Multilocus Phylogeny Research Articles

Integrative taxonomy and biogeographic affinities of the first freshwater sponge and mollusc association discovered in tropical Asia

Diverse associations of freshwater sponges with molluscs were recently described from the Xingu River, Amazon Basin. However, such associations in other parts of the world are almost unknown. Here, we report on the discovery of epifaunal associations of a freshwater sponge (Corvospongilla, Spongillidae) with a byssus-attaching clam (Limnoperna, Mytilidae) and a freshwater mussel (Hyriopsis, Unionidae) in tropical Asia (Mun River, Thailand). We used this association as a model system to show how the application of an integrative taxonomic approach can change modern views on the taxonomic status and biogeographic affinities of tropical invertebrates in a rather small sample. The freshwater sponge from the Mun River morphologically corresponds to the nominal taxon Corvospongilla siamensis but it is identical to Corvospongilla ultima from the Kaladan River, western Myanmar, based on the sequences of five DNA markers and the PTP species delimitation modeling. Hence, the first species is considered here to be a junior synonym of C. ultima. Conversely, the Limnoperna clam from the Mun River is found to be distant phylogenetically from the invasive golden mussel Limnoperna fortunei based on the sequences of three DNA markers. We therefore restore Limnoperna siamensis stat. rev. as a valid species. Our time-calibrated multi-locus phylogeny reveals that the split between L. siamensis and L. fortunei most likely occurred at the Miocene—Pliocene boundary. Finally, the freshwater mussel Hyriopsis khoratensis is an abundant species endemic to the Mun River. Our novel data highlight that associations of freshwater sponges with bivalves are present in Asia but were historically overlooked there and that the Mekong's sponge-mollusc association can be considered analogous to those discovered in South America.

Genetic diversity of Colletotrichum lupini and its virulence on white and Andean lupin

Lupin cultivation worldwide is threatened by anthracnose, a destructive disease caused by the seed- and air-borne fungal pathogen Colletotrichum lupini. In this study we explored the intraspecific diversity of 39 C. lupini isolates collected from different lupin cultivating regions around the world, and representative isolates were screened for their pathogenicity and virulence on white and Andean lupin. Multi-locus phylogeny and morphological characterizations showed intraspecific diversity to be greater than previously shown, distinguishing a total of six genetic groups and ten distinct morphotypes. Highest diversity was found across South America, indicating it as the center of origin of C. lupini. The isolates that correspond to the current pandemic belong to a genetic and morphological uniform group, were globally widespread, and showed high virulence on tested white and Andean lupin accessions. Isolates belonging to the other five genetic groups were mostly found locally and showed distinct virulence patterns. Two highly virulent strains were shown to overcome resistance of advanced white lupin breeding material. This stresses the need to be careful with international seed transports in order to prevent spread of currently confined but potentially highly virulent strains. This study improves our understanding of the diversity, phylogeography and pathogenicity of a member of one of the world’s top 10 plant pathogen genera, providing valuable information for breeding programs and future disease management.

Molecular reassessment of diaporthalean fungi associated with strawberry, including the leaf blight fungus, Paraphomopsis obscurans gen. et comb. nov. (Melanconiellaceae)

ABSTRACTPhytopathogenic fungi in the order Diaporthales (Sordariomycetes) cause diseases on numerous economically important crops worldwide. In this study, we reassessed the diaporthalean species associated with prominent diseases of strawberry, namely leaf blight, leaf blotch, root rot and petiole blight, based on molecular data and morphological characters using fresh and herbarium collections. Combined analyses of four nuclear loci, 28S ribosomal DNA/large subunit rDNA (LSU), ribosomal internal transcribed spacers 1 and 2 with 5.8S ribosomal DNA (ITS), partial sequences of second largest subunit of RNA polymerase II (RPB2) and translation elongation factor 1-α (TEF1), were used to reconstruct a phylogeny for these pathogens. Results confirmed that the leaf blight pathogen formerly known as Phomopsis obscurans belongs in the family Melanconiellaceae and not with Diaporthe (syn. Phomopsis) or any other known genus in the order. A new genus Paraphomopsis is introduced herein with a new combination, Paraphomopsis obscurans, to accommodate the leaf blight fungus. Gnomoniopsis fragariae comb. nov. (Gnomoniaceae), is introduced to accommodate Gnomoniopsis fructicola, the cause of leaf blotch of strawberry. Both of the fungi causing leaf blight and leaf blotch were epitypified. Fresh collections and new molecular data were incorporated for Paragnomonia fragariae (Sydowiellaceae), which causes petiole blight and root rot of strawberry and is distinct from the above taxa. An updated multilocus phylogeny for the Diaporthales is provided with representatives of currently known families.

