Number Of Cryptic Species Research Articles

Cytospora: an important genus of canker pathogens

Cytospora species have commonly been reported as important plant pathogenic fungi with wide host ranges and geographic distributions. With the increase in the number of cryptic species being described, a comprehensive global taxonomic revision of the genus Cytospora is required. The present study includes 399 isolates from 32 countries. These isolates were subjected to DNA sequence analysis for five genomic loci (ITS, act1, rpb2, tef1-α and tub2). Based on these data, it could be confirmed that Cytospora, Leucostoma, Valsa, Valsella and Valseutypella are congeneric. Furthermore, 111 species of Cytospora could also be reassessed, 44 species and four combinations newly introduced, and new typifications proposed for a further three species. Three asexual morphological groups (including 13 asexual morphological types) and three sexual morphological groups (including eight sexual morphological types) were designated. The present study explored the species diversity of Cytospora and re-evaluated the identity of all cultures in the Westerdijk Fungal Biodiversity Institute (Utrecht, The Netherlands) that were deposited as either Cytospora or as one of its related genera. This is the most comprehensive phylogenetic analysis thus far conducted on Cytospora and the results contribute to an increased understanding of the taxonomy of these important fungi. It is also hoped that the findings will lead to improved management strategies for diseases associated Cytospora species.

Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity.

Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.

Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability.

Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.

Consideration of Genetic Structure in the Ecologically or Biologically Significant Marine Areas Criteria: A Review of Convention on Biological Diversity Regional Workshops and A Case Study of Coral Reef Conservation Planning

In this study we reviewed the use of genetic information in the Ecologically or Biologically Significant Marine Areas (EBSA) of Convention on Biological Diversity (CBD). We also evaluated genetic indicators for each criterion of important marine areas. We proposed five genetic indices, mainly based on microsatellite analysis (e.g., private allele frequency and number of cryptic species), then selected EBSAs in tropical and temperate zones of Japan based on eight coral species as a case study. Finally, we compared the results with the findings from conventional species-based EBSAs. In the EBSAs genetic information was mainly used in the Northern Hemisphere, particularly in the Baltic Sea; it was rarely applied in the Southern Hemisphere and Asian regions. Although typically applied to large organisms, genetic information is used to various organisms, including benthic and bacterial communities. Genetic data are used as indicators of diversity and endemism. Genetic indices were available for all seven EBSA criteria, but only five indices of three criteria were used. Examination of important areas of corals in the temperate zone using these indices showed that the indices without genetic indicators extracted a large number of important areas in the tropics; however, the use of genetic indicators identified important locations, including in temperate zones. Comparison with conventional, mainly species-based non-genetic methods showed less than 50% agreement, although particularly important sites in marine protected areas were identified by both methods. While there is still more work to be done, such as consideration of the number of survey sites or target species, one reason is that species-based methods tend to evaluate tropical areas higher. Therefore, these genetic indices are useful for examining important regions, particularly in temperate zones; they revealed cryptic lineages, indicating that many unknown marine taxa should be considered in vulnerable marine areas. Some indicators could be extracted with additional effort, such as population size estimation, immigration, or the use of next-generation sequencing, thus guiding future studies. Because limited genetic information was available in the early stages of EBSA selection, there is a need for systematic surveys and evaluations, particularly in the Southern hemisphere, Asian region, and in small organisms.

Integrative taxonomy reveals three new species of European Lepidocyrtus lignorum-group (Collembola, Entomobryidae).

Lepidocyrtus is one of the genera of springtails with the largest number of species in the world. Molecular studies carried out to date on this genus have revealed the existence of a large number of cryptic species. Molecular and morphological studies done with four European populations of the genus have allowed us to describe three new species within the L. lignorum-group: L. fuscocephalus sp. nov., L. milagrosae sp. nov. and L. semicoloratus sp. nov. One of these species is made up of two geographically separate populations that represent two clearly separate but morphologically indistinguishable haplotypes.

Identification of the taxonomic status of Scinax nebulosus and Scinax constrictus (Scinaxinae, Anura) based on molecular markers.

The validation of many anuran species is based on a strictly descriptive, morphological analysis of a small number of specimens with a limited geographic distribution. The Scinax Wagler, 1830 genus is a controversial group with many doubtful taxa and taxonomic uncertainties, due a high number of cryptic species. One example is the pair of species Scinax constrictus and Scinax nebulosus, which share a similar morphology. Scinax constrictus is restricted to the Brazilian Cerrado savanna, while S. nebulosus is widely distributed throughout northern South America. Despite the validation of many anuran species, discriminations based only on morphological traits is quite difficult due to the high conservative morphology of some groups. In this context, the present study uses mitochondrial and nuclear genes to provide a more consistent diagnosis and test the validity of S. constrictus as a distinct species from S. nebulosus, as well as evaluate the position of these taxa within the Scinax genus. The topologies obtained herein uphold the monophyletic status of Scinax based on all molecular markers assessed in this study, in all analytical approaches, with high levels of statistical support.

