Tonnacypris glacialis (Ostracoda, Cyprididae): taxonomic position, (palaeo-) ecology, and zoogeography

Abstract. The freshwater ostracod Tonnacypris glacialis (Sars, 1890) is reported from the European Pleistocene for the first time. The historical allocation of the species is discussed, and the species composition and characteristics of Tonnacypris Diebel & Pietrzeniuk (1975) and its phylozoogeography are considered. The significance of T. glacialis is reviewed, particularly from the viewpoint of the possible implications of parthenogenesis (and occasional-male production) for the Quaternary history of the genus, and for the use of the species in palaeoenvironmental reconstruction. It is suggested that the Pleistocene fossil occurrence of T. glacialis in modern temperature latitudes is a robust indicator of mean summer temperatures of 6°C.     

Comparative phylogeography of three common Neotropical tree species

Aim To determine spatial and temporal commonalities in patterns of chloroplast DNA (cpDNA) variation in three widespread Neotropical tree species. We examine whether patterns of genetic variation are more consistent with Pliocene or Pleistocene divergence. Location Central American forests, located in El Salvador, Nicaragua, Costa Rica and Panama. Methods We collected sequences from two cpDNA loci from c. 30 locations for each of three species –Bursera simaruba (Burseraceae; n = 278), Brosimum alicastrum (Moraceae; n = 210) and Ficus insipida (Moraceae; n = 222) – and additionally sequenced one nuclear locus for Bursera simaruba (n = 45). We used Monmonier’s algorithm to detect genetic barriers between regions. Divergence times between these regions were estimated using coalescent analyses. Results Spatial genetic boundaries were found in similar areas for these species, namely between Costa Rica and Nicaragua for all three species, and between El Salvador and Nicaragua for two species. These boundaries visually coincide with the spatial delimitations of Pliocene islands and previously hypothesized Pleistocene refugia. Divergence time estimates between regions are more consistent with Pleistocene divergence in two of the three species. Main conclusions Our results point to strong commonalities in the spatial locations of genetic boundaries in these three species, despite the complex geological and climatological history of this region, and ecological differences between the species. While spatial genetic boundaries coincide conspicuously with possible Pliocene and Pleistocene barriers to gene flow, we cannot distinguish between the two scenarios because of the strong spatial overlap of both barriers. However, the temporal data tentatively suggest that some of this divergence occurred in the Pleistocene, although limitations in the analysis cannot confirm Pleistocene divergence without external, corroborating data. While we cannot definitively implicate a single historical process as driving patterns of genetic differentiation in all three species, our results represent an initial step towards identifying a common history of Central American tree species.     

A tale of the nearly tail‐less: the effects of Plio‐Pleistocene climate change on the diversification of the African avian genus Sylvietta

Sylvietta is a broadly distributed group of African species inhabiting a wide range of habitats and presents an interesting opportunity to investigate the historic mechanisms that have impacted the biogeography of African avian species. We collected sequence data from 50 individuals and used model‐based phylogenetic methods, molecular divergence estimates and ancestral area estimates to construct a time‐calibrated phylogeny and estimation of biogeographic history. We estimate a southern African origin for Sylvietta, with an initial divergence splitting the genus into two clades. The first consists of arid‐adapted species, with a southern African origin and subsequent diversification north into Ethiopia–Somalia. The second clade is estimated as having a Congolian forest origin with an eastward pattern of colonization and diversification as a result of Plio‐Pleistocene forest dynamics. Additionally, two members of the genus Sylvietta display interesting patterns of intraspecific diversification. Sylvietta rufescens is an arid‐adapted species inhabiting southern Africa, and we recover two subclades with a divergence dating to the Pleistocene, a unique pattern for avian species which may be explained via isolation in arid habitat fragments in the early Pleistocene. Second, Sylvietta virens, a species endemic to Afro‐tropical forests, is recovered with geographically structured genetic diversification across its broad range, an interesting result given that recent investigations of several avian forest species have found similar and substantial geographically structured genetic diversity relating to Plio‐Pleistocene forest fragmentation. Overall, Plio‐Pleistocene habitat cycling played a significant role in driving diversification in Sylvietta, and this investigation highlights the substantial impact of climate‐driven habitat dynamics on the history of sub‐Saharan species.     

