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Here we present a formal description of Biremis panamae Barka, Witkowski et Weisenborn sp. nov., which was isolated from the marine littoral environment of the Pacific Ocean coast of Panama. The description is based on morphology (light and electron microscopy) and the rbcL, psbC and SSU sequences of one clone of this species. The new species is included in Biremis due to its morphological features; i.e. two marginal rows of foramina, chambered striae, and girdle composed of numerous punctate copulae. The new species also possesses a striated valve face which is not seen in most known representatives of marine littoral Biremis species. In this study we also present the relationship of Biremis to other taxa using morphology, DNA sequence data and observations of auxosporulation. Our results based on these three sources point to an evolutionary relationship between Biremis, Neidium and Scoliopleura. The unusual silicified incunabular caps present in them are known otherwise only in Muelleria, which is probably related to the Neidiaceae and Scoliotropidaceae. We also discuss the relationship between Biremis and the recently described Labellicula and Olifantiella.
Nowadays a number of endemic mosquito species are known to possess vector abilities for various diseases, as e.g. the sibling species Culex pipiens and Culex torrentium. Due to their morphological similarity, ecology, distribution and vector abilities, knowledge about these species' population structure is essential. Culicidae from 25 different sampling sites were collected from March till October 2012. All analyses were performed with aligned cox1 sequences with a total length of 658 bp. Population structure as well as distribution patterns of both species were analysed using molecular methods and different statistical tests like distance based redundancy analysis (dbDRA), analysis of molecular variances (AMOVA) or McDonald & Kreitman test and Tajima's D. Within both species, we could show a genetic variability among the cox1 fragment. The construction of haplotype networks revealed one dominating haplotype for Cx. pipiens, widely distributed within Germany and a more homogeneous pattern for Cx. torrentium. The low genetic differences within Cx. pipiens could be a result of an infection with Wolbachia which can induce a sweep through populations by passively taking the also maternally inherited mtDNA through the population, thereby reducing the mitochondrial diversity as an outcome of reproductive incompatibility. Pairwise population genetic differentiation (FST) ranged significantly from moderate to very great between populations of Cx. pipiens and Cx. torrentium. Analyses of molecular variances revealed for both species that the main genetic variability exists within the populations (Cx. pipiens [88.38%]; Cx. torrentium [66.54%]). Based on a distance based redundancy analysis geographical origin explained a small but significant part of the species' genetic variation. Overall, the results confirm that Cx. pipiens and Cx. torrentium underlie different factors regarding their mitochondrial differentiation, which could be a result of endosymbiosis, dispersal between nearly located populations or human introduction.
It is commonly assumed that the colonization of restored river reaches by fish depends on the regional species pools; however, quantifications of the relationship between the composition of the regional species pool and restoration outcome are lacking. We analyzed data from 18 German river restoration projects and adjacent river reaches constituting the regional species pools of the restored reaches. We found that the ability of statistical models to describe the fish assemblages established in the restored reaches was greater when these models were based on ‘biotic’ variables relating to the regional species pool and the ecological traits of species rather than on ‘abiotic’ variables relating to the hydromorphological habitat structure of the restored habitats and descriptors of the restoration projects. For species presence in restored reaches, ‘biotic’ variables explained 34% of variability, with the occurrence rate of a species in the regional species pool being the most important variable, while ’abiotic’ variables explained only the negligible amount of 2% of variability. For fish density in restored reaches, about twice the amount of variability was explained by ‘biotic’ (38%) compared to ‘abiotic’ (21%) variables, with species density in the regional species pool being most important. These results indicate that the colonization of restored river reaches by fish is largely determined by the assemblages in the surrounding species pool. Knowledge of species presence and abundance in the regional species pool can be used to estimate the likelihood of fish species becoming established in restored reaches.
