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    Biological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus

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    The implication of metabolically active Vibrio spp. in the digestive tract of Litopenaeus vannamei for its post-larval development

    Sampling of organisms and bioassay experiments
    Shrimp post-larvae (PL5) of Litopenaeus vannamei were collected from the aquaculture farm Parque acuícola Cruz de Piedra, Guaymas, Sonora, Mexico (27° 51′ 05.9″ N 110° 31′ 57.0″ W). Afterward, post-larval shrimp were transported in aerated tanks with the same pond water as the farm to the Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora (DICTUS), where a lab-scale system was previously tested and used. The bioassay was conducted for 80 days with healthy shrimp, each weighing 0.5 ± 0.1 g, and post-larvae were randomly distributed in the lab-scale system. The system consisted of nine 80-L culture units linked to a recirculation aquaculture system (RAS), and sterile seawater was used to fill the units to an operating volume of 60 L. Influent seawater was filtrated and flowed through a UV lamp for sterilization, and the seawater was equally dispensed to all culture units, as depicted in the supplementary material (Fig. S2). The culture units were maintained under similar indoor conditions with artificial aeration (2000F heat bonded silica; pore size, 140 µm), and the salinity was maintained at around 35‰ with the addition of sterile freshwater (MilliQ grade, Millipore) to avoid the incorporation of outside bacteria and to compensate evaporation. Finally, the effluent generated by the system flowed through a biofilter containing nitrifying bacteria to control toxic nitrogen compounds in the recirculation system (Fig. S2). The unconsumed feed, feces, moults, and dead organisms (if any) were removed daily.
    The salinity, dissolved oxygen (DO), pH, and temperature were measured twice per day (07:00 and 18:00 h) using a YSI multiprobe system 556 (YSI Incorporated).
    The bioassay started with PL5 on day 0. At this point, 40 organisms were randomly introduced into each culture unit, and the experiment lasted 80 days. Throughout the experiment, shrimp were fed twice a day at a rate of 4% wet biomass day–1 using feeding trays with the same formulated feed consisting of commercial grow-out pelletized feed with 25% crude protein, 5% lipids, and 4% fiber.
    Water quality and productive response
    The water quality was monitored daily throughout the bioassay, and samples were collected weekly from each culture unit using sterile falcon tubes by filtering the water through 0.45 μm membranes (Millipore). Nitrite (NO2–N), nitrate (NO3–N), ammonia (NH3–NH4), and phosphate (P–PO4) concentrations were measured using commercial Hanna reagent kits HI 93707-01, HI 93728-01, HI 93700-01, and HI 93717-01, respectively (Hanna Instruments, Romania).
    Biometry analyses were performed at the four different developmental stages, denominated as I, II, III, and IV, corresponding to 0–20, 20–40, 40–60, and 60–80 culture days, respectively, and the productive response was calculated15.
    Collection of intestine and water samples and DNA and RNA extraction
    To discard the transitory microbiota, the shrimp were fasted for 6 h before sampling. Once the intestines were empty, these were dissected on the corresponding dates using a sterile dissection kit, placed in sterile cryogenic tubes, and stored at – 80 °C until nucleic acid extraction. Each sample date belongs to an experimental unit with three culture tanks. The intestine samples from culture tanks were pooled and considered as a replicate, giving three replicates per sampling time. At the same sampling points, 1 L samples of water (W) from each culture unit corresponding to an experimental replicate were collected and pooled for filtration through 0.22 µm sterile filters of mixed cellulose ester membrane (Whatman, Sigma, St Louis, USA) and placed in sterile, 50 mL falcon tubes for storage at – 80 °C until nucleic acid extraction.
