High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses

The schizothoracine fishes, also known as “mountain carps” are widely distributed in the Qinghai-Tibetan Plateau and its peripheral regions. Although they provide a prime example of high altitude adaptation, the phylogenetic relationships and the divergence times among these carp lineages are still controversial. Moreover, the genetic basis for high altitude adaptation is also poorly understood. In this study, we determined the mitochondrial genomes from two species of the schizothoracine fishes, representing a “morphologically primitive” clade and “morphologically specialized” clade, respectively. The phylogenetic tree and the divergence times were estimated within the evolutionary framework of the entire order Cypriniformes. Our results indicate a polyphylyetic relationship of the schizothoracine fishes and suggest two independent migration events into the Qinghai-Tibetan Plateau: one by the “morphologically primitive” clade in the Late Miocene and another by the “morphologically specialized” clade in the Eocene. Rapid speciation events of each clade from the Late Miocene to the Pliocene correspond to the timing of the geologic acceleration of the Qinghai-Tibetan Plateau. Interestingly, we found evidence for positive selection acting on the protein coding genes in the mitochondrial genomes of the “morphologically specialized” clade, implying a possible genetic basis for high altitude adaptation in this derived lineage of cypriniform fishes.     

A new duck from the Middle Miocene of Mongolia, with comments on Miocene evolution of ducks

A new relatively large duck, Chenoanas deserta gen. et sp. nov. from the Middle Miocene of the Sharga locality, which is morphologically intermediate between the extant genera Chenonetta and Tachyeres, is described. The diversity of Early and Middle Miocene ducks is discussed. It is noted that some Middle Miocene duck remains are incorrectly referred to the genus Mionetta. The distribution of morphological characters of the humerus in Neogene and extant ducks shows that the present day diversity of ducks apparently results from extinction of some taxa which were formed in the Oligocene-Early Miocene. The distribution of morphological characters in the evolution of diving ducks is evidence that not only the formation of different morphotypes but also so-called ??evolutionary maturation?? of taxa also explains the modern diversity.     

Middle Miocene Cephalotaxus (Taxaceae) from Yunnan,Southwest China,and its implications to taxonomy and evolution of the genus

The infrageneric taxonomy of the genus Cephalotaxus Siebold et Zuccarini ex Endlicher (Taxaceae) is controversial as morphological characters have been doubted to change coherently among species. Although the epidermal features are considered as important characters in the taxonomy of conifers, they have not been systematically studied in this genus. Neogene foliage shoots with well-preserved epidermal structure not only can provide systematic links to the extant species, but also have implications for the taxonomical definition of the extant species by their epidermal features. In this paper, the morphologies of leafy shoots combining epidermal structure of a Neogene Cephalotaxus, which was collected from the middle Miocene of Southwest China, and ten extant species (variants) were studied. Morphology as well as epidermal structures was compared among species (variants) in Cephalotaxus. Based on the comparisons, the taxonomical definition of extant species in genus Cephalotaxus are discussed. Our results indicate that leaf morphological characters in combination with the features of epidermal structure can distinguish species in genus Cephalotaxus. The fossil foliage shoots from the middle Miocene of Southwest China were assigned to a new species, C. maguanensis n. sp., which shows close affinities to the extant C. hainanensis. On the basis of leaf and epidermal information, we suggest there are seven extant species in Cephalotaxus. With global cooling and the uplift of the Qinghai-Tibet Plateau since the middle Miocene, the cooling climate induced the differentiation and southward expansions of C. maguanensis, and its extant offspring, C. hainanensis, is distributed to Hainan Island and the Indo-Chinese peninsula.     

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.     

