154 Works

Image-based taxonomic classification of bulk biodiversity samples using deep learning and domain adaptation

Tomochika Fujisawa, Víctor Noguerales, Emmanouil Meramveliotakis, Anna Papadopoulou & Alfried Vogler
Complex bulk samples of invertebrates from biodiversity surveys present a great challenge for taxonomic identification, especially if obtained from unexplored ecosystems. High-throughput imaging combined with machine learning for rapid classification could overcome this bottleneck. Developing such procedures requires that taxonomic labels from an existing source data set are used for model training and prediction of an unknown target sample. Yet the feasibility of transfer learning for the classification of unknown samples remains to be tested....

Spatial patterns of phylogenetic diversity and endemism in the Western Ghats, India: a case study using ancient predatory arthropods

D. K. Bharti, Greg Edgecombe, Praveen Karanth & Jahnavi Joshi
The Western Ghats (WG) mountain chain in peninsular India is a global biodiversity hotspot, one in which patterns of phylogenetic diversity and endemism remain to be documented across taxa. We used a well-characterized community of ancient soil predatory arthropods from the WG to understand diversity gradients, identify hotspots of endemism and conservation importance, and highlight poorly-studied areas with unique biodiversity. We compiled an occurrence dataset for 19 species of scolopendrid centipedes, which was used to...

Data from: Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae)

Anthony I. Cognato & Alfried P. Vogler
The possibility of gene tree incongruence in a species-level phylogenetic analysis of the genus Ips (Coleoptera: Scolytidae) was investigated based on mitochondrial 16S rRNA and nuclear Elongation factor-1α sequences, and existing Cytochrome Oxidase I and non-molecular data sets. Separate cladistic analyses of the data partitions resulted in partially discordant most-parsimonious trees but revealed only low conflict of the phylogenetic signal. Interactions among data partitions, which differed in the level of sequence divergence (COI > 16S...

Data from: Ancient plants with ancient fungi: liverworts associate with early-diverging arbuscular mycorrhizal fungi

William R. Rimington, Silvia Pressel, Jeffrey G. Duckett, Katie J. Field, David J. Read & Martin I. Bidartondo
Arbuscular mycorrhizas are widespread in land plants including liverworts, some of the closest living relatives of the first plants to colonise land 500 MYA. Previous investigations reported near-exclusive colonisation of liverworts by the most recently evolved arbuscular mycorrhizal fungi, the Glomeraceae, indicating a recent acquisition from flowering plants at odds with the widely-held notion that arbuscular mycorrhizal-like associations in liverworts represent the ancestral symbiotic condition in land plants. We performed an analysis of symbiotic fungi...

Data from: Plant controls on Late Quaternary whole ecosystem structure and function

Elizabeth S. Jeffers, Nicki J. Whitehouse, Adrian Lister, Gill Plunkett, Phil Barratt, Emma Smyth, Philip Lamb, Michael W. Dee, Stephen J. Brooks, Katherine J. Willis, Cynthia A. Froyd, Jenny E. Watson & Michael B. Bonsall
Plants and animals influence biomass production and nutrient cycling in terrestrial ecosystems; however their relative importance remains unclear. We assessed the extent to which mega-herbivore species controlled plant community composition and nutrient cycling, relative to other factors during and after the Late Quaternary extinction event in Britain and Ireland, when two-thirds of the region’s mega-herbivore species went extinct. Warmer temperatures, plant-soil and plant-plant interactions, and reduced burning contributed to the expansion of woody plants and...

Taxonomic identification using virtual palaeontology and geometric morphometrics: a case study of Jurassic nerineoidean gastropods

Yael Leshno Afriat, Yael Edelman-Furstenberg, Rivka Rabinovich, Jonathan Todd & Hila May
Taxonomic identification of fossils is fundamental to a wide range of geological and biological disciplines. Many fossil groups are identified based on expert judgment, which requires extensive experience and is not always available for the specific taxonomic group at hand. Nerineoideans, a group of extinct gastropods that formed a major component of Mesozoic shallow marine environments, have distinctive internal spiral folds that form the basis for their classification at the genus level. However, their identification...

