Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Spatial networks differ when food supply changes: Foraging strategy of Egyptian fruit bats

Animals are faced with a range of ecological constraints that shape their behavioural decisions. Habitat features that affect resource abundance will also have an impact, especially as regards spatial distribution, which will in turn affect associations between the animals. Here we utilised a network approach, using spatial and genetic data, to describe patterns in use of space (foraging sites) by free-ranging Egyptian fruit bats (Rousettus aegyptiacus) at the Dakhla Oasis in Egypt. We observed a decrease in home range size during spring, when food availability was lowest, which was reflected by differences in space sharing networks. Our data showed that when food was abundant, space sharing networks were less connected and more related individuals shared more foraging sites. In comparison, when food was scarce the bats had few possibilities to decide where and with whom to forage. Overall, both networks had high mean degree, suggesting communal knowledge of predictable food distribution.

Carnivore distribution across habitats in a central-European landscape: a camera trap study

Quantitative data on local variation in patterns of occurrence of common carnivore species, such as the red fox, European badger, or martens in central Europe are largely missing. We conducted a study focusing on carnivore ecology and distribution in a cultural landscape with the use of modern technology. We placed 73 automated infra-red camera traps into four different habitats differing in water availability and canopy cover (mixed forest, wetland, shrubby grassland and floodplain forest) in the Polabí region near Prague, Czech Republic. Each habitat was represented by three or four spatially isolated sites within which the camera traps were distributed. During the year of the study, we recorded nine carnivore species, including the non-native golden jackal. Habitats with the highest numbers of records pooled across all species were wetland (1279) and shrubby grassland (1014); fewer records were made in mixed (876) and floodplain forest (734). Habitat had a significant effect on the number of records of badger and marten, and a marginally significant effect on fox. In terms of seasonal dynamics, there were significant differences in the distribution of records among seasons in fox, marginally significant in least weasel, and the occurrence among seasons did not differ for badger and marten. In the summer, fox and marten were more active than expected by chance during the day, while the pattern was opposite in winter when they were more active during the night. Our findings on habitat preferences and circadian and seasonal activity provided the first quantitative data on patterns whose existence was assumed on the basis of conventional wisdom. Our study demonstrates the potential of a long-term monitoring approach based on infra-red camera traps. Generally, the rather frequent occurrence of recorded species indicates that most carnivore species are thriving in current central-European landscapes characterized by human-driven disturbances and urbanization.

Enamel apatite crystallinity significantly contributes to mammalian dental adaptations

The monophyodont molar teeth, prismatic enamel and the complexity of enamel microarchitecture are regarded as essential dental apomorphies of mammals. As prominent background factors of feeding efficiency and individual longevity these characters are crucial components of mammalian adaptive dynamics. Little is known, however, to which degree these adaptations are influenced by the crystallographic properties of elementary hydroxyapatite crystallites, the only inorganic component of enamel. In a miniature pig where individual molars differ significantly in duration of their development and in enamel resistance to attrition stress, we found highly significant differences between the molars in the size of crystallites, amount of microstrain, crystallinity and in enamel stiffness and elasticity, all clearly scaled with the duration of tooth calcification. The same pattern was found also in red deer bearing different molar type. The results suggest that the prolongation of tooth development is associated with an increase of crystallinity, i.e. the atomic order of enamel hydroxyapatite, an obvious component of micromechanical property of mature enamel. This relation could contribute to prolongation of dental development, characteristic of mammals in general. The aspects of enamel crystallinity, omitted in previous studies on mammalian and vertebrate dental evolution, are to be taken in account in these topics.

Late Pleistocene-Holocene paleobiogeography of the genus Apodemus in Central Europe

