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opencc-zeroAug 2020View details →

Data from: Chromosome-level assembly of Southern catfish (Silurus meridionalis) provides insights into visual adaptation to the nocturnal and benthic lifestyles

Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries with an important economic value but a drastically declining wild population. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7 Gb Nanopore long reads and 49.5 Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9 Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed that catfish possess a rod-dominated visual system which is responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of UV and violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow color vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio leaded to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of conserved noncoding elements (CNEs), which might be associated with the small eyes in catfish. Taken together, our study provided important clues for the adaptation of the catfish visual system to a benthic lifestyle. The draft genome of S. meridionalis represents a valuable resource for elucidation of molecular mechanism of ecological adaptation, as well as genetic breeding in aquaculture.

opencc-zeroDec 2018View details →

Data from: Lifestyle and socio-economic inequalities in diabetes prevalence in South Africa: a decomposition analysis

Background: Inequalities in diabetes are widespread and are exacerbated by differences in lifestyle. Many studies that have estimated inequalities in diabetes make use of self-reported diabetes which is often biased by differences in access to health care and diabetes awareness. This study adds to this literature by making use of a more objective standardised measure of diabetes in South Africa. The study estimates socio-economic inequalities in undiagnosed diabetes, diagnosed diabetes (self-reported), as well as total diabetes (undiagnosed diabetics + diagnosed diabetics). The study also examines the contribution of lifestyle factors to diabetes inequalities in South Africa. Methods: This cross sectional study uses data from the 2012 South African National Health and Nutrition Examination Survey (SANHANES-1) and applies the Erreygers Concentration Indices to assess socio-economic inequalities in diabetes. Contributions of lifestyle factors to inequalities in diabetes are assessed using a decomposition method. Results: Self-reported diabetes and total diabetes (undiagnosed diabetics + diagnosed diabetics) were significantly concentrated amongst the rich (CI = 0.0746; p < 0.05 and CI = 0.0859; p < 0.05). The concentration index for undiagnosed diabetes was insignificant but pro-poor. The decomposition showed that lifestyle factors contributed 22% and 35% to socioeconomic inequalities in self-reported and total diabetes, respectively. Conclusion: Diabetes in South Africa is more concentrated amongst higher socio-economic groups when measured using self-reported diabetes or clinical data. Our findings also show that the extent of inequality is worse in the total diabetes outcome (undiagnosed diabetics + diagnosed diabetics) when compared to the self-reported diabetes outcome. Although in comparison to other determinants, the contribution of lifestyle factors was modest, these contributions are important in the development of policies that address socio-economic inequalities in the prevalence of diabetes.

opencc-zeroDec 2018View details →

Data from: Do the high energy lifestyles of shorebirds result in high maximal metabolic rates? - Basal and maximal metabolic rates in least and pectoral sandpipers during migration

Shorebirds have high resting and field metabolic rates relative to many other bird groups, and this is posited to be related to their high-energy lifestyle. Maximum metabolic outputs for cold or exercise are also often high for bird groups with energetically demanding lifestyles. Moreover, shorebirds demonstrate flexible basal and maximal metabolic rates, which vary with changing energy demands throughout the annual cycle. Consequently, shorebirds might be expected to have high maximum metabolic rates, especially during migration periods. We captured least (Calidris minutilla) and pectoral (C. melanotos) sandpipers during spring and fall migration in southeastern South Dakota and measured maximal exercise metabolic rate (MMR; least sandpipers only), summit metabolic rate (Msum, maximal cold-induced metabolic rate) and basal metabolic rate (BMR, minimum maintenance metabolic rate) with open-circuit respirometry. BMR for both least and pectoral sandpipers exceeded allometric predictions by 3-14%, similar to other shorebirds, but Msum and MMR for both species were either similar to or lower than allometric predictions, suggesting that the elevated BMR in shorebirds does not extend to maximal metabolic capacities. Old World shorebirds show the highest BMR during the annual cycle on the Arctic breeding grounds. Similarly, least sandpiper BMR during migration was lower than on the Arctic breeding grounds, but this was not the case for pectoral sandpipers, so our data only partially support the idea of similar seasonal patterns of BMR variation in New World and Old World shorebirds. We found no correlations of BMR with either Msum or MMR for either raw or mass-independent data, suggesting that basal and maximum aerobic metabolic rates are modulated independently in these species.