Contribution to Chaetosphaeriaceae—Kionochaeta setosimplicia sp. nov. from Thailand

Species of Kionochaeta are saprobes commonly associated with decaying plant materials. As a part of surveys on freshwater microfungi, Kionochaeta-like taxon was found on a submerged decaying twig at a rivulet in the protected forest area of Khao Kheow Open Zoo (KKOZ), eastern Thailand. This taxon is microscopically similar to Kionochaeta, but clearly differs by its accessory lateral setiform branches and sterile setae arising beside the conidiophores. Multi-locus phylogenies inferred from four combined loci (SSU, ITS, LSU and RPB2) demonstrated that this taxon clustered as a unique clade with Kionochaeta species (Chaetosphaeriaceae, Chaetosphaeriales). Therefore, we introduce this taxon as K. setosimplicia, and it is phylogenetically close to K. castaneae, K. ramifera and K. pughii. Kionochaeta setosimplicia is separated from K. microspora and K. spissa. In Kionochaeta clade 1, K. nanophora forms a basal taxon. Kionochaeta ivoriensis forms a distinct Kionochaeta clade 2 distant from other Kionochaeta.

A new species of Pila (Gastropoda: Ampullariidae) from Mizoram, India

ABSTRACT Family Ampullariidae consists of 11 genera of freshwater snails distributed pan-tropically in the Old and the New World. One of the ampullarid genera, Pila, is distributed in Africa and Asia and consists of 28 species. Here we describe the sixth member of the genus Pila from India. Pila mizoramensis n. sp. was collected from the Northeast Indian state of Mizoram. We adopted an integrative taxonomic approach to describe this species. First, a multilocus phylogeny of the genus was built to determine its placement in the tree. Then we used pairwise distance in the cytochrome oxidase I gene to compare its divergence from its congeners. Finally morphometric data was used to show that this hill stream species of Pila does not overlap with other hill stream species in morphometric space. The morphology of the species is also discussed in detail. With the advent of molecular tools in taxonomy a plethora of new species have been described from India in the last few decades. We add this newest member of genus Pila to the growing list.ZooBank registration: http://www.zoobank.org/urn:urn:lsid:zoobank.org:pub:0ED40557-4595-49E5-99A6-8A684C5D6AB3

Characterization of a new strain of Metarhizium novozealandicum with potential to be developed as a biopesticide

ABSTRACT The fungal species Metarhizium novozealandicum, that occurs only in New Zealand and Australia has been poorly studied. In this work, a new strain of M. novozealandicum isolated from a larva of Wiseana sp. is described based on morphology, genomic multilocus (ITS, EF-1α and β-tubulin) phylogeny, growth in different culture media and insecticidal activity. The isolate AgR-F177 was clustered in the same clade with M. novozealandicum. AgR-F177 colonies developed faster on Sabouraud Dextrose Agar (SDA) than on Potato Dextrose Agar (PDA) when incubated at 25°C, with no growth observed at 30°C on either media. Conidia yield on an oat-based medium in semisolid fermentation was 7.41 x 108conidia/g of substrate and a higher yield of 1.68 x 109conidia/g of substrate was obtained using solid fermentation on cooked rice. AgR-F177 formed microsclerotia (MS) in liquid fermentation after 7 days reaching the maximum yield of 3.3 × 103 MS/mL after 10 days. AgR-F177 caused mortality in Wiseana copularis, Costelytra giveni and Plutella xylostella larvae with efficacies up to 100%, 69.2%, and 45.7%, respectively. The ease of production of AgR-F177 with different fermentation systems and its pathogenicity against different insect pests reveal its potential as a new biopesticide.

