Species Delimitation Research Articles

Integrative Systematics Reveals Cryptic Diversity in Paraphrynus Whip Spiders (Amblypygi: Phrynidae) from Southwestern North America

Due to their continuous growth, reclusive nature, and low vagility, the distributions and species limits of many whip spiders (Amblypygi Thorell, 1883) remain poorly understood, and much cryptic diversity remains unrecognized. Past attempts to separate the historical “forms” of Paraphrynus Moreno, 1940 into morphologically diagnosable species resulted, for example, in the division of Paraphrynus mexicanus (Bilimek, 1867) into three species—the nominotypical form, Paraphrynus cubensis Quintero, 1983, and Paraphrynus carolynae Armas, 2012. Nevertheless, the limitations of conservative morphology continue to hinder progress towards clarifying the diversity of Paraphrynus. One such example concerns P. carolynae, distributed from Arizona to central Mexico as currently defined. Through the acquisition of new, freshly collected material, the discovery of novel morphological characters, and molecular systematics analyses, it became apparent that P. carolynae comprises at least two morphologically diagnosable species. In this present contribution, the northernmost population of P. carolynae occurring in Arizona and California is described as a new species, Paraphrynus tokdod, sp. nov., raising the number of species in the genus to 22. This investigation also revealed more variation than expected in the secondary spine counts of the pedipalps and the trichobothrial counts of leg IV, previously used for species delimitation in Paraphrynus, suggesting that such characters should be used with caution.

Diving deeper into the taxonomy of the Neoscopelus species complex (Myctophiformes: Neoscopelidae) with the description of Neoscopelus serranoi sp. nov.

Previous studies have highlighted possible cryptic biodiversity in the genus Neoscopelus. This hypothesis was tested using new morphological, molecular and biogeographical data on species of this genus caught in the north Atlantic between 2010 and 2022. The information obtained has been combined with available data in an integrative approach, including a review of morphological characters reported in the ichthyological literature and DNA-based species delimitation analyses. The main outcome of the present study is the description of Neoscopelus serranoi sp. nov. from the Atlantic and southwestern Indian Oceans. The new species is morphologically very similar to Neoscopelus microchir from which differs in having a shorter anal-fin base, a shorter pelvic fin, more dorsal and pectoral-fin rays, less anal-fin rays, fewer gillrakers and fewer isthmus and lateral photophores. They also differ in geographic distribution, with the new species occurring in the Atlantic Ocean and the near southwestern Indian Ocean, whereas N. microchir was originally described from Japanese waters of the Pacific Ocean. A literature review of available morphological data between geographic areas for Neoscopelus macrolepidotus and Neoscopelus microchir showed a large intraspecific overlap and no boundaries. However, molecular species delimitation based on the mitochondrial COI gene revealed the existence of cryptic diversity in both species, with eight to ten molecular operational taxonomic units (MOTU), compared to three valid species. Neoscopelus serranoi sp. nov. was considered an independent MOTU in all analyses performed, supporting the morphological identification as a new species. These results highlight that the taxonomy of Neoscopelus is far from settled and show that a greater sampling effort is needed to resolve the uncertainties and to describe unknown putative species. This also exemplifies the virtues of integrative taxonomy in delving into the systematics of deep-sea fishes.

Voucher Specimens in Taxonomy and Simpson’s Hypodigm

The problem of specifying representative specimens to serve as vouchers or ground truth specimens for species is viewed from a perspective of object recognition based on training using exemplars recognized by personal perception. In taxonomy, an ‘exemplar’ mirrors the hypodigm concept of Simpson, which refers to certain specimens being unequivocal members of a species. His concept has been discarded in most taxonomies because he did not provide procedures that distinguished it from ‘material’ or ‘sample’. However, his underlying view of a morphospecies was of a group united by shared character resemblances, probabilistically related. On this basis, the hypodigm of a taxonomic species is here restricted to specimens demonstrated as likely belonging to one population. To raise objectivity in this task, personal perception should be supplemented by morphometric analyses, several of which are demonstrated using living and Holocene samples of the oceanic zooplankter Truncorotalia crassaformis (Galloway and Wissler) from the Atlantic and Caribbean Oceans.