opencc-zeroDec 2015View details →

Data from: The influence of slavemaking lifestyle, caste and sex on chemical profiles in Temnothorax ants: insights into the evolution of cuticular hydrocarbons

Chemical communication is central for the formation and maintenance of insect societies. Generally, social insects only allow nest-mates into their colony, which are recognized by their cuticular hydrocarbons (CHCs). Social parasites, which exploit insect societies, are selected to circumvent host recognition. Here, we studied whether chemical strategies to reduce recognition evolved convergently in slavemaking ants, and whether they extend to workers, queens and males alike. We studied CHCs of three social parasites and their related hosts to investigate whether the parasitic lifestyle selects for specific chemical traits that reduce host recognition. Slavemaker profiles were characterized by shorter-chained hydrocarbons and a shift from methyl-branched alkanes to n-alkanes, presumably to reduce recognition cue quantity. These shifts were consistent across independent origins of slavery and were found in isolated ants and those emerging in their mother colony. Lifestyle influenced profiles of workers most profoundly, with little effect on virgin queen profiles. We detected an across-species caste signal, with workers, for which nest-mate recognition is particularly important, carrying more and longer-chained hydrocarbons and males exhibiting a larger fraction of n-alkanes. This comprehensive study of CHCs across castes and species reveals how lifestyle-specific selection can result in convergent evolution of chemical phenotypes.

opencc-zeroFeb 2020View details →

Linking socioeconomic inequalities and type 2 diabetes through obesity and lifestyle factors among Mexican adults: a structural equations modeling approach

Objective. To assess the association between type 2 diabetes (DM2) and socioeconomic inequalities, mediated by the contribution of body mass index (BMI), physical activity (PA), and diet (diet-DII). Materials and methods. We conducted a cross-sectional analysis using data of adults participating in the Diabetes Mellitus Survey of Mexico City. Socioeconomic and demographic characteristics as well as height and weight, dietary intake, leisure time activity and the presence of DM2 were measured. We fitted a structural equation model (SEM) with DM2 as the main outcome, and BMI, diet-DII and PA served as mediator variables between socioeconomic inequalities index (SII) and DM2. Results. The prevalence of DM2 was 13.6%. From the fitted SEM, each standard deviation increases in the SII was associated with increased scores of DM2 (β=0.174, P<0.001). Conclusion. The results in the present study show how high scores in the index of SII may influence the presence of DM2.

FIGURE 1. A in The freshwater ostracod (Crustacea) genus Notodromas Lilljeborg, 1853 (Notodromadidae) from Japan; taxonomy, ecology and lifestyle

FIGURE 1. A. Map of localities where Notodromas has been reported in eastern Asia. Data from Brehm (1923; 1933); Chen (1982); Deb (1984); Klie (1938); Martens (1991); Mischke et al. (2002); Neale (1984); Neale & Zhao (1991); Okubo & Ida (1989); Okubo (2003); Pietrzeniuk (1977); Sars (1903); Schornikov (2004); Schornikov (1995); Zenina & Schornikov (2008); Zhao (1990). *1: Reported as N. monacha by Schornikov (1995), but considered to be N. sinensis by Schornikov & Trebukhova (2001). *2: Reported as N. monacha, but because only one juvenile was recovered (Pietrzeniuk 1977), it is considered to be in open nomenclature herein; see text for more details. *3: Bronshtein (1947) reported N. monacha from Kazakhstan, but as no specific localities were given, point is approximate. *4: Sub-fossil occurrence (Mischke et al. 2002). *5: Sars (1903) raised specimens of N. oculata from mud collected from Sumatra, but didn't specify which of two possibly localities the mud was collected from. Point is therefore approximate. N.B. Bronshtein (1947) reported N. monacha from "Western Siberia", but no specific localities were provided. All Japanese records of N. monacha are considered to be Notodromas trulla n. sp. herein. B. Localities where Notodromas trulla n. sp. has been collected. Numbers correspond to those in Table 1. Locality 3 is approximate, as no specific locality data was given. Note that some older records did not give any locality data.

