herbivores, were brought by hominins, but butchering took place somewhere else, not at the rear of the cave where they have been found. There is no evidence for simultaneous occupation of the cave by bears and hominins. There is also no evidence of human occupation at the rear of the cave, and they may have occupied the mouth of the cave during summer time. Cave bears could enter in winter-spring and occupied the rear of the cave. When the cave sediments reached close to the cave roof, bats occupied areas previously inhabited by bears and visited by hominins. Minerals neo-formed in fossils and sediments indicate seasonal changes in humidity and temperature inside the cave during the Pleistocene. Bat guano and corrosive fluid percolation caused strong corrosion on fossils after burial, damaging bones to such an extent that some of them could not be recovered. Bat guano was especially harmful to collagen, which is not preserved in most bones. Finally, during the Holocene, the top of the sequence was eroded by high energy water that removed the upper part of the sediments and opened the cave again to humans and animals.

The New Material of Large Mammals from Azokh and Comments on the Older Collections

During the 1960s to 1980s a human mandible, together with fossils of other animals and a lithic industry, were recovered from Units I to VI of Azokh Cave. After the year 2002, new excavations in Units I to V were undertaken. The new large mammal fossils are described and the fauna is revised, using part of the older collections. The only clear break in the sequence is the appearance of domestic mammals in Unit I. The following taxa recovered from Pleistocenic sediments were identified: Ursus spelaeus (the most abundant), Ursus sp. (U. aff. arctos/thibetanus), Vulpes vulpes, Canis aureus, Canis lupus, Meles meles, Martes cf. foina, Crocuta crocuta, Felis chaus, Panthera pardus, Equus hydruntinus, Equus ferus, Stephanorhinus hemitoechus, Stephanorhinus kirchbergensis, Sus scrofa, Capreolus pygargus, Dama aff. peleponesiaca, Dama sp., Megaloceros solilhacus, Cervus elaphus, Bison schoetensacki, Ovis ammon, Capra aegagrus and Saiga. Most species present are common in western Eurasia. All fossiliferous Units have taxa that in mid-latitude Europe are considered to be “interglacial” elements, while there are no clear “glacial” elements, which suggests temperate conditions despite the altitude of the cave. The evolutionary levels of various species suggest ages of about 300 ka for Units VI–IV, while Units III–II are slightly younger. Domestic mammals indicate a Holocene age for Unit I. Most sediments represent a normal transition between units. Processes of erosion, however, affected the top of the Pleistocene sediments recorded in the cave. Therefore, Unit I (Holocene sediments containing domestic animals) lies disconformably over Unit II (Late Pleistocene).

Introduction: Azokh Cave and the Transcaucasian Corridor

Azokh Cave (also known as Azikh or Azykh) contains Pleistocene and Holocene stratified sediment infill. The site was discovered by M. Huseinov (also named Guseinov by other authors) who led the previous phase of excavations. The geographic location of the site is at an important migratory route between Africa and Eurasia. The site has yielded Middle Pleistocene hominin remains (a mandible fragment) recovered in the 1960s during a previous phase of excavation work, together with Acheulean (Mode 2) stone tools and contemporaneous fauna. An important characteristic of the Azokh 1 cave site is a continuous sedimentary record along a 7 m section, ranging in age from Middle Pleistocene (MIS 9-8) to Late Pleistocene (Mousterian industry/Mode 3, MIS 5), and to Holocene periods at the top of the series. This detailed record documents three species of Homo: ancestors of Neanderthals, Homo neanderthalensis and Homo sapiens. In addition, two new fossiliferous sites, Azokh 2 and Azokh 5 (which are currently being explored), constitute a potential new source of information, especially about the Middle to Late Paleolithic transition and Holocene periods in the area. Plans for preservation and protection of the whole site are currently in progress.

Combustion at the late Early Pleistocene site of Cueva Negra del Estrecho del Río Quípar (Murcia, Spain)

Abstract Control of fire was a hallmark of developing human cognition and an essential technology for the colonisation of cooler latitudes. In Europe, the earliest evidence comes from recent work at the site of Cueva Negra del Estrecho del Río Quípar in south-eastern Spain. Charred and calcined bone and thermally altered chert were recovered from a deep, 0.8-million-year-old sedimentary deposit. A combination of analyses indicated that these had been heated to 400–600°C, compatible with burning. Inspection of the sediment and hydroxyapatite also suggests combustion and degradation of the bone. The results provide new insight into Early Palaeolithic use of fire and its significance for human evolution.

Paleoecology of Azokh 1

The fauna and flora from Azokh 1 are analyzed to provide evidence on past and present environments. The large mammal fauna was accumulated by carnivore and human agents, and it is dominated by woodland species. The small mammals, amphibians and reptiles were accumulated mainly by avian predators, barn owls and eagle owls which hunt over open areas, and their prey may have been brought to the cave from some distance away. The amphibians and reptiles indicate warm dry conditions, with some taxa specific to mountainous regions and many indicating warm arid conditions. The small mammals similarly indicate mainly arid environments with minor elements from deciduous woodland. The difference between small vertebrates and large mammals is taphonomic, and all four groups indicate slight transition to more arid conditions up the section. Bats are present in all units, and it appears likely that they are derived from natural deaths within the cave. They indicate woodland conditions low in the section changing to a treeless, arid and cold environment towards the top. Plant data from charcoal indicate that the regional vegetation was broadleaved deciduous woodland with mainly small trees and shrubs. The location of the cave on the lower slopes of the mountains of the Lesser Caucasus is close to the forest/steppe boundary, with forest on the mountain slopes and steppe on the lowlands to the east, and relatively minor fluctuations in climate would shift the boundary or and down slope, towards or away from the cave, with changes in climate. It is concluded, therefore, that the large mammals and flora represent the local woodland environment, and the small mammals, reptiles and amphibians represent prey species brought from further away.