Short sequence effect of ancient DNA on mammoth phylogenetic analyses

The evolution of Elephantidae has been intensively studied in the past few years, especially after 2006. The molecular approaches have made great contribution to the assumption that the extinct woolly mammoth has a close relationship with the Asian elephant instead of the African elephant. In this study, partial ancient DNA sequences of cytochrome b (cyt b) gene in mitochondrial genome were successfully retrieved from Late Pleistocene Mammuthus primigenius bones collected from Heilongjiang Province in Northeast China. Both the partial and complete homologous cyt b gene sequences and the whole mitochondrial genome sequences extracted from GenBank were aligned and used as datasets for phylogenetic analyses. All of the phylogenetic trees, based on either the partial or the complete cyt b gene, reject the relationship constructed by the whole mitochondrial genome, showing the occurrence of an effect of sequence length of cyt b gene on mammoth phylogenetic analyses.     

青海共和盆地猛犸象化石的发现及意义

在青海共和盆地晚更新世河湖相沉积地层中发现了象类化石,对化石的基本特征进行了描述,依据牙片的釉质层、齿脊频率等特征初步鉴定为猛犸象类化石,并在同一层位发现了钙化树木化石.结合区域地质以及产出猛犸象属化石地层的沉积学特征、孢粉组合等的简要分析认为,共和盆地晚更新世晚期为干燥寒冷的气候环境.这一发现有助于认识中国猛犸象属动物的迁徙过程,以及青藏高原晚更新世的生物演化、气候变化和构造活动.同时,也为研究青藏高原第四纪以来生物进化、湖泊与河流演化、气候变化、古地理与古环境变迁等提供了新资料.     

Mammoth tooth enamel growth rates inferred from stable isotope analysis and histology

Mammoth (Mammuthus sp.) teeth are relatively abundant in Quaternary deposits from Eurasia and North America, and their isotopic compositions can be used to reconstruct past seasonal patterns in precipitation, diet, and migration. Strategies for collecting and interpreting such data, however, are strongly dependent on growth rates, which can vary among species, individuals, and within teeth. In this study, we use histological and isotopic measurements to determine enamel growth rates for a Columbian mammoth (Mammuthus columbi) tooth in two directions. Using histology, the growth rate through the enamel thickness (ET; perpendicular to the height of the tooth) is estimated at 0.8 to 1.5 mm/yr. Isotopic sampling through the innermost 0.36 mm of the ET recovered less than half a period of variation (i.e., half an inferred year of growth), which is consistent with the histological estimate for ET growth rate. A combination of histological and isotopic measurements suggests that the enamel extension rate (growth in the height of the tooth) is 13–14 mm/yr. Knowledge of enamel growth rates should improve the design and interpretation of future isotopic studies of mammoth teeth. The combination of histological and isotopic measurements may also prove useful in determining growth rates for other extinct taxa.     

Pleistocene vertebrates of the Yukon Territory

Unglaciated parts of the Yukon constitute one of the most important areas in North America for yielding Pleistocene vertebrate fossils. Nearly 30 vertebrate faunal localities are reviewed spanning a period of about 1.6 Ma (million years ago) to the close of the Pleistocene some 10 000 BP (radiocarbon years before present, taken as 1950). The vertebrate fossils represent at least 8 species of fishes, 1 amphibian, 41 species of birds and 83 species of mammals. Dominant among the large mammals are: steppe bison (Bison priscus), horse (Equus sp.), woolly mammoth (Mammuthus primigenius), and caribou (Rangifer tarandus) – signature species of the Mammoth Steppe fauna (Fig. 1), which was widespread from the British Isles, through northern Europe, and Siberia to Alaska, Yukon and adjacent Northwest Territories. The Yukon faunas extend from Herschel Island in the north to Revenue Creek in the south and from the Alaskan border in the west to Ketza River in the east. The Yukon holds evidence of the earliest-known people in North America. Artifacts made from bison, mammoth and caribou bones from Bluefish Caves, Old Crow Basin and Dawson City areas show that people had a substantial knowledge of making and using bone tools at least by 25 000 BP, and possibly as early as 40 000 BP. A suggested chronological sequence of Yukon Pleistocene vertebrates (Table 1) facilitates comparison of selected faunas and indicates the known duration of various taxa.     