Lost in synonymy: Integrative species delimitation reveals two unrecognized species of Southern Asian tree squirrels (Rodentia: Sciuridae: Callosciurinae)

Abstract We present a comprehensive integrative taxonomic review of Callosciurus caniceps and Tamiops mcclellandii as they are currently defined. This review combines published molecular evidence, craniodental morphometrics, pelage and bacular variation, evaluations of potential hybrid zones using museum specimens and citizen science photographs, and, for C. caniceps, bioacoustic evidence. Our findings lead to the recognition of two species that had been lost in synonymy and highlight future perspectives on species delimitation in Sciuridae. By comparing phenotypic differentiation across climatic and vegetation transitions and contextualizing our results with the evolutionary history of our study systems, we provide insights into distribution, ecogeographical patterns, and speciation drivers in Southeast Asian vertebrates.

DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure

Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.

First support for phylogenetically segregated ecotypes and delineating thresholds for inter‐ and intraspecific ranks in phytophagous Central Asian beetles (Coleoptera)

AbstractAs defining various taxonomic ranks, especially at and within a specific level, can often be difficult, we used an evolutionarily young group of Central Asian beetles, the genus Anoplistes, to examine the limits between species, subspecies and ecotype. The molecular data (COI genetic distance, haplotype network and species delimitation) and detailed morphology (using SEM) of taxa assigned to the rank of species, subspecies and ecotype were used to verify their taxonomic status and attempt to more precisely establish the boundaries between these concepts. The minimum threshold for the COI genetic distance between species was found to be approximately 3%, while at the threshold of 4%–5% the morphology left no doubt as to the species distinctiveness. The threshold of approximately 2% was accepted as adequate for a subspecies rank, whereas intraspecific variability among individuals of the same subspecies (including its ecotypes) ranged from 0% to 2%. A newly presented colour/elytral pattern form, possibly another ecotype of A. halodendri distributed in western Mongolia, exemplifies adaptation to different environmental conditions via ecological speciation. Our results provide support that ecotypes can form phylogenetically distinct clades. Based on the results of the haplotype network, it can be tentatively concluded that the sand ecotype was the incipient form from which further ecotypes and subspecies developed.

Soil microbial community composition by crop type under rotation diversification

BackgroundCrop rotation is an important agricultural practice that often affects the metabolic processes of soil microorganisms through the composition and combination of crops, thereby altering nutrient cycling and supply to the soil. Although the benefits of crop rotation have been extensively discussed, the effects and mechanisms of different crop combinations on the soil microbial community structure in specific environments still need to be analyzed in detail.Materials and methodsIn this study, six crop rotation systems were selected, for which the spring crops were mainly tobacco or gramineous crops: AT (asparagus lettuce and tobacco rotation), BT (broad bean and tobacco rotation), OT (oilseed rape and tobacco rotation), AM (asparagus lettuce and maize rotation), BM (broad bean and maize rotation), and OR (oilseed rape and rice rotation). All crops had been cultivated for > 10 years. Soil samples were collected when the rotation was completed in spring, after which the soil properties, composition, and functions of bacterial and fungal communities were analyzed.ResultsThe results indicate that spring cultivated crops play a more dominant role in the crop rotation systems than do autumn cultivated crops. Crop rotation systems with the same spring crops have similar soil properties and microbial community compositions. pH and AK are the most important factors driving microbial community changes, and bacteria are more sensitive to environmental responses than fungi. Rotation using tobacco systems led to soil acidification and a decrease in microbial diversity, while the number of biomarkers and taxonomic indicator species differed between rotation patterns. Symbiotic network analysis revealed that the network complexity of OT and BM was the highest, and that the network density of tobacco systems was lower than that of gramineous systems.ConclusionsDifferent crop rotation combinations influence both soil microbial communities and soil nutrient conditions. The spring crops in the crop rotation systems had stronger dominating effects, and the soil bacteria were more sensitive than the fungi were to environmental changes. The tobacco rotation system can cause soil acidification and thereby affect soil sustainability, while the complexity of soil microbial networks is lower than that of gramineous systems. These results provide a reference for future sustainable applications of rotation crop systems.

