A Ceramic and Plant and Parasite Microfossil Record from Andarayan, Cagayan Valley, Philippines Reveals Cultigens and Human Helminthiases Spanning the Last ca. 2080 Years

Understanding the timing and nature of ancient agricultural development in the Philippines is hindered by a paucity of direct evidence of crops, that is, plant remains identified to taxa. Here we present analysis of plant microfossils (pollen, phytoliths, and starch) with the addition of ceramic and parasitological analyses of archaeological samples from Andarayan, Cagayan Valley, Northern Luzon to shed light on human activity in the region. Combined with previous ceramic and alluvial records from this area, the results are consistent with a continuity of a Neolithic subsistence tradition throughout the Cagayan Valley and its tributaries for the last 4000 to 500 years. Rice (Oryza sativa), taro (Colocasia esculenta), and cf. cassava (Manihot esculenta) starch provide evidence for cultivation of these taxa in the catchment. As plant taxa vary considerably in their production and preservation of different tissue types, the study also shows the value of a combined plant microfossil approach to cast the net widest when looking for direct evidence of horticulture. The parasitological analysis, showing a range of helminth parasites of humans and their commensals (dogs, pigs, and rats), to our knowledge represents the first ancient helminth eggs reported for the Philippines

Data from: Taxonomic quality of species descriptions varies over time and with the number of authors, but unevenly among parasitic taxa

Although concerns are being raised about a potential shortage of taxonomists and systematists, recent analyses suggest instead that the number of researchers involved in taxonomic descriptions is higher than ever and that the average number of new species described annually per taxonomist has declined in recent decades. Here, using nine metrics of taxonomic quality, such as the number of morphological traits measured, the number of separate line drawings included, and whether or not gene sequences are provided, we explore variation in taxonomic quality as a function of the number of authors and other potential determinants across 2366 descriptions of parasitic helminths published in 1337 articles between 1980 and 2014. Taxonomic quality has generally increased over time, but unequally among different groups of helminths. For example, the number of scanning electron micrographs per description has risen significantly over time in cestodes and nematodes, but decreased for digeneans. For most metrics used, the greater the number of authors per species description, the higher its quality, suggesting not more taxonomists but more collaborations between taxonomists and experts from other fields to produce more comprehensive species characterizations. Re-descriptions of species were of higher quality than their original descriptions, and the improved quality correlated with the number of years elapsed between them. However, the extent of this improvement varied among helminth species with different host taxa. Overall, our findings provide a note of caution for anyone using trends in the number of species described per author to extrapolate the total number of extant species. They also reveal cultural differences among taxonomists working on different groups of parasites that can serve to identify areas for potential improvement

Acanthocephalan Diversity and Host Associations Revealed from a Large-Scale Biodiversity Survey

Acanthocephalans constitute a relatively small phylum of dioecious helminths that infect invertebrate intermediate and vertebrate paratenic and definitive hosts. Like most parasites, acanthocephalans are usually overlooked in biodiversity studies, although they can have significant impacts on their host’s health and the structure of surrounding communities. In this study, we present morphological and molecular data from an extensive biodiversity survey of acanthocephalans infecting a range of marine animals in a coastal marine ecosystem in New Zealand. We recovered 13 acanthocephalan species infecting 32 of the 168 free-living animal species investigated, 1 of which is a new geographic record for New Zealand (Gorgorhynchoides queenslandensis), 9 of which constitute new host records, and at least 2 that are species new to science. The data presented here provide a baseline dataset to which future assessments of changes in diversity and distribution of acanthocephalans can be compared

Taxonomic quality REDESCRIPTION dataset

Detailed taxonomic quality data for original descriptions and subsequent re-descriptions of 574 helminth species

Appendix 1_Supplementary Material

Contains additional methodological details, and additional results in the form of figures and tables