Functional constraints during development limit jaw shape evolution in marsupials

Anne-Claire Fabre, Carys Dawling, Roberto Portela Miguez, Vincent Fernandez, Eve Noirault & Anjali Goswami
Differences in jaw function experienced through ontogeny can have striking consequences for evolutionary outcomes, as has been suggested for the major clades of mammals. In contrast to placentals, marsupial newborns have an accelerated development of the head and forelimbs, allowing them to crawl to the mother’s teats to suckle within just a few weeks of conception. The different functional requirements that marsupial newborns experience in early postnatal development have been hypothesized to have constrained their...

Data from: Metamorphosis revealed: time-lapse three-dimensional imaging inside a living chrysalis

Tristan Lowe, Russell J. Garwood, Thomas J. Simonsen, Robert S. Bradley & Philip J. Withers
Studies of model insects have greatly increased our understanding our animal development. Yet they are limited in scope to this small pool of model species: a small number of representatives for a hyperdiverse group with highly varied developmental processes. One factor behind this narrow scope is the challenging nature of traditional methods of study, such as histology and dissection, which can preclude quantitative analysis and do not allow the development of a single individual to...

Data from: Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

Jeffrey W. Streicher & John J. Wiens
Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae

Iker Irisarri, Miguel Vences, Diego San Mauro, Frank Glaw & Rafael Zardoya
BACKGROUND: Evolutionary novelties often appear by conferring completely new functions to pre- existing structures or by innovating the mechanism through which a particular function is performed. Sound production plays a central role in the behavior of frogs, which use their calls to delimit territories and attract mates. Therefore, frogs have evolved complex vocal structures capable of producing a wide variety of advertising sounds. It is generally acknowledged that most frogs call by moving an air...

Data from: A reliable DNA barcode reference library for the identification of the European shelf fish fauna

Thomas Knebelsberger, Gary R. Carvalho, Silke Laakmann, Michael J. Raupach, Hermann Neumann, Patrick D. Campbell, Monica Landi & Filipe O. Costa
Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based...

Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions

Cecilia Conte-Grand, Ralf Britz, Neelesh Dahanukar, Rajeev Raghavan, Rohan Pethiyagoda, Hoek Hui Tan, Renny Kurnia Hadiaty, Norsham S. Yaakob, Lukas Rüber & Heok Hui Tan
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group...

Data from: The first multi-gene phylogeny of the Macrostomorpha sheds light on the evolution of sexual and asexual reproduction in basal Platyhelminthes

Toon Janssen, Dita B. Vizoso, Gregor Schulte, D. Timothy J. Littlewood, Andrea Waeschenbach & Lukas Schärer
The Macrostomorpha—an early branching and species-rich clade of free-living flatworms—is attracting interest because it contains Macrostomum lignano, a versatile model organism increasingly used in evolutionary, developmental, and molecular biology. We elucidate the macrostomorphan molecular phylogeny inferred from both nuclear (18S and 28S rDNA) and mitochondrial (16S rDNA and COI) marker genes from 40 representatives. Although our phylogeny does not recover the Macrostomorpha as a statistically supported monophyletic grouping, it (i) confirms many taxa previously proposed...

Data from: Interspecific interactions through 2 million years: are competitive outcomes predictable?

Lee Hsiang Liow, Emanuela Di Martino, Kjetil Lysne Voje, Seabourne Rust & Paul D. Taylor
Ecological interactions affect the survival and reproduction of individuals. However, ecological interactions are notoriously difficult to measure in extinct populations, hindering our understanding of how the outcomes of interactions such as competition vary in time and influence long-term evolutionary changes. Here, the outcomes of spatial competition in a temporally continuous community over evolutionary timescales are presented for the first time. Our research domain is encrusting cheilostome bryozoans from the Wanganui Basin of New Zealand over...

Data from: Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

Wasiu A. Akanni, Karen Siu-Ting, Christopher J. Creevey, James O. McInerney, Mark Wilkinson, Peter G. Foster & Davide Pisani
The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an α-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the...

Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

Carmelo Andújar, Paula Arribas, Filip Ruzicka, Alexandra Crampton Platt, Martijn J. T. N. Timmermans, Alfried P. Vogler & Alex Crampton-Platt
High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum...