A new species of Friesea (Collembola: Neanuridae) from the Antarctic Continent

ABSTRACTA new species of Friesea was found in East Antarctica and is described here as Friesea eureka sp. nov. This is the first new collembolan species to be described from the Antarctic continent in 30 years, even though ice-free areas have been intensively surveyed over that time. It brings to five the number of described species of the genus Friesea known from the Antarctic continent and Peninsula, so is the most speciose genus of Collembola in the region. However, one of these, F. grisea Schäffer, comprises a number of cryptic species of different molecular lineages. The new species is distinguished by having 4 + 4 ocelli plus 1 + 1 hardly visible, a very reduced furca, up to four or five faintly clavate tenent hairs, four anal spines and four spinose chaetae in adult. The restricted distribution of the species emphasises the importance of protecting ice-free areas on the continent as they often contain at least one locally endemic faunal specieswww.zoobank.org/urn:lsid:zoobank.org:pub:865B9AE6-0428-4364-99A4-AF38A764D6D9

DNA barcoding, ecology and geography of the cryptic species of Aneura pinguis and their relationships with Aneura maxima and Aneura mirabilis (Metzgeriales, Marchantiophyta).

Aneura pinguis is a thalloid liverwort species with broad geographical distribution. It is composed of cryptic species, however, the number of cryptic species within A. pinguis is not known. Five cpDNA regions (matK, rbcL, rpoC1, trnH-psbA and trnL-trnF) and the entire nuclear ITS region were studied in 130 samples of A. pinguis from different geographical regions. The relationships between the cryptic species of A. pinguis, A. maxima and A. mirabilis were analyzed. All of the examined samples were clustered into 10 clades corresponding to 10 cryptic species of A. pinguis (marked A to J). Aneura mirabilis and A. maxima were nested among different cryptic species of A. pinguis, which indicates that A. pinguis is a paraphyletic taxon. Subgroups were found in cryptic species A, B, C and E. As single barcodes, all tested DNA regions had 100% discriminant power and fulfilled DNA barcode criteria for species identification; however, the only combination detected in all subgroups was trnL-trnF with trnH-psbA or ITS2. The distances between cryptic species were 11- to 35-fold higher than intraspecific distances. In all analyzed DNA regions, the distances between most pairs of cryptic A. pinguis species were higher than between A. maxima and A. mirabilis. All cryptic species of A. pinguis clearly differed in their habitat preferences, which suggests that habitat adaptation could be the main driving force behind cryptic speciation within this taxon.

A new species of the genus Takydromus (Squamata: Lacertidae) from Tianjingshan Forestry Station, northern Guangdong, China.

Many early descriptions of species of the genus Takydromus were based on limited diagnostic characteristics. This has caused considerable challenges in accurate species identification, meaning that a number of cryptic species have been erroneously identified as known species, resulting in substantially underestimated species diversity. We have integrated evidence from morphology and DNA sequence data to describe a new species of the Asian Grass Lizard, Takydromus albomaculosus sp. nov., based on two specimens from Tianjingshan Forestry Station, Ruyuan County, Guangdong Province, China. The new species can be distinguished from other known Takydromus species by distinctive morphological differences and significant genetic divergence in the mitochondrial COI gene. Morphologically, the new species differs from the known 22 congeners in the following combination of characters: relatively large body size, SVL 70.9 mm in female, 65.5 mm in male; presence of three or four pairs of femoral pores and four pairs of chin-shields; supraoculars three, rarely four, the posterior loreal either in contact with the anteriormost supraocular or not; the presence of supraciliary granules; the presence of six rows of ventral scales, strongly keeled in the male, and smooth but with the outermost row keeled in the female; the presence of enlarged and keeled lateral scales in a row above the ventrals, but shorter than the ventrals; subdigital lamellae 23-24 under the fourth finger and 29-30 under the fourth toe; dorsal surface brown, ventral surface green, flank dark brown or brown black with several prominent white round spots; the presence of a pair of white longitudinal dorsolateral stripes and a pair of white longitudinal ventrolateral stripes. Takydromus albomaculosus sp. nov. represents the twenty-third species of this genus, of which six species occur in northern Guangdong, where the biodiversity level of Takydromus is the second highest in the world, just below that of Taiwan.