Taxonomic quality MAIN dataset

Detailed taxonomic quality data for all 2366 descriptions of helminth species

Morphological and molecular characterisation of a new genus and species of acanthocephalan, Tenuisoma tarapungi n. g., n. sp. (Acanthocephala: Polymorphidae) infecting red-billed gulls in New Zealand, with a key to the genera of the Polymorphidae Meyer, 1931

Warner, LR ORCiD: 0000-0002-1587-8129Acanthocephalans of the family Polymorphidae Meyer, 1931 are cosmopolitan parasites that infect the intestines of fish-eating birds and mammals. Polymorphid acanthocephalans recovered from the intestines of red-billed gulls (Chroicocephalus scopulinus (Forster)) from the Otago coast, New Zealand, although morphologically similar to the genus Arhythmorhynchus Lühe, 1911 nevertheless have a unique molecular profile showing considerable genetic differentation, and are here diagnosed and described as Tenuisoma tarapungi n. g., n. sp. Characters which distinguish T. tarapungi include a very elongate, cylindrical hindtrunk, swollen anterior trunk with a spinose region, a secondary swelling in males only containing the testes, and hypodermal nuclei distributed throughout the length of the trunk. Molecular data (cox1, 18S, 28S) confirm that the representative of the new genus is closest to, but nonetheless strongly divergent from species of Pseudocorynosoma Aznar, Pérez-Ponce de León & Raga, 2006. Immature specimens are described and illustrated, demonstrating the extreme degree of hindtrunk inversion occurring in immature individuals of this species. We provide a key to the genera of the family Polymorphidae. © 2020, Springer Nature B.V

A new species of striped 'Ichthyophis' Fitzinger, 1826 (Amphibia: Gymnophiona: Ichthyophiidae) from Myanmar

A new species of striped ichthyophiid caecilian, 'Ichthyophis multicolor' sp. nov., is described on the basis of morphological and molecular data from a sample of 14 specimens from Ayeyarwady Region, Myanmar. The new species resembles superficially the Indian 'I. tricolor' Annandale, 1909 in having both a pale lateral stripe and an adjacent dark ventrolateral stripe contrasting with a paler venter. It differs from 'I. tricolor' in having many more annuli, and in many details of cranial osteology, and molecular data indicate that it is more closely related to other Southeast Asian 'Ichthyophis' than to those of South Asia. The caecilian fauna of Myanmar is exceptionally poorly known but is likely to include chikilids as well as multiple species of 'Ichthyophis'

Ichthyophis multicolor Wilkinson & Presswell & Sherratt & Papadopoulou & Gower 2014, sp. nov.

