Biology subjects

Straube, N.

Publications and source records attributed to Straube, N..

4 recordsLinked to original sources

bioRxiv2026

The proposed Baltic Sea endemic green alga Monostroma balticum represents a foliose morphotype of Ulva intestinalis (Ulvales, Ulvophyceae).

Green algae in Ulva, Monostroma and similar genera are notoriously difficult to identify morphologically, due to high phenotypic plasticity and the presence of cryptic species - which has historically resulted in a challenging taxonomy, poorly resolved species boundaries, and potentially numerous invalid species descriptions. DNA-based specimen identification, especially combined with analysis of historical herbarium voucher DNA, has huge potential in resolving many unresolved taxonomical problems in these algae. One such example is Monostroma balticum, which has been described as foliose, monostromatic green seaweed known only free-floating, and reported to be endemic to the Baltic Sea. Previous studies have highlighted major uncertainty in the status of this taxon. We conducted an extensive sampling campaign of monostromatic green algae across the Baltic Sea to molecularly, morphologically and ecologically characterise this enigmatic taxon. Additionally, we investigated original exciccate material of M. balticum by using a museomic approach. We show that Monostroma balticum represents a monostromatic, foliose morphotype of the cosmopolitan and ubiquitous species Ulva intestinalis. This foliose growth form is seen in low salinity conditions, and, so far, reported only from the inner basin of the Baltic Sea. Our work shows that using morphology- and DNA-based museomic approaches for contemporary and historical specimens is a powerful combination to resolve long-standing taxonomical uncertainties and to produce new biodiversity information, even in relatively well-studied regions.

plant biology↗

bioRxiv2025

A novel data filtering method resolves the controversy in the phylogeny of the Chondrichthyes

Phylogenomics, which uses genome-scale data for phylogenetic inference, has clarified many controversial nodes in the tree of life. Such extensive data improve tree resolution and better reflects organismal history compared to analyses based on single or a few genetic loci. However, some relationships within the tree of life remain unresolved, as increased data can yield high node support without ensuring accuracy due to systematic errors. For example, the order-level relationships among chondrichthyans are still contentious despite the use of phylogenomic data. To address systematic errors, complex models have been developed, and filtering for less erroneous data shows great promise. Current metric-based filtering methods rank loci based on overall tree statistics, but problematic signals are often local; and topology-based data filtering approaches struggle with circular assumptions. In this study, we introduced two novel metric-based data filtering methods based on the ratio of local branch length or GC content between problematic clades. We applied these methods to a dataset of 4,452 single-copy exons extracted from 98 chondrichthyan species. The results using all loci showed that the Hexanchiformes was positioned at the root of Elasmobranchii, pulling other squalomorphs to the basal position and rendering Squalomorphii paraphyletic. Contrastingly, filtering for loci with more even branch length, the branch ratio method (absRatioLen) strongly supported the monophyly of all superorders of the chondrichthyans as well as their higher classification grouping, such as Selachii and Batoidea. By concentrating on problematic nodes, our assumption-free filtering methods demonstrate significant potential in resolving contentious relationships in the tree of life.

evolutionary biology↗

bioRxiv2024

Museomics analyses inform about Channichthys icefish species diversity

The rapid diversification of notothenioid fishes in the waters surrounding the Antarctic continent is a prime example of the process of adaptive radiation. Within around 10 million years, Antarctic notothenioids have diversified into over 100 species with a broad range of lifestyles and ecological adaptations. However, the exact number of species within this radiation has long been unclear. Particularly challenging is the taxonomy of the genus Channichthys, for which between one and nine species have been recognized by different authors. The putative species from this genus are known from a limited number of representative specimens, of which most were sampled decades ago. Here, we investigated the mitochondrial genomes of museum specimens representing the four recently recognized species Unicorn Icefish (C. rhinoceratus), Red Icefish (C. rugosus), Sailfish Pike (C. velifer), and Charcoal Icefish (C. panticapaei), complemented by morphological analyses. All analyzed specimens were collected in the 1960s and 1970s and fixed in formaldehyde, and their DNA has thus been heavily degraded. Applying ancient-DNA protocols for DNA extraction and single-stranded library preparation, we were nevertheless able to obtain sufficient endogenous DNA to reconstruct the mitochondrial genomes of one specimen of each species. These mitochondrial genome sequences were nearly identical for the three specimens assigned to Unicorn Icefish, Red Icefish, and Sailfish Pike, while greater mitochondrial divergence was observed for the Charcoal Icefish specimens. We discuss possible explanations of the contrast between these molecular results and the recognizable morphological variation found among the four species, and recommend that at least the Charcoal Icefish be included the list of valid icefish and notothenioid species.

evolutionary biology↗

bioRxiv2023

From museum drawer to tree: historical DNA phylogenomics clarifies the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections

Although several methods exist for extracting and sequencing historical DNA originating from drypreserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol ([~] {euro}10 per sample), in combination with Ultraconserved Elements (UCEs), is an effective tool for insect phylogenomic studies. We successfully tested our approach by sequencing DNA from scarab dung beetles preserved in both wet and dry collections, including unique primary type and rare historical specimens from internationally important natural history museums in London, Paris and Helsinki. The focal specimens comprise enigmatic dung beetle genera (Nesosisyphus, Onychotechus and Helictopleurus) that varied in age and preservation. The oldest specimen, the holotype of the now possibly extinct Mauritian endemic Nesosisyphus rotundatus, was collected in 1944. We obtained high-quality DNA from all studied specimens to enable the generation of a UCE-based dataset that revealed an insightful and well-supported phylogenetic tree of dung beetles. The resulting phylogeny suggested the reclassification of Onychotechus (previously incertae sedis) within the tribe Coprini. Our approach demonstrates the feasibility and effectiveness of combining DNA data from historic and recent museum specimens to provide novel insights. The proposed archival DNA protocol is available at DOI 10.17504/protocols.io.81wgbybqyvpk/v1 HighlightsO_LIWe combined custom low-cost archival DNA extractions and Ultraconserved Element phylogenomics C_LIO_LIDNA from rare museum specimens of enigmatic dung beetles revealed their phylogenetic connections C_LIO_LIGenomic data was obtained from the holotype of a potentially extinct monoinsular endemic species C_LIO_LIGenomic data allowed a rare and enigmatic species of previously unknown affinity to be classified C_LIO_LIThe morphology of museum specimens remained intact following non-destructive DNA extraction C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/564347v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@34aad0org.highwire.dtl.DTLVardef@1ba597dorg.highwire.dtl.DTLVardef@1493c2dorg.highwire.dtl.DTLVardef@10dd2eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