Data from: A new exceptionally preserved Cambrian priapulid from the Chengjiang Lagerstätte

Xiaoya Ma, Richard J. Aldridge, David J. Siveter, Derek J. Siveter, Xianguang Hou & Gregory D. Edgecombe
A fossil priapulid, Eximipriapulus globocaudatus new genus new species, is described from the Cambrian Chengjiang Lagerstätte of Yunnan, China. The exceptional preservation of the animal reveals morphological details that allow direct comparison with extant priapulids. The body is divisible into a partially eversible pharynx, a smooth collar, a scalid-bearing introvert, a neck with triangular scalids, an unsegmented trunk with annulations, and a distinctly expanded terminal region. Several specialized regions of the alimentary canal are recognized:...

Data from: Exploring the universal ecological responses to climate change in a univoltine butterfly

Phillip B. Fenberg, Angela Self, John R. Stewart, Rebecca J. Wilson & Stephen J. Brooks
1. Animals with distinct life stages are often exposed to different temperatures during each stage. Thus, how temperature affects these life stages should be considered for broadly understanding the ecological consequences of climate warming on such species. For example, temperature variation during particular life stages may affect respective change in body size, phenology and geographic range, which have been identified as the “universal” ecological responses to climate change. While each of these responses has been...

Data from: Contrasting genetic structure of sympatric congeneric gastropods: do differences in habitat preference, abundance, and distribution matter?

Edward J.G. Wort, Mark A. Chapman, Stephen John Hawkins, Lucy Henshall, Alfonso Pita, Marc Rius, Suzanne T. Williams & Phillip B. Fenberg
Aim: The relationship of population genetics with the ecology and biogeography of species may be explored by comparing phenotypically similar but ecologically different congeners with overlapping ranges. We compared genetic differentiation between two congeneric rocky intertidal gastropods across a major portion of their sympatric range. We hypothesized that the habitat generalist with high abundance and continuous distribution would exhibit comparatively less genetic differentiation than the habitat specialist with low abundance and a fragmented distribution. Location:...

Evolution of body size and wing shape trade-offs in arsenurine silkmoths

Chris Hamilton, Nathalie Winiger, Juliette Rubin, Jesse Breinholt, Rodolphe Rougerie, Ian Kitching, Jesse Barber & Akito Kawahara
One of the key objectives in biological research is understanding how evolutionary processes have produced Earth's diversity. A critical step towards revealing these processes is an investigation of evolutionary tradeoffs – that is, the opposing pressures of multiple selective forces. For millennia, nocturnal moths have had to balance successful flight, as they search for mates or host plants, with evading bat predators. However, the potential for evolutionary trade-offs between wing shape and body size are...

Mineral chemistry and BSE-SEM images

Chiara M Petrone
Chemical analysis of pyroxenes and BSE-SEM images from pumices and lava flows from Popocatepetl Volcano, Mexico. Whole rock isotope data from pumices and lava flows from Popocatepetl Volcano, Mexico.

Data from: Sampling bias and the fossil record of planktonic foraminifera on land and in the deep sea

Graeme T. Lloyd, Paul N. Pearson, Jeremy R. Young & Andrew B. Smith
Large-scale trends in planktonic foraminiferal diversity have so far been based on utilization of synoptic biostratigraphic range charts. Although this approach ensures the taxonomic consistency and quality of the data being used, it takes no formal account of any sampling biases that might exist in the fossil record. We demonstrate that the occurrence data of planktonic foraminifera, as recorded in the primary literature, are strongly biased by sampling. We do this by demonstrating that raw...

Data from: Dramatic niche shifts and morphological change in two insular bird species

Per Alström, Jon Fjeldså, Knud Andreas Jønsson, Anders Ödeen, Per G. P. Ericson, Martin Irestedt, J. Fjeldsa, K. A. Jonsson, P. Alstrom & A. Odeen
Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has...

Data from: A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda)

Alain De Chambrier, Andrea Waeschenbach, Makda Fisseha, Tomas Scholz & Jean Mariaux
Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset...

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  • Natural History Museum
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  • University of Manchester
  • Royal Botanic Gardens
  • American Museum of Natural History
  • University of Otago