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.

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The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽

10.11646/phytotaxa.176.1.22 ◽

2014 ◽

Vol 176 (1) ◽

pp. 219 ◽

Cited By ~ 10

Author(s):

ASHA J. DISSANAYAKE ◽

RUVISHIKA S. JAYAWARDENA ◽

SARANYAPHAT BOONMEE ◽

KASUN M. THAMBUGALA ◽

QING TIAN ◽

...

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

The Family ◽

The Status ◽

Sexual State ◽

Morphological And Molecular Data ◽

Asexual State ◽

Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

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A widespread distribution for Arostrilepis tenuicirrosa (Eucestoda: Hymenolepididae) in Myodes voles (Cricetidae: Arvicolinae) from the Palearctic based on molecular and morphological evidence: historical and biogeographic implications

Acta Parasitologica ◽

10.2478/s11686-013-0170-6 ◽

2013 ◽

Vol 58 (4) ◽

Cited By ~ 6

Author(s):

Kurt Galbreath ◽

Kristina Ragaliauskaite ◽

Leonas Kontrimavichus ◽

Arseny Makarikov ◽

Eric Hoberg

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Intraspecific Diversity ◽

Myodes Glareolus ◽

Morphological Evidence ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Biogeographic History ◽

Mitochondrial Cytochrome B ◽

The Republic

AbstractHymenolepidid cestodes in Myodes glareolus from Lithuania and additional specimens originally attributed to Arostrilepis horrida from the Republic of Belarus are now referred to A. tenuicirrosa. Our study includes the first records of A. tenuicirrosa from the European (western) region of the Palearctic, and contributes to the recognition of A. horrida (sensu lato) as a complex of cryptic species distributed broadly across the Holarctic. Specimens of A. tenuicirrosa from Lithuania were compared to cestodes representing apparently disjunct populations in the eastern Palearctic based on structural characters of adult parasites and molecular sequence data from nuclear (ITS2) and mitochondrial (cytochrome b) genes. Morphological and molecular data revealed low levels of divergence between eastern and western populations. Phylogeographic relationships among populations and host biogeographic history suggests that limited intraspecific diversity within A. tenuicirrosa may reflect a Late Pleistocene transcontinental range expansion from an East Asian point of origin.

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Living and fossil placentals

The Origin and Evolution of Mammals ◽

10.1093/oso/9780198507604.003.0010 ◽

2004 ◽

Author(s):

T.S. Kemp

Keyword(s):

Sequence Data ◽

Sister Group ◽

Morphological Characters ◽

Molecular Data ◽

Molecular Sequence Data ◽

Minor Characters ◽

Molecular Sequence ◽

Large Sets ◽

Anterior Teeth ◽

Basal Group

The vast majority of living and fossil mammals are placentals. Today there are about 4,400 species, which are traditionally organised into 18 Orders, with an extra one if the Pinnipedia are separated from the Carnivora, and a twentieth if the recently extinct Malagasy order Bibymalagasia is recognised as such. There have been many attempts to discover supraordinal groupings from amongst these Orders based on morphological characters, though few proposals have been universally accepted. It is only with the advent of increasingly large sets of molecular sequence data in the last few years that a reasonably robust resolution looks imminent, although these contemporary analyses are remarkably and controversially at odds with the traditional ones. Novacek et al. (1988) summarised the then current situation regarding supraordinal classification of placentals, a time at which morphology was still dominant but molecular data was at the threshold of significance. They accepted a basal group Edentata that combined the Xenarthra of the New World with the Pholidota of the Old, based on a few cranial characters, loss of the anterior teeth, and reduction of the enamel of the remaining ones. This left the rest of the living placentals as a monophyletic group Epitheria, sharing such apparently minor characters as the shape of the stapes bone in the ear. They found very little resolution within the Epitheria, and concluded that there was a polychotomy of no less than nine lineages arranged as a ‘star’ phylogeny. No remnant of the previously recognised taxon Ferungulata, created by Simpson (1945) for the Carnivora plus the ungulate orders Artiodactyla, Perissodactyla, Proboscidea, Hyracoidea, Sirenia, and Tubulidentata remained. On the other hand, three supra ordinal taxa of earlier authors did survive. One was Gregory’s (1910) Archonta, consisting of generally conservative forms and by now composed of the Primates, Dermoptera, Scandentia, and Chiroptera, but excluding the Lipotyphla. The second was Glires, originating with Linnaeus (1758) and widely accepted ever since, for the Rodentia and Lagomorpha; Novacek et al. (1988) tentatively placed the Macroscelidea as the sister-group of the Glires. The third supraordinal taxon recognised was, like Glires, well-established if not universally accepted.