Identifying remains of extinct kangaroos in Late Pleistocene deposits using collagen fingerprinting

Our knowledge of past animal populations, including the geographical ranges of extinct species, has largely been derived from morphological analyses of skeletal fossil remains. However, a major barrier to the identification of the remains of extinct megafaunal species in archaeological and palaeontological sites is the highly fragmented nature of the material, which often precludes confident taxonomic identifications based on morphology. Biomolecular techniques are able to go beyond these limitations and are increasingly being used to make such identifications. Protein analysis offers a promising alternative to DNA techniques because they can be much cheaper, more amenable to high‐throughput processing and work on much older specimens. Here we demonstrate the potential of collagen fingerprinting in an Australian context by extracting collagen from 50‐ka kangaroo fossils from two caves in Tasmania, and identify several species including the extinct short‐faced kangaroo Simosthenurus occidentalis . Importantly, of the five fossil bones sampled that had hitherto been ascribed morphology‐based identifications below the family level, three had been incorrectly identified during an initial assessment of photographs taken in the field. Our results highlight the utility of using protein‐based methods for making genus‐level identification of marsupial bone, especially those that may form a basis for broader arguments such as that of late‐surviving megafaunal species.

     

The first water measurers from the Lower Cretaceous amber of Spain (Heteroptera,Hydrometridae, Heterocleptinae)

Two fossils belonging to a new genus and species of water measurer (Gerromorpha, Hydrometridae), Alavametra popovi Sánchez-García and Nel gen. n., sp. n., are described as first definitive record of the family in Lower Cretaceous (upper Albian) amber from the Utrillas Group (Peñacerrada I site) in Spain. Although several parts of the specimens are obscured due to preservation, a sufficient number of taxonomical characters are visible to consider adequate placement within Heterocleptinae, including the very long posterior pair of cephalic trichobothria inserted on tubercles and the preapical articulation between the first and second antennal segments. The new fossil taxon is included into a cladistic analysis with extinct and extant hydrometrids, and it results putatively basal among the subfamily Heterocleptinae, suggesting that this clade was already present 105 Ma ago.     

Chronology and new research on the Schaefer mammoth (?Mammuthus primigenius) site,Kenosha County,Wisconsin, USA

A summary of previous and new research on the Schaefer mammoth site is presented. The Schaefer site in extreme southeastern Wisconsin, USA was excavated in 1992 and 1993. Seventy-five percent of a mammoth ?Mammuthus primigenius, the woolly mammoth (but comparable as well with M. jeffersonii, the Jefferson mammoth) was recovered. Drifted wood specimens and plant macro fossils were also recovered from the site.Twenty-five specimens of wood have been identified as Picea sp., Picea/Larix sp., or unidentified hardwood. Macro fossils in the form of cones have been identified as black spruce (Picea mariana). These preliminary data do not appear to support the traditional environment inferred for the woolly mammoth and points to a need for study of the animal's attribution to species. The animal was a male, 36 years of age at death.Thirteen AMS 14C assays on bone cluster between 12,290 and 12,570 BP. Sixteen dates on wood specimens intimately associated with bone yield a range of dates from 11,980 to 12,940 BP.The remains exhibit multiple cut and wedge marks interpreted as cultural. Non-diagnostic cultural lithics were recovered. A disarticulated bone pile deposited in a low energy environment is consistent with human interaction.     

Taphonomy of two last glacial maximum mammoth sites in the central Great Plains of North America: A preliminary report on La Sena and Lovewell

Two mammoth sites from the central Great Plains of North America, each containing one adult Columbian mammoth (Mammuthus columbi), were excavated from Last Glacial Maximum (LGM) loess and fine-grained alluvial deposits, respectively. Taphonomic data from both sites indicate that the mammoth skeletons exhibit numerous spirally fractured limb elements. Dynamic loading points are present on midshafts of large limb bones. Bone flakes produced from the partial thickness of thick cortical bone are also present. Hypotheses of carnivore activity, mammoth trampling, and human-induced fracturing are evaluated as possible causes of the fractured limb bone. Testing the hypotheses using modern data from actualistic taphonomic studies of elephant skeletons, paleontological data from two proboscidean natural death sites, experimental data from elephant bone fracturing, and archaeologically derived data concerning late Pleistocene human modification of mammoth limb bone indicates that the first two hypotheses can be rejected, while the third hypothesis is supported.     

