Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation

GenBank accession numbers of cyt b, IRBP and RAG1 sequences of nemacheilids and one botiid species (B. lohachata). (XLSX 17 kb

Human IRF1 governs macrophagic IFN-γ immunity to mycobacteria

Inborn errors of human IFN-γ-dependent macrophagic immunity underlie mycobacterial diseases, whereas inborn errors of IFN-α/β-dependent intrinsic immunity underlie viral diseases. Both types of IFNs induce the transcription factor IRF1. We describe unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria and related intramacrophagic pathogens. These children have no history of severe viral disease, despite exposure to many viruses, including SARS-CoV-2, which is life-threatening in individuals with impaired IFN-α/β immunity. In leukocytes or fibroblasts stimulated in vitro, IRF1-dependent responses to IFN-γ are, both quantitatively and qualitatively, much stronger than those to IFN-α/β. Moreover, IRF1-deficient mononuclear phagocytes do not control mycobacteria and related pathogens normally when stimulated with IFN-γ. By contrast, IFN-α/β-dependent intrinsic immunity to nine viruses, including SARS-CoV-2, is almost normal in IRF1-deficient fibroblasts. Human IRF1 is essential for IFN-γ-dependent macrophagic immunity to mycobacteria, but largely redundant for IFN-α/β-dependent antiviral immunity

Fig. 1. Nemacheilus paucimaculatus, ZRC 52361 in Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae)

Fig. 1. Nemacheilus paucimaculatus, ZRC 52361, holotype, 47.1 mm SL, Malaysia: Johor, tributary of River Segamat.Published as part of <i>Bohlen, Jörg & Šlechtová, Vendula, 2011, Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae), pp. 201-204 in Raffles Bulletin of Zoology 59 (2)</i> on page 202, DOI: <a href="http://zenodo.org/record/10107205">10.5281/zenodo.10107205</a&gt