Wood mice of the genus Apodemus are an essential component of small mammal communities throughout Europe. Molecular data suggest the postglacial colonization of current ranges from south European glacial refugia, different in particular species. Yet, details on the course of colonization and Holocene history of particular species are not available, partly because of a lack of reliable criteria for species identification in the fossil record. Using a sample of extant species, we analyzed variation patterns and between-species overlaps for a large set of metric and non-metric dental variables and established the criteria enabling the reliable species identification of fragmentary fossil material. The corresponding biometrical analyses were undertaken with fossil material of the genus (2528 items, 747 MNI) from 22 continuous sedimentary series in the Czech Republic and Slovakia, from LGM to Recent. In Central Europe, the genus is invariantly absent in LGM assemblages but regularly appears during the Late Vistulian. All the earliest records belong to A. flavicollis, the species clearly predominating in the fossil record until the Late Holocene. A. uralensis accompanied it in all regions until the late Boreal when disappeared from the fossil record (except for Pannonia). A few items identified as A. sylvaticus had already appeared in the early Holocene assemblages, first in the western part of the region, yet the regular appearance of the species is mostly in the post-Neolithic age. A. agrarius appeared sparsely from the Boreal with a maximum frequency during the post-Neolithic period. The results conform well to the picture suggested by molecular phylogeography but demonstrate considerable differences among particular species in dynamic of the range colonization. Further details concerning Holocene paleobiogeography of individual species in the medium latitude Europe are discussed.

Mammalian enamel maturation: Crystallographic changes prior to tooth eruption

Using the distal molar of a minipig as a model, we studied changes in the microstructural characteristics of apatite crystallites during enamel maturation (16-23 months of postnatal age), and their effects upon the mechanical properties of the enamel coat. The slow rate of tooth development in a pig model enabled us to reveal essential heterochronies in particular components of the maturation process. The maturation changes began along the enamel-dentine junction (EDJ) of the trigonid, spreading subsequently to the outer layers of the enamel coat to appear at the surface zone with a 2-month delay. Correspondingly, at the distal part of the tooth the timing of maturation processes is delayed by 3-5 month compared to the mesial part of the tooth. The early stage of enamel maturation (16-20 months), when the enamel coat is composed almost exclusively of radial prismatic enamel, is characterized by a gradual increase in crystallite thickness (by a mean monthly increment of 3.8 nm); and an increase in the prism width and thickness of crystals composed of elementary crystallites. The late stage of maturation (the last two months prior to tooth eruption), marked with the rapid appearance of the interprismatic matrix (IPM) during which the crystals densely infill spaces between prisms, is characterized by an abrupt decrease in microstrain and abrupt changes in the micromechanical properties of the enamel: a rapid increase in its ability to resist long-term load and its considerable hardening. The results suggest that in terms of crystallization dynamics the processes characterizing the early and late stage of mammalian enamel maturation represent distinct entities. In regards to common features with enamel formation in the tribosphenic molar we argue that the separation of these processes could be a common apomorphy of mammalian amelogenetic dynamics in general.

Golden jackal (Canis aureus) in the Czech Republic: the first record of a live animal and its long-term persistence in the colonized habitat

A golden jackal (Canis aureus) individual was recorded ~40 km east of Prague in the Czech Republic. It is the first record of a living golden jackal in the country; up to now several individuals have been recorded but all of them were either shot dead or killed by a vehicle. The observed animal was documented by camera traps set up for research of carnivore diversity in different habitats in the study area. It was first photographed on 19 June 2015, and in total there were 57 records made by 12 traps until 24 March 2016 when the animal was still present in the area. Forty-nine of the 57 records were made in a shrubby grassland over an area of ~100 ha, 39% of sightings were during the day and 61% in the night. There were two distinct peaks in the circadian activity of the animal, from 4 to 10 a.m., and from 6 p.m. to midnight. We also review the verified records of the golden jackal in the Czech Republic, some of which were only published in local hunting magazines. However, the observation reported in this paper represents the first evidence of a long-term occurrence in Europe of the same golden jackal individual, that persisted for at least nine months and over winter, northwest of Hungarian-Austrian border where the population has been known to reproduce.

Deeply torpid bats can change position without elevation of body temperature

Because body temperature is tightly coupled to physiological function, hibernating animals entering deep torpor are typically immobile. We analysed thermal behaviour and locomotory activity of hibernating greater mouse-eared bats Myotis myotis and found two types of movement behaviour related to body temperature, i.e. movement at high fur temperature and at low fur temperatures (Tflow; <5°C). First Tflow movements appeared at the beginning of March and often occurred during long torpor bouts. In most cases, Tflow events represented slow displacements between clusters of bats. In several cases, however, departure or arrivals from and into clusters was also recorded without any elevation in body temperature. Distance travelled, flight duration and speed of locomotion during Tflow events was lower than in high fur temperature events. Such behaviour could allow bats to save energy long-term and prolong torpor bouts. Tflow movement in torpid bats significantly changes our understanding of basic hibernation principles and we strongly recommend further studies on the subject.

