Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes

Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki)

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

Thyreophagus tauricus sp. n., a New Subcortical Mite Species (Acari: Acaridae), with a COX1 DNA Sequence Analysis of Several Economically Important Species of Thyreophagus

As part of a survey of the subcortical astigmatic mites of Crimea, we discovered a new sexual acarid species, Thyreophagus tauricus sp. n. This species was cultured in the laboratory to correlate the adult and deutonymphal stages. Using specimens obtained by these rearing experiments, we provide a detailed description of Th. tauricus (light microscopy, SEM) based on females, males and heteromorphic deutonymphs. Furthermore, to facilitate molecular identification, the entire COX1 gene was also sequenced for this and three other Palearctic species reared in the lab as pure cultures. Adults of Th. tauricus sp. n. are distinct among all other species of the genus by the presence of flattened, button-shaped or minute spiniform setae s III and IV, which are well-developed spiniform in all other known species of Thyreophagus. Heteromorphic deutonymphs of Th. tauricus are distinct from all other species of Thyreophagus by the presence of well-developed setae cm on the dorsal part of the subcapitular remnant (absent all other species). Th. tauricus is morphologically very similar to Th. corticalis; however, COX1 K2P distances between these two species were large, 19.8%. COX1 K2P distances between Th. tauricus and other species (Th. entomophagus, Th. "entomophagus" NC 066986.1, Th. calusorum, Th. corticalis) ranged between 20.1 and 24.3%. We show that the GenBank sequence of Th. "entomophagus" from China (NC 066986.1) was probably misidentified.

Horizontal transmission maintains host specificity and codiversification of symbionts in a brood parasitic host

In host-symbiont systems, interspecific transmissions create opportunities for host switches, potentially leading to cophylogenetic incongruence. In contrast, conspecific transmissions often result in high host specificity and congruent cophylogenies. In most bird-feather mite systems, conspecific transmission is considered dominant, while interspecific transmission is supposedly rare. However, while mites typically maintain high host specificity, incongruent cophylogenies are common. To explain this conundrum, we quantify the magnitude of conspecific vs. interspecific transmission in the brood parasitic shiny cowbird (Molothrus bonariensis). M. bonariensis lacks parental care, allowing the assessment of the role of horizontal transmission alone in maintaining host specificity. We found that despite frequent interspecific interactions via foster parental care, mite species dispersing via conspecific horizontal contacts are three times more likely to colonize M. bonariensis than mites transmitted vertically via foster parents. The results highlight the previously underappreciated rate of transmission via horizontal contacts in maintaining host specificity on a microevolutionary scale. On a macroevolutionary scale, however, host switches were estimated to have occurred as frequently as codivergences. This suggests that macroevolutionary patterns resulting from rare events cannot be easily generalized from short-term evolutionary trends.

Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].

KNEMIDOKOPTES MITES AND THEIR EFFECTS ON THE GRIPPING POSITION OF THE FEET OF STELLER'S JAYS (CYANOCITTA STELLERI)

Steller's Jays (Cyanocitta stelleri) with swollen legs and feet resembling the signs of scaly leg have been commonly seen around Arcata, California, US. The clinical signs are thought to be caused by knemidokoptic mites, a group of parasites specialized on avian hosts. Between February 2019 and March 2020, we analyzed the long-term database of Steller's Jays collected by Humboldt State University for trends in the prevalence of signs of scaly leg, compared the gripping position in the feet of Steller's Jays with variable signs of this condition as an index of their ability to perch, identified the mites using a partial sequence of the cytochrome oxidase subunit I gene, and examined genetic distances between mites collected from different host species both sequenced in this study and from GenBank. Overall, 27% of jays recorded in the long-term database had shown signs of scaly leg. Jays with signs captured in this study had greater variability in and a reduced degree of contraction in the gripping position of their feet compared to jays without signs, suggesting that infestation may have an impact on the host's ability to perch. The cytochrome oxidase subunit I sequence (578 base pairs) from mites collected from Steller's Jays was compared to sequences from Knemidokoptes jamaicensis, Knemidokoptes derooi, and to unidentified Knemidokoptes spp. collected from different hosts. The mites from Steller's Jays were most closely related to Knemidokoptes jamaicensis but had a relatively high sequence divergence, 7.8%, supporting the possibility that the form infesting these jays may be an undescribed species.

Traveler Mites: Population Genetic Structure of the Wing Mites Periglischrus paracaligus (Acari: Mesostigmata: Spinturnicidae)

Wing mites of the genus Periglischrus are ectoparasites exclusively associated with phyllostomid bats. These mites show high host specificity and have been studied to understand the evolutionary history of their bat hosts mainly by using a morphological variation. Through a phylogeographic approach, we analyzed the genetic diversity and population genetic structure of the ectoparasite Periglischrus paracaligus Herrin and Tipton which parasitizes Leptonycteris yerbabuenae Martínez and Villa (lesser long-nosed bat) in Mexico. By the implementation of a multilocus approach, we found that P. paracaligus populations were diverse for haplotype diversity, and had values ranging from 0.5 to 1. No genetic structuring in the P. paracaligus parasites was observed along with the distribution of the host, L. yerbabuenae, in Mexico, nor when populations or regions were compared, but our results revealed a process of historical demographic expansion in all the analyzed markers. We discuss possible scenarios that could explain the lack of population structure in the light of the data analyzed for the parasites and the biology of L. yerbabuenae, such as the interplay between parasite and host traits being responsible for the genetic make-up of parasite populations. We also inferred its phylogenetic position among wing mites parasitizing the two other species of Leptonycteris bats. Long-nosed bats' monophyly helps to explain the observed presence of distinctive clades in the wing mite's phylogeny in specific association with each long-nosed bat host species.