A subterranean adaptive radiation of amphipods in Europe

Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.

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

ABSTRACT 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.

Phytophthora mediterranea sp. nov., a New Species Closely Related to Phytophthora cinnamomi from Nursery Plants of Myrtus communis in Italy

Monitoring surveys of Phytophthora related diseases in four forest nurseries in Italy revealed the occurrence of fourteen Phytophthora species to be associated with collar and root rot on fourteen plants typical of Mediterranean and alpine regions. In addition, a multilocus phylogeny analysis based on nuclear ITS and ß-tubulin and mitochondrial cox1 sequences, as well as micromorphological features, supported the description of a new species belonging to the phylogenetic clade 7c, Phytophthora mediterranea sp. nov. Phytophthora mediterranea was shown to be associated with collar and root rot symptoms on myrtle seedlings. Phylogenetically, P. mediterranea is closely related to P. cinnamomi but the two species differ in 87 nucleotides in the three studied DNA regions. Morphologically P. mediterranea can be easily distinguished from P. cinnamomi on the basis of its smaller sporangia, colony growth pattern and higher optimum and maximum temperature values. Data from the pathogenicity test showed that P. mediterranea has the potential to threaten the native Mediterranean maquis vegetation. Finally, the discovery of P. cinnamomi in alpine nurseries, confirms the progressive expansion of this species towards cold environments, probably driven by climate change.

Cryptic diversity, multilocus phylogeny, and pathogenicity of cercosporoid fungi associated with common bean and cowpea

AbstractIn recent years, common bean (Phaseolus vulgaris) and cowpea (Vigna unguiculata) plants in the north of Iran have exhibited symptoms resembling Cercospora leaf spot (CLS) disease. This study was initiated to elucidate the taxonomy and pathogenicity of cercosporoid taxa associated with leaf spot diseases of these two legume crops in Iran. A total of 138 samples with CLS symptoms were collected from cultivated common bean and cowpea species in northern Iran and subjected to microscopic examination, resulting in identification of 98 Cercospora and 59 Pseudocercospora samples. A six‐locus phylogenetic analysis (ITS, actA, tef1, gapdh, his3, and cmdA) coupled with examination of the morphology of 42 representative isolates from these samples confirmed that several cercosporoid fungi occur on common bean and cowpea in Iran. Five Cercospora species (C. iranica, C. cf. flagellaris, Cercospora sp. G, Cercospora sp. T, and C. vignigena) and two Pseudocercospora species (P. griseola f. griseola and P. cf. cruenta) were found; of these, C. cf. flagellaris was the dominant species, occurring on both common bean and cowpea. Pathogenicity tests confirmed that all seven species could infect leaves of common bean and/or cowpea. This is the first report of C. iranica, Cercospora sp. G, and Cercospora sp. T associated with common bean and/or cowpea in the world. In addition, C. vignigena was recorded for the first time in Iran. Results achieved in this study will assist strategies for the management of CLS disease of common bean and cowpea.

The Plant Family Asteraceae Is a Cache for Novel Fungal Diversity: Novel Species and Genera With Remarkable Ascospores in Leptosphaeriaceae.

In a cursory survey of fungi on Asteraceae in Yunnan Province, China, we report fungal species belonging to the family Leptosphaeriaceae (Pleosporales, Dothideomycetes). Two novel species have remarkable ascospores that are unusual for sexual ascomycetes. Multilocus phylogeny of large subunit, small subunit, and internal transcribed spacer sequence data showed one to be a novel genus, while the other is a new species. Praeclarispora artemisiae gen. et sp. nov. is introduced and is typical of Leptosphaeriaceae, but has unusual fusiform, versicolor ascospores with a brown median cell. Sphaerellopsis artemisiae sp. nov. has scolecosporous ascospores with deeply constricted septa that split into two parts, which resembles S. isthmospora but differs by ascospore dimension and molecular data. In addition, Plenodomus artemisiae is reported as a new collection from dead stems of Artemisia argyi in Qujing City. Plenodomus sinensis is reported as a new host record from Ageratina adenophora. All taxa are illustrated and described based on evidence of taxonomy and phylogeny.