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Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

Invertebrate Systematics ◽

10.1071/is13010 ◽

2014 ◽

Vol 28 (1) ◽

pp. 32 ◽

Cited By ~ 130

Author(s):

Rüdiger Bieler ◽

Paula M. Mikkelsen ◽

Timothy M. Collins ◽

Emily A. Glover ◽

Vanessa L. González ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Analytical Framework ◽

Morphological Characters ◽

Molecular Data ◽

Probabilistic Methods ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Protein Encoding ◽

Encoding Genes

To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.

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Diversification of Neoaves: integration of molecular sequence data and fossils

Biology Letters ◽

10.1098/rsbl.2006.0523 ◽

2006 ◽

Vol 2 (4) ◽

pp. 543-547 ◽

Cited By ~ 446

Author(s):

Per G.P Ericson ◽

Cajsa L Anderson ◽

Tom Britton ◽

Andrzej Elzanowski ◽

Ulf S Johansson ◽

...

Keyword(s):

Sequence Data ◽

Divergence Time ◽

Bird Species ◽

Molecular Data ◽

Molecular Evidence ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Divergence Time Estimates ◽

Time Estimates ◽

Early Tertiary

Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

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Morphological and molecular data supportLichina intermediaas a distinct austral-marine species in theL. pygmaeagroup

The Lichenologist ◽

10.1017/s0024282917000251 ◽

2017 ◽

Vol 49 (4) ◽

pp. 321-332 ◽

Cited By ~ 5

Author(s):

Matthias SCHULTZ

Keyword(s):

Sequence Data ◽

Morphological Characteristics ◽

Distribution Patterns ◽

Marine Species ◽

Molecular Data ◽

Separate Species ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Morphological And Molecular Data

AbstractMorphological characteristics and analyses of molecular sequence data (ITS, mtSSU) indicate that the austral-marine lichenLichina pygmaeavar.intermediais distinct from the chiefly European marine speciesL. confinisandL. pygmaea. It is thus proposed to treat var.intermediaas a separate species.Lichina intermediadiffers fromL. confinischiefly in the distinctly corticated branches, and deviates fromL. pygmaeain the shorter and thinner branches. Diagnostic differences between the three species are summarized and distribution patterns discussed.

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The Phylogeny of Rhizocephalan Parasites of the Genus Heterosaccus using Molecular and Larval Data (Cirripedia: Rhizocephala; Sacculinidae)

Israel Journal of Ecology and Evolution ◽

10.1080/15659801.2008.10639616 ◽

2008 ◽

Vol 54 (2) ◽

pp. 223-238 ◽

Cited By ~ 6

Author(s):

Henrik Glenner ◽

Philip Francis Thomsen ◽

Alexey V. Rybakov ◽

Bella S. Galil ◽

Jens T. Hoeg

Keyword(s):

Sequence Data ◽

Morphological Characters ◽

Molecular Data ◽

Sem Analysis ◽

Accurate Identification ◽

Generic Level ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

The Third ◽

The Family

Within parasitic barnacles of the family Sacculinidae, the genus Heterosaccus is the third largest, with 12 species infesting various brachyuran hosts throughout the world. As part of an effort to reconstruct rhizocephalan phylogeny we performed an analysis of four species of Heterosaccus and of selected sacculinid and non-sacculinid rhizocephalans. We used both molecular sequence data (16s rDNA and 18s rDNA) and morphological characters from an SEM analysis of the cypris larvae. Using Bayesian methods we obtained a highly supported tree in which the four species of Heterosaccus form a monophylum, whereas both the genus Sacculina and the family Sacculinidae are polyphyletic. The sistergroup to Heterosaccus is a clade consisting of the sacculinids Loxothylacus panopaei and the "classical" rhizocephalan Sacculina carcini. The molecular results found support in cypris morphology, where we identified two distinct synapomorphies for Heterosaccus, both present in male cyprids only: A large flap extending posteriorly from the third antennular segment, and the male-specific aesthetasc on the third segment being reduced to a rudiment or lacking completely. Female cyprids didn't show generic level apomorphies but resembled those of other sacculinid species. No morphological synapomorphies were identified between Heterosaccus, L. panopaei and S. carcini. While larval characters proved to be informative, we conclude that future studies on rhizocephalan taxonomy must rely primarily on molecular data, both to provide an overall phylogenetic framework and to assure an accurate identification of species for biogeographical and other biological purposes.