Smut fungi are well-suited to investigate the ecology and evolution of plant pathogens, as they are strictly biotrophic, yet cultivable on media. Here we report the genome sequence of Melanopsichium pennsylvanicum, closely related to Ustilago maydis and other Poaceae-infecting smuts, but parasitic to a dicot plant. To explore the evolutionary patterns resulting from host adaptation after this huge host jump, the genome of M. pennsylvanicum was sequenced and compared to the genomes of Ustilago maydis, Sporisorium reilianum, and Ustilago hordei. While all four genomes had a similar completeness in CEGMA analyses, gene absence was highest in M. pennsylvanicum, and most pronounced in putative secreted proteins, which are often considered as effector candidates. In contrast, the amount of private genes was similar among the species, highlighting that gene loss rather than gene gain is the hallmark of adaptation after the host jump to the dicot host. Our analyses revealed a trend of putative effectors to be next to another putative effector, but the majority of these are not in clusters and thus the focus on pathogenicity clusters might not be appropriate for all smut genomes. Positive selection studies revealed that M. pennsylvanicum has the highest number and proportion of genes under positive selection. In general, putative effectors showed a higher proportion of positively selected genes than non-effector candidates. The 248 putative secreted effectors found in all four smut genomes might constitute a core set needed for pathogenicity, while those 92 that are found in all grass-parasitic smuts, but have no ortholog in M. pennsylvanicum might constitute a set of effectors important for successful colonization of grass hosts.
Background: According to current taxonomy only three out of 27 Sinohimalayan leaf warbler species (Phylloscopidae) are considered genetically uniform across their entire breeding range along the Southeastern margin of the Qinghai-Tibetan Plateau, the Buff-barred Warbler (Phylloscopus pulcher) being one of them. Because marked differentiation among Himalayan and Chinese populations has been recently demonstrated for a number of Phylloscopus species (or sister species) we investigated the intraspecific variation of a mitochondrial gene, songs and morphology of P. pulcher in a phylogeographic approach.
Methods: We sequenced a fragment of the mitochondrial cytochrome b, reconstructed haplotype networks and analyzed DNA polymorphism among Himalayan and Chinese populations. We measured time and frequency parameters of two distinct song types and analyzed among population-differentiation in a principal component analysis and a discriminant analysis. We also compared measurements of body size dimensions taken from museum specimens.
Results: The mitochondrial haplotype network (cytb) was divided into two distinct clusters corresponding to geographic origin of samples. Pairwise genetic distances among Himalayan and Chinese mtDNA lineages account for 1.3% which coincides with Pleistocene lineage separation at roughly 650,000 years ago. Genetic diversity is slightly higher in the Chinese part of the species’ range with respect to haplotype and nucleotide diversity while the less diversified Himalayan population lineage shows signs of recent range expansion. The vocal repertoire of P. pulcher comprises two distinct verse types that are combined with short interspersed click notes to long continuous song displays. Trill verse types showed significant differences among regions in almost all measured frequency and time parameters: Chinese males displayed more rapid and more broad-banded trills at a lower pitch. In contrast, warbling verse types showed a distinctively different structure among regions: Himalayan songs consisted of repeated syllables while Chinese songs comprised repetitions of single, long and strongly modulated elements. Subtle morphological differences among specimens from the two study regions could only be confirmed for plumage coloration but not for metric characters.
Conclusions: Based on the genetic and bioacoustic distinctiveness of Chinese Buff-barred Warbler populations, we recommend that the name Phylloscopus pulcher vegetus Bangs, 1913 should be re-validated for this taxon.
Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3' end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3'UTR lengths, especially for chicken, and APADB provides necessary information to close this gap. Database URL: http://tools.genxpro.net/apadb/
Panama is a megadiverse country that together with Costa Rica constitutes Lower Central America (LCA). Western Panama's Cordillera Central accounts for the eastern part of the LCA highlands shared between these countries. The aim of the present study is to compile the most complete and updated picture possible of the taxonomy, diversity, and distribution of reptiles that occur from 500 m asl upwards along the Talamanca and Tabasará ranges. These two continuous mountain ridges account for the western two-thirds of the Cordillera Central between the Costa Rican border and 81°W Including specimens collected four own research travels, I morphologically examined more than 1800 specimens, analyzed 16S and/or COI barcodes of 300 specimens, and performed a thorough search in literature and databases to obtain locality records for specimens and species occurrences. My complete occurrence dataset comprises 14620 georeferenced occurrence records in three quality categories. Conceivable occurrences of species not yet documented from a given area are evaluated on the basis of existing data either as "plausible" or "possible". I provide all datasets which I generated for this study in Appendices. The previously published descriptions of Dactyloa ginaelisae Lotzkat, Hertz, Bienentreu & Köhler 2013, Norops benedikti (Lotzkat, Bienentreu, Hertz & Köhler 2011), Sibon perissostichon Köhler, Lotzkat & Hertz 2010, and Sibon noalamina Lotzkat, Hertz & Köhler 2012 are included in the present work. In the course of integrative taxonomic analyses, I classify 15 genealogical lineages revealed by DNA barcoding within 7 anole species as Deep Conspecific Lineages (DCLs) because they lack consistent morphological differences to their nominal conspecifics. I provisionally classify 18 mitochondrial lineages found within six other anole species as Unconfirmed Genealogical Lineages (UGLs) pending adequate analyses of their morphological variation. I regard the two additional UGLs Celestus sp. and Geophis sp. and the two Confirmed Genealogical Lineages (CGLs) Lepidoblepharis sp. 1 and 2 to represent undescribed species. My taxonomic analyses yield the hitherto most comprehensive survey of the variability exhibited by dozens of reptile species in western Panama. The 16S and/or COI barcodes I provide represent 65 species recognized herein and constitute the first DNA barcode reference library for LCA reptiles. The reptile fauna of Panama comprises 265 species, including the four UGLs and CGLs mentioned above and characterized for the first time in this study, as well as Dendrophidion crybelum Cadle 2012 whose presence in the country I consider plausible. My occurrence dataset reveals that 160 of these species have been documented to occur in my study area. Adding the 20 species whose occurrence therein I consider plausible, I report the total species richness of the Talamanca and Tabasará ranges as comprising 180 species representing 81 genera in 25 families. With 178.8 species per 10 000 km2, the relative species richness of the area is extremely high even in a tropical context. In view of their overall documented distribution, I regard the presence of 27 additional species in my study area as possible. For the 180 species occurring in my study area I provide standardized species accounts that, together with the taxonomic results, for the first time permit the doubtless identification of all 180 species, and illustrate 168 of these with color photographs. Concerning biogeography, my georeferenced dataset yields noteworthy distribution extensions for many species. Moreover, I present the hitherto most comprehensive, detailed, and reproducible assessments of the distribution patterns, historical origins, and conservation as well as of the occurrence among physiographic regions, climatic and altitudinal belts, political subdivisions, and protected areas, for my study area's reptile fauna. With 65 species, more than a third of the fauna is endemic to LCA. Among these, 42 Talamancan highland endemics are restricted to the LCA highlands, in the case of 16 small-scale highland endemics with documented ranges spanning less than 100 km. I assess many of these endemics as endangered. The fact that several of these species do not occur in any protected area renders the establishment of additional conservation areas necessary, especially in the central Serranía de Tabasará. Distributional range boundaries shared among different clades of highland anoles indicate physiographic and climatic barriers that may have effected in situ speciation within these lineages. As the largest study on Panamanian reptile diversity assembled to date, the present dissertation considerably increases our knowledge on the reptiles along the Cordillera Central and beyond, and thus constitutes a solid basis for future studies.
