A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae

Identification and characterization of a new species of Taxus - Taxus qinlingensis by multiple taxonomic methods

BACKGROUND

The taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.

RESULTS

Multiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500 m.

CONCLUSIONS

Four characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen & X. T. Wu, sp. nov.

Morphospecies and molecular diversity of ‘lace corals’: the genus Reteporella (Bryozoa: Cheilostomatida) in the central North Atlantic Azores Archipelago

Background

As in most bryozoans, taxonomy and systematics of species in the genus Reteporella Busk, 1884 (family Phidoloporidae) has hitherto almost exclusively been based on morphological characters. From the central North Atlantic Azores Archipelago, nine Reteporella species have historically been reported, none of which have as yet been revised. Aiming to characterise the diversity and biogeographic distribution of Azorean Reteporella species, phylogenetic reconstructions were conducted on a dataset of 103 Azorean Reteporella specimens, based on the markers cytochrome C oxidase subunit 1, small and large ribosomal RNA subunits. Morphological identification was based on scanning electron microscopy and complemented the molecular inferences.

Results

Our results reveal two genetically distinct Azorean Reteporella clades, paraphyletic to eastern Atlantic and Mediterranean taxa. Moreover, an overall concordance between morphological and molecular species can be shown, and the actual bryozoan diversity in the Azores is greater than previously acknowledged as the dataset comprises three historically reported species and four putative new taxa, all of which are likely to be endemic. The inclusion of Mediterranean Reteporella specimens also revealed new species in the Adriatic and Ligurian Sea, whilst the inclusion of additional phidoloporid taxa hints at the non-monophyly of the genus Reteporella.

Conclusion

Being the first detailed genetic study on the genus Reteporella, the high divergence levels inferred within the genus Reteporella and family Phidoloporidae calls for the need of further revision. Nevertheless, the overall concordance between morphospecies and COI data suggest the potential adequacy of a 3% cut-off to distinguish Reteporella species. The discovery of new species in the remote Azores Archipelago as well as in the well-studied Mediterranean Sea indicates a general underestimation of bryozoan diversity. This study constitutes yet another example of the importance of integrative taxonomical approaches on understudied taxa, contributing to cataloguing genetic and morphological diversity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02080-z.

Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny

Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.

A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution

Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we alleviate this issue by presenting the molecular sequences of 165 cheilostome bryozoan species from New Zealand waters. New Zealand is our geographic region of choice as its cheilostome fauna is taxonomically, functionally and ecologically diverse, and better characterized than many other such faunas in the world. Using this most taxonomically broadly-sampled and statistically-supported cheilostome phylogeny comprising 214 species, when including previously published sequences, and 17 genes (2 nuclear and 15 mitochondrial) we tested several existing systematic hypotheses based solely on morphological observations. We find that lower taxonomic level hypotheses (species and genera) are robust while our inferred trees did not reflect current higher-level systematics (family and above), illustrating a general need for the rethinking of current hypotheses. To illustrate the utility of our new phylogeny, we reconstruct the evolutionary history of frontal shields (i.e., a calcified body-wall layer in ascus-bearing cheilostomes) and ask if its presence has any bearing on the diversification rates of cheilostomes.

Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features

Bryozoans are aquatic colonial suspension-feeders abundant in many marine and freshwater benthic communities. At the same time, the phylum is under studied on both morphological and molecular levels, and its position on the metazoan tree of life is still disputed. Bryozoa include the exclusively marine Stenolaemata, predominantly marine Gymnolaemata and exclusively freshwater Phylactolaemata. Here we report the mitochondrial genome of the phylactolaemate bryozoan Cristatella mucedo. This species has the largest (21,008 bp) of all currently known bryozoan mitogenomes, containing a typical metazoan gene compendium as well as a number of non-coding regions, three of which are longer than 1500 bp. The trnS1/trnG/nad3 region is presumably duplicated in this species. Comparative analysis of the gene order in C. mucedo and another phylactolaemate bryozoan, Pectinatella magnifica, confirmed their close relationships, and revealed a stronger similarity to mitogenomes of phoronids and other lophotrochozoan species than to marine bryozoans, indicating the ancestral nature of their gene arrangement. We suggest that the ancestral gene order underwent substantial changes in different bryozoan cladesshowing mosaic distribution of conservative gene blocks regardless of their phylogenetic position. Altogether, our results support the early divergence of Phylactolaemata from the rest of Bryozoa.

A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group

Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air-dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.