FOSSIL MAMMALS FROM TAIWAN

Mammal fossils were first discovered on Taiwan by H. Saitō in 1926. Skulls and teeth fragments of Rhinoceros, Elephas, and Stegodon were discovered subsequently in transported float; the source bed, Tertiary gravels of the Kichō formation, was found in 1940 by Kaneko. The Tso-chen area alone has yielded specimens of all fossil mammals found in any of the 13 known fossil localities on Taiwan. Occurrences of these fossils with marine shells indicate deposition in the regressing sea of the late Pliocene. Similar fossils at Tso-chen and Hsin-chu indicate possible stratigraphic correlation. --M. Russell.     

Discovery of <Emphasis Type="Italic">Elephas</Emphasis> cf. <Emphasis Type="Italic">namadicus</Emphasis> from the late Pleistocene strata of Marginal Ganga Plain

We describe an elephant skull recovered from a cliff section of Dhasan river of Marginal Ganga Plain. The dental morphology and cranial features of the skull have been compared with the known species of Elephas from the Indian subcontinent. Although it shows very near resemblance to Elephas namadicus, but being an isolated specimen its specific identity cannot be proclaimed with certainty. As such, the specimen is provisionally referred as E. cf. namadicus. The Optically Stimulated Luminescence ages place this find at ~56 ka BP. This is the first chronologically well constrained report of E. cf. namadicus from the Ganga Plain.     

Preservation of the shell matrix protein dermatopontin in 1500 year old land snail fossils from the Bonin islands

Organic molecules such as proteins can be preserved in certain fossils. The bulk properties of fossil proteins of both vertebrates and invertebrates have been studied for over half a century. Named proteins have so far been identified, however, only in vertebrate fossils, such as collagen from mammoth bones. Using immunological assays, we examined 1500 year old fossils of the extinct land snail Mandarina luhuana from the Bonin islands for the presence of dermatopontin, a molluscan shell matrix protein. First, we examined the shell microstructure and mineralogy of the fossil shells using scanning electron microscopy (SEM) and powder X-ray diffraction (XRD) in order to estimate the extent of diagenetic alteration. The results suggest that the original microstructure and mineralogy of the shells are preserved. Antiserum raised against the Type-1 dermatopontin fragment of the living land snail Euhadra brandtii showed significant immunological reactivity with the extracts from the fossil shells of M. luhuana. Immunological binding curves drawn for the shell extracts of extant M. aureola and the extinct M. luhuana confirmed the presence of dermatopontin in the fossil shells and provided an estimate that about 75–98% of the original dermatopontin was lost from the M. luhuana fossils. This is the first report of a named protein being identified in invertebrate fossils.     

Mammoth tracks indicate a declining Late Pleistocene population in southwestern Alberta,Canada

Much debate has raged over the role that early humans played in this most recent large extinction. Fossil mammoth (Mammuthus primigenius) footprints were discovered at the St. Mary Reservoir in southwestern Canada (Wally's Beach DhPg-8). They are located in aeolian sediment dated at 11,300–11,000 years BP. By comparing the size distribution of these tracks with those of modern African elephants (Loxodonta africana), the age distribution of this mammoth population was determined. Containing far fewer juveniles than would be expected for an expanding or stable population, these tracks provide the first evidence that a living mammoth population, coexisting with human inhabitants, was in decline. Additionally, the same site provides corroborating evidence of humans hunting megafauna (horse and bovids). This suggests that humans, in addition to climate change, played a role in the end Pleistocene extinctions in North America.     