Introducing a new pleosporalean family Sublophiostomataceae fam. nov. to accommodate Sublophiostoma gen. nov.

Collections of microfungi on bamboo and grasses in Thailand revealed an interesting species morphologically resembling Lophiostoma, but which can be distinguished from the latter based on multi-locus phylogeny. In this paper, a new genus, Sublophiostoma is introduced to accommodate the taxon, S. thailandica sp. nov. Phylogenetic analyses using combined ITS, LSU, RPB2, SSU, and TEF sequences demonstrate that six strains of the new species form a distinct clade within Pleosporales, but cannot be assigned to any existing family. Therefore, a new family Sublophiostomataceae (Pleosporales) is introduced to accommodate the new genus. The sexual morph of Sublophiostomataceae is characterized by subglobose to hemisphaerical, ostiolate ascomata, with crest-like openings, a peridium with cells of textura angularis to textura epidermoidea, cylindric-clavate asci with a bulbous or foot-like narrow pedicel and a well-developed ocular chamber, and hyaline, fusiform, 1-septate ascospores surrounded by a large mucilaginous sheath. The asexual morph (coelomycetous) of the species are observed on culture media.

Diaporthe taoicola and D. siamensis, Two New Records on Citrus sinensis in China

Two Diaporthe species isolated from fruit of Citrus sinensis in China were characterized based on morphology and multilocus phylogeny of ITS, tef1, and tub2 gene sequences. The phylogeny indicated that the two species match Diaporthe taoicola and D. siamensis. A critical examination of phenotypic characteristics confirmed the phylogenetic results. Diaporthe taoicola was morphologically characterized by producing Alpha conidia with tapering toward both ends. Meanwhile, D. siamensis produced cylindrical or ellipsoidal Alpha conidia with two oil drops. Pathogenicity tests revealed that both species were pathogenic to fruit of C. sinensis. To our knowledge, the two species were firstly reported on Citrus sinensis in China.

Diversification of Prochilodus in the eastern Brazilian Shield: Evidence from complete mitochondrial genomes (Teleostei, Prochilodontidae)

The Neotropical fish genus Prochilodus includes five species occurring in the main drainages of the eastern Brazilian Shield: P. argenteus, P. costatus, P. lineatus, P. harttii, and P. vimboides. Multi and single locus phylogenies have questioned the monophyly of P. costatus and P. lineatus, and the biogeographic history of these species in the Brazilian Shield has never been explored. We characterized new mitogenomes for these species to reconstruct their evolutionary history, estimated the timing of Prochilodus cladogenesis, and discussed the implications of past geologic events on species diversification. The phylogeny supports the monophyly of both P. costatus and P. lineatus, and indicates a Miocene divergence of P. vimboides, much earlier than subsequent species diversification. The Early Pleistocene split of P. argenteus and P. harttii (~2.1 million years ago—MYA) is hypothesized to be related to recent Quaternary reactivations of the Rio Araçuaí Fault that promoted river captures between the eastern tributaries of the São Francisco basin and the upper Rio Jequitinhonha in the Serra do Espinhaço mountain range. The time-calibrated phylogeny also indicated a subsequent split of P. costatus and P. lineatus (~1.1 MYA) likely due to Quaternary activities of the Upper Rio São Francisco crustal discontinuity and Estrela Fault that catalyzed river captures between the upper Rio São Francisco and the Rio Grande of the Paraná basin in the Serra da Canastra mountain range. These results provide a temporal context for the diversification of Prochilodus and bring new insights to further study the historical biogeography of other riverine fish groups along the upland basins of the eastern Brazilian Shield.

Morpho-molecular characterization of Discosia ravennica sp. nov. and a new host record for Sporocadus rosigena.