ANATOMICAL REVISION OF THE GENUS MERYCOPOTAMUS (ARTIODACTYLA; ANTHRACOTHERIIDAE): ITS SIGNIFICANCE FOR LATE MIOCENE MAMMAL DISPERSAL IN ASIA

Abstract:  New fossil remains of the anthracothere genus Merycopotamus Falconer and Cautley, are described. Most of them were discovered by the Harvard University and Geological Survey of Pakistan joint research project (Y-GSP) in the well-dated Middle and Late Miocene deposits of the Potwar Plateau in northern Pakistan. This new material led us to revise the systematics of the genus with the validation of three species, M. nanus Falconer ( M. pusillus Lydekker), M. dissimilis Falconer and Cautley, and M. medioximus Lihoreau et al. , and allowed us to determine precisely their chronological distributions in a continuous Neogene sequence. Other specimens reported from the late Miocene deposits of the Khorat Plateau in north-east Thailand by the Department of Mineral Resources are the first remains of Merycopotamus to have been discovered in that region and are attributed to M. medioximus . These discoveries indicate a wider geographical distribution of the genus in the early Late Miocene. Anatomical investigations highlight the evolution of Merycopotamus through the Miocene towards more amphibious habits. Palaeobiogeographical and palaeoecological information for Merycopotamus stress the role of the Himalayan orogenesis as a dispersal barrier and the impact of a major global regression event on the evolution of Indian Subcontinent faunas from the Middle Miocene to the Late Pliocene.     

Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.     

Palaeoenvironmental significance of Miocene larger benthic foraminifera from the Xisha Islands,South China Sea

We studied 344 samples from Well XK-1 in Xisha Islands, South China Sea, and identified 66 species of larger benthic foraminifera, providing critical evidence for biostratigraphy and palaeoenvironmental interpretation of the Miocene reef carbonate sequence. Three assemblages are recognized, namely, Spiroclypeus higginsi–Borelis pygmaeus Assemblage (Letter Stage Te5, Early Miocene, 1256.28–1180.15 m), Nephrolepidina–Miogypsina Assemblage (Tf, Middle Miocene, 1031.10–577.04 m), and Cycloclypeus–Heterostegina Assemblage (Tg, Late Miocene, 468.13–380.42 m). On the basis of the palaeoecological preference of the larger foraminifera, we interpret that the Miocene carbonate sequence was deposited mainly in a warm tropical shallow water environment, characterized by five stages of continuous long-term evolution: backreef lagoon to shelf in the Early Miocene, normal to frontal reef in the early Middle Miocene, backreef lagoon to shelf in the later Middle Miocene, normal to frontal reef in the early Late Miocene, and proximal forereef shelf in the later Late Miocene.     

First fossil record of the catfish genus Sorubim (Siluriformes,Pimelodidae), from the Late Miocene of Paraná, Northeastern Argentina

The aim of the present contribution is to describe a partial fossil skull belonging to the catfish genus Sorubim. The specimen originates from the Late Miocene Ituzaingó Formation, at Paraná locality, Entre Ríos Province, Argentina. The material described here (MACN Pv-14224) was determined just to genus because the living species of Sorubim are morphologically similar. Presence of Sorubim is in concordance with the hypothesis indicating that most extant pimelodid genera were already present by the Late Miocene. Present finding constitutes the first fossil record for the genus.     

Firmiana (Malvaceae: Sterculioideae) fruits from the Upper Miocene of Yunnan,Southwest China

A new species of Firmiana Marsili is recognized and described based on capsules from the Late Miocene Lincang flora of Yunnan, China. Firmiana yunnanensis nov. sp. is represented by opened, dehiscent, membranous follicles with a weak, sinuous midvein, obtuse secondary veins and thick marginal vein. The follicles conform in shape and venation with those of extant species of Firmiana, a genus now distributed in eastern Africa, Indo-Malaysia, and eastern and southeastern Asia. This fossil species occurred within the native distribution of extant Firmiana species. It provides new information on fossil history, paleoecology, as well as on the plant diversity of the Lincang flora.     

Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome

Background

Indian muntjac (Muntiacus muntjak vaginalis) has an extreme mammalian karyotype, with only six and seven chromosomes in the female and male, respectively. Chinese muntjac (Muntiacus reevesi) has a more typical mammalian karyotype, with 46 chromosomes in both sexes. Despite this disparity, the two muntjac species are morphologically similar and can even interbreed to produce viable (albeit sterile) offspring. Previous studies have suggested that a series of telocentric chromosome fusion events involving telomeric and/or satellite repeats led to the extant Indian muntjac karyotype.