Leptobotia micra Bohlen & Šlechtová, 2017, new species

<i>Leptobotia micra,</i> new species <p>(Fig. 2, 3)</p> <p> <b>Holotype.</b> SNHM 10308, 45.6 mm SL; PR China: Guangxi province: market in Guilin, reportedly collected in River Li close to Guilin; Zhou <i>et al.</i>, 27 SEP 2013.</p> <p> <b>Paratypes.</b> SNHM 10309-10310, 2, 45.2–50.2 mm SL; ZRC 55399, 2, 45.8–45.9 mm SL; same data as holotype.</p> <p> <b>Diagnosis.</b> Member of the genus <i>Leptobotia</i> by having the suborbital spine simple and no mental lobes. <i>Leptobotia micra</i> is distinguished from all other species of <i>Leptobotia</i> by a combination of the following characters: no dark bars or dorsal saddles on body, a row of white dots along dorsal midline, 4+34 vertebrae, a predorsal distance of 58.1–59.0% SL, eye diameter 1.8‒2.0% SL, pelvic fins not reaching anus, an emarginated caudal fin (length of median rays 1.3‒1.4 times in length of lower lobe) and the anus positioned distinctly closer to anal-fin origin than to pelvic-fin base.</p> <p> <b>Description.</b> See Figure 2 for general appearance and Table 1 for morphometric data of holotype and 4 paratypes. A very small botiid loach (largest recorded size 50.2 mm SL) with elongated body (body depth 4.4‒6.1 times in SL). Body, head and caudal peduncle compressed. Dorsal outline from snout to end of dorsal-fin base slightly convex to convex; rising from snout to maximum body depth between base of pectoral and pelvic fins and then declines until end of dorsal-fin base. Dorsal outline behind dorsal-fin base nearly straight, tapering towards the caudal-fin base. Ventral outline of head slightly convex, ventral outline of body and caudal peduncle nearly straight with exception of belly, which is arched according to the degree of filling of stomach and gonads. Snout round or slightly pointed in ventral view. Depth of caudal peduncle 1.0‒1.2 times in its length. Axillary pelvic lobe present and with free tip. Very small adipose crests along dorsal and ventral midline of caudal peduncle.</p> <p>Dorsal fin with 4 simple and 7½ or 8½ branched rays. Distal margin of dorsal fin straight or slightly convex. Anal fin with 3 simple and 5½ branched rays, not reaching caudal-fin base, distal margin convex. Caudal fin with 9+8 branched rays, moderately forked (length of median rays 1.2‒1.4 times in length of upper lobe), lobes round or slightly pointed. Pelvic fins with 8 rays, origin under or slightly before origin of dorsal fin, reaching about half of distance between pelvic-fin base and anal-fin origin, not reaching anus, which is situated about 3 eye diameters in front of anal-fin origin. Pectoral fin with 11 to 13 rays, not reaching half of distance between pectoral-fin base and pelvic-fin origin. 4+34 vertebrae.</p> <p>Body covered by small scales except ventral side between head and anus. Lateral line nearly complete, always reaching vertical through end of anal-fin base, with 66‒86 pores. Cephalic lateral line system with 6 supraorbital, 4 + 10 infraorbital, 9 pre-operculo-mandibular and 3 supratemporal pores. Lips and barbels smooth.</p> <p>Anterior nostril pierced in front of side of a flap-like tube, reaching slightly behind posterior margin of posterior nostril, not reaching margin of eye, with a low anterior rim. Eye small (12.0‒14.6 times in lateral head length), eye diameter 1.9‒2.3 times in interorbital width. Mouth gape about same length as width. Posterior margin of upper lip reaching vertical through anterior margin of nostril. Processus dentiformes present, but very low and broadly rounded. No notch in lower lip. Lips thick, without furrows, upper lip with very small median incision; lower lip with a median interruption. Rostral barbels reaching about half of distance to corner of mouth, maxillary barbel just reaching behind level of posterior margin of nostrils, not reaching level of anterior margin of eye. Three dissected paratypes (42.2‒45.9 mm SL) are females with developing oocytes.</p> <p> <b>Sexual dimorphism.</b> None observed.</p> <p> <b>Colouration.</b> Ground colour of head and body in preserved specimens light beige. Body and head laterally peppered with grey pigment cells, whose density is increasing dorsally, so that dorsal side of head and body are grey. A row of white dots along dorsal midline from nape to caudal-fin base, single dots about size of eye, but usually at least some are fused to stripes. Dots are sometimes faint, in one paratype hardly visible, but present in all specimens. A faint dark grey stripe from mouth to eye, width slightly less than eye diameter. Base of rostral barbels and tip of mouth black. A dark grey band at base of caudal fin, width similar to eye diameter, continuous, reaching dorsal and ventral midline. 2 or 3 rows of dark grey faint blotches on caudal fin, 1 or 2 such rows in dorsal fin, single blotches in anal fin, paired fins without pigmentation.</p> <p> <b>Distribution.</b> The species is presently known only from the type series, which originated from the upper River Li around Guilin city in Guangxi province, PR China.</p> <p> <b>Etymology.</b> From micros, greek for ‘small’. The name refers to the fact that the species is the smallest known species of the genus, with females as small as 45 mm SL developing oocytes. An adjective.