Collections of fungal samples from two dead leaf specimens from Italy were subjected to morphological examination and phylogenetic analyses. Two coelomycetous taxa belonging to two different genera in Xylariomycetidae, Sordariomycetes, namely Discosia and Sporocadus, were identified. The Discosia taxon is revealed as a new species and is herein introduced as Discosia ravennicasp. nov. while the Sporocadus taxon is identified as Sporocadus rosigena. Multi-locus phylogeny based on DNA sequence data of the large subunit (LSU) and internal transcribed spacer (ITS) of nuclear ribosomal genes, β-tubulin (β-tub) and RNA polymerase II second largest subunit (rpb2) showed that D. ravennica is related to D. neofraxinea but it forms an independent lineage that supports its new species status. The new taxon also differs from other Discosia species by its unilocular to bilocular, superficial and applanate conidiomata with basal stroma composed of cells of textura angularis, elongate-ampulliform conidiogenous cells and conidia smaller in size. Sporocadus rosigena is here reported as a new host record from Quercus ilex from Italy. Descriptions, illustrations and molecular data for both species are provided in this paper.

Complexity of Gaeumannomyces species causing take-all root rot of St. Augustinegrass in Texas

ABSTRACT Gaeumannomyces graminis var. graminis (Ggg) has been the etiological agent of take-all root rot (TARR) in St. Augustinegrass (Stenotaphrum secundatum) and root decline of the other warm-season turfgrasses. Seventy-five Ggg isolates were obtained from St. Augustinegrass in central and east Texas. Evaluation of colony morphologies on potato dextrose agar (PDA) within 2 wk and follow-up multilocus phylogenic analyses revealed three phenotypic groups associated with different Gaeumannomyces species: (i) G. floridanus, highly melanized with round colony formation; (ii) G. arxii, none to slightly melanized with round colony formation; and (iii) G. graminicola, highly melanized with irregular colony formation. Further examination with representative isolates from each group revealed that their phenotypic characterizations supported the distinctive genetic groups within Ggg associated with St. Augustinegrass TARR. Gaeumannomyces floridanus isolates grew faster at warmer temperature (30 C) than G. arxii or G. graminicola. Pathogenicity assays using rice seedlings indicated that G. floridanus was more aggressive in disease symptom development than G. arxii or G. graminicola. A multilocus phylogeny reconstruction supported that most of Gaeumannomyces isolates tested in this study were separated into three phylogenetically distinct groups: G. floridanus, G. arxii, and G. graminicola. The resolution of intravarietal complexities of causal fungi of TARR is important for proper diagnostics and management strategies for TARR in St. Augustinegrass and other root-decline diseases in warm-season turfgrasses.

Diversity of marine fungi associated with wood baits in the estuary Ria de Aveiro, with descriptions of Paralulworthia halima, comb. nov., Remispora submersa, sp. nov., and Zalerion pseudomaritima, sp. nov.

ABSTRACT Lignicolous marine fungi are a particular group of microorganisms that are typically found in mangroves, salt marshes, and estuaries, normally associated with driftwood or submerged wood. During investigations of lignicolous fungi occurring in the estuary Ria de Aveiro, Portugal, wood baits were submerged in a marina for 1 year. Seventeen distinct marine fungal species were identified, with the most abundant taxa belonging to the family Lulworthiaceae. Through single- and multilocus phylogenies based on sequences of the internal transcribed spacer (ITS) region and large subunit (28S) and small subunit (18S) of the ribosomal RNA gene cluster in combination with morphological and physiological data, we describe Remispora submersa, sp. nov., and Zalerion pseudomaritima, sp. nov., as novel species. Additionally, we propose that Papulaspora halima, a species whose taxonomic placement has been somehow confusing, be transferred to the genus Paralulworthia as Paralulworthia halima.