Disentangling disjunctus: an integrated analysis of the patent leather beetle, Odontotaenius disjunctus complex (Passalidae: Coleoptera) with the description of two new species

The categorical rank of species is the fundamental taxonomic unit in characterizing biodiversity, and the accurate identification of species-level lineages is vital to all fields of biological research. This is particularly true for conservation biology, where state and federal agencies make conservation assessments based on recognized species’ distribution, ecology, and demography. Currently, there are two species of bess beetle in the conterminous United States, Odontotaenius flordianus (Schuster) and O. disjunctus (Illeger). Phylogeographic studies have proposed that O. disjunctus may represent a species complex harboring cryptic diversity. This study combines multi-locus species delimitation methods and multivariate analyses of morphological characters used to distinguish O. floridanus, to assess species diversity within the O. disjunctus complex. Delimitation methods inferred four well-supported species that diverged during the Pleistocene and whose formation was driven by historical isolation associated with shifting climatic conditions. We found a correlation between increased morphological differentiation and time since divergence. We described two new species, Odontotaenius jackmanicus sp. nov., based on morphological and molecular characters, and the cryptic species, Odontotaenius cryptodisjunctus sp. nov., diagnosed exclusively on molecular characters. We propose that the morphological similarities between O. disjunctus and O. cryptodisjunctus are due to a recent speciation combined with morphological conservatism and evolutionary stasis.

A revision of recent taxonomic changes to the eyelash palm pitviper, Bothriechis schlegelii (Serpentes, Viperidae)

The taxonomy of the Bothriechis schlegelii species group has recently been expanded, nearly doubling the number of recognized species within this genus. However, the validity of these new species, defined primarily by mitochondrial DNA and without a robust evaluation of nuclear DNA and morphological data, warrants critical reassessment. This study re-examines the integrative data used in the initial analysis and employs additional visualizations of the genetic and morphological datasets. The results suggest that the genetic differences previously interpreted as species boundaries may instead reflect clinal variation, not independent lineages. Furthermore, DELINEATE species delimitation analysis and morphological assessments challenge the distinction of the proposed taxa. The findings indicate that only three species in the B. schlegelii group should be maintained as valid (B. nigroadspersus, B. schlegelii, and B. supraciliaris), while most taxa proposed by Arteaga et al. (2024) should be considered junior synonyms, or at most, as subspecies. This has significant implications for conservation priorities and resource allocation. In highlighting the need for a cautious and thorough approach to species delimitation, this study contributes to the broader discussion of taxonomic practices, the issue of taxonomic inflation, and their impact on biodiversity conservation.

Description of larvae of three Opatrini species (Coleoptera: Tenebrionidae: Blaptinae) from China, with molecular species delimitation and diagnoses

Opatrini Brullé, 1832 is the most species-rich tribe in the subfamily Blaptinae Leach, 1815. In this study, a preliminary phylogenetic relationship among 14 species of five genera of Opatrini is hypothesized based on mitochondrial gene (COI) fragment. Based on the phylogenetic topology and the results of three molecular species delimitation analyses, three larval specimens are assessed for the adults. Additionally, the larvae of these three species are described and illustrated: Gonocephalum bilineatum (Walker, 1858), Gonocephalum gracile (Bates, 1879), and Mesomorphus latiusculus Chatanay, 1917.