</p> <p> <b>Remarks.</b> In three families of loaches (Botiidae, Cobitidae, Serpenticobitidae) the lateral ethmoid bone is developed as an erectable spine, called suborbital spine. In most cases, this spine is bifid, meaning it is divided into a main branch and a side branch, both pointed. In contrast to this common shape, the suborbital spine in all species of <i>Leptobotia</i> is simple, meaning it lacks the side branch. Within Botiidae, this character state is otherwise found only in <i>Sinibotia zebra</i> (Wu) (Wu 1939; Bohlen <i>et al.</i> 2016). <i>Sinibotia zebra</i> differs from all species of <i>Leptobotia</i> by having (vs. not having) the lower lip extended into mental lobes. The new species <i>L. micra</i> has a simple suborbital spine and no mental lobes, assigning it to the genus <i>Leptobotia</i>.</p> <p> Most species of <i>Leptobotia</i> have a prominent pigmentation pattern on the body and fins. Black bars are found in four species (<i>L. elongata</i>, <i>L. flavolineata</i> Wang, <i>L. orientalis</i> Xu <i>et al.</i>, <i>L. pellegrini</i> Fang), dorsal saddles in another four species (<i>L. guilinensis</i> Chen, <i>L. hengyangensis</i> Huang & Zhang, most specimens of <i>L. rubrilabris</i> Dabry de Thiersant, <i>L. tchangi</i> Fang) and a marbled (<i>L. taeniops</i> Sauvage) and a reticulated (<i>L. punctata</i>) pattern in one species each (Fang 1936, Wu 1939, Chen 1980, Li et al 2008, Nalbant 2002, Yu <i>et al.</i> 1981). <i>Leptobotia micra</i> differs from these species in having a plain grey body, darker at the dorsum, with a row of white dots along dorsal midline, a faint dark grey stripe from mouth to eye and a dark grey band at base of caudal fin (Fig. 2).</p> <p> <i>Leptobotia micra</i> bears a row of white dots along the complete dorsal midline, a character state otherwise encountered only in <i>L. citrauratea.</i> In <i>L. guilinensis</i>, <i>L. punctata</i> and some specimens of <i>L. posterodorsalis</i> and <i>L. taeniops</i>, such middorsal dots or a middorsal stripe are present in the posterior half of the dorsum between base of dorsal fin and caudal-fin origin (Fig. 4). <i>Leptobotia micra</i> differs from <i>L. citrauratea</i> by having 7½‒8½ (vs. 9½) branched dorsal-fin rays, a shorter caudal fin (1.1‒1.2 times in lateral head length vs. 0.9 times) and mildly emarginated caudal fin (length of median rays 1.3‒1.4 times in length of lower lobe; vs. strongly forked, length of median rays 1.7‒1.8 times in length of lower lobe). <i>Leptobotia micra</i> differs from <i>L. guilinensis</i> and <i>L. punctata</i> by having less vertebrae (4+34 vs. 4+ 39 in <i>L. punctata</i> and 4+ 35‒36 in <i>L. guilinensis</i>), a longer predorsal distance (58.1‒59.0% SL vs. 56.2% SL in <i>L. punctata</i> and 49.3‒55.9% SL in <i>L. guilinensis</i>) and the anus positioned distinctly closer to anal-fin origin than to pelvic-fin base (vs. in about equal distance in <i>L. punctata</i> and <i>L. guilinensis</i>). Additional differences in the pigmentation pattern between <i>L. micra</i> and <i>L. punctata</i> and <i>L. guilinensis</i> have been described above. <i>Leptobotia micra</i> differs from <i>L. posterodorsalis</i> by pelvic fins insert opposite or slightly in front of dorsal-fin origin (vs. remarkably before dorsal-fin origin), by having a deeper body (body depth 4.4‒6.1 times in standard length vs. 6.9‒8.3 times), more branched rays in pelvic (8 vs 6) fins, less vertebrae (4‒34 vs. 4+40‒41) and by not having (vs. having) prominent black blotches in the caudal fin.</p> <p> A simply grey or brown body is found in seven species of <i>Leptobotia</i>, namely <i>L. bellacauda</i> Bohlen & Šlechtová, <i>L. citrauratea</i>, <i>L. microphthalma</i> Fu & Ye, <i>L. posterodorsalis</i>, <i>L. tientaiensis</i> Wu and in few specimens of <i>L. elongata</i> and <i>L. rubrilabris</i> (Fig. 5). The differences between <i>L. micra</i> and <i>L. citrauratea</i> and <i>L. posterodorsalis</i> are given above. <i>Leptobotia micra</i> differs from <i>L. bellacauda</i> by not having (vs. having) prominent black blotches in the caudal fin, by having the anus closer to the anal fin origin than to base of pelvic fin (vs. closer to base of pelvic fin), a shorter caudal peduncle (11.8‒13.5% SL vs. 14.2‒18.2% SL), a larger eye (1.8‒2.0% SL vs. 2.2‒3.1% SL) and a less deeply emarginated caudal fin (length of median caudal rays 1.2‒1.4 times in length of upper lobe vs. 1.5‒2.0 times). <i>Leptobotia micra</i> differs from <i>L. microphthalma</i> by having larger eyes (eye diameter 1.8‒2.0 % SL vs. 0.8‒1.0 % SL), less deep forked caudal fin (length of median rays 1.2‒1.4 times in length of lower lobe vs. 2.7‒3.1 times), presence (vs. absence) of a black stripe from snout to eye, a black bar on caudal-fin base, and by having hyaline fins (vs having all fins in body colour). <i>Leptobotia micra</i> differs from <i>L. tientaiensis</i> by having 4+34 (vs. 4+35‒37) vertebrae, a row of white dots along middorsal line (vs. absent), by pelvic fins not reaching (vs. reaching) anus and anterior half of the axillary lobe being grown to the body (vs. free on whole