Snežna jama (Slovenia): Interdisciplinary dating of cave sediments and implication for landscape evolution

Caves are important markers of surface evolution, since they are, as a general rule, linked with ancient valley bottoms by their springs. However, caves can only be dated indirectly by means of the sediments they contain. If the sediment is older than common dating methods, one has to use multiple dating approaches in order to get meaningful results. U/Th dating, palaeomagnetic analysis of flowstone and sediment profiles, cosmogenic dating of quartz pebbles, and mammalian dating allowed a robust estimate of speleogenesis, sediment deposition, climatic change at the surface, and uplift history on the Periadriatic fault line during the Plio-Pleistocene. Our dates indicate that Snežna jama was formed in the (Upper) Miocene, received its sedimentary deposits during the Pliocene in a rather low-lying, hilly landscape, and became inactive due to uplift along the Periadriatic and Sava faults and climatic changes at the beginning of the Quaternary. Although it is only a single cave, the information contained within it makes it an important site of the Southern Alps.

Influence of sample preparation on the microstructure of tooth enamel apatite

X-ray powder diffraction and transmission electron microscopy are widely used for determination of the basic characteristics of the biological apatite structure. Many different techniques have been adopted for separation of the enamel part of the tooth for use in these analytical methods, but their influence on the sample itself has not yet been studied. In this paper, six different preparation techniques have been applied on pigs' teeth to see their effect on the microstructure of dental hydroxyapatite. Although the only inorganic component of the tooth is the hydroxyapatite, new phases, such as calcite, aragonite, calcium hydrogen phosphate and calcium carbonate hydroxide, appeared when a drilling technique or deproteination of the sample was used. In addition, the crystallite size (especially in thec-axis direction) varies within a wide range (330–700 Å) depending on the preparation technique. Thus, the results indicate a strong effect of the enamel separation on the phase composition and crystallite size. The method providing results most consistent with previous studies is manual disintegration.

Testing hypotheses of bat baculum function with 3D models derived from microCT

The baculum (os penis) has been extensively studied as a taxon-specific character in bats and other mammals but its mechanical function is still unclear. There is a wide consensus in the literature that the baculum is probably a sexually selected character. Using a novel approach combining postmortem manipulation and three-dimensional (3D) imaging, we tested two functional hypotheses in the common noctule bat Nyctalus noctula, the common pipistrelle Pipistrellus pipistrellus, and Nathusius' pipistrelle Pipistrellus nathusii: (i) whether the baculum can protect the distal urethra and urethral opening from compression during erection and copulation; and (ii) whether the baculum and corpora cavernosa form a functional unit to support both the penile shaft and the more distal glans tip. In freshly dead or frozen and thawed bats, we compared flaccid penises with artificially 'erect' penises that were inflated with 10% formalin. Penises were stained with alcoholic iodine and imaged with a lab-based high-resolution x-ray microtomography system. Analysis of the 3D images enabled us to compare the changes in relative positions of the baculum, corpora cavernosa, urethra, and corpus spongiosum with one another between flaccid and 'erect' penises. Our results support both functional hypotheses, indicating that the baculum probably performs two different roles during erection. Our approach should prove valuable for comparing and testing the functions of different baculum morphologies in bats and other mammals. Moreover, we have validated an essential component of the groundwork necessary to extend this approach with finite element analysis for quantitative 3D biomechanical modeling of penis function.

Environmental margin and island evolution in Middle Eastern populations of the Egyptian fruit bat

Here, we present a study of the population genetic architecture and microevolution of the Egyptian fruit bat (Rousettus aegyptiacus) at the environmental margins in the Middle East using mitochondrial sequences and nuclear microsatellites. In contrast to the rather homogenous population structure typical of cave-dwelling bats in climax tropical ecosystems, a relatively pronounced isolation by distance and population diversification was observed. The evolution of this pattern could be ascribed to the complicated demographic history at higher latitudes related to the range margin fragmentation and complex geomorphology of the studied area. Lineages from East Africa and Arabia show divergent positions. Within the northwestern unit, the most marked pattern of the microsatellite data set is connected with insularity, as demonstrated by the separate status of populations from Saharan oases and Cyprus. These demes also exhibit a reduction in genetic variability, which is presumably connected with founder effects, drift and other potential factors related to island evolution as site-specific selection. Genetic clustering indicates a semipermeability of the desert barriers in the Sahara and Arabian Peninsula and a corridor role of the Nile Valley. The results emphasize the role of the island environment in restricting the gene flow in megabats, which is also corroborated by biogeographic patterns within the family, and suggests the possibility of nascent island speciation on Cyprus. Demographic analyses suggest that the colonization of the region was connected to the spread of agricultural plants; therefore, the peripatric processes described above might be because of or strengthened by anthropogenic changes in the environment.

