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An updated inventory of the Bromeliaceae for Costa Rica is presented including citations of representative specimens for each species. The family comprises 18 genera and 198 species in Costa Rica, 32 species being endemic to the country. Additional 36 species are endemic to Costa Rica and Panama. Only 4 of the 8 bromeliad subfamilies occur in Costa Rica, with a strong predominance of Tillandsioideae (7 genera/150 spp.; 75.7% of all bromeliad species in Costa Rica). 124 species (62.6%) grow exclusively epiphytic, additional 59 spp. (29.8%) are facultative epiphytes. The most diverse genus is Werauhia, with 59 species (29.8% of the Costa Rican bromeliad flora), followed by Tillandsia with 40 species (20.2%) and Guzmania with 28 spp. (8.6%).
The LPJ-GUESS dynamic vegetation model uniquely combines an individual- and patch-based representation of vegetation dynamics with ecosystem biogeochemical cycling from regional to global scales. We present an updated version that includes plant and soil N dynamics, analysing the implications of accounting for C-N interactions on predictions and performance of the model. Stand structural dynamics and allometric scaling of tree growth suggested by global databases of forest stand structure and development were well-reproduced by the model in comparison to an earlier multi-model study. Accounting for N cycle dynamics improved the goodness-of-fit for broadleaved forests. N limitation associated with low N mineralisation rates reduces productivity of cold-climate and dry-climate ecosystems relative to mesic temperate and tropical ecosystems. In a model experiment emulating free-air CO2 enrichment (FACE) treatment for forests globally, N-limitation associated with low N mineralisation rates of colder soils reduces CO2-enhancement of NPP for boreal forests, while some temperate and tropical forests exhibit increased NPP enhancement. Under a business-as-usual future climate and emissions scenario, ecosystem C storage globally was projected to increase by c. 10 %; additional N requirements to match this increasing ecosystem C were within the high N supply limit estimated on stoichiometric grounds in an earlier study. Our results highlight the importance of accounting for C-N interactions not only in studies of global terrestrial C cycling, but to understand underlying mechanisms on local scales and in different regional contexts.
Fire is the primary disturbance factor in many terrestrial ecosystems. Wildfire alters vegetation structure and composition, affects carbon storage and biogeochemical cycling, and results in the release of climatically relevant trace gases including CO2, CO, CH4, NOx, and aerosols. One way of assessing the impacts of global wildfire on centennial to multi-millennial timescales is to use process-based fire models linked to dynamic global vegetation models (DGVMs). Here we present an update to the LPJ-DGVM and a new fire module based on SPITFIRE that includes several improvements to the way in which fire occurrence, behaviour, and the effects of fire on vegetation are simulated. The new LPJ-LMfire model includes explicit calculation of natural ignitions, the representation of multi-day burning and coalescence of fires, and the calculation of rates of spread in different vegetation types. We describe a new representation of anthropogenic biomass burning under preindustrial conditions that distinguishes the different relationships between humans and fire among hunter-gatherers, pastoralists, and farmers. We evaluate our model simulations against remote-sensing-based estimates of burned area at regional and global scale. While wildfire in much of the modern world is largely influenced by anthropogenic suppression and ignitions, in those parts of the world where natural fire is still the dominant process (e.g. in remote areas of the boreal forest and subarctic), our results demonstrate a significant improvement in simulated burned area over the original SPITFIRE. The new fire model we present here is particularly suited for the investigation of climate–human–fire relationships on multi-millennial timescales prior to the Industrial Revolution.
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
Molecular phylogenetic studies of Moraea Mill. and the inclusion of Barnardiella Goldblatt, Galaxia Thunb., Gynandriris Parl., Hexaglottis Vent., Homeria Vent. and Roggeveldia Goldblatt in the genus have rendered the existing infrageneric classification, dating from 1976, in need of substantial revision. In particular, subg. Moraea and subg. Vieusseuxia have been shown to be paraphyletic. We propose a new infrageneric classification, based, as far as current data permit, on phylogenetic principles. Monophyletic subgenera and sections are circumscribed based on molecular phylogenies alone or in combination with morphological considerations. We recognize 11 subgenera, 15 sections and three series, arranged as follows in phylogenetic sequence: Plumarieae; Visciramosae (with sect. Multifoliae and sect. Visciramosae); Moraea (with sect. Moraea and sect. Polyphyllae); Galaxia (with ser. Unguiculatae, ser. Eurystigma and ser. Galaxia); Monocephalae; Acaules; Polyanthes (with sect. Serpentinae, sect. Deserticola, sect. Hexaglottis, sect. Gynandriris, sect. Polyanthes and sect. Pseudospicatae); Grandifl orae; Vieusseuxia (with sect. Integres, sect. Vieusseuxia and sect. Villosae); and Homeria (with sect. Stipanthera, sect. Flexuosae, sect. Homeria and sect. Conantherae). Most are moderately to well circumscribed at the morphological level either by floral or vegetative characters, except subg. Moraea, which includes a small number of unspecialized species apparently not linked by any apomorphic features. With over 27 new species described in the past 25 years and another 60 transferred to the genus, Moraea now includes 214 species. We provide a full taxonomic synopsis of the genus.