Results

We used a comparative mapping and sequencing approach to characterize the sites of ancestral chromosomal fusions in the Indian muntjac genome. Specifically, we screened an Indian muntjac bacterial artificial-chromosome library with a telomere repeat-specific probe. Isolated clones found by fluorescence in situ hybridization to map to interstitial regions on Indian muntjac chromosomes were further characterized, with a subset then subjected to shotgun sequencing. Subsequently, we isolated and sequenced overlapping clones extending from the ends of some of these initial clones; we also generated orthologous sequence from isolated Chinese muntjac clones. The generated Indian muntjac sequence has been analyzed for the juxtaposition of telomeric and satellite repeats and for synteny relationships relative to other mammalian genomes, including the Chinese muntjac.

Conclusions

The generated sequence data and comparative analyses provide a detailed genomic context for seven ancestral chromosome fusion sites in the Indian muntjac genome, which further supports the telocentric fusion model for the events leading to the unusual karyotypic differences among muntjac species.     

Neogene phasianids (Aves: Phasianidae) of Central Asia: 2. Genera <Emphasis Type="Italic">Perdix,Plioperdix</Emphasis>, and <Emphasis Type="Italic">Bantamyx</Emphasis>

The phasianid genera Perdix, Plioperdix, and Bantamyx from the Neogene of Mongolia and Transbaikalia are reviewed. Based on published data and new material, the diagnoses of Late Pliocene Perdix margaritae Kurochkin and Plioperdix ponticus (Tugarinov) and Late Miocene Bantamyx georgicus Kurochkin are emended. It is shown that a tarsometatarsus from the Upper Miocene of the Pavlodar locality belongs to the genus Palaeoperdix rather than Palaeortyx, as was proposed in the previous studies. Small Neogene Asian phasianids are compared in detail with Neogene taxa from Europe and extant genera.     

The Evolution and Paleobiogeography of Flying Squirrels (Sciuridae, Pteromyini) in Response to Global Environmental Change

Flying squirrels are strictly arboreal squirrels adopting a special gliding form of locomotion. This group of animals has a long history that has mirrored the vicissitude of forests. The discrepancy in the distribution between fossils and extant species indicates a mysterious evolution history requiring further exploration. This study compiles the worldwide fossils of Pteromyini to the species level in order to reproduce the spatiotemporal distribution pattern of flying squirrels and deduce the ancestral distribution according to dispersal-vicariance analysis of a phylogeny of the extant species. In addition, we reconstruct the paleoenvironmental background and find that flying squirrels probably originated in the Oligocene–Miocene transition from Europe and immediately dispersed to Asia and North America. Influenced by glaciation, CO₂ reduction, geologic movements and the Paratethys retreat, the Northern Hemisphere underwent climate deterioration and grassland expansion during the late Miocene, and thus the diversity of Pteromyini dramatically decreased. The uplift of the Tibet Plateau in addition to the strengthened Asian monsoons intensified the aridity in central Asia, but brought sufficient water to the densely forested regions of South and Southeast Asia. These forests are likely both refugia and diversification center for flying squirrels during glacial periods in the Quarternary. The subsequent connection and separation events among these heterogeneous habitats has probably been a driving force in the speciation of flying squirrels. Based on this work, we predict a bleak future for the flying squirrels, one which is closely associated with the fate of forests in Asia.     