FIGURE 4. Notodromas trulla n in The freshwater ostracod (Crustacea) genus Notodromas Lilljeborg, 1853 (Notodromadidae) from Japan; taxonomy, ecology and lifestyle

FIGURE 4. Notodromas trulla n. sp. A, internal view of a male left valve (LBM 1430005751). B, internal view of anteriorventral margin of a male left valve (LBM 1430005751). C, internal view of anterior-ventral margin of a male right valve (LBM 1430005751). D, internal view of a male right valve (LBM 1430005751). E, internal view of posterior-ventral margin of a female left valve (LBM 1430005752). F, internal view a female left valve (LBM 1430005752). G, internal view a female right valve (LBM 1430005752). H, internal view of adductor muscle scars of a female right valve (LBM 1430005752). I, internal view of posterior-ventral margin of a female right valve (LBM 1430005752). Scale bar = 303 µm for A, D, F & G, 134 µm for B, C, E, H & I.

FIGURE 3. A–F. Notodromas trulla n in The freshwater ostracod (Crustacea) genus Notodromas Lilljeborg, 1853 (Notodromadidae) from Japan; taxonomy, ecology and lifestyle

FIGURE 3. A–F. Notodromas trulla n. sp. A, dorsal view of male, anterior to left (LBM 1430005757). B, dorsal view of female, anterior to left (LBM 1430005754). C, oblique ventral view of famale, anterior to right (LBM 1430005756). D, ventral view of female, anterior to left (LBM 1430005756). E, lateral left view of female anterior margin (LBM 1430005756). F, ventral view of female, detail of posterior region, anterior to left (LBM 1430005755). G, Notodromas monacha, ventral view of female, detail of posterior region, anterior to left. H, Notodromas persica, ventral view of female, detail of posterior region, anterior to left. Scale bar = 303 µm for A–D, 70 µm for E–H.

FIGURE 8. A, Notodromas trulla n in The freshwater ostracod (Crustacea) genus Notodromas Lilljeborg, 1853 (Notodromadidae) from Japan; taxonomy, ecology and lifestyle

FIGURE 8. A, Notodromas trulla n. sp., hemipenis (LBM 1430005748). B, Notodromas monacha, hemipenis. C, Notodromas persica, hemipenis.

FIGURE 2. A & B, Notodromas trulla n in The freshwater ostracod (Crustacea) genus Notodromas Lilljeborg, 1853 (Notodromadidae) from Japan; taxonomy, ecology and lifestyle

FIGURE 2. A & B, Notodromas trulla n. sp. A, left lateral view of male carapace (LBM 1430005758). B, left lateral view of female carapace (LBM 1430005753). C & D, Notodromas monacha. C, left lateral view of male carapace. D, left lateral view of female carapace. E & F, Notodromas persica. E, left lateral view of male carapace. F, left lateral view of female carapace. G, Notodromas trulla n. sp., left lateral view of posterior region of female carapace (LBM 1430005754). H, Notodromas monacha, left lateral view of posterior region of female carapace. I, Notodromas persica, left lateral view of posterior region of female carapace. Scale bar = 303 µm for A–F, 70 µm for G–I.

