Xenopus fraseri: Mr. Fraser, where did your frog come from?

A comprehensive, accurate, and revisable alpha taxonomy is crucial for biodiversity studies, but is challenging when data from reference specimens are difficult to collect or observe. However, recent technological advances can overcome some of these challenges. To illustrate this, we used modern approaches to tackle a centuries-old taxonomic enigma presented by Fraser’s Clawed Frog, Xenopus fraseri, including whether X. fraseri is different from other species, and if so, where it is situated geographically and phylogenetically. To facilitate these inferences, we used high-resolution techniques to examine morphological variation, and we generated and analyzed complete mitochondrial genome sequences from all Xenopus species, including >150-year-old type specimens. Our results demonstrate that X. fraseri is indeed distinct from other species, firmly place this species within a phylogenetic context, and identify its minimal geographic distribution in northern Ghana and northern Cameroon. These data also permit novel phylogenetic resolution into this intensively studied and biomedically important group. Xenopus fraseri was formerly thought to be a rainforest endemic placed alongside species in the amieti species group; in fact this species occurs in arid habitat on the borderlands of the Sahel, and is the smallest member of the muelleri species group. This study illustrates that the taxonomic enigma of Fraser’s frog was a combined consequence of sparse collection records, interspecies conservation and intraspecific polymorphism in external anatomy, and type specimens with unusual morphology

A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Furman, B. L. S., Cauret, C. M. S., Knytl, M., Song, X. Y., Premachandra, T., Ofori-Boateng, C., Jordan, D. C., Horb, M. E., & Evans, B. J. (2020). A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome. PLoS Genetics, 16(11), e1009121, doi:10.1371/journal.pgen.1009121.In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among—and even within—species. To understand these systems more, we investigated a rare example of a frog with three sex chromosomes: the Western clawed frog, Xenopus tropicalis. We demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a very similar genomic location as a previously known female-determining factor on the W chromosome. Nucleotide polymorphism of expressed transcripts suggests genetic degeneration on the W chromosome, emergence of a new Y chromosome from an ancestral Z chromosome, and natural co-mingling of the W, Z, and Y chromosomes in the same population. Compared to the rest of the genome, a small sex-associated portion of the sex chromosomes has a 50-fold enrichment of transcripts with male-biased expression during early gonadal differentiation. Additionally, X. tropicalis has sex-differences in the rates and genomic locations of recombination events during gametogenesis that are similar to at least two other Xenopus species, which suggests that sex differences in recombination are genus-wide. These findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes, demonstrate that several characteristics of old and established sex chromosomes (e.g., nucleotide divergence, sex biased expression) can arise well before sex chromosomes become cytogenetically distinguished, and show how these characteristics can have lingering consequences that are carried forward through sex chromosome turnovers.This work was supported by the Natural Science and Engineering Research Council of Canada (RGPIN-2017-05770) (BJE), Resource Allocation Competition awards from Compute Canada (BJE), the Whitman Center Fellowship Program at the Marine Biological Laboratory (BJE), the Museum of Comparative Zoology at Harvard University (BJE), and National Institutes of Health grants R01-HD084409 (MEH) and P40-OD010997 (MEH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015

Topological Anomaly Detection in Dynamic Multilayer Blockchain Networks

Motivated by the recent surge of criminal activities with cross-cryptocurrency trades, we introduce a new topological perspective to structural anomaly detection in dynamic multilayer networks. We postulate that anomalies in the underlying blockchain transaction graph that are composed of multiple layers are likely to also be manifested in anomalous patterns of the network shape properties. As such, we invoke the machinery of clique persistent homology on graphs to systematically and efficiently track evolution of the network shape and, as a result, to detect changes in the underlying network topology and geometry. We develop a new persistence summary for multilayer networks, called stacked persistence diagram, and prove its stability under input data perturbations. We validate our new topological anomaly detection framework in application to dynamic multilayer networks from the Ethereum Blockchain and the Ripple Credit Network, and demonstrate that our stacked PD approach substantially outperforms state-of-art techniques

FIGURE 8. Inset shows a in A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana

