Exploring species boundaries with multiple genetic loci using empirical data from non-biting midges

Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction, and haploweb calculation

Motivation

Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other datasets in the framework of integrative taxonomy. In diploid organisms, this often requires separating (phasing) sequences with heterozygotic positions, and typically separate programs are required for phasing, reformatting of input files, and haplotype network construction. We therefore developed Hapsolutely, a user-friendly program with an ergonomic graphical user interface that integrates haplotype phasing from single-locus sequences with five approaches for network/genealogy reconstruction.

Results

Among the novel options implemented, Hapsolutely integrates phasing and graphical reconstruction steps of haplotype networks, supports input of species partition data in the common SPART and SPART-XML formats, and calculates and visualizes haplowebs and fields for recombination, thus allowing graphical comparison of allele distribution and allele sharing among subsets for the purpose of species delimitation. The new tool has been specifically developed with a focus on the workflow in alpha-taxonomy, where exploring fields for recombination across alternative species partitions may help species delimitation.

Availability and implementation

Hapsolutely is written in Python, and integrates code from Phase, SeqPHASE, and PopART in C++ and Haxe. Compiled stand-alone executables for MS Windows and Mac OS along with a detailed manual can be downloaded from https://www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/Hapsolutely).

Fauna and taxonomy of Diamesinae (Diptera, Chironomidae) from the Caucasus, with a morphological description and DNA barcoding of new taxa and a discussion of diagnostic problems for Diamesa Meigen and Pseudodiamesa Goetghebuer

As a result of the revision of adult males as well as available literature data, 26 species of the subfamily Diamesinae are registered for the Caucasus, belonging to 5 genera. Four species are recorded for the first time for this region, one species, D. elbrusica sp. nov., and one subspecies, D. sakartvella gidanica subsp. nov., are new to science and are described. Six species are classified as endemics of the Caucasus. Distribution of other species of Caucasian Diamesinae is discussed. DNA barcodes of 102 specimens and 20 species of four genera, Boreoheptagyia Brundin, Diamesa Meigen, Pseudodiamesa Goetghebuer and Syndiamesa Kieffer were obtained in this study. Of these, 12 species were deposed in the GenBank and BOLD systems for the first time. We have established that D. cinerella group includes D. kasymovi and probably D. lavillei whereas D. zernyi group includes D. vaillanti and D. valentinae. Highly supported phylogeny and results of species delimitation suggest the description of D. elbrusica sp. nov. and D. sakartvella gidanica subsp. nov. Ps. aff. branickii and Ps. aff. nivosa are new species based on DNA barcoding. The results of species delimitation show that genus Pseudodiamesa includes 10 (ASAP, GMYC), 14 (mPTP) or 21 (BOLD) distinct molecular taxonomic units (mOTUs) among which only Ps. stackelbergi have an undoubted species status that requires a large revision using both morphological and molecular approaches.

Integrative taxonomy delimits and diagnoses cryptic arboreal species of the Cyrtodactylusbrevipalmatus group (Squamata, Gekkonidae) with descriptions of four new species from Thailand

Species delimitation and species diagnosis must remain separate operations to avoid constructing taxonomies comprised of non-monophyletic species based on morphological similarity as opposed to phylogenetic propinquity. This is particularly true for highly specialized species such as the range-restricted upland taxa in the Cyrtodactylusbrevipalmatus group of Indochina where strong selection pressure for an arboreal lifestyle has contributed to morphologically similar but distantly related species. This in turn, has resulted in a history of erroneous taxonomies that have actually obscured rather than revealed the diversity within this group. A Bayesian phylogeny of the C.brevipalmatus group recovered at least 15 putative species-level lineages, at least seven of which are undescribed, and of which four are described herein. A total evidence morphological data set comprised of 16 normalized morphometric, 15 meristic, and seven categorical characters scored across 51 individuals was subjected to a multiple factor analysis (MFA) and an analysis of variance (ANOVA) to diagnose the putative species. These new species descriptions contribute to focusing attention to the unrealized diversity in upland tropical ecosystems, which due to climate change, are some of the most impearled ecosystems on the planet. Thus, it is paramount that taxonomies do not conflate species identities and underrepresent true diversity.

Re-evaluating the case for poecilogony in the gastropod Planaxis sulcatus (Cerithioidea, Planaxidae)

Background

Planaxis sulcatus has been touted as a textbook example of poecilogony, with members of this wide-ranging Indo-Pacific marine gastropod said to produce free-swimming veligers as well as brooded juveniles. A recent paper by Wiggering et al. (BMC Evol Biol 20:76, 2020) assessed a mitochondrial gene phylogeny based on partial COI and 16S rRNA sequences for 31 individuals supplemented by observations from the brood pouch of 64 mostly unsequenced individuals. ABGD and bGYMC supported three reciprocally monophyletic clades, with two distributed in the Indo-Pacific, and one restricted to the northern Indian Ocean and Red Sea. Given an apparent lack of correlation between clade membership and morphological differentiation or mode of development, the reported 3.08% maximum K2P model-corrected genetic divergence in COI among all specimens was concluded to represent population structuring. Hence, the hypothesis that phylogenetic structure is evidence of cryptic species was rejected and P. sulcatus was concluded to represent a case of geographic poecilogony.