<i>Ichthyophis multicolor</i> sp. nov. <p>urn:lsid:zoobank.org:act: AAE62A6A-B689-4B18-9A58-599C2993EDED</p> <p> Figs. 1 <i>–</i> 3; Tables 1 <i>–</i> 2</p> <p> <b>Holotype</b>. CAS 212264, an adult female, collected by villagers for Jens V. Vindum on 25 April 2000 from the vicinity of Mwe Hauk Village (26°16’39.2’’N, 94°45’32.5’’E; c. 10 m asl), Ayeyarwady Region, Myanmar.</p> <p> <b>Paratypes</b> (n = 13). CAS 212254 <i>–</i> 63 and 212265 <i>–</i> 67 (eleven females and two males) collected along with holotype.</p> <p> <b>Diagnosis</b>. A striped <i>Ichthyophis</i> that differs from all other striped congeners except <i>I. tricolor</i> in having a pale venter, typically with whitish markings mid-ventrally, bordered by a darker ventrolateral longitudinal stripe immediately below the pale yellowish lateral stripe on each side. Differs from <i>I. tricolor</i> in having many more AGs (> 325) and vertebrae (> 120) and TAs nearly or more than twice as far from nares than from eyes (N–TA/E–TA> 1.8).</p> <p> <b>Description of holotype</b>. Some morphometric and meristic data are given in Table 1. Mostly good condition, damaged skin dorsally c. 55 mm anterior to terminus, small depressed scar on right about eight annuli anterior to the vent, several scale pockets opened, small (<15 mm) midventral longitudinal incision 125 mm behind ST with some viscera protruding including bean-shaped eggs (9 x 6.5 mm). Head, nuchal region and trunk dorsoventrally compressed. Girth maximal throughout midbody, increasing very gradually over first 60 mm, decreasing less gradually over last c. 30 mm, L/W = c. 25. Tail upturned towards tip, short (about as long as ST–TA). Head somewhat more V- than U-shaped in dorsal view. In lateral view, distance of CM from top of head a little greater than distance from bottom of head. In ventral view, lower jaws inset from upper jaws, not notably more so anteriorly than at level of TAs. Eye equidistant from lip and top of head in lateral view, not surrounded by narrow whitish ring, eye diameter (c. 0.7 mm) distinctly larger than that of naris and TA, about equal to TP. TAs more than twice as distant from nares as from eyes, fairly close to lips (0.6 mm), on imaginary lines between nares and CMs. Naris approximately level with AM; in lateral view equidistant from top and bottom of head and ST; close to but inset from side of head in dorsal view. Teeth slender, strongly recurved, OM series extends approximately one quarter to one third the length of IM series (with three to five OMs on each side) behind posteriormost IMs. Bluntly tipped tongue strongly plicate (with approximately a dozen longitudinal ridges and grooves) posteriorly, lacking a distinct longitudinal medial groove, margin overlying all except anteriormost IMs. Choanae very narrow, distance between them six or seven times each of their greatest widths. Collar region more massive than adjacent head and body, delimited by strong constrictions. C2 slightly longer than C1 measured laterally. NG1 incomplete dorsally, not pale ventrally. NG3 with gentle middorsal anterior flexure. Four anteromedially flexed, evenly spaced TGs on C2 dorsally, first two short and third poorly developed on right, last longer, crossing midline, not extending as far as lateral stripes.</p> <p>The first three AGs widely incomplete on venter, otherwise mostly complete midventrally with five (on left) or six (on right) widely incomplete near (i.e. interrupted by) the vent, and five more narrowly incomplete on tail. Dorsally, AGs are mostly complete, those on first two thirds of the body and last eight curve anteromedially, the former gently, the latter very strongly angulate and narrowly incomplete (giving the appearance of a notch) at midline. Ventrally, anterior AGs angulate, degree of posteromedial curvature increasing from two to 2.5 times the length of an annulus at midbody, decreasing posteriorly, orthoplicate by 36th AG anterior to vent. The last few annuli shorter. The terminus ends in a short (1.3 mm) cap, approximately the length of the three preceding tail annuli or two body annuli.</p> <p>Small (0.6 x 0.4 mm) scattered scales present in a single row in very shallow pocket of first AG on dorsum; posteriorly, four to five rows of large (1.7 x 1.8 mm) scales present in very deep pockets on dorsum, reducing to deep pockets with three to four scale rows on the venter. Margins of vent slightly elevated, formed of twelve main denticulations, six on each side, with some irregular subdivisions. No associated papillae.