Combining citizen science, phylogenetics, and bioacoustics to inform taxonomy and conservation of the Near Threatened Proceratophrys paviotii (Anura, Odontophrynidae).

Herein, basel on novel data gathered by citizens scientists and specialists, we contribute to the improvement of scientific knowledge and conservation of the Near Threatened Proceratophrys paviotii in order to: 1) test for the first time the phylogenetic position and a species delimitation of P. paviotii through a molecular approach; 2) describe a larger sample of its advertisement call to properly encompass the species intraspecific variation; 3) describe for the first time the P. paviotii release call; and 4) provide novel insights on the species conservation status. Our 16S tree confidently grouped P. paviotii with P. cururu, P. renalis, and P. laticeps. The average sequence divergence between P. paviotii and its congeners ranged from 2.2% (P. laticeps) to 9.1% (P. redacta). Advertisement calls consisted of a single note with duration of 0.26-0.58 s, 17-41 pulses emitted at rate of 54.19-77.49 pulses/s and peak frequency of 775.19-947.46 Hz. Release calls consisted of a single note with duration of 0.04-0.43 s, 2-13 pulses emitted at rate of 21.17-81.58 pulses/s and peak frequency of 689.1-1,722.6 Hz. Additionally, our study strongly supports the notion that Citizen Science approaches can yield invaluable information concerning species' geographic distribution and conservation.

Molecular phylogenetic studies on Trigonella section Ellipticae (Trifolieae, Fabaceae) from India utilising nrDNA (ITS) and cpDNA (trnL–trnF & petL–psbE)

This study highlights the critical importance of species delimitation in biodiversity conservation, focusing on the poorly understood Indian Trigonella species, with focus on T. sect. Ellipticae. Despite their ecological and socio-economic significance, these species, primarily found in the northwest Himalayas, have been inadequately catalogued and preserved. Adapted to harsh, dry environments, T. sect. Ellipticae exhibits morphological traits that complicate traditional species delimitation due to significant overlap among species boundaries. To address these challenges, we integrated molecular sequence data (nrDNA ITS and cpDNA (trnL–trnF & petL–psbE)) with morphological analysis, confirming the monophyly of Trigonella and revealing distinct evolutionary lineages within T. sect. Ellipticae. While nrDNA ITS sequences alone proved insufficient for resolving species relationships, phylogenetic investigations utilizing plastid data identified three distinct clades, enhancing taxonomic clarity. The study also suggests that observed morphological variations in T. cachemiriana may be due to phenotypic plasticity rather than distinct evolutionary lineages. We propose a new combination, T. emodi var. gracilis, to better represent the diversity within this group. Overall, this research underscores the necessity of combining molecular and morphological approaches for effective species delimitation, contributing to broader biodiversity conservation efforts in India, where many species remain inadequately catalogued. As the urgency for conservation increases, refining taxonomic frameworks is essential for ensuring that conservation strategies are based on accurate biological data.

The Vitextrifolia complex (Lamiaceae) in the Philippines.

The Vitextrifolia complex in the Philippines comprises economically important medicinal species, but its taxonomic status has become ambiguous due to numerous historical nomenclatural revisions. We assembled the complete chloroplast genomes of five species belonging to this species complex to provide additional evidence for their species delimitation. Based on a detailed analysis of specimens which combined molecular and morphological data, we propose reinstating V.elmeri Moldenke and delineating V.arvensis Gentallan, Sengun & M.B.Bartolome as a new endemic species belonging to this complex. The new species is a putative hybrid between V.bicolor Willd. and V.elmeri Moldenke. The specific epithet arvensis reflects its predominantly cultivated nature, both on a commercial scale and in home gardens, as a valued medicinal plant. We also provided a key to identify the five species belonging to the V.trifolia complex in the Philippines.

