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Data from: Ambient noise tomography of upper crustal structures and Quaternary faults in the Seoul metropolitan area and its geological implications

We investigate the upper-crustal seismic velocity structure in the Seoul metropolitan area, where about 20 million people live. The Chugaryeong fault zone (CFZ) is placed in this area, but the seismic hazard potential remains unclear. We conducted ambient noise tomography to illuminate the high-resolution upper-crustal structure in the Seoul metropolitan area. We analyzed continuous vertical seismic records for ~5 months from a dense seismic array with 77 broadband stations. Group velocity dispersion curves and tomographic maps were extracted between 0.5 and 10 s periods. We inverted 3-D group velocity tomography models up to a depth of ~10 km from the group velocity maps. The shear-wave velocity model is consistent with the geological features. High-velocity anomalies at shallow depths are correlated with the surface topography and geology. The CFZ is located at a low velocity below the 5 km depth and presented as the simplified model. The large VS contrast regions are located beneath NS-trending faults. The cross-sections coincide with the near-vertical strike-slip faults in this area. In the southern region of the Seoul metropolitan area, low-velocity anomalies correlate with high heat flow regions. Our results effectively suggest high resolution upper-crustal structures and subsurface hidden faults in the urban area.

opencc-by-4.0Nov 2021View details →

Data set for the paper "Temperatures and cooling rates recorded by the New Caledonia ophiolite: implications for cooling mechanisms in young forearc sequences"

Tables 1-3 and Tables S1-S4

opencc-by-4.0Nov 2021View details →

Figure 7 from: Zhao W, Liu D, Jia Q, Wu X, Zhang H (2021) Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses. ZooKeys 1070: 13-30. https://doi.org/10.3897/zookeys.1070.72742

Figure 7 The phylogenetic relationships of PCG+rRNA using BI and ML methods. Numbers above each node indicate Bayesian posterior probabilities values and ML bootstrap values.

opencc-by-4.0Nov 2021View details →

Figure 2 from: Zhao W, Liu D, Jia Q, Wu X, Zhang H (2021) Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses. ZooKeys 1070: 13-30. https://doi.org/10.3897/zookeys.1070.72742

Figure 2 The rates of nonsynonymous substitution (Ka), the rates of synonymous substitution (Ks), and the ratio of Ka/Ks for each PCGs of Myrmus lateralis mitogenome

Extreme rainfall events and cooling of sea turtle clutches: implications in the face of climate warming

Understanding how climate change impacts species and ecosystems is integral to conservation. When studying impacts of climate change, warming temperatures are a research focus, with much less attention given to extreme weather events and their impacts. Here we show how localized, extreme rainfall events can have a major impact on a species that is endangered in many parts of its range. We report incubation temperatures from the world's largest green sea turtle rookery, during a breeding season when two extreme rainfall events occurred. Rainfall caused nest temperatures to drop suddenly and the maximum drop in temperature for each rain-induced cooling averaged 3.6°C (n = 79 nests, min = 1.0°C, max = 7.4°C). Since green sea turtles have temperature-dependent sex determination, with low incubation temperatures producing males, such major rainfall events may have a masculinization effect on primary sex ratios. Therefore, in some cases, extreme rainfall events may provide a "get-out-of-jail-free card" to avoid complete feminization of turtle populations as climate warming continues.

Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications

Chamaerhodos is a small genus with ca 7–8 species with a disjunct distribution in Asia and western North America. Due to limited sampling of species and genes in previous studies, little is known about the phylogenetic relationships among the species. Moreover, chloroplast genomic resources for Chamaerhodos have been limited. Herein, we conducted a comparative analysis of the complete chloroplast (cp) genomes of five Chamaerhodos species. The five cp genomes had a typical quadripartite structure with high conservation of gene content and gene order. These five cp genomes encoded an identical set of 129 genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes. Comparison of the boundaries between the IRs and single copy regions revealed only very slight boundary differences and the five cp genomes showed only little sequence divergence. Seven regions (trnR-UCU-atpA, trnS-GCU- trnG-UCC, TrnG-GCC-trnfM-CAU, trnL-UAA intron, trnH-GUG-psbA, trnF-GAA- ndhJ, matK-5′-trnK-UUU) were identified as excellent candidate markers. A total of 117, 108, 116, 117 and 118 perfect SSRs were detected in the cp genomes of Ch. altaica, Ch. canescens, Ch. erecta, Ch. sabulosa and Ch. trifida, respectively. A phylogenetic analysis support the monophyly of Chamaerhodos and place it as part of the Fragariinae clade sister to the clade of Dasiphora, Drymocallis and Potaninia. Within Chamaerhodos, Ch. canescens was inferred sister to a clade containing the other four species. The detailed characterization of the Chamaerhodos chloroplast genomes sets the foundation for further studies on the genus and its close relatives in the economically important Rosaceae.

Identification of the first Japanese family with PDX1-MODY (MODY4): a novel PDX1 frameshift mutation, clinical characteristics, and implications

Context The PDX1 encodes pancreatic and duodenal homeobox, a critical transcription factor for pancreatic β-cell differentiation and maintenance of mature β-cells. Heterozygous loss-of-function mutations cause PDX1-MODY (MODY4). Case description The patient is an 18-year-old lean man who developed diabetes at 16 years of age. Given his early-onset age and leanness, we performed genetic testing. Targeted-next generation sequencing and subsequent Sanger sequencing detected a novel heterozygous frameshift mutation (NM_00209.4:c.218delT. NP_000200.1: p.Leu73Profs*50) in the PDX1 transactivation domain that resulted in loss-of-function and was validated by an in vitro functional study. The proband and his 56-year-old father, who had the same mutation, both showed markedly reduced insulin and gastric inhibitory polypeptide (GIP) secretion compared to the dizygotic twin sister, who was negative for the mutation and had normal glucose tolerance. The proband responded to sitagliptin, suggesting its utility as a treatment option. Notably, the proband and his father showed intriguing phenotypic differences: the proband had been lean for his entire life but developed early-onset diabetes requiring an antihyperglycemic agent. In contrast, his father was overweight, developed diabetes much later in life, and did not require medication, suggesting the oligogenic nature of PDX1-MODY. A review of all reported cases of PDX1-MODY also showed heterogeneous phenotypes regarding onset age, obesity, and treatment, even in the presence of the same mutation. Conclusions We identified the first Japanese family with PDX1-MODY. The similarities and differences found among the cases highlight the wide phenotypic spectrum of PDX1-MODY.

Implications for the mesopelagic microbial gardening hypothesis as determined by experimental fragmentation of Antarctic krill faecal pellets

1. Detritivores need to upgrade their food to increase its nutritional value. One method is to fragment detritus promoting the colonisation of nutrient-rich microbes, which consumers then ingest along with the detritus; so-called microbial gardening. Observations and numerical models of the detritus-dominated ocean mesopelagic zone have suggested microbial gardening by zooplankton is a fundamental process in the ocean carbon cycle leading to increased respiration of carbon-rich detritus. However, no experimental evidence exists to demonstrate that microbial respiration rates are higher on recently fragmented sinking detrital particles. 2. Using aquaria-reared Antarctic krill faecal pellets we showed fragmentation increased microbial particulate organic carbon (POC) turnover by 1.8x, but only on brown faecal pellets, formed from the consumption of other pellets. Microbial POC turnover on un-and fragmented green faecal pellets, formed from consuming fresh phytoplankton, was equal. Thus, POC content, fragmentation, and potentially nutritional value together drive POC turnover rates. 3. Mesopelagic microbial gardening could be a risky strategy, as the dominant detrital food source is settling particles. Even though fragmentation decreases particle size and sinking rat, it is unlikely that an organism would remain with the particle long enough to nutritionally benefit from attached microbes. We propose 'communal gardening' occurs whereby additional mesopelagic organisms nearby or below the site of fragmentation consume the particle and the colonised microbes. 4. To determine how fragmentation impacts the remineralisation of sinking carbon-rich detritus, and to parameterise microbial gardening in mesopelagic carbon models, three key metrics from further controlled experiments and observations are needed; how particle composition (here, pellet colour/krill diet) impacts the response of microbes to the fragmentation of particles; the nutritional benefit to zooplankton from ingesting microbes after fragmentation along with identification of which essential nutrients are being targeted; how both these factors vary between physical (shear) and biological particle fragmentation.