Germination characteristics and frost tolerance of seedlings are crucial parameters for establishment and invasion success of plants. The characterization of differences between populations in native and invasive ranges may improve our understanding of range expansion and adaptation. Here, we investigated germination characteristics of Ambrosia artemisiifolia L., a successful invader in Europe, under a temperature gradient between 5 and 25 °C. Besides rate and speed of germination we determined optimal, minimal and maximal temperature for germination of ten North American and 17 European populations that were sampled along major latitudinal and longitudinal gradients. We furthermore investigated the frost tolerance of seedlings. Germination rate was highest at 15 °C and germination speed was highest at 25 °C. Germination rate, germination speed, frost tolerance of seedlings, and the temperature niche width for germination were significantly higher and broader, respectively, for European populations. This was partly due to a higher seed mass of these populations. Germination traits lacked evidence for adaptation to climatic variables at the point of origin for both provenances. Instead, in the native range, seedling frost tolerance was positively correlated with the risk of frosts which supports the assumption of local adaptation. The increased frost tolerance of European populations may allow germination earlier in the year which may subsequently lead to higher biomass allocation—due to a longer growing period—and result in higher pollen and seed production. The increase in germination rates, germination speed and seedling frost tolerance might result in a higher fitness of the European populations which may facilitate further successful invasion and enhance the existing public health problems associated with this species.
We review the diving-beetle genus Rhantus Dejean of Madagascar (Coleoptera, Dytiscidae, Colymbetinae) based on museum collection holdings and recently collected expedition material. Both morphology and DNA is used to test species boundaries, in particular whether newly collected material from the Tsaratanana mountains in the north represent a new species or are conspecific with Rhantus manjakatompo Pederzani and Rocchi 2009, described based on a single male specimen from the central Ankaratra mountains. DNA of the holotype of R. manjakatompo was successfully extracted in a non-destructive way and sequenced. The general mixed Yule coalescent model applied to an ultrametric tree constructed from mitochondrial cytochrome c oxidase subunit I (COI) sequence data delimited three species. Morphological characters supported the same species unambiguously. We therefore recognise three species of Rhantus to occur in Madagascar: R. latus (Fairmaire, 1869), R. bouvieri Régimbart, 1900 and R. manjakatompo Pederzani and Rocchi, 2009. All three species are endemic to Madagascar and restricted to the highlands of the island. Rhantusstenonychus Régimbart, 1895, syn. n., is considered a junior synonym of R. latus. We designate lectotypes for R. bouvieri and R. goudoti Sharp, 1882, the latter a junior synonym of R. latus. We provide descriptions, a determination key, SEM-images of fine pronotal and elytral structures, distribution maps, habitus photos, and illustrations of male genitalia and pro- and mesotarsal claws. We discuss the role of the Manjakatompo forest as a refugium for Madagascan Rhantus diversity and other endemics of the montane central high plateau.
State-of-the-art general circulation models (GCMs) are tested and challenged by the ability to reproduce paleoclimate key intervals. In order to account for climate changes associated with soil dynamics we have developed a soil scheme, which is asynchronously coupled to a state-of-the-art atmosphere ocean GCM with dynamic vegetation. We test the scheme for conditions representative of a warmer (mid-Holocene, 6 kyr before present, BP) and colder (Last Glacial Maximum, 21 kyr BP) than pre-industrial climate. The computed change of physical soil properties (i.e. albedo, water storage capacity, and soil texture) for these different climates leads to amplified global climate anomalies. Especially regions like the transition zone of desert/savannah and taiga/tundra, exhibit an increased response as a result of the modified soil treatment. In comparison to earlier studies, the inclusion of the soil feedback pushes our model simulations towards the warmer end in the range of mid-Holocene studies and beyond current estimates of global cooling during the Last Glacial Maximum based on PMIP2 (Paleoclimate Modelling Intercomparison Project 2) studies. The main impact of the interactive soil scheme on the climate response is governed by positive feedbacks, including dynamics of vegetation, snow, sea ice, local water recycling, which might amplify forcing factors ranging from orbital to tectonic timescales.
In old and heavily weathered soils, the availability of P might be so small that the primary production of plants is limited. However, plants have evolved several mechanisms to actively take up P from the soil or mine it to overcome this limitation. These mechanisms involve the active uptake of P mediated by mycorrhiza, biotic de-occlusion through root clusters, and the biotic enhancement of weathering through root exudation. The objective of this paper is to investigate how and where these processes contribute to alleviate P limitation on primary productivity. To do so, we propose a process-based model accounting for the major processes of the carbon, water, and P cycle including chemical weathering at the global scale. We use simulation experiments to assess the relative importance of the different uptake mechanisms to alleviate P limitation on biomass production. Implementing P limitation on biomass synthesis allows the assessment of the efficiencies of biomass production across different ecosystems.