The Chacoan peccary,Catagonus wagneri (Mammalia,Tayassuidae), in the late Pleistocene (northern Uruguay,South America): paleoecological and paleobiogeographic considerations

Catagonus wagneri has the most restricted geographical distribution among extant Tayassuidae and inhabited semi-arid thorny forests of dry Chaco in Paraguay, Bolivia and Argentina. Until now, C. wagneri has only been recorded in archaeological, pre-Hispanic deposits from the Santiago del Estero Province, Argentina. A new partially complete skull from the Sopas Formation (Late Pleistocene; Uruguay) is identified as C. wagneri. This is the only fossil record of the species which extends its biochron until the late Pleistocene, and the first one substantially far from its current range; the first fossil record of the species in Uruguay; the most complete fossil material of the species; and it provides relevant ecological and climatic information. According to the ecological and climatic available information of C. wagneri, the presence of this mammal in the late Pleistocene of northern Uruguay indicates a warm climate and arid to semi-arid environments. Even though not associated with the fossil remains of C. wagneri, some mammals included in the sedimentary levels of the Sopas Formation also suggest arid to semi-arid environments. Climatic changes, in particular in the late Pleistocene and Holocene, could be invoked to explain modifications of its geographic range.http://zoobank.org/ECF04BCF-8246-4F11-AAB8-5FAA9F437BDA     

Phylogeny of African fruit bats (Chiroptera,Pteropodidae) based on complete mitochondrial genomes

Members of the family Pteropodidae, also known as Old World fruit bats, are represented in Africa by 14 genera and 44 species. Here, we sequenced 67 complete mitochondrial genomes from African and Asian pteropodids to better understand the evolutionary history of the subfamily Rousettinae, which includes most of the African species. An increased frequency of guanine to adenine transitions is detected in the mtDNA genomes of Macroglossus sobrinus and all species of Casinycteris and Scotonycteris. Our phylogenetic and molecular dating analyses based on 126 taxa and 15,448 characters indicate a low signal for deep relationships within the family, suggesting a rapid diversification during the Late Oligocene period of “warming.” Within the subfamily Rousettinae, most nodes are highly supported by our different analyses (all nucleotide sites, SuperTRI analyses of a sliding window, transversions only, coding genes only, and amino acid sequences). The results indicate the existence of four tribes: Rousettini—distributed from Africa through Mediterranean region and South Asia to South-East Asia; Eonycterini—found in Asia; and Epomophorini and Scotonycterini—restricted to sub-Saharan Africa. Although most interspecies relationships are highly supported, three parts of the Rousettinae mitochondrial tree are still unresolved, suggesting rapid diversification: (a) among the three subtribes Epomophorina (Epomophorus sensu lato, i.e., including Micropteropus, Epomops, Hypsignathus, Nanonycteris), Plerotina (Plerotes), and Myonycterina (Myonycteris, Megaloglossus) in the Late Miocene; (b) among Epomops, Hypsignathus, and other species of Epomophorina at the Pliocene–Pleistocene boundary; and (c) among Myonycteris species in the Early Pleistocene. Within the Epomophorini, Stenonycteris lanosus emerged first, suggesting that lingual echolocation may have appeared in the common ancestor of Epomophorini and Rousettini. Our analyses suggest that multiple events of mtDNA introgression occurred within the Epomophorus species complex during the Pleistocene.     

A new genus of red‐toothed shrew (Mammalia,Soricidae) from the Early Pleistocene of Gran Dolina (Atapuerca,Burgos, Spain), and a phylogenetic approach to the Eurasiatic Soricinae

This paper describes a new genus and species of shrew from the Pleistocene (levels 4, 5, and 6) of the Gran Dolina site, located in the Sierra de Atapuerca (Burgos, Spain). Dolinasorex glyphodon gen. et sp. nov. (Mammalia, Soricidae) is a type of large‐sized soricine, endemic in character, which inhabited the Sierra de Atapuerca in the last part of the Early Pleistocene (c. 780–900 kya). Morphometric and phylogenetic analyses indicate that the new species is more closely related to Asiatic forms than to the species Beremendia fissidens with its primarily European distribution. The main palaeoecological and palaeobiogeographical implications of the new taxon in the area around Atapuerca and in the Iberian Peninsula in general are discussed. The paper also presents a tentative phylogeny for the Soricinae subfamily in Eurasia, including for the first time exclusively fossil species, producing results that may prove to be of great interest for more complete studies in the future. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 904–925.     