FIG. 8. — Sindhochelys ragei n. gen., n in First report of a bothremydid turtle, Sindhochelys ragei n. gen., n. sp., from the early Paleocene of Pakistan, systematic and palaeobiogeographic implications

FIG. 8. — Sindhochelys ragei n. gen., n. sp., holotype CPAG-RANKT-V-3, from the Paleocene of Ranikot, locality K18-12, Southern Pakistan. A-D, decoration in various parts of the shell: A, isolated piece with the imprint of the mesoplastral external surface; B, marginal part of peripheral 10, dorsal view; C, left costal 1 part, posterior border at mid-width, dorsal view; D, a costal lateral border, in dorsal view; E, right hyoplastral part, ventral view. Scale bar: 5 cm.

FIG. 7. — Sindhochelys ragei n. gen., n in First report of a bothremydid turtle, Sindhochelys ragei n. gen., n. sp., from the early Paleocene of Pakistan, systematic and palaeobiogeographic implications

FIG. 7. — Sindhochelys ragei n. gen., n. sp., holotype CPAG-RANKT-V-3, from the Paleocene of Ranikot, locality K18-12, Southern Pakistan. Medioanterior part of the shell, the nuchal being removed, showing a part of the dorsal face of the anterior lobe with the sulci limiting the overlapping scales. Scale bar: 5 cm.

opencc-by-4.0Dec 2021View details →

Figure 2 from: Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA (2021) Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. ZooKeys 1076: 25-41. https://doi.org/10.3897/zookeys.1076.73262

Figure 2 Phylogenetic relationships among the Hylobates species as represented by the NJ analysis. ML (Log Likelihood= -4326.23) and BI analysis produced similar topologies. Numbers above/below the branches represents bootstrap values for NJ, ML, and BI posterior probability, respectively. Only bootstrap values greater than 50% are shown.

Supplementary material 3 from: Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA (2021) Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. ZooKeys 1076: 25-41. https://doi.org/10.3897/zookeys.1076.73262

Table S3

opencc-by-4.0Dec 2021View details →

Figure 1 from: Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA (2021) Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. ZooKeys 1076: 25-41. https://doi.org/10.3897/zookeys.1076.73262

Figure 1 Geographical distribution of Hylobates lar subspecies throughout South-East Asia (adapted from Thinh et al. 2010; Brockelman and Geissmann, 2020). Black squares represent individuals of known exact locations while blue squares indicated the approximate locations of the confiscated and surrendered individuals used in this study. Numbers on the map corresponds to the location in Table 1. The approximate location of the Isthmus of Kra, the Surat Thani-Krabi depression, and the Kangar-Pattani line are indicated by the grey, red, and green lines, respectively, marking the possible break among the Indochinese (carpenteri, entelloides, and yunnannesis) from the lar subspecies.

Supplementary material 2 from: Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA (2021) Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. ZooKeys 1076: 25-41. https://doi.org/10.3897/zookeys.1076.73262

Table S2

Supplementary material 1 from: Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA (2021) Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. ZooKeys 1076: 25-41. https://doi.org/10.3897/zookeys.1076.73262

Table S1.

opencc-by-4.0Dec 2021View details →

Figure 3 from: Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA (2021) Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. ZooKeys 1076: 25-41. https://doi.org/10.3897/zookeys.1076.73262

Figure 3 Median-joining network (MJN) constructed showing the relationships among the H. lar haplotypes. Each circle size is proportional to the number of individuals in each haplotype. The numbers next to the nodes correspond to the haplotype designation as listed in Supplementary Material, Table S1. The lines connecting the haplotypes represent single mutations unless indicated otherwise (numbers in parentheses). Hypothetical haplotypes (median vectors) are represented by white circles.

