- Senckenbergische Naturforschende Gesellschaft (47)
A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)
Verena E. Kutschera
Alexander A. Sokolov
- Background: Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass.
Results: Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene.
Conclusions: The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan’s northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges
- Background: There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus riparius and C. piger).
Results: More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection.
Conclusions: Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species’ ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution.
Integrating movement ecology with biodiversity research - exploring new avenues to address spatiotemporal biodiversity dynamics
Carsten M. Buchmann
Jana A. Eccard
- Movement of organisms is one of the key mechanisms shaping biodiversity, e.g. the distribution of genes, individuals and species in space and time. Recent technological and conceptual advances have improved our ability to assess the causes and consequences of individual movement, and led to the emergence of the new field of ‘movement ecology’. Here, we outline how movement ecology can contribute to the broad field of biodiversity research, i.e. the study of processes and patterns of life among and across different scales, from genes to ecosystems, and we propose a conceptual framework linking these hitherto largely separated fields of research. Our framework builds on the concept of movement ecology for individuals, and demonstrates its importance for linking individual organismal movement with biodiversity. First, organismal movements can provide ‘mobile links’ between habitats or ecosystems, thereby connecting resources, genes, and processes among otherwise separate locations. Understanding these mobile links and their impact on biodiversity will be facilitated by movement ecology, because mobile links can be created by different modes of movement (i.e., foraging, dispersal, migration) that relate to different spatiotemporal scales and have differential effects on biodiversity. Second, organismal movements can also mediate coexistence in communities, through ‘equalizing’ and ‘stabilizing’ mechanisms. This novel integrated framework provides a conceptual starting point for a better understanding of biodiversity dynamics in light of individual movement and space-use behavior across spatiotemporal scales. By illustrating this framework with examples, we argue that the integration of movement ecology and biodiversity research will also enhance our ability to conserve diversity at the genetic, species, and ecosystem levels.
Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes) : research article
Jan Ole Kriegs
- Background The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades. Results We analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae. Conclusions The TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well.
The Evolutionary Paradox of Tooth Wear: Simply Destruction or Inevitable Adaptation?
Huynh Nhu Nguyen
Ian R. Grosse
- Over the last century, humans from industrialized societies have witnessed a radical increase in some dental diseases. A severe problem concerns the loss of dental materials (enamel and dentine) at the buccal cervical region of the tooth. This “modern-day” pathology, called non-carious cervical lesions (NCCLs), is ubiquitous and worldwide spread, but is very sporadic in modern humans from pre-industrialized societies. Scholars believe that several factors are involved, but the real dynamics behind this pathology are far from being understood. Here we use an engineering approach, finite element analysis (FEA), to suggest that the lack of dental wear, characteristic of industrialized societies, might be a major factor leading to NCCLs. Occlusal loads were applied to high resolution finite element models of lower second premolars (P2) to demonstrate that slightly worn P2s envisage high tensile stresses in the buccal cervical region, but when worn down artificially in the laboratory the pattern of stress distribution changes and the tensile stresses decrease, matching the results obtained in naturally worn P2s. In the modern industrialized world, individuals at advanced ages show very moderate dental wear when compared to past societies, and teeth are exposed to high tensile stresses at the buccal cervical region for decades longer. This is the most likely mechanism explaining enamel loss in the cervical region, and may favor the activity of other disruptive processes such as biocorrosion. Because of the lack of dental abrasion, our masticatory apparatus faces new challenges that can only be understood in an evolutionary perspective.
Intermediate Coupling between Aboveground and Belowground Biomass Maximises the Persistence of Grasslands
Steven I. Higgins
- Aboveground and belowground biomass compartments of vegetation fulfil different functions and they are coupled by complex interactions. These compartments exchange water, carbon and nutrients and the belowground biomass compartment has the capacity to buffer vegetation dynamics when aboveground biomass is removed by disturbances such as herbivory or fire. However, despite their importance, root-shoot interactions are often ignored in more heuristic vegetation models. Here, we present a simple two-compartment grassland model that couples aboveground and belowground biomass. In this model, the growth of belowground biomass is influenced by aboveground biomass and the growth of aboveground biomass is influenced by belowground biomass. We used the model to explore how the dynamics of a grassland ecosystem are influenced by fire and grazing. We show that the grassland system is most persistent at intermediate levels of aboveground-belowground coupling. In this situation, the system can sustain more extreme fire or grazing regimes than in the case of strong coupling. In contrast, the productivity of the system is maximised at high levels of coupling. Our analysis suggests that the yield of a grassland ecosystem is maximised when coupling is strong, however, the intensity of disturbance that can be sustained increases dramatically when coupling is intermediate. Hence, the model predicts that intermediate coupling should be selected for as it maximises the chances of persistence in disturbance driven ecosystems.