Shedding light on some dark branches: The under‐appreciated diversity of gymnosome pteropods and their coiled thecosome prey in the Neotropics

AbstractHoloplanktonic organisms are thought to have enormous populations sizes, expansive geographic ranges, and low species diversity. Previous work suggests that pelagic gastropods are no exception to this generalization. However, most of these data are derived from temperate species, whereas the bulk of pteropod diversity occurs in the tropics. Here, we present DNA barcode data for COI focused on the under‐studied limacinoid, gymnosome, and pseudothecosome pteropods collected from the coastal waters of Panama. We applied four molecular species delimitation approaches to determine the number of operational taxonomic units (OTUs) identifiable from our sequences and all data available from Barcode of Life Database (BOLD) and GenBank and compared these to the Barcode Index Number generated by the BOLD. Assemble Species by Automatic Partitioning (ASAP), Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and Generalized Mixed Yule Coalescent (GMYC) methods generally gave congruent results and suggest that pteropod diversity in the tropics is significantly underrepresented both in DNA sequence databases and in the number of named OTUs. Of 42 specimens collected and sequenced, we recovered 16 OTUs, only one of which belonged to an OTU already represented in sequence databases. Neighbor‐joining trees including the previously published sequences show that in all three groups morphospecies can include genetically divergent lineages. Many very divergent (>15% from nearest neighbor) taxa are also still represented by only a single sequence, suggesting that there is a large amount of cryptic or pseudo‐cryptic diversity still to be described. To aid this future endeavor, we include some preliminary 16S data derived from new pteropod‐specific primers.

Massive citizen science sampling and integrated taxonomic approach unravel Danish cryptogam-dwelling tardigrade fauna

Tardigrade diversity and distribution are enigmatic in most parts of the globe, and only some European countries can boast of a relatively well-studied water bear fauna. However, even these suffer from the lack of genetic data, which would substantiate faunistic data and make biogeographic comparisons easier. Denmark has never been intensively and systematically researched in this regard, thus a citizen science sampling of cryptogams (mosses, liverworts, and lichens) was launched in spring 2023, aiming at a comprehensive biodiversity survey across this insular country. Nearly 700 samples were selected out of 8.000 sent to NHMD, based on the quality of samples, representativeness of various regions of Denmark, and the type of substrate to allow unravelling of potential ecological associations between tardigrades and cryptogams. Importantly, a large fraction of morphological identifications was backed up by DNA barcode data based on ITS-2 (1001 sequences), and in some cases also on COI (93 sequences) and ITS-1 (22 sequences) molecular markers, which are recognised DNA fragments used in species delimitation. We quadruple the number of known Danish limno-terrestrial tardigrade species (55 spp. reported in this paper vs. 14 spp. reported in literature so far, most of which were contentious due to the insufficient knowledge on tardigrade taxonomy), demonstrating the power of integrative taxonomy. No fewer than nine spp. are new to science. This is the first case where tardigrade fauna of an entire country is examined both from morphological and DNA barcoding data perspective.

The ornate rubbernose pleco (Siluriformes, Loricariidae, Chaetostoma), a new species from the Ucayali River Basin, Peru

A new species in the rubbernose catfish genus Chaetostoma is described from the Aguaytia, Pisqui and Palcazu Rivers, which drain the Pampa de Sacramento Region in the Ucayali River drainage of central Peru. The new species is distinguished from congeners, except C. anomalum, C. branickii, C. dorsale, C. leucomelas, C. microps, C. nudirostre, C. palmeri and C. thomsoni by having distinct, white, variably-shaped spots or vermiculations ½–2× nostril diameter on dark grey to black background on the head (vs. spots absent or black on light-coloured background). The new species is distinguished from C. anomalum, C. branickii, C. dorsale, C. microps, C. nudirostre and C. thomsoni by having highly variable, distinct white spots, vermiculations or bands ½–10× nostril diameter on the body, from C. leucomelas by having dorsal and caudal fin indistinctly and variably-patterned with zero to four bands (vs. dorsal and caudal fin consistently having five or more uniform bands) and from C. palmeri by having two predorsal plates (vs. three), supraoccipital excrescence present (vs. absent) and pelvic-fin insertion slightly posterior to dorsal-fin insertion (vs. pelvic-fin insertion at middle of dorsal-fin base). Species delimitation analyses of the COI and Cytb genes further support the recognition of this new species.