    Total DNA and RNA were extracted and purified from the membrane filters previously used to filter seawater samples and from intestines that were also previously sampled, both of them with the FastDNA Spin Kit for Soil15, and the FastRNA Pro Blue Kit (MP-Bio, Santa Ana, CA, USA) in combination with mechanical lysis using the FastPrep Systems (MP-BIO, Santa Ana, CA, USA). The obtained RNA samples were digested according to the TURBO DNA protocol (Ambion, Life Technologies Corporation, Carlsbad, CA, USA) and EDTA to stop the DNase activity and to ensure that any DNA residuals were presented. Finally, samples were purified according to the RNA Cleanup protocol from the RNeasy Mini Kit (Qiagen, Hamburg, Germany). The quality and concentration of nucleic acids were tested as previously described Maza-Márquez et al.39.
    qPCR and RT-qPCR assays
    Real-time polymerase chain reaction (qPCR) assays have been widely implemented for estimating total cell count based on DNA gene markers, regardless of their level of metabolic activity40,41, while reverse transcription qPCR (RT-qPCR) is a useful method for analyzing the expression of specific genes. RT-qPCR is also used because of its high sensitivity, accuracy, specificity, and rapidity in analyzing the time-specific expression of particular genes, allowing for the detection of low-abundance transcripts42. The absolute abundance of total and metabolically active populations of bacteria and Vibrio in both target samples were measured by qPCR and RT-qPCR, respectively, using a StepOne Real-Time PCR system (Applied Biosystems, USA). For RT-qPCR, the synthesis of cDNA was performed by reverse transcription of RNA with the aid of SuperScript III Reverse Transcriptase (Invitrogen, Life Technologies Corporation, Carlsbad, CA, EEUU), following the manufacturer’s specifications, in a final volume of 20 µL and using 150–200 ng of total RNA as a template (specific primers described in Table S4) (Sigma Aldrich; St. Louis, MO, USA) and dNTPs (Invitrogen; Carlsbad, USA). In addition, the cDNA quality and concentration were measured using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific Waltham, MA USA). The number of copies (nbc) of 16S rRNA genes (16S rDNA) and 16S rRNA (16S rRNA) were evaluated in each sample using either extracted DNA or cDNA, respectively, as templates with a set of primers previously described (Table S4) based on the increasing fluorescence intensity of the SYBR Green dye during amplification. For the amplification and detection of specific fragments, the iTaq Universal SYBR Green Supermix (Biorad, USA) was used in a final volume of 15 µL for each reaction. All quantitative amplifications were performed in triplicate. The qPCR reaction mixtures contained 1.8 µL of cDNA or DNA, 250 ng of T4 gene 32 (QBiogene, Illkirch, France), 1.2 µL of each primer (10 mM), supplied by Sigma Aldrich (St. Louis, MO, USA), and 1 × SYBR Green Supermix. The amplification and detection conditions are described in Table S5.
    To provide absolute quantification of the target microorganisms, standard curves were constructed with the aid of a standard plasmid that contained the inserts of the targeted genes. Amplicons of the 16S rDNA were generated from culture strains of Pseudomonas putida NCB957 (quantification of bacteria) and Vibrio parahaemolyticus ATCC17802 (quantification of Vibrio). The PCR products were cloned with the aid of the pCR2.1-TOPO plasmid vector using the TOPO TA cloning system (Invitrogen, Life Technologies Corporation, Carlsbad, CA, USA), following the manufacturer’s protocols. The calibration curves for absolute quantification in the DNA samples (16S rDNA) were generated using serial ten-fold dilutions of linearized plasmid standards, and for absolute quantification in RNA samples (16S rRNA), non-linearized plasmid standards were used as templates for in vitro transcription of the target genes into RNA39,40,43. The copy number per ng was calculated as previously described43. All calibration curves had a correlation coefficient (r2) of  > 0.99 in all assays, and the efficiency of PCR amplification was always between 90 and 110%. Finally, the number of copies of the targeted genes was expressed per gram of tissue sampled, while for water samples these were expressed as the number of copies per mL.
    Statistical analyses
    All statistical analyses were performed in R Studio (version 3.6.0)44 using the following R packages: maggrittr45, ade446, factoextra47, vegan48, and gplots49. Analyses of variance (ANOVA) and multiple-range tests (Student’s-test) were used with a significance level of 95% (p  More