Ceriodaphnia (Cladocera: Daphniidae) in China: Lineage diversity, phylogeography and possible interspecific hybridization

The distribution and species/lineage diversity of freshwater invertebrate zooplankton remains understudied in China. Here, we explored the species/lineage diversity and phylogeography of Ceriodaphnia species across China. The taxonomy of this genus is under-explored. Seven morphospecies of Ceriodaphnia (C. cornuta, C. laticaudata, C. megops, C. pulchella, C. quadrangula, C. rotunda and C. spinata) were identified across 45 of 422 water bodies examined. Rather little morphological variation was observed within any single morphospecies regardless of country of origin. Nevertheless, we recognized that some or all of these morphospecies might represent species complexes. To investigate this, phylogenetic relationships within and among these morphospecies were investigated based on mitochondrial (partial cytochrome c oxidase subunit I gene) and nuclear (partial 28S rRNA gene) markers. The mitochondrial marker placed these populations in nine lineages corresponding to the morphospecies: C. laticaudata and C. pulchella were each represented by two lineages, suggesting that both are species complexes. The remaining five morphospecies were each represented by a single mtDNA lineage. Three of the nine mitochondrial lineages (belonging to C. pulchella, C. rotunda and C. megops) are newly reported and exhibited a restricted distribution within China. The nuclear-DNA phylogeny also recognized seven Ceriodaphnia taxa within China. We detected occasional mito-nuclear discordances in Ceriodaphnia taxa across China, suggesting interspecific introgression and hybridization. Our study contributes to an understanding of the species/lineage diversity of Ceriodaphnia, a genus with understudied taxonomy.

An integrative approach reveals high species diversity in the primitively segmented spider genus

Accurate species delimitation is crucial for our understanding of evolution, biodiversity and conservation. However, morphology-based species delimitation alone appears to be prone to taxonomic errors and ineffective for taxa with high interspecific morphological homogeneity or intraspecific morphological variations, as is the case for mesothele and mygalomorph spiders. Combined molecular–morphology species delimitation has shown great potential to delimit species boundaries in such ancient lineages. In the present study, molecular and morphological evidence were integrated to delimit species of the primitively segmented spider genus Songthela Ono, 2000. The cytochrome c oxidase subunit I gene (COI) was sequenced for 192 novel specimens belonging to 12 putative morphospecies. The evolutionary relationships within Songthela and the 12-morphospecies hypothesis were tested in two steps – species discovery and species validation – using four single-locus species delimitation approaches. All species delimitation analyses supported the 12-species hypothesis. Phylogenetic analyses yielded three major clades in Songthela, which are consistent with morphology. Accordingly, we assigned 19 known and 11 new species (S. aokoulong, sp. nov., S. bispina, sp. nov., S. dapo, sp. nov., S. huayanxi, sp. nov., S. lianhe, sp. nov., S. lingshang, sp. nov., S. multidentata, sp. nov., S. tianmen, sp. nov., S. unispina, sp. nov., S. xiujian, sp. nov., S. zizhu, sp. nov.) of Songthela to three species-groups: the bispina-group, the multidentata-group and the unispina-group. Another new species, S. zimugang, sp. nov., is not included in any species groups, but forms a sister lineage to the bispina- and unispina-groups. These results elucidate a high species diversity of Songthela in a small area and demonstrate that integrating morphology with COI-based species delimitation is fast and cost-effective in delimiting species boundaries. http://zoobank.org/urn:lsid:zoobank.org:pub:AF0F5B31-AFAF-4861-9844-445AE8678B67

Molecular identification and DNA barcode screening of acaroid mites in ground flour dust

Molecular identification of acaroid mites is difficult because of the scarcity of molecular data in GenBank. Here, acaroid mites collected from ground flour dust in Xi'an, China, were preliminarily morphologically classified/grouped. Universal primers were then designed to amplify and screen suitable DNA barcodes for identifying these mites. Sixty mite samples were morphologically classified into six groups. Groups 1-2 were identified to Dermatophagoides farinae and Tyrophagus putrescentiae, while Groups 3-6 were not identified to the species level. ITS2 exhibited higher efficiency in molecular identification in comparison with COI, 12S, and 16S. Groups 1-6 were identified as D. farinae, T. putrescentiae, Suidasia nesbitti, Chortoglyphus arcuatus, Lepidoglyphus destructor, and Gohieria sp., respectively. The phylogenetic results were consistent with the morphological classification. Group 6 was further identified as G. fusca according to the morphology of the reproductive foramen. We conclude that the use of ITS2 and the availability of universal primers provide an ideal DNA barcode for molecular identification of acaroid mites. The use of multiple target genetic markers in conjunction with morphological approaches will improve the accuracy of Acaridida identification.