FIGURE 5. Notodromas trulla n in The freshwater ostracod (Crustacea) genus Notodromas Lilljeborg, 1853 (Notodromadidae) from Japan; taxonomy, ecology and lifestyle

FIGURE 5. Notodromas trulla n. sp. Colour image of a female, right lateral view. Note the position of the eye lens. This feature occurs on both valves.

Figure 10. Amphibioplana onnisi. A, holotype RMNH.VER. 19956.a in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle

Figure 10. Amphibioplana onnisi. A, holotype RMNH.VER. 19956.a, photomicrograph of a horizontal section of the left ovary (lo) with tuba (tu) and origin of the left oviduct (lod), testes (t) and vitellaria (vi); B, RMNH.VER. 19956.d, photomicrograph of a sagittal section at the level of the left ovary (lo), with testes (t) and vitellaria (vi); C, CGAS Pla 19.2, photomicrograph of a sagittal section at the level of the left ovary (lo), showing in detail the dorsal (de) and ventral epidermis (ve) with the subepidermal musculature, some vitellaria (vi), and the ventral nerve cord (vnc).

Figure 14 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle

Figure 14. Amphibioplana onnisi. Photomicrographs of the copulatory apparatus; sagittal sections. A, holotype RMNH. VER. 19956.a, showing penis bulb (pb), penis papilla (pp), genital atrium (ga), and the gonopore (go) opening into the cupshaped chamber (csc); anterior to the right; B, CGAS Pla 19. 2, showing copulatory bursa (cb), penis bulb, penis papilla and genital atrium; anterior to the right; C, RMNH.VER. 19958.d, showing copulatory bursa with a voluminous mass of sperm (s) in its lumen, penis bulb, penis papilla and genital atrium; anterior to the left; D, CGAS Pla 19.1b, showing copulatory bursa with sperm in its lumen, penis bulb, penis papilla and genital atrium; anterior to the left; E, CGAS Pla 24.5, sagittal section showing the proximal tract of the bursal canal (bc) with its diaphragm-like protrusion (bcd) into the copulatory bursa; anterior to the left; F, CGAS Pla 22. 6, transverse section showing the penis papilla with the two vasa deferentia (vd) running parallel before their fusion to form the ejaculatory duct.

Figure 3. Amphibioplana onnisi. A in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle

Figure 3. Amphibioplana onnisi. A single, curled up specimen from under a stone in the Grutta 'e Pauli Cave. Scale bar not available.

Figure 9. Amphibioplana onnisi. A, RMNH.VER. 19956.d in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle

Figure 9. Amphibioplana onnisi. A, RMNH.VER. 19956.d, photomicrograph of a sagittal section of the prepharyngeal region, showing the brain (b), the anterior intestinal branch (aib), the most anterior testes (t) and vitellaria (vi) and the left ovary (lo); B, photograph of a preserved specimen from the Grutta 'e Pauli Cave in ventral view, showing the vitellaria (vi), testes (t), pharynx (ph), and copulatory apparatus (ca).

Figure 8 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle

Figure 8. Amphibioplana onnisi. Photomicrographs of the pharynx, sagittal sections. A, CGAS Pla 19.2, oesophageal protrusion (oep) and convoluted tract of the pharynx (cph); anterior to the right; B, RMNH.VER. 19956.c, oesophageal protrusion (oep), also showing xanthophil (xg) and erythrophil (eg) secretions in the pharynx; anterior to the left.

Figure 5 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle

Figure 5. Amphibioplana onnisi. Habitus of live specimens from the Grutta 'e Pauli Cave. A, specimen with constriction just behind copulatory apparatus; B, C, anterior portion of specimen with regenerating blastema (rb) at the margin of the prepharyngeal part of the body; D, specimen with caudal tip located just behind the pharynx, suggesting a recent postpharyngeal fission; E, specimen with caudal tip located just behind the copulatory apparatus (ca), suggesting a recent caudal fission; F, specimen with a regenerating blastema behind the copulatory apparatus. Scale bars not available.