length). <i>Leptobotia micra</i> differs from plain grey specimens of <i>L. elongata</i> by having a shorter head (lateral head length 23.6‒25.9% SL vs. 29.0‒29.2% SL), a lower head (head depth at nape 12.1‒14.8% SL vs. 15.6‒16.8% SL), a less strongly emarginated caudal fin (length of median rays 1.3‒1.4 times in length of lower lobe; vs. strongly forked, length of median rays 2.2‒2.6 times in length of lower lobe) and a smaller eye (1.8‒2.0% SL vs. 2.3‒2.7% SL). It differs from plain brown specimens of <i>L. rubrilabris</i> by having the anus closer to the anal-fin origin than to base of pelvic fin (vs. equally distanced), all fins much shorter (e.g. length of upper lobe of caudal peduncle 18.7‒23.9% SL vs. 29.0‒34.7% SL, length of anal fin 15.3‒16.8% SL vs. 18.1‒21.2% SL), a more compressed body (body width at dorsal-fin origin 8.6‒9.8% SL vs. 11.6‒11.8% SL).</p> <p> <i>Leptobotia micra</i> occurs in the River Li, which drains into the River Gui, a northern tributary of the Pearl River. The River Li is particularly rich in botiid loaches; including <i>L. micra</i> up to now nine species have been recorded from this river (Fang 1936, Chen 1980, pers. observ.). Among them are four species of <i>Leptobotia</i>, namely <i>L. guilinensis</i>, <i>L. micra</i>, <i>L. microphthalma</i>, <i>L. pellegrini.</i> The differences between <i>L. micra</i> and <i>L. guilinensis</i> and <i>L. microphthalma</i> have been described above. <i>Leptobotia micra</i> differs from <i>L. pellegrini</i> by not having (vs. having) broad black dorsal saddles and/or bars on the body, by pelvic fins not reaching (vs. reaching) anus, by having smaller eyes (1.8‒2.0% SL vs. 2.3‒2.9% SL) and a less strongly forked caudal fin (length of median lobe 1.3‒1.4 times in length of lower lobe vs. 1.8‒2.0 times). Other species of <i>Leptobotia</i> recorded from the Pearl River basin are <i>L. punctata</i> and <i>L. posterodorsalis</i>; for differences between these two species and <i>L. micra</i> see above.</p> <p> <i>Leptobotia micra</i> seems to be an exceptionally small species of this genus. Although the limited number of known specimens does not allow conclusions on the maximum size of the species, the fact that females of less than 5 cm SL bear developing oocytes indicates a small size at maturation.</p> <p> <b>Comparative material.</b> <i>Leptobotia bellacauda</i>: SNHM 20160220, holotype, 70.1 mm SL; PR China, Anhui province, Qiupu River; SNHM 20160221‒20160224, paratypes, 4 specimens, 64.6‒76.7 mm SL, ZRC 54802, paratypes, 2 specimens, 71.7‒73.4 mm SL; same data as holotype; <i>Leptobotia citrauratea</i>: AMNH 8402, holotype, 50 mm SL; China: Hunan prov.: Lake Dongting (by photographs); <i>Leptobotia elongata</i>: IAPG A8553-8560 (normally banded form), 8 specimens, 68.7‒85.2 mm SL, IAPG A8550-8551 (plain grey form), 2 specimens, 82.2‒86.5 mm SL; both PR China: Sechuan prov., Yangtze River; <i>Leptobotia flavolineata</i>: BMAM 762196, holotype, about 84 mm SL; PR China: Beijing prov.: Juma River (by photographs); <i>Leptobotia guilinensis</i>: IAPG A8861‒8883, 23 specimens, 62.7‒80.3 mm SL; PR China: Guangxi: Li River. <i>Leptobotia hengyangensis</i>: IHASW 80013, syntype, 1; PR China: Hunan: Xiang River (by photographs). <i>Leptobotia microphthalma</i>: IAPG A8536‒8543, 9 specimens, 66.3‒81.4 mm SL; PR China: Sichuan: Min River. <i>Leptobotia orientalis</i>: BMAM 80 VI0030, paratype, 80 mm SL; PR China: Beijing prov.: Juma River (by photographs); <i>Leptobotia pellegrini</i>: IAPG A 1813-1815, 3 specimens, 110.0‒ 146.3 mm SL, IAPG A8561, 1 specimen, 81.2 mm SL; both: PR China: Sichuan prov.: Yangtze River; <i>Leptobotia punctata</i>: IAPG A9101, 1 specimen, 53.2 mm SL; PR China: Guangxi: Yong River. <i>Leptobotia rubrilabris</i>: IAPG A8552; 1 specimen, 85.7 mm SL; PR China: Sichuan prov.: Yangtze River; IAPG A10065, 1 specimen, 93.8 mm SL; PR China: Anhui prov.: Qiantang River; <i>Leptobotia taeniops</i>: IAPG A8562-8566, 5 specimens, 75.1‒91.5 mm SL; PR China: Jiangxi prov.: Gan Jiang; <i>Leptobotia tientaiensis</i>: IHASW 790940 (syntype of <i>L. tientaiensis hansuiensis</i> Fang & Hsu), 1, PR China: Shaanxi: Langao (by photographs); IAPG A10063, 1, XX mm SL; PR China: Hubei prov.: Hansui River basin; AMNH 9682 (holotype of <i>L. compressicauda</i> Nichols), 93.2 mm SL; PR China: Fujian prov.: Chungan Hsien (by photographs); AMNH 11131 (paratypes of <i>L. compressicauda</i>), 7 specimens, 64.5‒94.6 mm SL; PR China: Fujian prov.: Chungan Hsien (by photographs); IAPG A9173, 1 specimen, 51.3 mm SL; PR China: Zhejiang: River in Tiantai Mountains. <i>Leptobotia tchangi</i>: IAPG 9167‒9172, 6 specimens, 62.6‒111.8 mm SL, PR China: Zhejiang: Qiantang River.</p> <p> Further data taken from Aquatic Research Institute of Guangxi (2006), Bohlen & Šlechtová (2016), Li <i>et al.</i> (2008), Xu <i>et al.</i> (1981), and Ye <i>et al.</i> (2015).</p>Published as part of <i>Bohlen, Jörg & Šlechtová, Vendula, 2017, Leptobotia micra, a new species of loach (Teleostei: Botiidae) from Guilin, southern China, pp. 90-100 in Zootaxa 4250 (1)</i> on pages 91-99, DOI: 10.11646/zootaxa.4250.1.7, <a href="http://zenodo.org/record/439818">http://zenodo.org/record/439818</a&gt