On the systematic position of the large-sized deer from Apollonia,Early Pleistocene,Greece

The revision of the large-sized deer association from the early Pleistocene site Apollonia (Early Pleistocene; Greece), revealed the presence of two species,Praemegaceros pliotarandoides (De Alessandri, 1903) and a giant representative of the genusArvernoceros. P. pliotarandoides (=Psekupsoceros orientalis Radulesco & Samson, 1967) is characterized by advanced dental morphology, lack of the middle antler tine, and dichotomously branched distal part of the antlers and is regarded as the direct forerunner of middle PleistoceneP. verticornis. The species attribution of the ApollonianArvernoceros is not clear enough because of the incomplete data, and for this reason we keep this form under the nameArvernoceros cf.verestchagini. The presence ofArvernoceros in Apollonia certainly extends its chronological occurrence to early Pleistocene and a new generic definition is proposed. Several taxonomic and systematic questions on early Pleistocene large-sized deer of Europe are also discussed.     

Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N_e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma. The inferred ancestral N_e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10^?9) or third glaciation (mutation rate = 9 × 10^?9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.     

A NEW SPECIES OF DICERORHINUS (RHINOCEROTIDAE) FROM THE PLIO‐PLEISTOCENE OF MYANMAR

Abstract: A skull and mandible of the new species Dicerorhinus gwebinensis sp. nov. of Rhinocerotidae (Mammalia, Perissodactyla) is described. The material is collected from the upper part of the Irrawaddy sediments (Plio‐Pleistocene) in central Myanmar. D. gwebinensis sp. nov. is morphologically more similar to the extant species D. sumatrensis (Sumatran rhinoceros) than to other species of the genus but differs from D. sumatrensis in having the comparatively shorter nasal, the more concave dorsal profile of the skull, the more elevated occiput and presence of molar crista in M3/. This is the first discovery of Dicerorhinus in the upper Miocene to lower Pleistocene of the Indian subcontinent and Mainland Southeast Asia, and fills the chronological and geographical gap of this lineage in Asia. The Dicerorhinus clade probably migrated into Southeast Asia from East Asia by the Pliocene or early Pleistocene. This hypothesis is supported by the scarcity or absence of this clade in the Neogene mammalian fauna of the Indian Subcontinent.     

The Boxgrove,England, middle Pleistocene herpetofauna: Paleogeographic,evolutionary, stratigraphic,and paleoecological relationships

Triturus vulgaris (smooth newt), Triturus helveticus or T. vulgaris (palmate or smooth newt), Triturus sp. (newt), Pelobates fuscus (common spadefoot), Bufo bufo (common toad), Bufo calamita (natterjack toad), Bufo sp. (toad), Rana arvalis (moor frog), Rana temporaria (common frog), Rana sp. (frog), Anguis fragilis (slow worm), Lacerta cf. L. vivipara (common lizard), Natrix natrix (grass snake), and Natrix sp. (grass, viperine, or dice snake) were identified at the Middle Pleistocene Boxgrove Site, West Sussex, England. This is the first British fossil record of Pelobates fuscus and the earliest fossil record in Britain for the endangered species Bufo calamita. All of these herpetological species are extant and all of them occur in Britain today with the exception of Pelobates fuscus and Rana arvalis that presently live on the European continent.

The Boxgrove, Westbury, and West Runton British pre‐Anglian Middle Pleistocene herpetofaunas show no apparent differences among themselves in patterns of species composition, diversity, or number of exotics. But these three herpetofaunas together have [1] less species diversity and [2] fewer exotic continental species than in the Cudmore Grove British post‐Anglian Middle Pleistocene herpetofauna.