We find that active P-uptake is an essential mechanism for sustaining P availability on long time scales, whereas biotic de-occlusion might serve as a buffer on time scales shorter than 10 000 yr. Although active P uptake is essential for reducing P losses by leaching, humid lowland soils reach P limitation after around 100 000 yr of soil evolution. Given the generalized modeling framework, our model results compare reasonably with observed or independently estimated patterns and ranges of P concentrations in soils and vegetation. Furthermore, our simulations suggest that P limitation might be an important driver of biomass production efficiency (the fraction of the gross primary productivity used for biomass growth), and that vegetation on older soils becomes P-limited leading to a smaller biomass production efficiency.
With this study, we provide a theoretical basis for investigating the responses of terrestrial ecosystems to P availability linking geological and ecological time scales under different environmental settings.
Mosquitoes and other arthropods may transmit medically important pathogens, in particular viruses such as West Nile virus. The presence of suitable hosts and competent vectors for those zoonotic viruses is essential for an enzootic transmission, which is a prerequisite for epidemics. To establish reliable risk projections, it is an urgent need for an exact identification of mosquito species, which is especially challenging in the case of sibling species, such as Culex. pipiens pipiens biotypes pipiens and molestus. To facilitate detection of different Culex pipiens forms and their hybrids we established a multiplex real-time PCR. Culex pipiens samples were obtained by egg raft collection and rearing until imago stage or adult sampling using CO2 baited traps and gravid traps. In total, we tested more than 16,500 samples collected all over Germany in the years 2011 and 2012. The predominant species in Germany are Culex pipiens pipiens biotype pipiens and Culex. torrentium, but we also detected Culex pipiens pipiens biotype molestus and hybrids of the two pipiens biotypes at sites where both species occur sympatrically. This report of a potentially important bridge vector for West Nile virus might have major impact in the risk projections for West Nile virus in Germany.
Tree migration-rates : narrowing the gap between inferred post-glacial rates and projected rates
(2013)
Faster-than-expected post-glacial migration rates of trees have puzzled ecologists for a long time. In Europe, post-glacial migration is assumed to have started from the three southern European peninsulas (southern refugia), where large areas remained free of permafrost and ice at the peak of the last glaciation. However, increasing palaeobotanical evidence for the presence of isolated tree populations in more northerly microrefugia has started to change this perception. Here we use the Northern Eurasian Plant Macrofossil Database and palaeoecological literature to show that post-glacial migration rates for trees may have been substantially lower (60–260 m yr–1) than those estimated by assuming migration from southern refugia only (115–550 m yr–1), and that early-successional trees migrated faster than mid- and late-successional trees. Post-glacial migration rates are in good agreement with those recently projected for the future with a population dynamical forest succession and dispersal model, mainly for early-successional trees and under optimal conditions. Although migration estimates presented here may be conservative because of our assumption of uniform dispersal, tree migration-rates clearly need reconsideration. We suggest that small outlier populations may be a key factor in understanding past migration rates and in predicting potential future range-shifts. The importance of outlier populations in the past may have an analogy in the future, as many tree species have been planted beyond their natural ranges, with a more beneficial microclimate than their regional surroundings. Therefore, climate-change-induced range-shifts in the future might well be influenced by such microrefugia.
Background: Mitochondrial genes are among the most commonly used markers in studies of species’ phylogeography and to draw conclusions about taxonomy. The Hyles euphorbiae complex (HEC) comprises six distinct mitochondrial lineages in the Mediterranean region, of which one exhibits a cryptic disjunct distribution. The predominant mitochondrial lineage in most of Europe, euphorbiae, is also present on Malta; however, it is nowadays strangely absent from Southern Italy and Sicily, where it is replaced by 'italica'. A separate biological entity in Italy is further corroborated by larval colour patterns with a congruent, confined suture zone along the Northern Apennines. By means of historic DNA extracted from museum specimens, we aimed to investigate the evolution of the mitochondrial demographic structure of the HEC in Italy and Malta throughout the Twentieth Century.
Results: At the beginning of the Twentieth Century, the European mainland lineages were also present at a moderate frequency in Southern Italy and Sicily. The proportion of 'italica' then steadily increased in this area from below 60 percent to near fixation in about 120 years. Thus, geographical sorting of mitochondrial lineages in the HEC was not as complete then as the current demography suggests. The pattern of an integral 'italica' core region and a disjunct euphorbiae distribution evolved very recently. To explain these strong demographic changes, we propose genetic drift due to anthropogenic habitat loss and fragmentation in combination with an impact from recent climate warming that favoured the spreading of the potentially better adapted 'italica' populations.
Conclusions: The pattern of geographically separated mitochondrial lineages is commonly interpreted as representing long term separated entities. However, our results indicate that such a pattern can emerge surprisingly quickly, even in a widespread and rather common taxon. We thus caution against drawing hasty taxonomic conclusions from biogeographical patterns of mitochondrial markers derived from modern sampling alone.
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.
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.