Molecules, morphometrics and new fossils provide an integrated view of the evolutionary history of Rhinopomatidae (Mammalia: Chiroptera)

Background

The Rhinopomatidae, traditionally considered to be one of the most ancient chiropteran clades, remains one of the least known groups of Rhinolophoidea. No relevant fossil record is available for this family. Whereas there have been extensive radiations in related families Rhinolophidae and Hipposideridae, there are only a few species in the Rhinopomatidae and their phylogenetic relationship and status are not fully understood.

Results

Here we present (a) a phylogenetic analysis based on a partial cytochrome b sequence, (b) new fossils from the Upper Miocene site Elaiochoria 2 (Chalkidiki, Greece), which represents the first appearance datum of the family based on the fossil record, and (c) discussion of the phylogeographic patterns in both molecular and morphological traits. We found deep divergences in the Rhinopoma hardwickii lineage, suggesting that the allopatric populations in (i) Iran and (ii) North Africa and the Middle East should have separate species status. The latter species (R. cystops) exhibits a shallow pattern of isolation by distance (separating the Middle East and the African populations) that contrasts with the pattern of geographic variation in the morphometrical traits. A deep genetic gap was also found in Rhinopoma muscatellum (Iran vs. Yemen). We found only minute genetic distance between R. microphyllum from the Levant and India, which fails to support the sub/species distinctness of the Indian form (R. microphyllum kinneari).

Conclusion

The mtDNA survey provided phylogenetic tree of the family Rhinopomatidae for the first time and revealed an unexpected diversification of the group both within R. hardwickii and R. muscatellum morphospecies. The paleobiogeographic scenario compiled in respect to molecular clock data suggests that the family originated in the region south of the Eocene Western Tethyan seaway or in India, and extended its range during the Early Miocene. The fossil record suggests a Miocene spread into the Mediterranean region, followed by a post-Miocene retreat. Morphological analysis compared with genetic data indicates considerable phenotypic plasticity in this group.

The Trabecula cranii: development and homology of an enigmatic vertebrate head structure

Abstract

The vertebrate cranium consists of three parts: neuro-, viscero- and dermatocranium, which differ in both developmental and phylogenetic origin. Traditionally, developmental origin has been used as a criterion for homology, but this becomes problematic when skull elements such as the parietal bone are now shown, by modern fate-mapping studies, to have different developmental origins in different groups of tetrapods. This indicates a flexibility of developmental programmes and regulatory pathways which has probably been very important in cranial evolution. The trabecula cranii is an intriguing cranial element in the anterior cranial base in vertebrates. It forms a viscerocranial part of the neurocranium and is believed to be neural crest-derived in gnathostomes, but a similarly named structure in lampreys has been shown to have a mesodermal origin. Topographically, this trabecula seems to be homologous to the gnathostome trabecula cranii, and might also have the same function: to form a border between adjacent morphogenetic domains, to constrain and redirect growth of both brain and stomodeum and thus to refine developmental schedules of both. We suggest that such a border zone can recruit cells from either the mesoderm (as in the lamprey) or from the neural crest (as in the gnathostomes investigated), and still retain its homology. In our view, the trabecula is an interface element that integrates the respective divergent morphogenetics programs of the preotic head into a balanced unit; we suggest that such a definition can be used to define "the sameness" of this element throughout vertebrates.