Geopalaeontological setting,chronology and palaeoenvironmental evolution of the Baccinello-Cinigiano Basin continental successions (Late Miocene,Italy)

The Latest Miocene succession of the Baccinello-Cinigiano Basin in southern Tuscany (Italy) recorded a faunal turnover documenting the extinction of an older, insular, endemic faunal complex characterised by the extinct ape Oreopithecus bambolii and the setting of a new, continental, European faunal complex including the colobine monkey Mesopithecus. A similar turnover pattern (Late Miocene ape/Latest Miocene Cercopithecidae) is generally observed in Late Miocene continental successions of Eurasia, from Spain to central Europe, Southwest Europe, the near East, and Southwest Asia. Abundant literature reports that the Late Miocene Eurasian hominoid primate distribution closely tracks the climatic/environmental changes occurring during the 12–9 Ma interval, until their extinction in western Europe. In the primate record, the dispersion of Cercopithecidae and the contraction of hominids is interpreted as an event depicting a pattern of “continentalisation” in the Old World. The sedimentary succession of the Baccinello-Cinigiano basin, one of the longest continuous vertebrate-bearing continental successions in the Neogene Italian record, contributes to the debate on this hypothesis. This paper provides an overview of the main characteristics of the sedimentary succession, the chronological constraints (biochronology, radiometric datings, magnetostratigraphy), and the palaeoenvironmental evolution as derived from palaeobiological approaches and from the study of stable carbon and oxygen isotope contents along the entire sedimentary succession. The 2 myr geological history of the Baccinello Cinigiano Basin, which documents the evolutionary history of Oreopithecus and associated faunas, does not have a direct relation with the event of the Messinian Salinity Crisis. The evolutionary history of Baccinello-Cinigiano Basin and its palaeontological record have been mainly driven by the regional tectonism and palaeogeographic changes that affected the northern Tyrrhenian regions in Late Miocene (Latest Tortonian–Messinian) times.     

On the Middle Miocene avifauna of Maboko Island,Kenya

The Middle Miocene sediments of Maboko Island (Lake Victoria) in western Kenya yielded numerous avian bones, which remained, however, little studied. The significance of this material is shown by the recent identification of an opisthocomiform bird. In the present study, further avian remains from Maboko Island are described. Most of the specimens belong to aquatic or semi-aquatic groups, of which some are closely related to taxa known from Early and Middle Miocene European avifaunas, that is, Nectornis cormorants (N. africanus nov. sp.) and Laricola-like Laromorphae. The fossil material also includes Ciconiidae (cf. Ciconia), Pelecanidae, Phoenicopteridae (Leakeyornis aethiopicus), Musophagidae, and a species of Ardeidae, which closely resembles the taxon Pikaihao from the Early Miocene of New Zealand. Some avian remains from Maboko Island belong to higher-level taxa unknown from the Middle Miocene of Europe. The occurrence of a giant Jacanidae (?Nupharanassa mabokoensis nov. sp.) is of particular interest, because these are globally absent in extant avifaunas and were previously only known from the Late Eocene/Early Oligocene of Egypt. Further unknown from contemporaneous European sites are small representatives of Jacanidae, Bucerotidae, and Alcedinidae, with the fossils of the latter two taxa being among the earliest published records of their respective groups. Several of the taxa that are common in contemporaneous European avifaunas have not been found in Maboko, and in spite of less pronounced climatic differences, Middle Miocene Afrotropical avifaunas already appear to have been distinct from contemporaneous European ones.     

The Hand of Cercopithecoides williamsi (Mammalia,Primates): Earliest Evidence for Thumb Reduction among Colobine Monkeys

Thumb reduction is among the most important features distinguishing the African and Asian colobines from each other and from other Old World monkeys. In this study we demonstrate that the partial skeleton KNM-ER 4420 from Koobi Fora, Kenya, dated to 1.9 Ma and assigned to the Plio-Pleistocene colobine species Cercopithecoides williamsi, shows marked reduction of its first metacarpal relative to the medial metacarpals. Thus, KNM-ER 4420 is the first documented occurrence of cercopithecid pollical reduction in the fossil record. In the size of its first metacarpal relative to the medial metacarpals, C. williamsi is similar to extant African colobines, but different from cercopithecines, extant Asian colobines and the Late Miocene colobines Microcolobus and Mesopithecus. This feature clearly links the genus Cercopithecoides with the extant African colobine clade and makes it the first definitive African colobine in the fossil record. The postcranial adaptations to terrestriality in Cercopithecoides are most likely secondary, while ancestral colobinans (and colobines) were arboreal. Finally, the absence of any evidence for pollical reduction in Mesopithecus implies either independent thumb reduction in African and Asian colobines or multiple colobine dispersal events out of Africa. Based on the available evidence, we consider the first scenario more likely.     