Only the Terrestral Sequence Unit at Boxgrove yielded enough herpetological species for paleoecological interpretation. These taxa indicate a quiet pool surrounded by a somewhat humid vegetated area that gave way to a more xerophytic sandy area, and a paleoclimate at least as warm and perhaps somewhat warmer than occurs in the area today.     

The integration of multiple independent data reveals an unusual response to Pleistocene climatic changes in the hard tick Ixodes ricinus

In the last few years, improved analytical tools and the integration of genetic data with multiple sources of information have shown that temperate species exhibited more complex responses to ice ages than previously thought. In this study, we investigated how Pleistocene climatic changes affected the current distribution and genetic diversity of European populations of the tick Ixodes ricinus, an ectoparasite with high ecological plasticity. We first used mitochondrial and nuclear genetic markers to investigate the phylogeographic structure of the species and its Pleistocene history using coalescent‐based methods; then we used species distribution modelling to infer the climatic niche of the species at last glacial maximum; finally, we reviewed the literature on the I. ricinus hosts to identify the locations of their glacial refugia. Our results support the scenario that during the last glacial phase, I. ricinus never experienced a prolonged allopatric divergence in separate glacial refugia, but persisted with interconnected populations across Southern and Central Europe. The generalist behaviour in host choice of I. ricinus would have played a major role in maintaining connections between its populations. Although most of the hosts persisted in separate refugia, from the point of view of I. ricinus, they represented a continuity of ‘bridges’ among populations. Our study highlights the importance of species‐specific ecology in affecting responses to Pleistocene glacial–interglacial cycles. Together with other cases in Europe and elsewhere, it contributes to setting new hypotheses on how species with wide ecological plasticity coped with Pleistocene climatic changes.     

Palaeobiology of <Emphasis Type="Italic">Euowenia grata</Emphasis> (Marsupialia: Diprotodontinae) and its Presence in Northern South Australia

Recovery of a specimen of Euowenia grata (De Vis, 1887) from mid Pliocene sediments of the Tirari Formation on the bank of the Warburton River in the Lake Eyre Basin provides the first recorded account of this species in South Australia. The specimen comprises a partial skull including left and right premaxillae, maxillae, and left zygomatic arch, along with an almost complete upper dentition (missing the left I2). An articulated hind leg and pes found downstream at the same stratigraphic level, as well as both fore- and hind-feet of a single individual, are also referred to E. grata and represent the first postcranial material assigned to the species. A reconstruction of the pes indicates that much more of the body weight was borne by the tarsus in this species than in plesiomorphic diprotodontids, such as Nimbadon Hand et al., 1993, or Ngapakaldia Stirton, 1967, although E. grata does not exhibit the more extreme enlargement of the tarsus seen in graviportal Pleistocene diprotodontids. E. grata is found here also to be the only known Australian marsupial, extant or extinct, to exhibit fusion of all three cuneiform bones in the tarsus. We suggest that the diprotodontine hind limb and pes had evolved graviportal adaptations in the Pliocene as well as in the Pleistocene members. We also suggest that E. grata may have been able to rear up against trees while browsing.     

Vegetation history from archaeological charcoals in central Australia: The late Quaternary record from Puritjarra rock shelter

Archaeological charcoals from Puritjarra rock shelter provide the first direct information about the vegetation of central Australia during the late Pleistocene and early Holocene. During the late Pleistocene there appears to have been a more open vegetation than today with fewer trees and shrubs, though with many of the taxa that are important in the modern central Australian flora. The persistence of species such as Acacia macdonnelliensis, Callitris glaucophylla and Eucalyptus opaca throughout the time of the last glacial maximum and the presence of appreciable quantities of wood charcoal in the archaeological deposits at this time indicate that the region was not a tree-less steppe even during full glacial aridity. From 13,000 B.P. onwards, acacias are strongly represented in the charcoal assemblage both quantitatively and in terms of the number of species present. Acacia aneura is for the first time a major component of the assemblage indicating that it had by this time become a significant element of the local vegetation. These changes coincide with evidence elsewhere in the Australian arid zone for the onset of wetter conditions in the early Holocene.     