</p> <p>In preservation, dorsum brownish grey, more grey on head. A distinct pale spot, wider than long (4.5 x 4 mm), forming a disc around the vent. Narrow, irregular, pale yellowish bilateral stripes, extend unbroken from just in front of CMs to the fifth or sixth last annulus, fading gradually on first annulus behind the vent, almost broken on C2, not visible ventrally on collars, not connecting with or curving towards disc. Immediately below each lateral stripe, running from C2 to the level of the vent, a mostly slightly narrower brown line, a little paler than the dorsal colour, with a gradual but rapid transition to a much paler tan colour that predominates on the venter but which is interrupted by small whitish patches midventrally. Narrow, pale lines along upper margins of lower jaw. TPs and ST pale. Pale midventral line extends across nuchal region to the level of CMs. Except where crossing pale lateral stripes, AGs appear mostly paler than adjacent skin, especially on venter.</p> <p> <b>Variation</b>. Morphometric and meristic data for the type series are given in Table 1. The sample is trimodal in total length, with eight specimens less than 200 mm, five greater than 350 mm and one at 256 mm. Relative overall proportions (L/W = 25.1 to 28.4) and some features of the head (N– TA /E <i>–</i> TA = 1.9 to 2.6; E <i>–</i> ST/E <i>–</i> E = 1.0 to 1.1) show no correlation with total length and are seemingly unaffected by growth. In contrast, there are some substantial differences related to size. For example, W/S ranges from 4.4 to 5.4 in the eight smallest specimens and from 6.1 to 7.2 in larger specimens, indicating that the width of the stripe does not grow as fast as the width of the body. Similar allometries are apparent in the relative lengths of the head (L/H) and of the tail (L/ T), and the tail appears to lengthen more slowly than the head. The sample includes only two males (both small), and we can reject the hypothesis that it is an unbiased sample from a population with an even sex ratio (<i>p</i> = 0.0129, two-tailed binomial test). The five largest females all have large yolky eggs and all other females have small, non-yolky eggs (<0.5 mm) and might therefore be considered subadult.</p> <p>The tail is upturned only in the holotype. All paratypes have the stripe beginning closer to the eye than in the holotype, with some slight downturn of the stripe near the vent, and pale markings on the throat are not apparent in CAS 212255. Ventral colour varies substantially. All specimens have dark stripes immediately below the pale lateral stripes that give way to a paler tan ground colour on the venter, and all but one (CAS 212257) have some white mid-ventrally, either as patches or forming an irregular but unbroken stripe that may be very broad (e.g. CAS 212267). In general, the colours are a little more intense in the smaller specimens. Scales are less well developed in the smallest specimens, with no scales in anteriormost annuli and only a single scale row in shallow pockets at midbody and posteriorly in the smallest paratype (CAS 212259). The right naris of the largest paratype (CAS 212267) is malformed and especially large. Larger specimens have more teeth in all series but the relative numbers between series does not vary much with size.</p> <p> <b>Molecular systematics.</b> There is very little variation among the eight specimens of <i>Ichthyophis multicolor</i> sequenced for the three mt gene fragments (mean nucleotide p-distance <i>16s</i>: 0.0008, cytb: 0.0010; no variation in <i>12s</i>), consistent with the interpretation that they are conspecific. Visual inspection of transition and transversion plots (not shown) indicated substantial saturation of <i>cytb</i> third codon positions across the multiple alignment. Partitioning by gene and codon position was favoured over partitioning by gene only in both ML and BI analyses, but the different partitioning schemes had little effect on the phylogenetic results (Fig. 2) which are very similar to those reported by Gower <i>et al.</i> (2002) in that sampled South Asian <i>Ichthyophis</i> are paraphyletic with respect to the monophyletic Southeast Asian <i>Ichthyophis</i> and the relationships among sampled peninsular Indian (<i>I. beddomei</i> Peters 1879, <i>I. tricolor</i>) and Sri Lankan (<i>I. glutinosus</i> L, <i>I. orthoplicatus</i> Taylor 1960) <i>Ichthyophis</i> are not particularly well-supported. <i>I. multicolor</i> is distinct genetically from other sampled species, and is recovered as sister to all other sampled Southeast Asian <i>Ichthyophis</i>.</p> <p> <b>Cranial and mandibular osteology.</b> A reconstruction of the skull and mandible of one large, female paratype (CAS 212266) of <i>Ichthyophis multicolor</i> is shown in Figure 3 and similar illustrations of <i>Ichthyophis kohtaoensis</i> Taylor 1960 (a ‘typical’, or at least not obviously unusual, Southeast Asian congener) and <i>I. tricolor</i> (the most similarly coloured congener) are shown in Figures 4 and 5. There are no differences between these species and the type species of the genus, <i>I. glutinosus</i>, in terms of the number of separate skull bones and their general arrangement (Wilkinson <i>et al.