Results

Our goal was to reassess the case for poecilogony in Planaxis sulcatus with a larger molecular dataset and expanded geographic coverage. We sequenced an additional 55 individuals and included published and unpublished sequence data from other sources, including from Wiggering et al. Our dataset comprised 108 individuals (88 COI, 81 16S rRNA) and included nine countries unrepresented in the previous study. The expanded molecular dataset yielded a maximum K2P model-corrected genetic divergence among all sequenced specimens of 12.09%. The value of 3.08% erroneously reported by Wiggering et al. is the prior maximal distance value that yields a single-species partition in ABGD, and not the maximum K2P intraspecific divergence that can be calculated for the dataset. The bGMYC analysis recognized between two and six subdivisions, while the best-scoring ASAP partitions recognized two, four, or five subdivisions, not all of which were robustly supported in Bayesian and maximum likelihood phylogenetic analyses of the concatenated and single gene datasets. These hypotheses yielded maximum intra-clade genetic distances in COI of 2.56–6.19%, which are more consistent with hypothesized species-level thresholds for marine caenogastropods.

Conclusions

Based on our analyses of a more comprehensive dataset, we conclude that the evidence marshalled by Wiggering et al. in support of Planaxis sulcatus comprising a single widespread, highly variable species with geographic poecilogony is unconvincing and requires further investigation in an integrative taxonomic framework.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01961-7.

Type specimen sequencing, multilocus analyses, and species delimitation methods recognize the cosmopolitan Corallina berteroi and establish the northern Japanese C. yendoi sp. nov. (Corallinaceae, Rhodophyta)

A partial rbcL sequence of the lectotype specimen of Corallina berteroi shows that it is the earliest available name for C. ferreyrae. Multilocus species delimitation analyses (ABGD, SPN, GMYC, bPTP, and BPP) using independent or concatenated COI, psbA, and rbcL sequences recognized one, two, or three species in this complex, but only with weak support for each species hypothesis. Conservatively, we recognize a single worldwide species in this complex of what appears to be multiple, evolving populations. Included in this species, besides C. ferreyrae, are C. caespitosa, the morphologically distinct C. melobesioides, and, based on a partial rbcL sequence of the holotype specimen, C. pinnatifolia. Corallina berteroi, not C. officinalis, is the cosmopolitan temperate species found thus far in the NE Atlantic, Mediterranean Sea, warm temperate NW Atlantic and NE Pacific, cold temperate SW Atlantic (Falkland Islands), cold and warm temperate SE Pacific, NW Pacific and southern Australia. Also proposed is C. yendoi sp. nov. from Hokkaido, Japan, which was recognized as distinct by 10 of the 13 species discrimination analyses, including the multilocus BPP.

Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956

Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.

Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles

Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.

DNA barcoding to characterize biodiversity of freshwater fishes of Egypt

The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity (π) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.

DNA-based species delimitation reveals cryptic and incipient species in synchronous flashing fireflies (Coleoptera: Lampyridae) of Southeast Asia

Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet fundamental knowledge about their biodiversity is lacking. Recent studies have revealed notable population-level phylogeographical structure within the Pteroptyx tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Additionally, morphological and genetic similarities between P. balingiana and P. malaccae have raised questions about the former’s validity as a distinct species. We collected samples from previously unsampled populations and assembled the most comprehensive genetic dataset for Pteroptyx to date, to characterize species boundaries within the P. tener, P. bearni and P. malaccae groups. Using a suite of species delimitation analyses, we show that P. tener along the west coast of Peninsular Malaysia (PM) is distinct from populations from the east coast and Borneo despite the absence of morphological differentiation. However, analyses could not conclusively differentiate P. bearni from Borneo and eastern PM, nor identify P. balingiana and P. malaccae as distinct species, indicating that these populations may be conspecific or represent incipient species. This study underlines the need to increase geographical, taxonomic and genetic sampling of Southeast Asian fireflies to provide a better understanding of their biodiversity.

Molecular diversity and species delimitation in the family Gasteruptiidae (Hymenoptera: Evanioidea)

Gasteruptiidae Ashmead is an easily recognised family of wasps with ∼589 described species worldwide. Although well characterised by traditional taxonomy, multiple authors have commented on the extreme morphological uniformity of the group, making species-level identification difficult. This problem is enhanced by the lack of molecular data and molecular phylogenetic research for the group. We used 187 cytochrome c oxidase subunit I (COI) barcodes to explore the efficiency of sequence data to delimitate species in Gasteruptiidae. We undertook a graphical and discussion-based comparison of six methods for species delimitation, with the success of methods judged based on known species boundaries and morphology. Both distance-based (ABGD and jMOTU threshold analysis) and tree-based (GMYC and PTP) methods compared across multiple parameters recovered variable molecular operational taxonomic units (MOTUs), ranging from 55 to 123 MOTUs. Tree-based methods tended to split known morphological species less than distance-based methods, with the single-threshold GMYC method the most concordant with known morphospecies. Our results suggest that the incorporation of molecular species delimitation techniques provides a powerful tool to assist in the interpretation of species and help direct informed decisions with taxonomic uncertainty in the family.

Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae)

The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.