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    The density of anthropogenic features explains seasonal and behaviour-based functional responses in selection of linear features by a social predator

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    Gainers and losers of surface and terrestrial water resources in China during 1989–2016

    Surface water frequency maps and surface water areas during 1989–2016
    Surface water frequencies (FW) of individual pixels in 2016 varied substantially across China (Fig. 1a). There were 1444 million pixels with annual surface water frequency of FW  > 0 in 2016, amounting to ~1.3 × 106 km2 maximum SWA in 2016. Based on the surface water frequency in a year, a water pixel was defined as year-long surface water (FW ≥ 0.75), seasonal surface water (0.05 ≤ FW  More

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    Synergy effect of peroxidase enzymes and Fenton reactions greatly increase the anaerobic oxidation of soil organic matter

    Study sites and sampling
    Three soil types were selected (Table 2). The first was an Andisol31 (Volcanic–allophanic) formed from recent Volcanic ash deposited in the Andes. This was collected from a native temperate rainforest dominated by old growth Nothofagus betuloides (Mirb.) located in Puyehue National Park, where mean annual precipitation is typically  > 8,000 mm year−112. The soils are derived from basaltic scoria with high levels of allophane, imogolite, and ferrihydrite material32. The second soil type was an Ultisol (Metamorphic) sampled in Alerce Costero National Park in the coastal range. It is derived from Metamorphic-schist with high levels of illite-kaolinite33. Finally, an Inceptisol (Granitic) was selected from an ancient Araucaria araucana and Nothofagus pumilio forest in Nahuelbuta National Park. This soil type originates from intrusive Granitic rock parent materials. Mean annual precipitation in this ancient forest reaches  > 1,491 mm and mean annual temperatures reach 13.3 °C34 (Table 2). From each soil sample, four composite soil samples were taken from the Ah mineral horizon (5–10 cm) after removing litter and organic horizons. The samples were then transported to a laboratory under cold conditions. All soils were homogenized and sieved ( More

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    The earliest domestic cat on the Silk Road

    Burials of domestic and wild cats remain a rarity in the archaeological record, especially in comparison to dogs, which are recovered so frequently that they have their own depositional typologies1,2,3,4,5. Finds of individual, articulated animals in archaeological contexts, particularly those exhibiting osteopathologies, are ideal for a social zooarchaeological approach which encourages the investigation of human animal interaction as a facet of social and cultural structures beyond productive capacity6. This type of integrated social-cultural approach in archaeology has largely been utilised in pre- and protohistoric contexts in which there are limited written sources in order to access and interpret the worldview of past cultures. However, there is value in utilising this framework in historical contexts as some animals, such as the domestic cat, are often not frequently and explicitly mentioned in the written record. Such animals act as signifiers of changing cultural attitudes and evidence of human-mediated species dispersal that accompanied expanding human connectivity through the end of the first millennium CE7, 8. The unique and rare find of the remains of a small felid, found in the medieval urban center of Dzhankent in Kazakhstan, is ripe for this approach. Below, we combine multiple lines of scientific enquiry to: explore the ancestry of this cat and ascertain its domestic status; characterise its diet in comparison to other fauna; and reconstruct its life history. Thus, this osteobiography reflects changing human attitudes towards animals that are part of bigger social and cultural changes taking place along the medieval Silk Road.
    In the semi-arid and arid steppe of Central Asia, particularly in modern day Kazakhstan, domestic cats were not widespread before the colonial period of the eighteenth and nineteenth centuries. There are no published archaeological remains of domestic felines from any prehistoric archaeological sites in the Kazakh steppe9,10,11,12 despite the fact that there is increasing evidence for sedentary settlements and agricultural activity dating from the Late and Final Bronze Age within this region which would encourage the presence and utility of commensal rodent hunters such as cats13,14,15. Along the southern border of the Central Asian steppe, in Uzbekistan and Turkmenistan, single bones from felines of uncertain domesticated status have been found in Bronze Age urban contexts, such as at the sites of Kavat 3 and Ulug Depe, as well as in Iron Age contexts from Geoktchick Depe and Kyzyltepe (Fig. 1)16, 17. Remains of small felines are similarly sparse throughout the Archaic and Antique periods in this region (fourth century BCE to eighth century CE) and only single bones were found at urban sites such as at Kugaitepe, Tukatepe, Tok-Kala, Toprak-Kala, Koi Krilgan Kala, Kuruk Kala and at the Gorgon Gates16,17,18, More

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    Drivers of piscivory in a globally distributed aquatic predator (brown trout): a meta-analysis

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    Fossils reshape the Sternorrhyncha evolutionary tree (Insecta, Hemiptera)