Molecular markers reveal reproductive strategies of non‐pollinating fig wasps

1. Fig wasps have proved extremely useful study organisms for testing how reproductive decisions evolve in response to population structure. In particular, they provide textbook examples of how natural selection can favour female‐biased offspring sex ratios, lethal combat for mates and dimorphic mating strategies.2. However, previous work has been challenged, because supposedly single species have been discovered to be a number of cryptic species. Consequently, new studies are required to determine population structure and reproductive decisions of individuals unambiguously assigned to species.3. Microsatellites were used to determine species identity and reproductive patterns in three non‐pollinating Sycoscapter species associated with the same fig species. Foundress number was typically one to five and most figs contained more than one Sycoscapter species. Foundresses produced very small clutches of about one to four offspring, but one foundress may lay eggs in several figs.4. Overall, the data were a poor match to theoretical predictions of solitary male clutches and gregarious clutches with n − 1 females. However, sex ratios were male‐biased in solitary clutches and female‐biased in gregarious ones.5. At the brood level (all wasps in a fig), a decrease in sex ratio with increasing brood size was only significant in one species, and sex ratio was unrelated to foundress number. In addition, figs with more foundresses contain more wasp offspring.6. Finally, 10–22% of females developed in patches without males. As males are wingless, these females disperse unmated and are constrained to produce only sons from unfertilised eggs.

The development of a preliminary rock reef fish multimetric index for assessing thermal and urban impacts in a tropical bay

We developed a multimetric index for assessing ecological conditions in rocky reefs areas to evaluate thermal and urban influences on fish community. Eight metrics were selected to assess thermal influence: (1) total number of species; (2) number of water column species; (3) number of transient species; (4) density of individuals with low resilience; (5) density of omnivores; (6) density of carnivores; (7) number of cryptic species; (8) density of herbivores. For urban influence, six metrics were selected: (1) total density; (2) ratio between the number of rare species and the total number of species; (3) density of individuals with heavy fishing pressure; (4) number of resident species; (5) number of cryptic species; (6) density of herbivores. This preliminary index succeed in discriminating control/impacted sites and proved to be an important tool to assess impacts that alter fish community and have potential to be used in tropical rock reef coastal areas.

Cryptic Species in Putative Ancient Asexual Darwinulids (Crustacea, Ostracoda)

BackgroundFully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied.Methodology/Principal FindingsWe used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG) species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/θ method and the General Mixed Yule Coalescent model (GMYC). We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis), five to six (D. stevensoni) and two (P. aotearoa), respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies.Conclusions/SignificanceOur results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated.

Parmelia sulcata(Ascomycota:Parmeliaceae), a sympatric monophyletic species complex

AbstractRecently, the number of cryptic species known has increased considerably, showing that species diversity has in many cases been underestimated in the past.Parmelia sulcatais a widely distributed species and one of the most common taxa in temperate Europe. The first intra-specific molecular studies onP. sulcatashowed an unexpectedly high genetic variability. In the present work, we study the biodiversity of this taxon including specimens from four continents and using three molecular markers (nuITS, nuIGS rDNA, and partial β-tubulin gene). Two monophyletic groups ofP. sulcatawere encountered; one of these is epitypified asP. sulcatas. str and the other one is segregated as the new cryptic speciesP. encryptatasp. nov. Issues surrounding the lectotypification ofParmelia sulcatahave also been elucidated.

Another example of cryptic diversity in lichen-forming fungi: the new species Parmelia mayi (Ascomycota: Parmeliaceae)

In the last decade, a number of cryptic species have been discovered in lichenized fungi, especially in species with a cosmopolitan or disjunctive distribution. Parmelia saxatilis is one of the most common and widely distributed species. Recent molecular studies have detected two species, P. ernstiae and P. serrana, within P. saxatilis s. lat., suggesting the existence of considerable genetic diversity that may not yet be expressed at the phenotypic level. Due to the complexity in the P. saxatilis s. lat. group, we used this as a model to study the species boundary and identify cryptic lineages. We used Phylogenetic (Bayes, ML and MP) and genetic distance approaches to analyze ITS and β-tubulin sequences. Our results confirm the existence of another cryptic lineage within P. saxatilis s. lat. This lineage is described herein as a new species, P. mayi. It forms an independent, strongly supported, monophyletic lineage, distantly related to the morphologically similar species P. ernstiae, P. saxatilis and P. serrana. Morphologically, it is indistinguishable from P. saxatilis but the new species is separated by molecular, bioclimatic, biogeographic and chemical characters. At present, P. mayi appears to have a restricted distribution in the northern Appalachian mountain territories of North America. It is found in climatic conditions ranging from hemiboreal and orotemperate to cryorotemperate ultrahyperhumid bioclimates.

