Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

Pragmatic Assignment of Species Groups Based on Primary Species Hypotheses: The Case of a Dominant Component of the Southern Ocean Benthic Fauna

Ecological studies that enhance our understanding of the structure and function of the natural world rely heavily on accurate species identification. With rapid sample accumulation and declining taxonomic expertise, cladistics, phylogenetics and coalescent-based analyses have become key tools for identification or discrimination of species. These tools differ in effectiveness and interpretation depending on researcher perspective and the unique evolutionary histories of the taxa. Given the cost and time required for taxonomic assessment of ambiguous species groups, we advocate a pragmatic approach to clarify species assignment. We carried out a case-study on species from the diverse ophiuroid genus Ophiacantha common in shelf habitats around the Southern Ocean. Although several of the species are formally described with clear and distinctive morphological characters and reproductive strategies (O. vivipara, O. pentactis, O. densispina, O. antarctica, and O. wolfarntzi), recent molecular data has highlighted issues with these morphospecies, the characters that formally define them and their evolutionary histories. Here we provide evidence that key morphological features of species can be deceptive and show that six-armed O. vivipara, for example, is not a widely distributed Southern Ocean species as currently accepted, rather, three disparate clades. Ophiacantha pentactis, described as having five arms, frequently has six arms and the six-armed form is mistakenly classified as O. vivipara. All six-armed specimens collected from the Antarctic continental shelf fall into the O. pentactis species clade. Molecular tools designed for species delimitation appear to fail to reflect the “true” species composition. Rather than rely on a single tool for species recognition, we advocate an integrated approach using traditional detailed taxonomic morphology, summary statistics of molecular sequence data from populations, robust phylogenies, sufficient geographical sampling and local biological knowledge to ensure that species hypotheses can be built on mutually supporting lines of evidence.

Disporella guada sp. nov., an erect-ramose rectangulate cyclostome (Bryozoa, Stenolaemata) from the Caribbean Sea: convergent evolution in bryozoan colony morphology

The taxonomy of cyclostome bryozoans is founded on characters of the skeleton, but molecular sequence data have increasingly shown that established higher taxa are not monophyletic. Here we describe the skeletal morphology of a new species from Guadeloupe (French West Indies) with erect ramose colonies consisting of long, curved zooids that are typical of the suborder Cerioporina among living cyclostomes. However, molecular evidence from nuclear ribosomal RNA genes 18S and 28S places the new taxon in the suborder Rectangulata, where this colony-form has not been previously recorded. It nests firmly within the genus Disporella Gray, 1848, in a strongly supported clade that also includes Plagioecia patina (Lamarck, 1816) (Tubuliporina) and the sister taxa Doliocoitis cyanea Gordon & Taylor, 2001 (Rectangulata) and Favosipora rosea Gordon & Taylor, 2001 (Cerioporina). The short and robust branches of the new Guadeloupe cyclostome, here named Disporella guada Harmelin, Taylor & Waeschenbach sp. nov., are well adapted to life in shallow rocky sites exposed to severe wave action, which appear to be its exclusive habitat.

Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank

Molecular sequence data is an essential component for many biological fields of study. The strength of these data is in their ability to be centralised and compared across research studies. There are many online repositories for molecular sequence data, some of which are very large accumulations of varying data types like NCBI’s GenBank. Due to the size and the complexity of the data in these repositories, challenges arise in searching for data of interest. While data repositories exist for molecular markers, taxa and other specific research interests, repositories may not contain, or be suitable for, more specific applications. Manually accessing, searching, downloading, accumulating, dereplicating and cleaning data to construct project-specific datasets is time-consuming. In addition, the manual assembly of datasets presents challenges with reproducibility. Here, we present the MACER package to assist researchers in assembling molecular datasets and provide reproducibility in the process.

An annotated checklist of the chaetonotidan Gastrotricha from India

India has a long history of research on freshwater and marine Gastrotricha. In more than 110 years of study on Order Chaetonotida, two families consisting of 11 genera and 39 species have been described. Thirty of these species are taxa originally described from other continents, while only nine species (7 freshwater, 2 marine) are only known from India. The large percentage (77%) of so-called cosmopolitan species in India has contributed to the phenomenon known as the “meiofauna paradox”. However, a careful review of the pertaining literature provides a different biogeographical picture of the chaetonotidan fauna of India. Herein we show that the high incidence of European and North American species reported from India is mainly due to a mixture of misidentification and species lumping. In fact, for only 12 species there are enough data that would make the Indian specimens morphological similar to taxa previously reported from Europe and/or North America. However, without the appropriate molecular sequence data for comparison, there is no way to rule out the possibility of cryptic speciation.We conclude that further sampling throughout India and the use of more powerful microscopical techniques (e.g., DIC optics) and molecular sequencing will reveal more species and improve the quality of re-descriptions of those (9 spp.) that so far appear to be endemic to the subcontinent. Here we recommend six species to be excluded from the fauna of India while another 11 species (non endemic to India) should be considered dubitatively present in the Indian fauna.

