By how much do we underestimate species diversity of liverworts using morphological evidence? An example from Australasian Plagiochila (Plagiochilaceae: Jungermanniopsida)

Integrative approaches to a revision of the liverwort in genus Aneura (Aneuraceae, Marchantiophyta) from Thailand

Background

The genus Aneura Dumort. is a simple thalloid liverwort with cosmopolitan distributions. Species circumscription is problematic in this genus due to a limited number of morphological traits. Two species are currently reported from Thailand, including A. maxima and A. pinguis. At the global scale, A. pinguis is considered a cryptic species, as the species contains several distinct genetic groups without clear morphological differentiation. At the same time, the identity of A. maxima remains unclear. In this work, we examined the level of diversity of Aneura species found in Thailand using both morphological and molecular data.

Methods

We measured the morphological traits and generated the molecular data (four markers: trnL-F, trnH-psbA, rbcL, and ITS2) from the Thai specimens. The concatenated dataset was then used to reconstruct phylogeny. Species delimitation with GMYC, bPTP, ASAP, and ABGD methods was performed to estimate the number of putative species within the genus.

Results

The samples of A. pinguis formed several clades, while A. maxima sequences from Poland were grouped in their clade and nested within another A. pinguis clade. We could not recover a sample of A. maxima from Thailand, even from the reported locality. Two putative species were detected among Thai Aneura samples. However, no morphological trait could distinguish the specimens from the two observed genetic groups.

Discussion

The previously observed paraphyletic nature of A. pinguis globally was also found among Thai samples, including several putative species. However, we could not confirm the identity of A. maxima from Thai specimens. The previous report could result from misidentification and problematic species circumscription within Aneura. The results highlighted the need to include multiple lines of evidence for the future taxonomic investigation of the group.

Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda)

In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.

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

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.

Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus

Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.

Rates and patterns of molecular evolution in bryophyte genomes, with focus on complex thalloid liverworts, Marchantiopsida

Plants commonly referred to as "bryophytes" belong to three major lineages of non-vascular plants: the liverworts, the hornworts and the mosses. They are unique among land plants in having a dominant haploid generation and a short-lived diploid sporophytic generation. The dynamics of selection acting on a haploid genome differs from those acting on a diploid genome: new mutations are directly exposed to selection. The general aim of this paper is to investigate the diversification rateof bryophytes - measured as silent site substitution rate representing neutral evolution (mutation rate) and the nonsynonymous to synonymous substitution rate ratio (dN/dS) representing selective evolution - and compare it with earlier studies on vascular plants. Results show that the silent site substitution rate is lower for liverworts as compared to angiosperms, but not as low as for gymnosperms. The selection pressure, measured as dN/dS, isnot remarkably lower for bryophytes as compared to other diploid dominant plants as would be expected by the masking hypothesis, indicating that other factors are more important than ploidy.

SPART: A versatile and standardized data exchange format for species partition information

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.

Three new species of Trichoderma in the Harzianum and Longibrachiatum lineages from Peruvian cacao crop soils based on an integrative approach

The hyperdiverse genus Trichoderma is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (acl1, act, rpb2, and tef1) to delimit species of two lineages of Trichoderma. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, T.awajun, sp. nov., T. jaklitschii, sp. nov., and T. peruvianum, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in Trichoderma.

Differentiation in the eastern Asian Periphyllus koelreuteriae (Hemiptera: Aphididae) species complex driven by climate and host plant

Divergent adaptation to different ecological conditions is regarded as important for speciation. For phytophagous insects, there is limited empirical evidence on species differentiation driven by climate and host plant. The recent application of molecular data and integrative taxonomic practice may improve our understanding of population divergence and speciation. Periphyllus koelreuteriae aphids feed exclusively on Koelreuteria (Sapindaceae) in temperate and subtropical regions of eastern Asia, and show morphological and phenological variations in different regions. In this study, phylogenetic and haplotype network analyses based on four genes revealed that P. koelreuteriae populations comprised three distinct genetic clades corresponding to climate and host plants, with the populations from subtropical highland regions and on Koelreuteria bipinnata host plants representing the most basal clade. These genetic lineages also showed distinct characteristics in terms of morphology and life cycle. The results indicate that P. koelreuteriae is a species complex with previously unrevealed lineages, whose differentiation may have been driven by climatic difference and host plant.