    Phylogenetic analysis
    We conducted Bayesian Inference (BI) and Maximum Parsimony (MP) analyses using morphological data to place the fossil taxa and resolve the relationships within Sternorrhyncha. Therefore, we mainly included those morphological characters that were also discernible in the fossils that were selected. The data matrix used for the analysis consisted of 10 taxa (Fulgoromorpha taken as an outgroup, and 9 Sternorrhyncha ingroups, including extinct groups, see Supplementary information 1 Table S1) and 42 characters (see Supplementary information 1 Table S2). The characters were treated as non-additive and unordered. The list of characters and the nexus file containing the character matrix is available in Appendix (Tables S1 and S2).
    The detailed results of phylogenetic analyses are presented in the Appendix. Both phylogenetic methods (MP and BI) were highly congruent in their resultant topologies (Supplementary information 1 Figs S1, S2a–c). According to the resulting phylogenies, the fossil described below forms a group of its own (Fig. 1), included in a clade of Psylliformes, related to Psyllodea and Aleyrodomorpha, but deserving of recognition as a different infraorder.
    Figure 1

    Phylogenetic position of Dingla shagria gen. sp. nov. on most parsimonius tree. Numbers at nodes represent posterior probabilities and bootstrap values. Image of planthopper Pyrops candelaria: Max Pixel Public Domain CC0 (modified); pincombeid Pincombea sp. redrawn from46; male scale insect: Pavel Kirillov CC-BY-SA2.0 (modified); Coccavus supercubitus redrawn from46; aphid Macrosiphum rosae: Karl 432 CC-BY-SA4.0 (modified); protopsyllidiid Poljanka hirsuta redrawn from47; liadopsyllid Liadopsylla apedetica redrawn from48; whitefly Aleyrodes proletella: Amada44 CC-BY-SA4.0 (modified); psyllid Trioza urticae photo by Jowita Drohojowska.

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    Systematic palaeontology
    Order Hemiptera Linnaeus, 1758.
    Suborder Sternorrhyncha Amyot et Audinet-Serville, 1843.
    Clade Psylliformes sensu Schlee, 1969.
    Dinglomorpha Szwedo & Drohojowska infraord. nov
    Diagnosis
    Fore wing with costal veins complex carinate (Pc carinate as in Psylliformes), ScP present as separate fold at base of common stem R + MP + CuA (unique character); common stem R + MP + CuA weakened at base (unique character); areola postica reduced (homoplasy with Aleyrodoidea); clavus present, with single claval vein A1. Hypandrium present as small plate (as in Psylliformes).
    Dingloidea Szwedo & Drohojowska superfam. nov
    Diagnosis
    Fore wing membranous with modified venation—veins thickened, areola postica reduced; antennae 10-segmented; 3 ocelli present; stem MP present, connected with RP and CuA; abdomen widely fused with thorax; no wax glands on sternites.
    Dinglidae Szwedo & Drohojowska fam. nov
    urn:lsid:zoobank.org:act:D0A1C785-62D3-4E07-9A3B-FFAE3C13B704.
    Type genus Dingla
    Szwedo et Drohojowska gen. nov.; by present designation.
    Diagnosis
    Imago. Head with compound eyes narrower than thorax. Eyes entirely rounded, postocular tumosity present; lateral ocelli placed dorsolaterally, near anterior angle of compound eye in dorsal view, median ocellus present. Antennae 10-segmented, with bases in frons to compound eyes, rhinaria scarce (?). Pronotum in mid line longer than mesopraescutum. Fore wing with thickened costal margin, basal portion of stem R + MP + CuA weak, distal portion of stem R + MP + CuA convex, forked at about half of fore wing length, branch RA short; pterostigmal area thickened. Common stem MP + CuA short, branches RP, MP and CuA parallel on membrane. Rostrum reaching metacoxae. Metacoxa without meracanthus. Metadistitarsomere longer than metabasitarsomere, claws distinct, long and narrow, no distinct additional tarsal structures. Male anal tube long. Hypandrium in form of small plate, styli long, narrow and acutely hooked at apex.
    Dingla Szwedo & Drohojowska gen. nov
    LSID urn:lsid:zoobank.org:act:5053D386-4A13-445C-8036-9C69D885561F.
    Type species Dingla shagria
    Szwedo et Drohojowska sp. nov.; by present designation and monotypy.
    Etymology
    The generic name is derived from the adjective ‘dingla’ meaning ‘old’ in Jingpho language, which is spoken in Kachin state where the amber originates from. Gender: feminine.
    Diagnosis
    Vertex in mid line about as long as wide between compound eyes. Frons flat, widely triangularly incised at base. Antenna with 10th antennomere longer than penultimate one, widened, membranous apically, with terminal concavity. Pronotum about twice as wide as long. Mesopraescutum narrow, about as wide as pronotum; mesoscutum wide, with scutellar sutures not reaching anterior margin; mesoscutellum widely pentagonal. Fore wing with branch R forked anteriad of branch MP + CuA forking. Tip of clavus at level of MP + CuA forking. Hind wing with terminals RP and M subparallel and weakened in apical portion. Metafemur not thickened, metatibia without apical spines.
    Dingla shagria Szwedo & Drohojowska sp. nov
    LSID urn:lsid:zoobank.org:act:3EA05FB0-B783-4D7A-98EA-10B02F50B83D (Figures 2, 3).
    Figure 2

