The enigmatic Placozoa part 2: Exploring evolutionary controversies and promising questions on earth and in space

The placozoan Trichoplax adhaerens has been bridging gaps between research discilplines like no other animal. As outlined in part 1, placozoans have been subject of hot evolutionary debates and placozoans have challenged some fundamental evolutionary concepts. Here in part 2 we discuss the exceptional genetics of the phylum Placozoa and point out some challenging model system applications for the best known species, Trichoplax adhaerens

Character-based barcoding, a symbiosis and potential successor of traditional taxonomy and modern DNA barcoding

Classic taxonomy is a powerful tool for identifying animals based on morphology but has shown to be problematic on similar looking, cryptic species. A solution to this problem has been found within the bauplan of life, the DNA (deoxyribonucleic acid). DNA is used to create and regulate proteins. The structure of DNA has highly unique sections that are conserved within species, but diverse between species. One particular section, a 648 bp long fragment of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, has become a popular barcode for species identification. Here, a new barcoding technique, character-based barcoding more similar to traditional approaches is tested. This thesis investigates whether CO1 is suitable as a single marker (a) or should be complemented by others (b). Performance of distance- and character-based barcoding (c) is evaluated and it is tested whether character-based barcoding can be used to identify cryptic species (d). In the first manuscript, CO1 sequences of endangered turtle species are compared (a). Having a reliable tool for species identification is an important asset in species protection surveillance. Variability within the barcode region is assessed and the utility of both distance- and character-based methods for species identification are evaluated (c). Odonata is an old order rich in species. As many species have evolved in a short time, it was observed that intra- and interspecific variety is overlapping in some sister groups. This observation made Odonata the ideal candidate for testing CO1 (a), ND1 (b), as well as distance- and character-based-barcoding (c) in the second manuscript. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. As combinations of multiple marker regions seemed to be a better approach to barcoding, three markers (CO1, 28S rDNA, rhodopsin) are tested (b) in the third manuscript. A combined, layered approach to character-based barcoding is evaluated and unique diagnostics specific to geolocations are identified (d). The results of all three studies show that combining multiple markers improves identification success. The character-based approach provides better identification in the tested animal groups. This method can be used to estimate presence, absence or frequency of cryptic species

Utilizing DeepSqueak for automatic detection and classification of mammalian vocalizations: a case study on primate vocalizations

Bioacoustic analyses of animal vocalizations are predominantly accomplished through manual scanning, a highly subjective and time-consuming process. Thus, validated automated analyses are needed that are usable for a variety of animal species and easy to handle by non-programing specialists. This study tested and validated whether DeepSqueak, a user-friendly software, developed for rodent ultrasonic vocalizations, can be generalized to automate the detection/segmentation, clustering and classification of high-frequency/ultrasonic vocalizations of a primate species. Our validation procedure showed that the trained detectors for vocalizations of the gray mouse lemur (Microcebus murinus) can deal with different call types, individual variation and different recording quality. Implementing additional filters drastically reduced noise signals (4225 events) and call fragments (637 events), resulting in 91% correct detections (N(total) = 3040). Additionally, the detectors could be used to detect the vocalizations of an evolutionary closely related species, the Goodman’s mouse lemur (M. lehilahytsara). An integrated supervised classifier classified 93% of the 2683 calls correctly to the respective call type, and the unsupervised clustering model grouped the calls into clusters matching the published human-made categories. This study shows that DeepSqueak can be successfully utilized to detect, cluster and classify high-frequency/ultrasonic vocalizations of other taxa than rodents, and suggests a validation procedure usable to evaluate further bioacoustics software

The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches

<div><p>The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent “Folmer region”, a 648 basepair fragment at the 5’ end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the “Folmer region”, the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the “Folmer region” using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic “environment”, this new marker will further enhance the discrimination power at the species level.</p></div

Information on anisoptera odonate samples.

<p>Information on anisoptera odonate samples.</p

Information on zygoptera odonate samples.

<p>Information on zygoptera odonate samples.</p

Sequence information.

<p>Sequence information.</p

Diagnostic characters for sister taxa.

<p>Diagnostic characters for sister taxa.</p