Miocene hyaenids (Hyaenidae; Carnivora) from Siwaliks of Pakistan

Newly discovered Miocene hyaenid specimens, recently collected from the Siwalik Group, are described and discussed. A careful comparison with the known material reveals that these specimens belong to the early hyaenid species Thalassictis cf. T. proava, Ictitherine indet. and Lepthyaena sivalensis. The stratigraphic range of T. proava extended up to the Dhok Pathan Formation (Middle Miocene to Early Pliocene). The stratigraphic range of T. proava comprises the Middle to Late Miocene, with the youngest record in Hasnot, Potwar Plateau in the Siwalik Group. The material is of great interest because Siwalik carnivoran material is rare.     

Tertiary crocodylians from Puerto Rico: Evidence for Late Tertiary endemic crocodylians in the West Indies?

Fragmentary fossils from northwestern Puerto Rico document the existence of crocodyliforms during the Late Oligocene and Early Miocene. The remains are insufficient to establish new named species, but they are inconsistent with any other crocodylian known from the western hemisphere during the Cenozoic, including extant Alligator and Crocodylus. They are thus consistent with the hypothesis that Crocodylus is a comparatively recent immigrant into the West Indies and suggest that, as with Australasia and Africa, the Antilles hosted an endemic clade of crocodylians during the Tertiary, later replaced by Crocodylus.     

Phylogeny ofMuntiacus (Cervidae) based on mitochondrial DNA restriction maps

Mitochondrial DNA restriction maps for 12 restriction enzymes of four species of muntjacs—Indian muntjac(M. muntjak), Gongshan muntjac(M. gongshanensis), black muntjac(M. crinifrons), and Chinese muntjac(M. reevesi)—were compared to estimate the phylogenetic relationships among them. Phylogenetic trees were constructed by both distance and parsimony methods. The two resulting trees share a similar topology, which indicates that the black muntjac and the Gongshan muntjac are closely related, followed by the Chinese muntjac; the Indian muntjac is the sister taxon to all the other muntjacs.     

Change in diversity,ecological significance and biogeographical relationships of the Mediterranean Miocene toothed whale fauna

The main evolutionary trend in the Mediterranean Miocene toothed whale fauna is related (1) to the change in diversity and (2) to the turnover in community structure. Diversity increases from Upper Aquitanian–Lower Burdigalian to Burdigalian–Langhian, when it reaches its maximum. Starting from this time, diversity decreases progressively. The Early Miocene (Upper Aquitanian–Lower Burdigalian) Mediterranean toothed whale fauna, as well as the extramediterranean ones, is characterised by a high number of endemic taxa and by the prevalence of longirostral forms living in estuarine-neritic environments. A more diversified fauna spreading in neritic and pelagic environments characterises the Burdigalian–Langhian age, while an increase in pelagic forms and the nearly complete disappearance of some archaic longirostral taxa is typical of the Serravallian–Messinian fauna. Decrease in diversity and disappearance of archaic longirostral taxa are also recorded, at more general scale, in the Late Miocene extramediterranean fossil bearing deposits. These events can be related to the progressive global climatic deterioration, starting from Middle Miocene. From a biogeographic point a view, we can outline some relationships between the Mediterranean and western North Atlantic Miocene faunas. Closer affinities are observed between the Baltringen fauna and the northern Atlantic one, because of the presence of the genera Pomatodelphis and Zarhachis (platanistids) in both areas. In the Miocene Mediterranean and in North Atlantic, the delphinids are apparently absent as well as other extant delphinoid groups even if erroneously recorded in the past.