The knowledge of phenotypic variation in the European range of the highly allergenic Ambrosia artemisiifolia L. (common ragweed) is not entirely complete, even though it is an invasive species of utmost concern. We hypothesized the prevalence of phenotypic differentiations between common ragweed populations in the introduced range, and we assumed that those differentiations were related to environmental conditions at the points of origin. Using a common garden experiment, we investigated biomass allocation, growth rates, and flowering phenology of 38 European common ragweed populations originating from a major geographical gradient. We observed considerable phenotypic variation in growth parameters and flowering phenology, e.g. mean aboveground biomass varied from 23.3 to 47.3 g between the populations. We were able to relate most measured traits with environmental parameters prevailing at the points of origin. For example, early growth of ruderal populations was highly correlated with temperature and precipitation at the point of origin. Late growth and flowering phenology were highly correlated with latitude, i.e. individuals from northern populations grew smaller and flowered and dispersed their pollen and seeds up to 5 weeks earlier than individuals from southern populations. We also found a longitudinal gradient in flowering phenology which has not yet been described. The existence of such a high variability in the introduced range may facilitate further range expansion. We suggest that the correlation with environmental variables rests upon genetic variation possibly due to adaptations to the respective environment. To clarify if such adaptation results from multiple events of introduction or as evolutionary response after introduction, genetic investigations are needed.
Understanding major causes of biodiversity and range dynamics requires research on evolutionary processes under consideration of environmental changes. In my thesis, I investigated the spatio-temporal evolution of the Neotropical tree genus Cedrela from the Meliaceae family by studying its genetic diversity, taxonomy, colonization history, climatic niche changes and dynamics of species distributions. My results show that climatic and geological changes are major drivers of biological diversification in Cedrela.
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
Drought stress is one of the major abiotic factors diminishing crop productivity world wide. In the course of climate change, regions which already experience dry seasons nowadays will suffer from elongated drought periods and water shortage. These climatic changes will not only have an impact on the regional flora and fauna but also on the people inhabiting these areas. It is therefore of great importance to understand the reactions of plants to drought stress to help breeding and biotechnological approaches for the benefit of new robust cereal cultures growing under low water regimes. In this dissertation four grasses of the genus Panicum, P. bisulcatum (C3), P. laetum, P. miliaceum and P. turgidum (all C4 NAD-ME) were subjected to drought stress. The plants diverse reactions were investigated on a physiological as well as on a molecular level to deepen the understanding of drought stress responses. Drought stress was imposed for a species-specific period until a relative leaf water content (RWC) of ~50 % was reached in each grass. Physiological measurements were conducted on leaves with a RWC of ~50 % investigating chlorophyll a fluorescence parameters with a Plant Efficiency Analyzer (PEA) and gas exchange parameters like the photosynthesis rate and stomatal conductance with a Gas Fluorescence Chamber (GFS-3000). Subsequent molecular analysis were conducted on leaf samples taken (RWC = 50 %) analysing different proteins and the transcriptome of the Panicum species. The physiological measurements revealed a higher photosynthesis rate for the C4 grasses under drought stress with no significant differences between the C4 species. Also the water use efficiency was significantly higher in the C4 species in comparison to the C3 species independent from the water regime supporting results from the literature. The chlorophyll a measurements revealed the strongest adaptation to water shortage in the C4 species P. turgidum followed by the C3 species P. bisulcatum. It has been shown before (GHANNOUM 2009) that the C4 photosynthesis apparatus is more prone to drought stress than the C3 apparatus – despite the higher water use efficiency. Results also suggested that the great adaptation of P. turgidum to drought stress arose from its ability to recover from drought stress (all JIP test parameters showed no significant differences between control and recovery samples). The additional down-regulation of PS II but not of PS I under drought stress also helped the plant to endure times of water shortage and facilitated the recovery when water was available again. Protein analyses on the content of PEPC, OEC and RubisCO (LSU and SSU) revealed no changes. Dehydrin 1 in contrast was strongly up-regulated under drought stress and Summary 108 recovery in all four Panicum species. The stable content of the OEC protein was therefore not the catalyst of rising K peaks measured by chlorophyll a fluorescence and a reduced OEC activity was supposed. Transcriptomic analyses revealed a myriad of differentially regulated tags. Due to unsequenced genomes, tags could only be partially (8 % maximum for P. turgidum) annotated to their specific genes. Diverse methods were therefore used to annotate the most highly regulated tags to their genes and their products. Special emphasis was put on the regulation of five gene products confirming the regulation schemata from the HT-SuperSAGE analyses. Interestingly one protein – the NCED1 – was down-regulated under stress conditions, in contrast to results from the literature. It is therefore of great importance to investigate longer lasting drought to understand the full range of drought stress adaptation. Future genome sequencing projects might also include the Panicum species investigated in this dissertation and important gene candidates with no hits (maybe completely new to the research community) might help breeding and biotechnology approaches to produce more drought resistant crop species.