</i> 2011: fig 5). Comparison of these three reconstructions (Figs. 3 <i>–</i> 5) immediately suggests several notable differences among the three species. However, some of these differences do not stand scrutiny as interspecific because they are variable among the other specimens examined. Thirteen characters that, based on our sampling, do represent interspecific differences separating one of the three species are reported in Table 2. Several of these differences are substantial and obvious, such as the relative size of teeth in the outer rows, and whether the tentacular canal is open within the maxillopalatine or roofed with bone.</p> <p> Notable differences among the three specimens illustrated in Figs. 3 <i>–</i> 5 which vary within species are: the presence or absence of prefrontal-septomaxilla contact; the relative size of the upper temporal fenestra; the relative breadth of the pterygoid in palatal view; the relative width of the skull roof level with the parietal-frontal suture. In a simple count of similarities summarized in Table 2, <i>Ichthyophis multicolor</i> and <i>I. tricolor</i> are about as similar to each other as are <i>I. multicolor</i> and <i>I. kohtaoensis</i>, with the least similar pair of species being <i>I. tricolor</i> and <i>I. kohtaoensis</i>.</p> <p> <b>Etymology</b>. Named for its having more distinct colours than most other <i>Ichthyophis</i>. For nomenclatural purposes the specific epithet is considered to be a noun in apposition.</p> <p> <b>Suggested English name</b>. Colourful Ichthyophis or Colourful Ich.</p> <p> <b>Distribution and natural history</b>. This species is known only from the type locality. Specimens were collected on the surface after heavy rain from an area of secondary forest and agriculture. The soil was sandy and hard packed. Local people brought the field team to the locality in response to questions about where ichthyophiids could be found. Although the type series includes no larval specimens it seems very likely that the species, like all other <i>Ichhyophis</i> as far as is known, is oviparous with an aquatic larval stage. This life history is also suggested by the large size of the unlaid eggs (e.g. Wilkinson & Nussbaum 1998).</p>Published as part of <i>Wilkinson, Mark, Presswell, Bronwen, Sherratt, Emma, Papadopoulou, Anna & Gower, David J., 2014, A new species of striped Ichthyophis Fitzinger, 1826 (Amphibia: Gymnophiona: Ichthyophiidae) from Myanmar, pp. 45-58 in Zootaxa 3785 (1)</i> on pages 47-53, DOI: 10.11646/zootaxa.3785.1.4, <a href="http://zenodo.org/record/4910742">http://zenodo.org/record/4910742</a&gt

Biases in parasite biodiversity research: why some helminth species attract more research than others

As the number of known and described parasite species grows every year, one might ask: how much do we actually know about these species beyond the fact they exist? For free-living taxa, research effort is biased toward a small subset of species based on their properties or human-centric factors. Here, using a large data set on over 2500 helminth parasite species described in the past two decades, we test the importance of several predictors on two measures of research effort: the number of times a species description is cited following its publication, and the number of times a species’ name is mentioned in the scientific literature. Our analysis highlights some taxonomic biases: for instance, descriptions of acanthocephalans and nematodes tend to receive more citations than those of other helminths, and species of cestodes are less frequently mentioned in the literature than other helminths. We also found that helminths infecting host species of conservation concern receive less research attention, perhaps because of the constraints associated with research on threatened animals, while those infecting host species of human use receive greater research effort. Intriguingly, we found that species originally described by many co-authors subsequently attract more research effort than those described by one or few authors, and that research effort correlates negatively with the human population size of the country where a species was discovered, but not with its economic strength, measured by its gross domestic product. Overall, our findings reveal that we have conducted very little research, or none at all, on the majority of helminth parasite species following their discovery. The biases in study effort we identify have serious implications for future research into parasite biodiversity and conservation