    Dingla shagria gen. sp. nov., holotype male, No. MAIG 5,979: body in dorsal view (a); body in ventral view (b); drawing of body in dorsal view (c); drawing of head in ventral view with clypeus (d); fore wing (e); apical antennomere (f); antennomeres 6th—10th (g); head in dorsal view (h); head in ventral view (i); head in lateral view (j); male genitalia in dorsal view (k); male genitalia in ventral view (l); male genitalia in lateral view (m); scale bars: 0.5 mm a, b, c, e; 0.1 mm f, g, k, l, m; 0.2 mm j, h, i; 0.25 mm d.

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    Figure 3

    Dingla shagria gen. sp. nov., paratype male, No. MAIG 5,980: body in dorsal view (a); body in ventral view (b); head in ventral view with median ocellus (c); paratype male, No. NIGP172398, body in dorsal view (d); body in ventral view (e); fore tibia (f); paratype male, No. NIGP172399 body in dorsal view (g); body in ventral view (h); mid leg (i); hind leg (j); scale bars: 0.5 mm a, b, g, h, j; 0.4 mm d, e, f; 0.2 mm c; 0.25 mm i.

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    Etymology
    The specific epithet is derived from the noun ‘shagri’ meaning ‘insect’ in Jingpho language spoken in the Kachin State, when the amber was collected.
    Material
    Holotype male. MAIG 5979, Paratype male, MAIG 5980, deposited in Museum of Amber Inclusions, Laboratory of Evolutionary Entomology and Museum of amber Inclusions, Department of Invertebrate Zoology and Parasitology, Faculty of Biology, University of Gdańsk, Gdańsk, Poland; paratype male NIGP172398, paratype male NIGP172399, deposited in Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China.
    Locality and horizon
    Kachin amber, Noije Bum hill, Hukawng Valley, Kachin State, northern Myanmar. Terminal Aptian/earliest Cenomanian.
    Diagnosis
    Pedicel (2nd antennomere) elongate, slightly thickened, 3rd antennomere longer than second and 4th; antennomeres 4th to 8th subequal in length. Protibia with row of thin setae in apicad half. Probasitarsomere about half as long as prodistitarsomere. Subgenital plate small, subquadrate, parameres long and narrow, parallel; about 3 times as long as wide at base, with hooked acute apex. Male anal tube tubular, slightly widening apicad, merely shorter than parameres.
    Description
    Male. Measurements (in mm): Total length 1.76 to 2.13; Body length total (including claspers) 1.76–2.13; Head including compound eyes width 0.37–0.52; head length along mid line 0.18–0.24; vertex width 0.2–0.26; Forewing length 1.32–1.79; forewing width 0.62–0.74; Claspers length 0.2–032; Antennomere 1st 0.04–0.08; antennomere 2nd 0.8–0.13; antennomere 3rd 0.08–0.16; antennomere 4th 0.06–0.12; antennomere 5th 0.06–0.09; antennomere 6th 0.06–0.1; antennomere 7th 0.06–0.09; antennomere 8th 0.0–0.09; antennomere 9th 0.06–0.09; antennomere 10th 0.0.8–0.01; Profemur + protrochanter cumulative length 0.26–0.46; protibia length 0.29–0.34; probasitarsomere length 0.06–0.09; prodistitarsomere length 0.08–0.13; mesofemur + mesotrochanter cumulative length 0.3–0.4; mesotibia length 0.36–0.4; mesobasitarsomere length 0.05–0.1; mesodistitarsomere length 0.13–015; metafemur + metatrochanter cumulative length 0.39–0.56; metatibia length 0.5–0.68; metabasitarsomere length 0.1–0.15; metadistitarsomere length 0.1–0.18.