Revealing the endophytic mycoflora in tea (Camellia sinensis) leaves in Sri Lanka: the first comprehensive study

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.

A new species of Aspicilia (Megasporaceae), with a new lichenicolous Sagediopsis (Adelococcaceae), from the Falkland Islands

The new species Aspicilia malvinae is described from the Falkland Islands. It is the first species of Megasporaceae to be discovered on the islands and only the seventh to be reported from South America. It is distinguished from other species of Aspicilia by the unusual secondary metabolite chemistry (hypostictic acid) and molecular sequence data. The collections of the new species support two lichenicolous fungi: Endococcus propinquus s. lat., which is new to the Falkland Islands, and a new species of Sagediopsis with small perithecia and 3-septate ascospores c. 18–20 × 4–5 μm, which is described here as S. epimalvinae. A total of 60 new DNA sequences obtained from species of Megasporaceae (mostly Aspicilia) are also introduced.

On the systematics and the phylogenetic position of the poorly known, montane dragon-lizard species Pseudocalotes austeniana (Annandale, 1908) (Squamata, Agamidae, Draconinae)

The montane agamid species Pseudocalotes austeniana has had a complicated taxonomic history, as the species was initially described as a member of the genus Salea Gray, 1845. Later, the species was placed in a monotypic genus Mictopholis Smith, 1935, which was erected only to include this species; however, the species was later on transferred to the genus Pseudocalotes Fitzinger, 1843, owing to the morphological similarities, and lack of strong characters to diagnose the genus Mictopholis. Nonetheless, its precise phylogenetic and systematic position has remained unresolved due to the lack of molecular sequence data. During a herpetological expedition to Arunachal Pradesh, specimens of P. austeniana were collected from the hills near the type locality. The mitochondrial 16S rRNA, ND2 and ND4, and the nuclear RAG1 regions were subjected to molecular phylogenetics. Maximum Likelihood and Bayesian Inference gene trees revealed that P. austeniana is a member of the subfamily Draconinae. The analyses showed that the genus Pseudocalotes is polyphyletic, and P. austeniana was embedded within the genus Japalura Gray, 1853 sensu stricto. We here, thus, propose to transfer the species P. austeniana to the genus Japlaura, as Japalura austenianacomb. nov. Biogeographic and evolutionary significance of the findings are discussed.

Unravelling unexplored diversity of cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) in tropical Africa

Cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) are one of the largest and most diverse groups of hyphomycetes causing a wide range of diseases of economically important plants as well as of plants in the wild. Although more than 6000 species are known for this group, the documentation of this fungal group is far from complete. Especially in the tropics, the diversity of cercosporoid fungi is poorly known. The present study aims to identify and characterise cercosporoid fungi collected on host plants belonging to Fabaceae in Benin, West Africa. Information on their morphology, host species and DNA sequence data (18S rDNA, 28S rDNA, ITS and tef1) is provided. DNA sequence data were obtained by a simple and non-culture-based method for DNA isolation which has been applied for cercosporoid fungi for the first time in the context of the present study. Among the loci used for the phylogenetic analysis, tef1 provided the best resolution together with the multigene dataset. Species delimitation in many cases, however, was only possible by combining molecular sequence data with morphological characteristics. Based on forty specimens recently collected in Benin, 18 species are presented with morphological descriptions, illustrations and sequence data. Among these, six species in the genus Cercospora and two species in Pseudocercospora are proposed as species new to science. The newly described species are Cercospora (C.) beninensis on Crotalaria macrocalyx, C. parakouensis on Desmodium tortuosum, C. rhynchophora on Vigna unguiculata, C. vignae-subterraneae on Vigna subterranea, C. tentaculifera on Vigna unguiculata, C. zorniicola on Zornia glochidiata, Pseudocercospora sennicola on Senna occidentalis and Pseudocercospora tabei on Vigna unguiculata. Eight species of cercosporoid fungi are reported for Benin for the first time, three of them, namely C. cf. canscorina, C. cf. fagopyri and C. phaseoli-lunati are new for West Africa. The presence of two species of cercosporoid fungi on Fabaceae previously reported from Benin, namely Nothopassalora personata and Passalora arachidicola, is confirmed.