Three Mitochondrial Genomes of Chrysochroinae (Coleoptera, Buprestidae) and Phylogenetic Analyses

Three mitochondrial genomes of Chrysochroinae (Buprestidae) were sequenced and analyzed. The mitogenomes of the genera Catoxantha and Nipponobuprestis are first reportedand Chrysochroa opulenta is a first record for China. The complete mitogenomes of Catoxantha luodiana, Nipponobuprestis guangxiensis and Chrysochroa opulenta exhibit striking similarities in their lengths and composition. Specifically, their lengths are 15,594 bp, 15,775 bp and 15,587 bp, respectively. Each of these genomes encodes 37 typical mitochondrial genes. The overwhelming majority of protein-coding genes (PCGs) have the typical ATN (ATT, ATA, ATG or ATC) as the start codon and terminate with TAR (TAA or TAG) as the stop codon or an incomplete stop codon T-. Among the three mitogenomes, Leu2, Ser2 and Phe were the most frequently encoded amino acids. In the PCGs, the Ka/Ks ratio of cox1 is the lowest, whereas atp6 has the highest value. This suggests that cox1 can be used as a molecular barcode for species delimitation and phylogeny in Chrysochroinae. The phylogenetic results showed that C. luodiana and two Chrysochroa species formed a clade. Based on the topology of the phylogenetic tree, the genus Catoxantha should be reassigned as a subgenus of Chrysochroa.

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources.

Host population structure and species resolution reveal prophage transmission dynamics.

Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages, we show that most prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are cosmopolitan and the most abundant species. Prophages in the same bacterial genome are very divergent, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. This study shows how integrating the host population structure and clustering at the species level allows us to better appreciate phage diversity and its transmission dynamics.

Is it all Phacelia pinnatifida? Molecular delimitations and taxonomic revision of Phacelia sect. Glandulosae in South America based on ddRADseq

AbstractPhacelia sect. Glandulosae, with ca. 62 taxa, is the most diverse of the 11 sections of the genus Phacelia (Hydrophyllaceae). The family is largely restricted to North and Central America, but the genus Phacelia has an amphitropical distribution with nine species reported from western South America, five of which have been assigned to P. sect. Glandulosae. These species are found in arid to semi‐arid Andean habitats between 1000 and 5000 m a.s.l. Species delimitation has long been confounded for this plant group in South America by some degree of taxonomic chaos – lack of typifications, dozens of synonyms, different names used for the same taxon between different countries – and poor representation in molecular phylogenies. Here, we try to improve our understanding by employing a ddRADseq strategy to investigate phylogenetic relationships of all South American representatives of P. sect. Glandulosae based on a total of 33 sampled specimens. Both maximum likelihood and species tree inference analyses of the ddRADseq data resulted in a well‐resolved topology. All five species currently recognized in P. sect. Glandulosae in South America form a highly supported monophylum including P. nana, previously considered as belonging to P. sect. Euglypta. However, the currently recognized morphospecies form a clade with very short branch lengths indicating coalescence processes at the level of population, except for P. artemisioides, which is clearly sister to the rest. Additionally, different morphospecies and ecotypes are largely retrieved as poly‐ and/or paraphyletic. Based on these results and on re‐evaluation of the morphological characters traditionally used to delineate species within P. sect. Glandulosae, we argue that these characters are of limited diagnostic value. We recommend recognizing only two South American species within this section: polymorphic P. pinnatifida and its closely related sister species P. artemisioides. A revised formal taxonomy is provided.