opencc-zeroJan 2022View details →

Genetic diversity of Horsfieldia tetratepala (Myristicaceae), an endangered plant species with extremely small populations to China: implications for its conservation

Genetic variation determines the evolutionary potential of a species and is vital for fully understanding the evolution of a species, as well as for developing optimal conservation strategies. Horsfieldia tetratepala is an economically important rainforest tree which has declined steadily, mainly though habitat destruction, and an endangered, narrow endemic in China where it is also classified as a Plant Species with Extremely Small Populations (PSESP). Effective conservation strategies for H. tetratepala are required urgently, but limited information about its genome is available. Accordingly, restriction site-associated DNA sequencing (RAD_seq) was used to sequence sixty-three H. tetratepala trees covering ten isolated populations to assess genome-level diversity and population structure, generating 8,103 high-quality SNPs. Low genetic diversity and moderate genetic differentiation was observed among populations, but Bayesian clustering divided the sampled H. tetratepala populations into two genetic clusters, though with some populations from Guangxi and Yunnan intermixed. Because of increasing of habitat fragmentation and human disturbance, conservation priority should be placed on populations with higher genetic variation (e.g., BB, TKH, DWS, and GLQ). Overall, our study provides valuable genomic resources for H. tetratepala that will significantly advance the formulation of effective conservation strategies.

opencc-zeroJan 2022View details →

Data for: Local contributions to beta-diversity in urban pond networks: implications for biodiversity conservation and management

Aim: An understanding of how biotic communities are spatially organised is necessary to identify and prioritize habitats within landscape-scale biodiversity conservation. Local Contribution to Beta diversity (LCBD) identifies individual habitats that make a significant contribution to beta-diversity and may have important practical implications, particularly for conservation of habitat networks. In this study, we develop and apply a conservation prioritisation approach based on LCBD in aquatic invertebrate communities from 132 ponds. Location: Five urban settlements in the UK: Halton, Loughborough, Stockport, Birmingham, Huddersfield. Methods: We partition LCBD into richness difference (nestedness: RichDiffLCBD) and species replacement (turnover: ReplLCBD) and identify key environmental variables driving LCBD. We examine LCBD at two scales relevant to conservation planning: within urban settlements and nationally across the UK. Results: Significant differences in LCBD values were recorded among the five settlements. In four of the five urban settlements studied, pond sites with the greatest LCBD values typically showed high replacement values. Significant LCBD sites and sites with high taxonomic diversity together supported more of the regional species pool (70%-97%) than sites with high taxonomic diversity alone (54% to 94%) or what could be protected by the random selection of sites. LCBD was significantly associated with vegetation shading, surface area, altitude and macrophyte cover. Main conclusions: Conservation prioritisation that incorporates LCBD and sites with high taxonomic diversity improves the effectiveness of conservation actions within pond habitat networks, ensures site supporting high biodiversity are protected, and provides a method to define a spatial network of protected sites. Identifying new, effective conservation approaches, particularly in urban areas where resources may be scarce and conflicts regarding land use exist, is essential to ensure biodiversity is fully supported and detrimental anthropogenic effects are reduced.

opencc-by-4.0Jan 2022View details →

Figure 1 from: Sánchez D, Vázquez-Benítez B, Vázquez-Sánchez M, Aquino D, Arias S (2022) Phylogenetic relationships in Coryphantha and implications on Pelecyphora and Escobaria (Cacteae, Cactoideae, Cactaceae). PhytoKeys 188: 115-165. https://doi.org/10.3897/phytokeys.188.75739

Figure 1 Phylogenetic relationships of Coryphantha and close related genera. Majority rule phylogram, from the BI analysis using cpDNA sequences and indels partitions (molecular analysis). Numbers in nodes indicate posterior probabilities. Labels indicate the main recovered clades and subclades.