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A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)
(2013)
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
(2013)
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.
Future climate change is predicted to advance faster than the postglacial warming. Migration may therefore become a key driver for future development of biodiversity and ecosystem functioning. For 140 European plant species we computed past range shifts since the last glacial maximum and future range shifts for a variety of Intergovernmental Panel on Climate Change (IPCC) scenarios and global circulation models (GCMs). Range shift rates were estimated by means of species distribution modelling (SDM). With process-based seed dispersal models we estimated species-specific migration rates for 27 dispersal modes addressing dispersal by wind (anemochory) for different wind conditions, as well as dispersal by mammals (dispersal on animal's coat – epizoochory and dispersal by animals after feeding and digestion – endozoochory) considering different animal species. Our process-based modelled migration rates generally exceeded the postglacial range shift rates indicating that the process-based models we used are capable of predicting migration rates that are in accordance with realized past migration. For most of the considered species, the modelled migration rates were considerably lower than the expected future climate change induced range shift rates. This implies that most plant species will not entirely be able to follow future climate-change-induced range shifts due to dispersal limitation. Animals with large day- and home-ranges are highly important for achieving high migration rates for many plant species, whereas anemochory is relevant for only few species.
Stakeholder dialogues can be used not only to introduce and discuss the various demands of the participants. Under certain circumstances they can also serve to smoothen out and solve conflicts that arise in connection with the use and conservation of biodiversity. In order to be successful in this respect, it is crucial to create a situation enabling a process of joint learning. A positive effect might also be achieved by the formation of groups that evolve in the course of a succession of workshops as well as speeches and special items on the agenda. In order for the workshops to be successful, they should be supported by frequent stakeholder analyses. In this guideline we are listing related principles and indications from the literature as well as our own experiences geared towards jointly solving biodiversity conflicts and creating islands of consensus.
Allgemein ist anerkannt, dass gute Kompensationsprojekte nicht nur Kohlenstoff festlegen, sondern möglichst weitere Nachhaltigkeitsleistungen aufweisen, die jedoch bisher bei der Durchführung und der Bewertung der Projekte häufig nicht angemessen berücksichtigt werden. In der vorliegenden Untersuchung wird erhoben, ob brauchbare Indikatoren vorliegen, die zur Bewertung weiterer ökologischer und sozialer Nutzen derartiger Projekte verwendet werden können.
Um den Kritiken gegenüber Waldprojekten zu begegnen, sollten Indikatoren zur Bewertung der Projekte möglichst so gewählt werden, dass sich mit ihnen auch räumliche Verlagerungseffekte erfassen lassen. Ebenso wichtig ist die Betrachtung ausreichender Zeiträume Waldprojekte haben aufgrund der langen Lebensdauer von Bäumen eine längere Laufzeit, als sie derzeit in vielen Bewertungssystemen berücksichtigt wird. Der langfristige Sequestrierungseffekt eines Projektes hängt entscheidend davon ab, ob das Holz alter Bäume im Wald wieder in den Kohlenstoffkreislauf kommt oder dem Wald entzogen wird. Bei ausschließlicher energetischer Nutzung des Holzes und auch bei Verarbeitung zu Zellstoff, Papier und Pappe wird kurze Zeit nach der Holzernte wieder Kohlendioxid freigesetzt. Dagegen schlagen langlebige Nutzungen des Holzes und insbesondere eine tatsächliche Substitution von Produkten aus Erdöl und Erdgas positiv zu Buche.
Wichtige Zusammenhänge bestehen zwischen dem Kohlendioxid-Minderungspotential von Waldprojekten und deren erheblichen ökologischen und sozialen Nutzen; diese entstehen bei optimalem Management in einer Art Ko-Produktion und sollten bewusst gestaltet werden; entsprechende Trade-offs sind bekannt.
Für die Beschreibung der gesamtökologischen und der sozialen Leistungen von Waldprojekten kann weitgehend auf bereits bekannten Kriterien aufgebaut werden; sie sollten aber um die Betrachtung der relevanten Ökosystemdienstleistungen ergänzt werden. Die Kohlenstofffestlegung ist eng mit zahlreichen dieser Ökosystemdienstleistungen (z.B. Humusbildung, Pufferungspotential gegenüber Stickstoff usw.) verknüpft. Waldprojekte mit hoher Biodiversität sind zudem in der Regel besser in der Lage, das Kriterium der Permanenz eines Kohlenstofflagers zu erfüllen. Auch lassen sich über die Ökosystemdienstleistungen bisher ausgeblendete sozio-kulturelle Dimensionen besser als bisher einbeziehen.
Auf diese Weise lässt sich die Darstellung der Nachhaltigkeitsleistung von Waldprojekten auf eine breitere Basis als bisher stellen – sowohl in ökologischer als auch in sozialer Hinsicht können die Kriterienkataloge der bisherigen Standards erweitert werden, die besonders auf Umweltwirkungen und sozioökonomische Effekte abheben. In den meisten Fällen sind bereits ausreichend geeignete Indikatoren bzw. Parameter vorhanden, um weitere wichtige Leistungen der Waldprojekte nachvollziehbar zu beschreiben. Für einige der betrachteten Dimensionen und Kriterien sind bisher noch keine Indikatoren vorhanden; zumeist gibt es aber auch dort Parameter, die Situationen anzeigen, welche unter Umständen genauer betrachtet werden müssten.