Multilocus sequencing reveals multiple geographically structured lineages of Coniophora arida and C. olivacea (Boletales) in North America

Coniophora arida and C. olivacea (Coniophoraceae, Boletales) are widespread wood-decay fungi in temperate and boreal regions, occurring both in buildings and natural environments. Genetic variation and geographic structure among isolates of C. arida and C. olivaceae were investigated in this study, with an emphasis on North America. Multilocus sequencing of three DNA regions revealed three main lineages in C. arida and six in C. olivacea, some of which might represent cryptic species. Most of the lineages are present in North America, mainly in allopatry, suggesting recent or ongoing geographic speciation. One of the C. arida isolates included a high number of heterozygous sites and might represent a hybrid between two cryptic C. arida lineages. The data indicate out-crossing reproductive modes in both C. arida and C. olivacea. Together with other recent investigations of Coniophora species our data suggest that the genus comprises a significant number of cryptic species and is much more diverse than previously deduced from morphological characteristics.

MULTIPLE CRYPTIC SPECIES: MOLECULAR DIVERSITY AND REPRODUCTIVE ISOLATION IN THE BOSTRYCHIA RADICANS/B. MORITZIANA COMPLEX (RHODOMELACEAE, RHODOPHYTA) WITH FOCUS ON NORTH AMERICAN ISOLATES

Red algae of the Bostrychia radicans/B. moritziana complex are common in warm temperate areas of North America. Phylogenetic analysis of both plastid and mitochondrial DNA sequence data revealed seven distinct evolutionary lineages among worldwide samples. Although only two haplotypes (plastid and mitochondrial) were found in Pacific Mexico, four plastid and 11 mitochondrial haplotypes were found in a similar latitudinal spread along the Atlantic coast of the United States. On the U.S. Atlantic coast only one plastid haplotype was found in northern samples (Connecticut to North Carolina), whereas further south several plastid haplotypes were found. Phylogenetic analyses suggested that this single plastid haplotype found among northern samples could be the result of a northward range expansion possibly since the last glacial maximum. Crossing data of samples within the same evolutionary lineage showed that samples with the same plastid haplotypes were generally sexually compatible; samples with different plastid haplotypes were reproductively isolated. Samples from Pacific Mexico were partially reproductively compatible with some samples from the Atlantic USA (plastid haplotype C) and were more closely related to these samples than these U.S. samples were to other U.S. Atlantic samples. Compatible solute types mirrored the plastid haplotype, with plastid haplotype B having only sorbitol, whereas all other haplotypes also contained dulcitol. Samples from Atlantic USA, with different plastid haplotypes (e.g. B vs. C), but within the same evolutionary lineage, were reproductively isolated from each other. Data indicate that reproductive isolation occurs between and within supported evolutionary lineages and that the number of cryptic species is high.

Genetic Heterogeneity ofLeucostomaSpecies in Michigan Peach Orchards

ABSTRACT The pathogens causing perennial canker of peach, Leucostoma spp., were characterized in Michigan orchards to identify which species and subgroups (cryptic species) were prevalent on a highly susceptible peach cultivar, Loring, and a less susceptible cultivar, Redhaven. Four hundred and three strains of Leucostoma were isolated from cankers in three southwest Michigan orchards where 'Loring' occurred adjacent to 'Redhaven' in side-by-side plots. Based on colony morphology and small nuclear rDNA size polymorphisms, three cryptic species were detected; 89% of the isolates were identified as L. persoonii phenetic group 1, 10% were L. cincta group 4, and 1% were L. persoonii group 2. Pathogen profiles differed significantly between cankers on small branches of 'Loring' and 'Redhaven', and between cankers on small branches and trunks. Of 1,232 random pairings among isolates of L. persoonii group 1, 95% were vegetatively incompatible. A minimum of 11 and a maximum of 17 maternal lines were identified based upon mitochondrial DNA restriction fragment length polymorphisms among 69 isolates of L. persoonii group 1 from one split-cultivar block of 72 trees. Vegetative compatibility loci were randomly associated with maternal lines. Evidence of clonality was absent in L. persoonii group 1, as no correlation occurred between these two sets of independent genetic markers and no genotype was over-represented. The number of cryptic species, the number of maternal lines, and the frequency of incompatibility within maternal lines indicate that considerable genetic variation exists within the Leucostoma populations in Michigan peach orchards, and that sexual recombination is common.

Electrophoretic variability ofAlcyonidium mytiliDalyell, 1847 (Bryozoa, Ctenostomida) from European coasts

Abstract An electrophoretic study using polyacrylamide gradient gels and isoelectric focusing has confirmed that the ctenostome bryozoan Alcyonidium mytili Dalyell, 1847, to date considered a valid species, in fact comprises a number of cryptic species, of which three are present on the French, Danish, and Swedish coasts.