Hiding in plain sight: DNA barcoding suggests cryptic species in all ‘well-known’ Australian flower beetles (Scarabaeidae: Cetoniinae)

DNA barcode data is presented for Australian cetoniine flower beetles to aid with species discovery and guide revisionary taxonomy. Sequences of the COI gene’s DNA barcode region were acquired from 284 cetoniine specimens, covering 68 described species and 33 genera. This equates to 48% of the known species and 83% of the genera which occur in Australia. Results suggest up to 27 putative undescribed species in our sample, only 11 of which were suspected to be undescribed before this study, leaving 16 unexpected (“cryptic”) species. The Australian cetoniine fauna may hence be increased by up to 19%. An unanticipated result of the work is that each of the five most visible and commonly collected Australian cetoniine species, Eupoecila australasiae (Donovan, 1805), Neorrhina punctatum (Donovan, 1805), Glycyphana (Glycyphaniola) stolata (Fabricius, 1781), Chondropyga dorsalis (Donovan, 1805) and Bisallardiana gymnopleura (Fischer, 1823), have unexpectedly high diversity in DNA barcode sequences and were consequently split into multiple clusters, possibly indicating the presence of cryptic species.

Systematics of the Peripatopsis clavigera species complex (Onychophora : Peripatopsidae) reveals cryptic cladogenic patterning, with the description of five new species

During the present study, DNA sequence data, gross morphology and scanning electron microscopy (SEM) were used to examine cryptic species boundaries in the velvet worm, Peripatopsis clavigera species complex, from the southern Cape Afrotemperate forest belt in South Africa. Sequence data were generated for the mitochondrial COI and the nuclear 18S rRNA loci and phylogenetically analysed using both a Bayesian inference and a maximum-likelihood approach. Both the COI data and the combined DNA sequence topology (COI+18S) revealed the presence of five clades within the Peripatopsis clavigera species complex, and revealed that specimens from Tulbagh were distantly related and represented a sixth clade. The evolutionary distinction of the five clades was corroborated to varying degrees by the four species-delimitation methods (ABGD, PTP, GMYC and STACEY); however, both the gross morphological data and the SEM provided limited diagnostic differences between the five clades. Furthermore, the COI haplotype network and phylogeographic analyses provided evidence of genetic isolation between lineages that are currently syntopic. The distribution of genealogically exclusive and widespread maternal lineages was atypical among velvet worms and did not reflect the general trend of genetic and geographical isolation. Instead, lineages exhibited admixture among localities, a result most likely due to fluctuations in climatic conditions affecting the southern Cape Afrotemperate forest during the Pliocene–Pleistocene period as evident from our divergence time estimations. Four novel, narrow-range endemic species – P. ferox, sp. nov., P. mellaria, sp. nov., P. edenensis, sp. nov. and P. mira, sp. nov. – are described within the P. clavigera species complex, whereas the Tulbagh specimens are described as P. tulbaghensis, sp. nov. Collectively, these results demonstrate that Peripatopsis likely contains several undescribed species.

Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus

With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.

Persistence of single species of symbionts across multiple closely-related host species

Some symbiont species are highly host-specific, inhabiting only one or a very few host species, and typically have limited dispersal abilities. When they do occur on multiple host species, populations of such symbionts are expected to become genetically structured across these different host species, and this may eventually lead to new symbiont species over evolutionary timescales. However, a low number of dispersal events of symbionts between host species across time might be enough to prevent population structure and species divergence. Overall, processes of evolutionary divergence and the species status of most putative multi-host symbiont systems are yet to be investigated. Here, we used DNA metabarcoding data of 6,023 feather mites (a total of 2,225 OTU representative sequences) from 147 infracommunities (i.e., the assemblage consisting of all mites of different species collected from the same bird host individual) to investigate patterns of population genetic structure and species status of three different putative multi-host feather mite species Proctophyllodes macedo Vitzthum, 1922, Proctophyllodes motacillae Gaud, 1953, and Trouessartia jedliczkai (Zimmerman, 1894), each of which inhabits a variable number of different closely related wagtail host species (genus Motacilla). We show that mite populations from different host species represent a single species. This pattern was found in all the mite species, suggesting that each of these species is a multi-host species in which dispersal of mites among host species prevents species divergence. Also, we found evidence of limited evolutionary divergence manifested by a low but significant level of population genetic structure among symbiont populations inhabiting different host species. Our study agrees with previous studies showing a higher than expected colonization opportunities in host-specific symbionts. Indeed, our results support that these dispersal events would allow the persistence of multi-host species even in symbionts with limited dispersal capabilities, though additional factors such as the geographical structure of some bird populations may also play a role.

Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia)

BACKGROUND

Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library.

METHODS

We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels.

RESULTS

A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6-6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels.

CONCLUSIONS

Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.

Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda)

The recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.