Chemical composition of modern and fossil hippopotamid teeth and implications for paleoenvironmental reconstructions and enamel formation – Part 2: Alkaline earth elements as tracers of watershed hydrochemistry and provenance
Thomas C. Brachert
Dieter F. Mertz
- This study demonstrates that alkaline earth elements in enamel of hippopotamids, in particular Ba and Sr, are tracers for water provenance and hydrochemistry in terrestrial settings. The studied specimens are permanent premolar and molar teeth found in modern and fossil lacustrine sediments of the Western Branch of the East African Rift system (Lake Kikorongo, Lake Albert, and Lake Malawi) and from modern fluvial environments of the Nile River.
Concentrations in enamel vary by two orders of magnitude for Ba (120–9336 μg g−1) as well as for Sr (9–2150 μg g−1). The variations are partially induced during post-mortem alteration and during amelogenesis, but the major contribution originates ultimately from the variable water chemistry in the habitats of the hippopotamids which is controlled by the lithologies and weathering processes in the watershed areas. Amelogenesis causes a distinct distribution of MgO, Ba and Sr in modern and fossil enamel, in that element concentrations increase along profiles from the outer rim towards the enamel–dentin junction by a factor of 1.3–1.9. These elements are well correlated in single specimens, thus suggesting that their distribution is determined by a common, single process, which can be described by closed system Rayleigh crystallization of bioapatite in vivo.
Enamel from most hippopotamid specimens has Sr/Ca and Ba/Ca which are typical for herbivores. However, Ba/Sr ranges from 0.1 to 3 and varies on spatial and temporal scales. Thus, Sr concentrations and Ba/Sr in enamel differentiate between habitats having basaltic mantle rocks or Archean crustal rocks as the ultimate sources of Sr and Ba. This provenance signal is modulated by climate change. In Miocene to Pleistocene enamel from the Lake Albert region, Ba/Sr decreases systematically with time from 2 to 0.5. This trend can be correlated with changes in climate from humid to arid, in vegetation from C3 to C4 biomass as well as with increasing evaporation of the lake water. The most plausible explanation is that Ba mobility decreased with increasing aridification due to preferential deposition with clay and Fe-oxide-hydroxide or barite on the watershed of Lake Albert.
Coalescent-based genome analyses resolve the early branches of the euarchontoglires
Björn M. Hallström
- Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.
Physico-chemical variables determining the invasion risk of freshwater habitats by alien mollusks and crustaceans
- The aim of this study was to assess the invasion risk of freshwater habitats and determine the environmental variables that are most favorable for the establishment of alien amphipods, isopods, gastropods, and bivalves. A total of 981 sites located in streams and rivers in Germany. Therefore we analyzed presence-absence data of alien and indigenous amphipods, isopods, gastropods, and bivalves from 981 sites located in small to large rivers in Germany with regard to eight environmental variables: chloride, ammonium, nitrate, oxygen, orthophosphate, distance to the next navigable waterway, and maximum and minimum temperature. Degraded sites close to navigable waters were exposed to an increased invasion risk by all major groups of alien species. Moreover, invaded sites by all four groups of alien species were similar, whereas the sites where indigenous members of the four groups occurred were more variable. Increased temperature and chloride concentration as well as decreased oxygen concentration were identified as major factors for the invasibility of a site. Species-specific analyses showed that chloride was among the three most predictive environmental variables determining species assemblage in all four taxonomic groups. Also distance to the next navigable waterways was similarly important. Additionally, the minimum temperature was among the most important variables for amphipods, isopods, and bivalves. The bias in the occurrence patterns of alien species toward similarly degraded habitats suggests that the members of all four major groups of freshwater alien species are a non-random, more tolerant set of species. Their common tolerance to salinity, high temperature, and oxygen depletion may reflect that most alien species were spread in ballast water tanks, where strong selective pressures, particularly temperature fluctuations, oxygen depletion, and increased salinity may create a bottleneck for successful invasion. Knowledge on the major factors that influence the invasion risk of a habitat is needed to develop strategies to limit the spread of invasive species.
Die Gamma-Strahlen-Meßkurve der Oberjura-Gesteinsfolgen in Preußisch Oldendorf und Wehrendorf (Westliches Wiehengebirge, Nordwestdeutschland)
Franz Jürgen Harms
- Im Wiehengebirge (Osnabrücker Bergland) wurden die lithostratigraphisch gegliederten Gesteinsfolgen des Oberjura (Oxford, Kimmeridge, Gigas-Schichten bis Eimbeckhäuser Platten kalk) in zwei Tagesaufschlüssen am Linken-Berg bei Preußisch Oldendorf und am Osterberg bei Wehrendorf mit einer Gamma-Sonde nach dem Scintillometer-Prinzip vermessen. Oie synthetisch erzeugten Gamma- Kurven lassen sich eindeutig mit den Gamma-ray-Kurven der in der Nähe niedergebrachten Bohrungen vergleichen.