河北蔚县大南沟晚更新世草原猛犸象(长鼻目|哺乳动物纲)

在泥河湾盆地真象化石十分常见。  近年来,在泥河湾层中新发现了世界上最早的草原猛犸象(Mammuthus trogontherii)化石,过去被归入古菱齿象的部分材料也被转移到该种;  但以往报道的材料都很零碎,并且时代也较早。本研究的发现于蔚县大南沟东陡壁附近的长鼻类下颌骨(完好下颌体带左右m3)亦可归入该种,主要依据如下特征: 喙突(或吻突)不发育、下颌联合部短、下颌体前缘陡直、具有舌侧神经孔、颊齿齿板中间突不发育和釉质环无菱形结构、下第三臼齿有×18个齿板、齿板较薄、齿板频率为6、釉质层较薄但褶皱不强烈等。蔚县大南沟的化石是迄今在我国所发现的材料最完好和地质时代最晚的草原猛犸象化石记录,距今约4.5万年。     

Mid-Holocene vertebrate bone Concentration-Lagerstätte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus)

Although the recent history of human colonisation and impact on Mauritius is well documented, virtually no records of the pre-human native ecosystem exist, making it difficult to assess the magnitude of the changes brought about by human settlement. Here, we describe a 4000-year-old fossil bed at Mare aux Songes (MAS) in south-eastern Mauritius that contains both macrofossils (vertebrate fauna, gastropods, insects and flora) and microfossils (diatoms, pollen, spores and phytoliths). With >250 bone fragments/m² and comprising 50% of all known extinct and extant vertebrate species (n_s = 44) of Mauritius, MAS may constitute the first Holocene vertebrate bone Concentration-Lagerstätte identified on an oceanic volcanic island. Fossil remains are dominated by extinct giant tortoises Cylindraspis spp. (63%), passerines (～10%), small bats (7.8%) and dodo Raphus cucullatus (7.1%). Twelve radiocarbon ages [four of them duplicates] from bones and other material suggest that accumulation of fossils took place within several centuries. An exceptional combination of abiotic conditions led to preservation of bones, bone collagen, plant tissue and microfossils. Although bone collagen is well preserved, DNA from dodo and other Mauritian vertebrates has proved difficult. Our analysis suggests that from ca 4000 years ago (4 ka), rising sea levels created a freshwater lake at MAS, generating an oasis in an otherwise dry environment which attracted a diverse vertebrate fauna. Subsequent aridification in the south-west Indian Ocean region may have increased carcass accumulation during droughts, contributing to the exceptionally high fossil concentration. The abundance of floral and faunal remains in this Lagerstätte offers a unique opportunity to reconstruct a pre-human ecosystem on an oceanic island, providing a key foundation for assessing the vulnerability of island ecosystems to human impact.     

New palaeontological evidence suggests an early Middle Pleistocene age for the lower levels of Sun Hole Cave,Cheddar, Somerset,UK

Sun Hole, a small fissure cave on the north side of Cheddar Gorge, Somerset, is best known as the site where late Upper Palaeolithic artefacts are associated with human and other mammal remains that immediately pre-date the Lateglacial interstadial. These remains from the upper levels (Unit I) overlie sediments (Unit II) that are thought to have accumulated during a full glacial period, below which are sediments (Unit III) attributed to an interglacial stage. The extinct land snail Retinella (Lyrodiscus) sp., which in Britain was only known from the Hoxnian Stage, had previously been recovered from Unit III. The interglacial at the base of the sequence was therefore assigned to the Hoxnian Stage (Marine Isotope Stage (MIS) 11, 424–374 kyr). Here we provide additional analyses of samples from Unit III, which as well as containing further Retinella (Lyrodiscus), also yielded a specimen of Monachoides incarnatus, its first record from the British Pleistocene. An associated assemblage of small mammals included a few that are rare in the British Pleistocene, such as birch mouse (Sicista cf. betulina) and garden dormouse (Eliomys quercinus). The vole Lasiopodomys gregaloides and the shrew Sorex (Drepanosorex) savini do not occur as late as the Hoxnian and therefore suggest an older age in the early Middle Pleistocene. The record from Sun Hole therefore has parallels with the well-known sequence from the upper Calcareous Member in the nearby cavern system at Westbury-sub-Mendip.     

Stratigraphic and geochronologic contexts of mammoth (Mammuthus) and other Pleistocene fauna,Upper Missouri Basin (northern Great Plains and Rocky Mountains), U.S.A.