Fig. 3. Nemacheilus paucimaculatus, ZRC 52361 in Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae)

Fig. 3. Nemacheilus paucimaculatus, ZRC 52361, holotype, 47.1 mm SL; mouth, ventral view (scale bar = 5 mm).Published as part of <i>Bohlen, Jörg & Šlechtová, Vendula, 2011, Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae), pp. 201-204 in Raffles Bulletin of Zoology 59 (2)</i> on page 203, DOI: <a href="http://zenodo.org/record/10107205">10.5281/zenodo.10107205</a&gt

Fig. 4 in Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae)

Fig. 4. Southern part of Malay Peninsula showing selected rivers and the collection points of Nemacheilus paucimaculatus. The type locality is indicated as solid circle, other localities as solid squares. Grey dotted lines outline governmental states.Published as part of <i>Bohlen, Jörg & Šlechtová, Vendula, 2011, Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae), pp. 201-204 in Raffles Bulletin of Zoology 59 (2)</i> on page 203, DOI: <a href="http://zenodo.org/record/10107205">10.5281/zenodo.10107205</a&gt

Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae)

Bohlen, Jörg, Šlechtová, Vendula (2011): Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae). Raffles Bulletin of Zoology 59 (2): 201-204, DOI: http://doi.org/10.5281/zenodo.1010720

Fig. 2. Nemacheilus paucimaculatus, A, B ZRC 52361 in Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae)

Fig. 2. Nemacheilus paucimaculatus, A, B ZRC 52361, holotype, 47.1 mm SL, Malaysia: Johor, tributary of River Segamat; C CMK 22255, 43.0 mm SL, same data as A; D ZRC 2063, 52.4 mm SL, Malaysia: Negeri Sembilan, Sungai Jelai; E ZRC 2063, 44.4 mm SL, same data as D.Published as part of <i>Bohlen, Jörg & Šlechtová, Vendula, 2011, Nemacheilus Paucimaculatus, A New Species Of Loach From The Southern Malay Peninsula (Teleostei: Nemacheilidae), pp. 201-204 in Raffles Bulletin of Zoology 59 (2)</i> on page 203, DOI: <a href="http://zenodo.org/record/10107205">10.5281/zenodo.10107205</a&gt

Using Species Groups to Approach the Large and Taxonomically Unresolved Freshwater Fish Family Nemacheilidae (Teleostei: Cypriniformes)

Large animal families with unresolved taxonomy are notoriously difficult to handle with respect to their biodiversity, systematics, and evolutionary history. We approach a large and taxonomically unresolved family of freshwater fishes (Nemacheilidae, >600 species) by proposing, on the basis of morphologic data, a species group within the family and study its phylogeny with conclusions regarding its diversity, taxonomy, and biogeographic history. Phylogenetic analyses of two mitochondrial and three nuclear genes of 139 specimens, representing about 46 species (17 candidate species from the proposed species-group, plus 29 comparative species), revealed that the proposed species group does not form a distinct monophyletic lineage, but that the candidate and comparative species mixed in three different lineages. However, the results revealed more than 20% of undescribed species within the ingroup and showed that species do not cluster according to the presently recognised genera. At least one of the genetic clades shows signs of an eastward range expansion during the second half of Miocene from north India via Myanmar into Laos, western China, and western Thailand. We conclude that the approach of picking monophyletic lineages to study biodiversity, systematics, and evolutionary history helps to open the door to large animal families