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Halenia coreana (Gentianaceae), a new species from Korea: Evidence from morphological and molecular data

Phytotaxa ◽

10.11646/phytotaxa.403.2.2 ◽

2019 ◽

Vol 403 (2) ◽

pp. 86

Author(s):

SU-MIN HAN ◽

HYOSIG WON ◽

CHAE EUN LIM

Keyword(s):

New Species ◽

Sequence Data ◽

Its Region ◽

Molecular Data ◽

Rbcl Gene ◽

Species Status ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Morphological And Molecular Data ◽

A New Species

A new species of Halenia (Gentianaceae) from Korea, H. coreana S.M.Han, H.Won & C.E.Lim, is recognized based on morphological and molecular data, and its description and illustration are provided. It is distinct from H. corniculata in having long, narrower and incurved spurs and attenuated leaf apex. Molecular sequence data of nuclear ribosomal ITS region, nuclear XDH gene, and chloroplast rbcL gene also strongly support its species status.

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Rediscovery of Mus nitidulus Blyth (Rodentia: Muridae), an endemic murine rodent of the central basin of Myanmar

Zootaxa ◽

10.11646/zootaxa.1498.1.4 ◽

2007 ◽

Vol 1498 (1) ◽

pp. 45-68 ◽

Cited By ~ 7

Author(s):

TOMOFUMI SHIMADA ◽

KENNETH P. APLIN ◽

PAULINA JENKINS ◽

HITOSHI SUZUKI

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Species Group ◽

Central Basin ◽

Mammal Species ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Rainfed Rice ◽

South Central ◽

Murine Rodent

A genetically distinct population of mice from south central Myanmar is identified as Mus nitidulus Blyth, a taxon described in 1859 but subsequently treated as a synonym of a more widely distributed Asian mouse—Mus cervicolor Hodgson, 1845. We present molecular sequence data from mitochondrial and nuclear genes which demonstrate that M. nitidulus is distinct from M. cervicolor and from all other species of Mus currently recognized in the Asian region. The molecular data further show that M. nitidulus is a member of the Mus booduga Species Group within subgenus Mus, and thus phylogenetically remote from M. cervicolor. We stabilize the nomenclature of M. nitidulus by designating a lectotype with associated molecular sequence data. We review and illustrate the morphology of M. nitidulus and reassess all previously referred material. Mus nitidulus appears to be confined to the central basin of Myanmar, an area that formerly supported a mosaic of evergreen and deciduous monsoon forests. Today, this region is largely cleared and employed for rainfed rice cultivation. Mus nitidulus is only the second mammal species recorded as endemic to Myanmar. It can be locally abundant in ricefield habitat and is regarded locally as an agricultural pest.

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Isorchis cannonin. sp. (Digenea: Atractotrematidae) from Great Barrier Reef rabbitfishes and the molecular elucidation of its life cycle

Journal of Helminthology ◽

10.1017/s0022149x17000906 ◽

2017 ◽

Vol 92 (5) ◽

pp. 604-611 ◽

Cited By ~ 4

Author(s):

D.C. Huston ◽

S.C. Cutmore ◽

T.H. Cribb

Keyword(s):

Great Barrier Reef ◽

Sequence Data ◽

Molecular Data ◽

Reproductive Organs ◽

Barrier Reef ◽

Larval Form ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Moreton Bay ◽

Single Testis

AbstractWe describeIsorchis cannonin. sp. from the rabbitfishesSiganus fuscescens(Houttuyn) andSiganus lineatus(Valenciennes) (Siganidae) collected off Heron Island, southern Great Barrier Reef, Australia and, using molecular data, demonstrate that ‘Cercariae queenslandaeII’ of Cannon (1978) from the gastropodClypeomorus batillariaeformisHabe & Kosuge (Cerithiidae) is the larval form of this new species. The cercariae ofI.cannonin. sp. develop in rediae, encyst in the environment after emergence, and are inferred to then be consumed by grazing rabbitfish. Additionally, we provide a new report ofIsorchis curraniAndres, Pulis & Overstreet, 2016 from the type host,Selenotoca multifasciata(Richardson) (Scatophagidae) collected in Moreton Bay, south-east Queensland, Australia, greatly expanding the known geographical range of this species. Molecular sequence data (ITS1, ITS2 and 28S rDNA) generated forI.cannonin. sp. and the new specimens ofI.currani, confirm the identification ofI.curraniand demonstrate a distinct genotype forI.cannonin. sp. relative to other species ofIsorchisDurio & Manter, 1969, for which molecular data are available.Isorchis cannonin. sp. is morphologically distinct from all other species in the genus, and is further distinguished by utilizing species of Siganidae as definitive hosts, rather than species of Chanidae or Scatophagidae. Because haploporid and atractotrematid cercariae have well-developed reproductive organs, we find cercariae of these closely related families morphologically distinguishable in the same way as adult trematodes: atractotrematids have two symmetrical testes and haploporids have a single testis or, rarely, two tandem or oblique testes.

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