The Cueva del Azufre in Tabasco, Mexico, is a nutrient-rich cave and its inhabitants need to cope with high levels of dissolved hydrogen sulfide and extreme hypoxia. One of the successful colonizers of this cave is the poeciliid fish Poecilia mexicana, which has received considerable attention as a model organism to examine evolutionary adaptations to extreme environmental conditions. Nonetheless, basic ecological data on the endemic cave molly population are still missing; here we aim to provide data on population densities, size class compositions and use of different microhabitats. We found high overall densities in the cave and highest densities at the middle part of the cave with more than 200 individuals per square meter. These sites have lower H2S concentrations compared to the inner parts where most large sulfide sources are located, but they are annually exposed to a religious harvesting ceremony of local Zoque people called La Pesca. We found a marked shift in size/age compositions towards an overabundance of smaller, juvenile fish at those sites. We discuss these findings in relation to several environmental gradients within the cave (i.e., differences in toxicity and lighting conditions), but we also tentatively argue that the annual fish harvest during a religious ceremony (La Pesca) locally diminishes competition (and possibly, cannibalism by large adults), which is followed by a phase of overcompensation of fish densities.
Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
Background: The invasive eel parasite Anguillicoloides crassus (syn. Anguillicola crassus) is considered one of the major causes for the decline of the European eel (Anguilla anguilla) panmictic population. It impairs the swim bladder function and reduces swimming performance of its host. The life cycle of this parasite involves different intermediate and paratenic hosts. Despite an efficient immune system of the paratenic fish hosts acting against infections with A. crassus, levels of parasitized eels remain high in European river systems. Recently, the round goby Neogobius melanostomus (Gobiidae) has become dominant in many rivers in Europe and is still spreading at a rapid pace. This highly invasive species might potentially act as an important, so far neglected paratenic fish host for A. crassus.
Methods: Based on own observations and earlier single sightings of A. crassus in N. melanostomus, 60 fresh individuals of N. melanostomus were caught in the Rhine River and examined to assess the infection levels with metazoan parasites, especially A. crassus. Glycerin preparations were used for parasite identification.
Results: The parasite most frequently found in N. melanostomus was the acanthocephalan Pomphorhynchus sp. (subadult stage) which occurred mainly encysted in the mesenteries and liver. Every third gobiid (P = 31.7%) was infected by A. crassus larvae (L3) which exclusively occurred inside the acanthocephalan cysts. No intact or degenerated larvae of A. crassus were detected elsewhere in the goby, neither in the body cavity and mesenteries nor in other organs. Affected cysts contained the acanthocephalan larvae and 1-12 (mI =3) living A. crassus larvae. Additionally, encysted larvae of the nematode Raphidascaris acus were detected in the gobies, but only in the body cavity and not inside the acanthocephalan cysts.
Conclusions: Based on our observations, we suggest that A. crassus might actively bypass the immune response of N. melanostomus by invading the cysts of acanthocephalan parasites of the genus Pomphorhynchus using them as "Trojan horses". Providing that eels prey on the highly abundant round goby and that the latter transfers viable infective larvae of A. crassus, the new paratenic host might have a strong impact on the epidemiology of A. crassus.