Mammoth fossils and other Pleistocene vertebrates from the Upper Missouri Basin, in the northern Plains and Rocky Mountains of the western interior of North America, have been dated to the late Pleistocene and are associated with Wisconsinan deposits. Mammoth remains have also been found in older stratigraphic contexts. For example, Mammuthus columbi and other fossils from the Doeden Locality are in pre-Wisconsinan terrace gravels along the Yellowstone River; the deposits are likely Illinoian or Sangamonian. Faunas that appear to be associated with the Wisconsinan interstadial, before the Last Glacial Maximum, are found in intermountain valleys and mountain settings (the Merrell Locality, Blacktail Cave, Natural Trap Cave) and on the Plains in both glaciated and unglaciated regions (Box Creek, Wibaux gravel pit). Localities containing faunas dated to the time interval from about the Last Glacial Maximum to the end of the Younger Dryas chronozone (late Wisconsinan) include the youngest fossil-bearing strata at Merrell, Blacktail Cave, Natural Trap Cave; deposits at Sheep Rock Spring, Indian Creek, MacHaffie, False Cougar Cave, Shield Trap Cave; and mammoths found at Sun River, Glendive, Colby, and the Deer Creek drainage.     

The first record of “spelaeoid” bears in Arctic Siberia

For a long time, “spelaeoid” (cave-bear-like) bears, Ursus (Spelearctos) spp., were believed to be almost purely European animals. Their geographic range has recently been extended to the east, in southern Siberia, Transbaikalia, Kirghizia, Mongolia and Korea. Two unexpected new findings, presented here in detail, significantly change existing views on the distribution of cave bears; both were found in North-Eastern Siberia, far beyond the Arctic Circle, more than 1500 km to the north-east of the previously accepted range.One of the fossils is a mandible, found near the town of Cherskiy at 68.73°N, 161.38°E. The analysis of local geology and accompanying mammal fossils suggests that it comes from the Olyorian Fauna (Early to early Middle Pleistocene). Morphologically, the Cherskiy mandible is closest to Ursus savini, a small middle Pleistocene cave bear from the British Cromer Forest-bed Formation, but differs in having a slightly more advanced dentition, and thus it is described as a new subspecies Ursus savini nordostensis. Another newly recognized fossil of the “spelaeoid” bear is an astragalus found at the Oskhordokh site at 67.54°N, 135.67°E, on a large gravel bar on the right bank of the Adycha River. This specimen is attributed to Ursus cf. deningeri.The paper also presents an interesting example of the interaction between classical and “molecular” palaeontology.The new finds significantly change existing ideas on the ecology and evolution of cave bears, some of the most remarkable members of the extinct Pleistocene megafauna.     

Pleistocene mammals from the southern Brazilian continental shelf

Fossils of terrestrial mammals preserved in submarine environment have been recorded in several places around the world. In Brazil such fossils are rather abundant in the southernmost portion of the coast, associated to fossiliferous concentrations at depths up to 10 m. Here is presented a review of such occurrences and the first record of fossils in deeper areas of the continental shelf. The fossils encompass several groups of both extinct and extant mammals, and exhibit several distinct taphonomic features, related to the marine environment. Those from the inner continental shelf are removed and transported from the submarine deposits to the coast during storm events, thus forming large konzentrat-lagerstätte on the beach, called “Concheiros”. The only fossils from deeper zones of the shelf known so far are a portion of a skull, a left humerus and of a femur of Toxodon sp. and a lower right molar of a Stegomastodon waringi, all collected by fishermen at depths around 20 m. The presence of fossils at great depths and distances from the present coastline, without signs of abrasion and far from areas of fluvial discharges does indicate that these remains have not been transported from the continent to the shelf, but have been preserved directly on the area that today correspond to the continental shelf. These remains indicate the existence of large fossiliferous deposits that have developed during periods of sea-level lowstand (glacial maxima) and have been submerged and reworked by the sea-level rise at the end of the last glaciation.     

Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications

Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel (Camelus bactrianus); dromedary camel (Camelus dromedarius) and guanaco (Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp₉, deamidation of Gln₃₅ and Gln₃₉, and oxidation of Met₃₆. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation.A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro₄ for His₄ defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a complete character analysis aimed at determining the evolutionary history of this functionally significant protein. We emphasize that ancient protein sequencing and phylogenetic analyses using amino acid sequences must pay close attention to post-translational modifications, amino acid substitutions due to diagenetic alteration and the impacts of isobaric amino acids on mass shifts and sequence alignments.