Pátek, Levousy a Chlumčany – významné fosiliferní středopleistocénní lokality na pravém břehu Ohře mezi Louny a Libochovicemi [Pátek, Levousy and Chlumčany – important mid-pleistocene localities on the right bank of the Ohře River between Louny and Libochovice]

Due to a complete predominance of non-calcareous fluvial sediments in the Czech Republic, any find of fossil malacofauna is always considered as rare. The present work describes three localities in the Ohře river area, which contain, especially in the case of the Pátek locality, very abundant mid-Pleistocene malacofaunas. They were mainly collected in the floodplain fine-grained loam and back swamp deposits but also in sandy gravels. The molluscan thanatocenoses from localities near the Pátek village indicate the interglacial maximum (with up to 25 forest species s.l.), which developed directly on a 30 m thick river terrace dating back to the period, during which the Ohře river established its present-day easterly course. The fossil molluscs from the Levousy locality come from floodplain loam deposits as well as from the underlying sandy terrace gravels. The species distribution, nevertheless, indicates only a transitional glacial-interglacial period. The somewhat higher morphologic position of the locality, as well as that of another section at Chlumčany, and complete predominance of local late Cretaceous material indicates that the Ohře river did not flow to the east yet during the accumulation of the floodplain deposits with molluscs, but still to the north, towards Bílina. The terrestrial malacofauna from the Chlumčany section came from floodplain marls, particularly from sandy tufa deposits in the alluvium, which contains no forest-biotope elements, but the presence of the species Columella columella – distinct representative of our „coldest“ loess deposits – is an absolute surprise, since the peak of production of the sandy tufa deposits has always been associated with climate optima of the interglacials and of the Holocene.Therefore, the described malacofaunas come from a boundary period, during which the Ohře river did not use its present-day valley (Levousy and Clumčany) yet. Then, from the oldest time span, it took up for the first time its eastward course. Stratigraphy of the localities cannot be determined with a reasonable certainty in regard to the current controversial situation in Pleistocene chronology both in the northern foothills of the Alps and in the area of the „classic“ localities belonging to the continental ice-sheet region in northern Germany (Kovanda 2005a). Altogether 12 mid-Pleistocene species of small mammals were found in thanaotocoenoses at localities Pátek and Levousy. Ostracod assemblages analysis was also undertaken (11 species in 8 samples were determined)

Pátek, Levousy a Chlumčany – významné fosiliferní středopleistocénní lokality na pravém břehu Ohře mezi Louny a Libochovicemi [Pátek, Levousy and Chlumčany – important mid-pleistocene localities on the right bank of the Ohře River between Louny and Libochovice]

Due to a complete predominance of non-calcareous fluvial sediments in the Czech Republic, any find of fossil malacofauna is always considered as rare. The present work describes three localities in the Ohře river area, which contain, especially in the case of the Pátek locality, very abundant mid-Pleistocene malacofaunas. They were mainly collected in the floodplain fine-grained loam and back swamp deposits but also in sandy gravels. The molluscan thanatocenoses from localities near the Pátek village indicate the interglacial maximum (with up to 25 forest species s.l.), which developed directly on a 30 m thick river terrace dating back to the period, during which the Ohře river established its present-day easterly course. The fossil molluscs from the Levousy locality come from floodplain loam deposits as well as from the underlying sandy terrace gravels. The species distribution, nevertheless, indicates only a transitional glacial-interglacial period. The somewhat higher morphologic position of the locality, as well as that of another section at Chlumčany, and complete predominance of local late Cretaceous material indicates that the Ohře river did not flow to the east yet during the accumulation of the floodplain deposits with molluscs, but still to the north, towards Bílina. The terrestrial malacofauna from the Chlumčany section came from floodplain marls, particularly from sandy tufa deposits in the alluvium, which contains no forest-biotope elements, but the presence of the species Columella columella – distinct representative of our „coldest“ loess deposits – is an absolute surprise, since the peak of production of the sandy tufa deposits has always been associated with climate optima of the interglacials and of the Holocene.Therefore, the described malacofaunas come from a boundary period, during which the Ohře river did not use its present-day valley (Levousy and Clumčany) yet. Then, from the oldest time span, it took up for the first time its eastward course. Stratigraphy of the localities cannot be determined with a reasonable certainty in regard to the current controversial situation in Pleistocene chronology both in the northern foothills of the Alps and in the area of the „classic“ localities belonging to the continental ice-sheet region in northern Germany (Kovanda 2005a). Altogether 12 mid-Pleistocene species of small mammals were found in thanaotocoenoses at localities Pátek and Levousy. Ostracod assemblages analysis was also undertaken (11 species in 8 samples were determined)