FIGURE 8. Inset shows a map of West Africa showing the location of the Atewa Range in Ghana (upper left), known localities of Conraua sagyimase sp. nov. are shown in red and know localities of Conraua derooi in yellow. Stars indicate type localities. Altitudinal range is indicated with shading from lowlands (light) to high elevation (dark). Sources: OpenStreetMap (2020), U.S. Geological Survey (2020).Published as part of <i>NEIRA-SALAMEA, KARLA, OFORI-BOATENG, CALEB, KOUAMÉ, N'GORAN G., BLACKBURN, DAVID C., SEGNIAGBETO, GABRIEL H., HILLERS, ANNIKA, BAREJ, MICHAEL F., LEACHÉ, ADAM D. & RÖDEL, MARK-OLIVER, 2021, A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana, pp. 71-95 in Zootaxa 4995 (1)</i> on page 86, DOI: 10.11646/zootaxa.4995.1.4, <a href="http://zenodo.org/record/10086923">http://zenodo.org/record/10086923</a&gt

FIGURE 7 in A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana

FIGURE 7. Conraua sagyimase sp. nov. from the Atewa Range Forest Reserve, southern Ghana (photos by Alan Channing); specimen not collected.Published as part of <i>NEIRA-SALAMEA, KARLA, OFORI-BOATENG, CALEB, KOUAMÉ, N'GORAN G., BLACKBURN, DAVID C., SEGNIAGBETO, GABRIEL H., HILLERS, ANNIKA, BAREJ, MICHAEL F., LEACHÉ, ADAM D. & RÖDEL, MARK-OLIVER, 2021, A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana, pp. 71-95 in Zootaxa 4995 (1)</i> on page 85, DOI: 10.11646/zootaxa.4995.1.4, <a href="http://zenodo.org/record/10086923">http://zenodo.org/record/10086923</a&gt

FIGURE 1 in A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana

FIGURE 1. Conraua derooi from the type locality Misahöhe, Togo (a – c) and Biakpa in the Volta area (d), Ghana; a: adult male, note bulging neck and posterior part of head, b & c: adult females; d: half-grown specimen. Specimens not collected.Published as part of <i>NEIRA-SALAMEA, KARLA, OFORI-BOATENG, CALEB, KOUAMÉ, N'GORAN G., BLACKBURN, DAVID C., SEGNIAGBETO, GABRIEL H., HILLERS, ANNIKA, BAREJ, MICHAEL F., LEACHÉ, ADAM D. & RÖDEL, MARK-OLIVER, 2021, A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana, pp. 71-95 in Zootaxa 4995 (1)</i> on page 77, DOI: 10.11646/zootaxa.4995.1.4, <a href="http://zenodo.org/record/10086923">http://zenodo.org/record/10086923</a&gt

FIGURE 3. a in A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana

FIGURE 3. a) Spectrogram and oscillogram of advertisement call of male Conraua sagyimase sp. nov. from Atewa Range Forest, individual not collected (call 1); b) Spectrogram and oscillogram of advertisement call of male Conraua derooi from Biakpa, Ghana, individual not collected. FFT = 256 points.Published as part of <i>NEIRA-SALAMEA, KARLA, OFORI-BOATENG, CALEB, KOUAMÉ, N'GORAN G., BLACKBURN, DAVID C., SEGNIAGBETO, GABRIEL H., HILLERS, ANNIKA, BAREJ, MICHAEL F., LEACHÉ, ADAM D. & RÖDEL, MARK-OLIVER, 2021, A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana, pp. 71-95 in Zootaxa 4995 (1)</i> on page 78, DOI: 10.11646/zootaxa.4995.1.4, <a href="http://zenodo.org/record/10086923">http://zenodo.org/record/10086923</a&gt

FIGURE 9 in A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana

FIGURE 9. Habitat from Conraua sagyimase sp. nov. in the Atewa Range Forest Reserve (a–b), southern Ghana (photos: courtesy of Piotr Naskrecki); and type locality of Conraua derooi, Misahöhe, Togo (c–d).Published as part of <i>NEIRA-SALAMEA, KARLA, OFORI-BOATENG, CALEB, KOUAMÉ, N'GORAN G., BLACKBURN, DAVID C., SEGNIAGBETO, GABRIEL H., HILLERS, ANNIKA, BAREJ, MICHAEL F., LEACHÉ, ADAM D. & RÖDEL, MARK-OLIVER, 2021, A new critically endangered slippery frog (Amphibia, Conrauidae, Conraua) from the Atewa Range, central Ghana, pp. 71-95 in Zootaxa 4995 (1)</i> on page 87, DOI: 10.11646/zootaxa.4995.1.4, <a href="http://zenodo.org/record/10086923">http://zenodo.org/record/10086923</a&gt