An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru

The assignment of accurate species names is crucial, especially for those with confirmed agronomic potential such as highland papayas. The use of additional methodologies and data sets is recommended to establish well-supported boundaries among species of Vasconcellea. Accordingly, six chloroplast (trnL-trnF, rpl20-rps12, psbA-trnH intergenic spacers, matK and rbcL genes) and nuclear (ITS) markers were used to delimit species in the genus Vasconcellea using phylogeny and four DNA-based methods. Our results demonstrated congruence among different methodologies applied in this integrative study (i.e., morphology, multilocus phylogeny, genetic distance, coalescence methods). Genetic distance (ABGD, SPN), a coalescence method (BPP), and the multilocus phylogeny supported 22–25 different species of Vasconcellea, including the following five new species from northern Peru: V. badilloi sp. nov., V. carvalhoae sp. nov., V. chachapoyensis sp. nov., V. pentalobis sp. nov., and V. peruviensis sp. nov. Genetic markers that gave better resolution for distinguishing species were ITS and trnL-trnF. Phylogenetic diversity and DNA-species delimitation methods could be used to discover taxa within traditionally defined species.

Dimeric and esterified sesquiterpenes from the liverwort Chiastocaulon caledonicum

This is the first chemical investigation of Chiastocaulon caledonicum, an endemic liverwort from New Caledonia. We herein present the isolation of thirteen compounds including seven undescribed sesquiterpenoids, namely four barbatane- and three myltaylane-type sesquiterpenes. The structures of these compounds were elucidated based on the interpretation of their chemical and spectroscopic/spectrometric data. Chiastocaulins A and B are the first examples of dimers based on two myltaylane units. The chemotaxonomic importance and the biosynthesis of the chiastocaulin structure are discussed. Terpenoid dimers formed via a Diels-Alder cyclization are thought to be specific to the Plagiochilaceae family.

Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta) in relation to taxonomy and geography

PREMISE

The Sphagnum recurvum complex comprises a group of closely related peat mosses that are dominant components of many northern wetland ecosystems. Taxonomic hypotheses for the group range from interpreting the whole complex as one polymorphic species to distinguishing 6-10 species. The complex occurs throughout the Northern Hemisphere, and some of the putative species have intercontinental ranges. Our goals were to delimit the complex and assess its phylogenetic structure in relation to morphologically defined species and intercontinental geography.

METHODS

RADseq analyses were applied to a sample of 384 collections from Europe, North America, and Asia. The data were subjected to maximum likelihood phylogenetic analyses and analyses of genetic structure using the software STRUCTURE and multivariate ordination approaches.

RESULTS

The S. recurvum complex includes S. angustifolium, S. fallax, S. flexuosum, S. pacificum, and S. recurvum as clades with little evidence of admixture. We also resolved an unnamed clade that is referred to here as S. "pseudopacificum." We confirm that S. balticum and S. obtusum are nested within the complex. Species with bluntly acute to obtuse stem leaf apices are sister to those with acute to apiculate leaves. Most of the species exhibit some differentiation between intraspecific population systems disjunct on different continents.

CONCLUSIONS

We recognize seven species in the amended S. recurvum complex, including S. balticum and S. obtusum, in addition to the informal clade S. "pseudopacificum." Although we detected some geographically correlated phylogenetic structure within widespread morphospecies, our RADseq data support the interpretation that these species have intercontinental geographic ranges.

LIMES: a tool for comparing species partition

Motivation

Species delimitation (SD) is on the verge of becoming a fully fledged research field in systematics, but the variety of available approaches tends to result in significant—sometimes striking—incongruences, when tested comparatively with a given taxonomic sampling.

Results

We present LIMES, an automatic calculation tool which qualitatively compares species partitions obtained by distinct SD approaches, regardless of their respective theoretical backgrounds, and even in absence of reference topology. The program implements four different previously published indexes, and allows their automated calculation.

Availability and implementation

LIMES is freely downloadable at www.limes.cnrs.fr.

Supplementary information

Supplementary data are available at Bioinformatics online.