Morphotypic variability of masticatory surface pattern of molars in the recent and Pleistocene Lemmus and Myopus (Rodentia,Cricetidae) of Europe and Western Siberia

In this article, we present the results of morphological study, applying multivariate statistical analysis, of seven samples of recent Lemmini species (Lemmus lemmus, L. sibiricus, Myopus schisricolor) and eight samples of the ancient Siberian lemmings from the Middle and Late Pleistocene localities, mainly in northeastern Europe. On the basis of studying variability of masticatory surface pattern of molars, 24 morphotypes have been described. The differences in morphotypes frequencies were found between the recent Myopus and Lemmus and between the two Norwegian lemming samples. There are some indications of an evolutionary trend in molar morphology of the Siberian lemmings of the Middle, Late Pleistocene, and the recent of Eastern Europe. The distinctions, at least, between the Middle Pleistocene and modern lemmings exceed a species level.     

Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong)

The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.     

Phylogeny of slug species of the genus Arion: evidence of monophyly of Iberian endemics and of the existence of relict species in Pyrenean refuges

The Iberian Peninsula contains the majority of the Paleartic land slug species of the genus Arion, which exhibits diverse taxonomic problems. The present study investigated Arion taxonomy on the basis of analyses of the mitochondrial ND1 gene and nuclear internal transcribed spacer 1 (ITS1) sequences. The Iberian endemic species were monophyletically clustered in two divergent sister clades. The topotype specimens of Arion lusitanicus and the closely related species Arion nobrei and Arion fuligineus, as well as Arion hispanicus and Arion flagellus, were grouped into an ‘Atlantic’ clade, whereas Arion baeticus, Arion gilvus, Arion anguloi, Arion wiktori and Arion paularensis were included in a ‘Continental–Mediterranean’ clade. Calibration of mutation rate in the ND1 gene suggested that the divergence of these two clades occurred around the Pliocene–Pleistocene boundary, with subsequent speciation events during the Pleistocene. A group of ancestral and divergent endemic species with distribution centred in the Pyrenean mountain range (Arion molinae, Arion lizarrusti, Arion antrhacius and Arion iratii) arose in the Pliocene and survived through the Pleistocene in geographically confined small populations. Arion lusitanicus showed up to be polyphyletic: specimens, sampled outside the geographic range of the topotype in the north‐western Iberian Peninsula, were included in a non‐monophyletic clade together with the widely distributed species Arion ater and Arion rufus. The divergent species with a wide European distribution (Arion subfuscus, Arion hortensis, Arion fagophilus and Arion intermedius) were located in basal positions in all topologies. The evolutionary history of these slug species (highly sensitive to climatic factors, with capacity for both outcrossing and selfing, and with low dispersal ability) appears to have been moulded by Pliocene–Pleistocene climate events and by the rugged topography of southern Europe, giving rise to repeated cycles of population isolation during periods of glaciation alternating with interglacial expansions limited by geographic barriers.     

Tayassu pecari (Link, 1795) (Mammalia,Cetartiodactyla): comments on its South American fossil record,taxonomy and paleobiogeography

Tayassu pecari is widely distributed across the Neotropical region, from northern Argentina to south-eastern Mexico. However, its fossil record is scarce; it is recorded since the middle Pleistocene to Holocene in Argentina, Brazil and Uruguay. This paper aims to: (1) update the systematic synonymy of this species; (2) review and update its geographic chronologic distribution and provide a new Lujanian record of Tayassu pecari in Buenos Aires Province and (3) discuss the paleoenvironmental and paleobiogeographical implications of this record. Considering the quantitative analysis performed, the fossil here recorded clearly integrates the group of Tayassu pecari. This specimen corresponds to the first record of Tayassu pecari in the central-northern region of the Buenos Aires Province. During Late Pleistocene, Tayassu pecari was distributed southern to its recent range, probably evidencing different paleoenvironment conditions. This species is the better adapted peccary to tropical and subtropical rainforests, but may also be present in arid environments. Consequently, Tayassu by itself is insufficient to infer the prevailing environmental conditions. However, according to the fauna associated with the specimen described here, it is possible to infer an open or semi-open and arid or semi-arid environment for the central-northern Buenos Aires region by Late Pleistocene times.