Freshwater ecosystems are increasingly impacted by alien invasive species which have the potential to alter various ecological interactions like predator-prey and host-parasite relationships. Here, we simultaneously examined predator-prey interactions and parasitization patterns of the highly invasive round goby (Neogobius melanostomus) in the rivers Rhine and Main in Germany. A total of 350 N. melanostomus were sampled between June and October 2011. Gut content analysis revealed a broad prey spectrum, partly reflecting temporal and local differences in prey availability. For the major food type (amphipods), species compositions were determined. Amphipod fauna consisted entirely of non-native species and was dominated by Dikerogammarus villosus in the Main and Echinogammarus trichiatus in the Rhine. However, the availability of amphipod species in the field did not reflect their relative abundance in gut contents of N. melanostomus. Only two metazoan parasites, the nematode Raphidascaris acus and the acanthocephalan Pomphorhynchus sp., were isolated from N. melanostomus in all months, whereas unionid glochidia were only detected in June and October in fish from the Main. To analyse infection pathways, we examined 17,356 amphipods and found Pomphorhynchus sp. larvae only in D. villosus in the river Rhine at a prevalence of 0.15%. Dikerogammarus villosus represented the most important amphipod prey for N. melanostomus in both rivers but parasite intensities differed between rivers, suggesting that final hosts (large predatory fishes) may influence host-parasite dynamics of N. melanostomus in its introduced range.
Speolepta leptogaster (Winnertz, 1863) is frequently occurring in European subterranean environments. As for most cave animals, studies addressing non-anatomical aspects are sparse. Here we present the first molecular study on S. leptogaster. We investigated the demographic structure (i.e. COI locus) of 69 specimens from 36 underground populations in Hesse (Central German Uplands) to get first insights into the species’ dispersal ability.
In total, 14 haplotypes were revealed. Haplotype diversity was relatively high, whereas nucleotide diversity was low. Furthermore, a significant but low pattern of isolation-by-distance and (a) past population expansion event(s) were detected.
Our genetic results suggest a (good) active dispersal ability for Speolepta leptogaster. The occurrence of several surface records of adult specimens corroborates this hypothesis. We discuss the developmental stages of S. leptogaster in the context of the ecological classification system and regard the species as a eutroglophile. Evidence has been found to distinguish two larval types. A reconstructed life-cycle of the species is provided.
High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
Background: The current taxonomy of the African giraffe (Giraffa camelopardalis) is primarily based on pelage pattern and geographic distribution, and nine subspecies are currently recognized. Although genetic studies have been conducted, their resolution is low, mainly due to limited sampling. Detailed knowledge about the genetic variation and phylogeography of the South African giraffe (G. c. giraffa) and the Angolan giraffe (G. c. angolensis) is lacking. We investigate genetic variation among giraffe matrilines by increased sampling, with a focus on giraffe key areas in southern Africa.
Results: The 1,562 nucleotides long mitochondrial DNA dataset (cytochrome b and partial control region) comprises 138 parsimony informative sites among 161 giraffe individuals from eight populations. We additionally included two okapis as an outgroup. The analyses of the maternally inherited sequences reveal a deep divergence between northern and southern giraffe populations in Africa, and a general pattern of distinct matrilineal clades corresponding to their geographic distribution. Divergence time estimates among giraffe populations place the deepest splits at several hundred thousand years ago.
Conclusions: Our increased sampling in southern Africa suggests that the distribution ranges of the Angolan and South African giraffe need to be redefined. Knowledge about the phylogeography and genetic variation of these two maternal lineages is crucial for the development of appropriate management strategies.
Mehr als 6.600 Doktorandinnen und Doktoranden forschen an der Goethe-Universität Frankfurt am Main. Das und vieles mehr ergab die erste repräsentative Umfrage unter Promovierenden und ihren Betreuern, die im Auftrag der Universität durch das Berliner Institut für Forschungsinformation und Qualitätssicherung (iFQ) durchgeführt wurde. Das gute Ergebnis ist nicht zuletzt auf GRADE, die Goethe Graduate Academy, zurückzuführen, dem universitätsübergreifenden Zentrum für die Doktorandenausbildung. ...