    Vertex about half as long as width of head with compound eyes; slightly narrower than wide at base; disc of vertex slightly concave; sutura coronalis absent. Scapus cyllindrical, longer than wide, pedicel slightly longer than scapus, barrel-shaped, wider than 3rd antennomere. Antennomere 3rd longer than 2nd antennomere (pedicel) antennomeres 5th to 9th subequal in length; antennomere 9th with subapical rhinarium; antennomere 10th (apical) longer then penultimate one, spoon-like widened apically, with rhinarium placed subapically. Median and lateral ocelli visible from above. Compound eyes large, not divided, with distinct, non-differentiated ommatidia; postocular protuberances narrow. Frons convex, with distinct triangular, concave median portion; median ocellus at margin with vertex; postclypeus and apical portion of loral plates distinctly incised to frons; postclypeus about twice as long as wide; anteclypeus tapering ventrad; lora semicircular, long, with upper angles slightly below upper margin of postclypeus, lower angles not exceeding half of anteclypeus length. Rostrum with apex reaching metacoxae; scapus short, wide, placed in distinct anterolateral concavity.
    Pronotum large, as long lateral as in midline; about 2.6 times as wide as long in mid line; disc of pronotum convex; anterior margin convex, slightly protruding between compound eyes; posterior margins converging posteriad; posterior margin slightly concave. Mesopraescutum with anterior margin covered by pronotum, with anterior margin convex, lateral margins expanded posterolaterad, with posterior margin convex posteriomediad, slightly concave posterolaterad. Mesoscutum distinctly wider than long in mid line; anterior margin merely concave medially, lateral margins distinctly diverging posteriad, posterolateral angles acute, distinct, posterior margin W-shaped, with distinct median concavity; disc of mesoscutum convex with indistinct longitudinal concavities (apodemes? sutures?). Mesoscutellum narrow, with anterior margin acutely convex, lateral margins subparallel, posterior margin straight, disc of mesoscutellum concave, with posteromedian furrow. Metascutum and metascutellum not visible.
    Fore wing about 2.5 times as long as wide; narrower at base, widening posteriad, rounded in apical margin; widest at ¾ of its length. Costal margin thickened, veins thick, distinctly elevated; basal portion of stem R + MP + CuA weak, distal portion of stem R + MP + CuA convex, forked at about half of forewing length, branch RA short; pterostigmal area thickened; common stem MP + CuA short, branches RP, MP and CuA parallel on membrane; areola postica absent; clavus present, with apex exceeding half of forewing, with single claval vein A1.
    Hind wing about 0.8 times as long as forewing, with costal margin with two groups of regularly dispersed setae, basal group with seven longer and stiff setae and median group with 10 shorter, stout setae; terminals RP and M subparallel and weakened in apical portion.
    Profemur and mesofemur subequal in length; protibia slightly shorter than mesotibia; pro- and metadistitarsomeres slightly longer than pro- and mesobasitarsomeres. Metacoxa without meracanthus; metafemur longer than pro- and mesofemur; metatibia distinctly longer than pro- and mesotibia; metadistitarsomere distinctly longer than metabasitarsomere; tarsal claws long, narrow, without arolium or empodium.
    Abdomen with segments III to VIII almost homonomic in length, widely connected to thorax, subgenital portion narrowing. Subgenital plate small, subquadrate, parameres long and narrow, parallel; about 3 times as long as wide at base, with hooked acute apex. Male anal tube tubular, slightly widening apicad, merely shorter than parameres. More