Bisher liegen keine allgemein anerkannten Standards hinsichtlich der Nachhaltigkeitskriterien von Waldprojekten vor. Eine neuerliche Debatte über eine Erweiterung des Kriteriensets ist notwendig, damit die zugehörigen Leistungsindikatoren allgemein akzeptiert werden. Diese Diskussion sollte jenseits der Nachhaltigkeitsleistungen der Waldprojekte selbst auch deren Vergleichbarkeit mit technischen Kompensationsprojekten im Blick haben. Die Kriteriendebatte war bisher durch die technischen Projekte dominiert und leider auch auf deren Bewertung verengt. Anders als technische Projekte haben Waldprojekte häufig sowohl für den Naturhaushalt als auch für die Gesellschaft viele weitere Nutzen, die eine nachhaltige Entwicklung begünstigen. Diese werden aber bisher nur unzureichend für die Qualitätssicherung und Kommunikation der Projekte genutzt.
Analog zum Gold Standard (GS) sollten die diskutierten Kriterien zu einem Standard für Waldprojekte verknüpft werden, mit dem sich die Nachhaltigkeitsleistungen dieser Kompensationsprojekte verlässlich bestimmen und überprüfen lassen. In Testläufen könnten die identifizierten Kriterien und Indikatorvorschläge erprobt und dabei modifiziert bzw. verfeinert werden.
Venomous secretions from marine snails of the Terebridae family target acetylcholine receptors
(2013)
Venoms from cone snails (Conidae) have been extensively studied during the last decades, but those from other members of the suborder Toxoglossa, such as of Terebridae and Turridae superfamilies attracted less interest so far. Here, we report the effects of venom and gland extracts from three species of the superfamily Terebridae. By 2-electrode voltage-clamp technique the gland extracts were tested on Xenopus oocytes expressing nicotinic acetylcholine receptors (nAChRs) of rat neuronal (α3β2, α3β4, α4β2, α4β4, α7) and muscle subtypes (α1β1γδ), and expressing potassium (Kv1.2 and Kv1.3) and sodium channels (Nav1.2, 1.3, 1.4, 1.6). The extracts were shown to exhibit remarkably high inhibitory activities on almost all nAChRs tested, in particular on the α7 subtype suggesting the presence of peptides of the A-superfamily from the venom of Conus species. In contrast, no effects on the potassium and sodium channels tested were observed. The venoms of terebrid snails may offer an additional source of novel biologically active peptides.
Reduction of greenhouse gas (GHG) emissions to minimize climate change requires very significant societal effort. To motivate this effort, it is important to clarify the benefits of avoided emissions. To this end, we analysed the impact of four emissions scenarios on future renewable groundwater resources, which range from 1600 GtCO2 during the 21st century (RCP2.6) to 7300 GtCO2 (RCP8.5). Climate modelling uncertainty was taken into account by applying the bias-corrected output of a small ensemble of five CMIP5 global climate models (GCM) as provided by the ISI-MIP effort to the global hydrological model WaterGAP. Despite significant climate model uncertainty, the benefits of avoided emissions with respect to renewable groundwater resources (i.e. groundwater recharge (GWR)) are obvious. The percentage of projected global population (SSP2 population scenario) suffering from a significant decrease of GWR of more than 10% by the 2080s as compared to 1971–2000 decreases from 38% (GCM range 27–50%) for RCP8.5 to 24% (11–39%) for RCP2.6. The population fraction that is spared from any significant GWR change would increase from 29% to 47% if emissions were restricted to RCP2.6. Increases of GWR are more likely to occur in areas with below average population density, while GWR decreases of more than 30% affect especially (semi)arid regions, across all GCMs. Considering change of renewable groundwater resources as a function of mean global temperature (GMT) rise, the land area that is affected by GWR decreases of more than 30% and 70% increases linearly with global warming from 0 to 3 ° C. For each degree of GMT rise, an additional 4% of the global land area (except Greenland and Antarctica) is affected by a GWR decrease of more than 30%, and an additional 1% is affected by a decrease of more than 70%.
Tropical forest soils are a significant source for the greenhouse gas N2O as well as for NO, a precursor of tropospheric ozone. However, current estimates are uncertain due to the limited number of field measurements. Furthermore, there is considerable spatial and temporal variability of N2O and NO emissions due to the variation of environmental conditions such as soil properties, vegetation characteristics and meteorology. In this study we used a process-based model (ForestDNDC-tropica) to estimate N2O and NO emissions from tropical highland forest (Nyungwe) soils in southwestern Rwanda. To extend the model inputs to regional scale, ForestDNDC-tropica was linked to an exceptionally large legacy soil dataset. There was agreement between N2O and NO measurements and the model predictions though the ForestDNDC-tropica resulted in considerable lower emissions for few sites. Low similarity was specifically found for acidic soil with high clay content and reduced metals, indicating that chemo-denitrification processes on acidic soils might be under-represented in the current ForestDNDC-tropica model. The results showed that soil bulk density and pH are the most influential factors driving spatial variations in soil N2O and NO emissions for tropical forest soils. The area investigated (1113 km2) was estimated to emit ca. 439 ± 50 t N2O-N yr−1 (2.8–5.5 kg N2O-N ha−1 yr−1) and 244 ± 16 t NO-N yr−1 (0.8–5.1 kg N ha−1 yr−1). Consistent with less detailed studies, we confirm that tropical highland rainforest soils are a major source of atmospheric N2O and NO.
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.
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.