Unveiling the unknown phylogenetic position of the scallop Austrochlamys natans and its implications for marine stewardship in the Magallanes Province

Two species of scallop, Austrochlamys natans (“Ostión del Sur”) and Zygochlamys patagonica (“Ostión patagonico”) are presently exploited in the southern part of the Magallanes Province (MP). The lack of clarity in taxonomic identification and ecological aspects is generating both erroneous extraction statistics and an unperceived harvesting pressure on A. natans and Z. patagonica. We aim to discriminate these Magallanes scallops accurately, improve our understanding of their complex natural history and discuss possible implications for their management and conservation status, given the current fisheries statistics. To achieve these goals, we present a complete review of the historical identification of the Magallanes scallop and a multi-locus molecular phylogeny which allowed us to recover the phylogenetic position of A. natans. We sampled 54 individuals from five localities across the southern Pacific coast of the MP. We calculated the depth of the byssal notch (BND) and shell height (VH) ratio from morphological characters and conducted phylogenetic reconstructions with mitochondrial (12S and 16S) and nuclear markers (28S) using Bayesian and maximum likelihood analyses. Both morphology and molecular phylogeny identified two distinct entities, Z. patagonica and a distinct, highly divergent lineage that corresponds to A. natans. Our study provides integrative evidence to alert the current fishery management and the need for further conservation studies.

Artabotrys angustipetalus (Annonaceae), a new species from Thailand, including a plastid phylogeny and character evolutionary analyses of thorn occurrence in Artabotrys

Artabotrys R. Br. is one of the larger genera of Annonaceae with over 100 species distributed throughout the palaeotropics plus northern Australia. Although the genus is morphologically very well circumscribed, species delimitation is quite problematic owing to overlapping morphological characteristics. In Thailand, 20 species of Artabotrys have been reported, including A. multiflorus C. E. C. Fisch. Detailed comparisons with the type specimen from Myanmar revealed that A. multiflorus occurring in Kanchanaburi Province of Thailand represents a new species herein described as A. angustipetalus Photikwan & Chaowasku. The new species differs from A. multiflorus by having fewer flowers per hook, linear (vs oblong to oblong-lanceolate) petals, acute (vs obtuse) petal apex, longer and narrower petals and fewer carpels per flower. A multi-locus plastid phylogeny including an accession of A. angustipetalus and 30 accessions of other species of Artabotrys has been reconstructed. The results uncover a well-supported clade consisting of thorn-bearing species of Artabotrys, with A. angustipetalus recovered outside this clade. To understand the evolution of thorns in Artabotrys, ancestral character-state reconstructions were carried out; this trait is inferred to have evolved only once in Artabotrys. The benefits of thorns in Artabotrys species are discussed and hypothesized.Citation: Photikwan E., Damthongdee A., Jongsook H. & Chaowasku T. 2021: Artabotrys angustipetalus (Annonaceae), a new species from Thailand, including a plastid phylogeny and character evolutionary analyses of thorn occurrence in Artabotrys. – Willdenowia 51: 69–82.Version of record first published online on 23 March 2021 ahead of inclusion in April 2021 issue.

Entangled Aeglidae (Decapoda, Anomura): Additional evidence for cryptic species

AbstractCryptic species are a major challenge for morphologically based species identification. Molecular approaches to species delimitation can be a valuable tool to provide preliminary taxonomic hypotheses and significantly complements morphological taxonomy. In South America, the freshwater crabs of the genus Aegla have sparked much interest as they are key species in the often‐endangered freshwater ecosystems and themselves are often considered endangered species. Morphological similarity among Aegla species is not always positively correlated with genetic relatedness and growing evidence suggests that several putative single taxa are actually assemblages of cryptic species. We coupled broad geographically sampling (Argentina, Brazil and Uruguay) with multilocus (COI, 16S and ANT) phylogenies to investigate the diversity of Aegla uruguayana. Our species delimitation analyses suggested that 19 aeglid populations form a well‐supported clade, although individuals from 10 populations possibly represent a complex of cryptic species. The significant amount of cryptic diversity found in aeglids seem to rely on several factors, including habitat fragmentation, life history features, morphological stasis, convergent evolution and recent divergence. The search for new diagnostic characters and the description of the cryptic species that remain unnamed will probably be the next challenge for this unique group of crustaceans.