Do mosses really exhibit so large distribution ranges? Insights from the integrative taxonomic study of the Lewinskya affinis complex (Orthotrichaceae, Bryopsida)

The strikingly lower number of bryophyte species, and in particular of endemic species, and their larger distribution ranges in comparison with angiosperms, have traditionally been interpreted in terms of their low diversification rates associated with a high long-distance dispersal capacity. This hypothesis is tested here with Lewinskya affinis (≡ Orthotrichum affine), a moss species widely spread across Europe, North and East Africa, southwestern Asia, and western North America. We tested competing taxonomic hypotheses derived from separate and combined analyses of multilocus sequence data, morphological characters, and geographical distributions. The best hypothesis, selected by a Bayes factor molecular delimitation analysis, established that L. affinis is a complex of no less than seven distinct species, including L. affinis s.str., L. fastigiata and L. leptocarpa, which were previously reduced into synonymy with L. affinis, and four new species. Discriminant analyses indicated that each of the seven species within L. affinis s.l. can be morphologically identified with a minimal error rate. None of these species exhibit a trans-oceanic range, suggesting that the broad distributions typically exhibited by moss species largely result from a taxonomic artefact. The presence of three sibling western North American species on the one hand, and four Old World sibling species on the other, suggests that there is a tendency for within-continent diversification rather than recurrent dispersal following speciation. The faster rate of diversification as compared to intercontinental migration reported here is in sharp contrast with earlier views of bryophyte species with wide ranges and low speciation rates.

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios

Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Bayesian Phylogenetics and Phylogeography (BPP) explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.

Does Calypogeia azurea (Calypogeiaceae, Marchantiophyta) occur outside Europe? Molecular and morphological evidence

Oil bodies are the unique feature of most liverworts. Their shape, color and distribution pattern in leaf and underleaf cells are important taxonomic features of the genus Calypogeia. Most species of the genus Calypogeia have pellucid and colorless oil bodies, whereas colored, including gray to pale brown, purple-brown or blue oil bodies, are rare. To date, C. azurea was the only species with blue oil bodies to have been considered as a species of the Holarctic range. This species has been noted in various parts of the northern hemisphere-from North America, through Europe to the Far East. The aim of this study was to determine the genetic diversity of C. azurea from different parts of its distribution range and to ascertain whether blue oil bodies appeared once or several times in the evolution of the genus Calypogeia. The phylogenetic analyses based on four plastid regions (rbcL, trnG, trnL, trnH-psbA) and one nuclear region (ITS2) revealed that C. azurea is presently a paraphyletic taxon, with other Calypogeia species nested among C. azurea accessions that were clustered into four different clades. Based on the level of genetic divergence (1.03-2.17%) and the observed morphological, ecological and geographical differences, the evaluated clades could be regarded as previously unrecognized species. Four species were identified: C. azurea Stotler & Crotz (a European species corresponding to the holotype), two new species from Pacific Asia-C. orientalis Buczkowska & Bakalin and C. sinensis Bakalin & Buczkowska, and a North American species which, due to the lack of identifiable morphological features, must be regarded as the cryptic species of C. azurea with a provisional name of C. azurea species NA.

Quantification of complex modular architecture in plants

Morphometrics, the assignment of quantities to biological shapes, is a powerful tool to address taxonomic, evolutionary, functional and developmental questions. We propose a novel method for shape quantification of complex modular architecture in thalloid plants, whose extremely reduced morphologies, combined with the lack of a formal framework for thallus description, have long rendered taxonomic and evolutionary studies extremely challenging. Using graph theory, thalli are described as hierarchical series of nodes and edges, allowing for accurate, homologous and repeatable measurements of widths, lengths and angles. The computer program MorphoSnake was developed to extract the skeleton and contours of a thallus and automatically acquire, at each level of organization, width, length, angle and sinuosity measurements. Through the quantification of leaf architecture in Hymenophyllum ferns (Polypodiopsida) and a fully worked example of integrative taxonomy in the taxonomically challenging thalloid liverwort genus Riccardia, we show that MorphoSnake is applicable to all ramified plants. This new possibility of acquiring large numbers of quantitative traits in plants with complex modular architectures opens new perspectives of applications, from the development of rapid species identification tools to evolutionary analyses of adaptive plasticity.

Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.