Species Delimitation and Analysis of Cryptic Species Diversity in the XXI Century

The potentials and limitations of different approaches to revealing species boundaries and describing cryptic species are discussed. Both the traditional methods of species delimitation, mostly based on morphological analysis, and the approaches using molecular markers are considered. Besides, the prospects of species identification using digital image recognition and machine learning are briefly considered. It is concluded that molecular markers provide very important material for species delimitation; the value of these data increases manifold if they can be compared with information on morphology, geographic distribution, and ecological preferences of the studied taxa. In many cases, only a practicing taxonomist who knows his or her group thoroughly can correctly interpret the molecular data and incorporate them into the existing knowledge system in order to make a taxonomic decision.

     

The sister group relation of parmeliaceae (Lecanorales, Ascomycota)

The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Gypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae.     

Not as Ubiquitous as We Thought: Taxonomic Crypsis,Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae,Hypocreales, Ascomycota)

The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.     

Cetradonia,a new genus in the new family Cetradoniaceae (Lecanorales,Ascomycota)

Abstract:A taxonomic revision of the lichen genus Gymnoderma Nyl. sensu Yoshimura & Sharp (Cladoniaceae) based on an integrative analysis of polyphasic characters supports the segregation of a new genusCetradonia J.-C.Wei & Ahti in a new family Cetradoniaceae J.-C.Wei & Ahti. The monotypic genus and family are based on Cladonia linearis Evans. In addition, two species are recognized in genus Neophyllis F. Wilson and two species are retained in the genus Gymnoderma Nyl. of the Cladoniaceae.     

Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin

The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras.     

中国鹅膏菌属(担子菌)的物种多样性

鹅膏菌属（Ａｍａｎｉｔａ）是一个近世界性广布的大属,全球已被描述而又被承认的有近５００种。在文献中,我国此属已记载约２００种。然而,许多种都是原初描述于欧洲或北美的种类。近来的研究表明,东亚的鹅膏菌独特且有其自身的分布范围。东亚的有些种虽与产于欧洲或北美的某些种相似,但仔细的野外观察,详尽的形态解剖学和分子进化生物学研究结果表明,东亚的鹅膏菌是独立的分类群。在欧洲,人们有采集著名食菌恺撒鹅膏菌的习     

中国块菌属多样性

在中国特别是西南地区块菌属Tuber资源调查的基础上,本文综合形态特征、生态特征以及分子系统学分析,对比研究了欧洲和北美的部分块菌属标本,对中国块菌属已知种类进行了分类订正和系统的总结.研究确认我国分布有17种块菌,其中3/4的种类分布于西南地区.尚有6种因未观察到可靠的标本而存疑,3种排除在我国分布.文中对该属在我国...     

Hypocrealean (Hypocreales,Ascomycota) Fungal Diversity in Different Stages of Tropical Forest Succession in Costa Rica1

The relationship between forest succession and microfungal diversity has been poorly studied. Fungi provide important ecosystem services that may deteriorate in deforested or highly disturbed forests. To determine the possible effects of deforestation and forest succession on microfungi, species diversity of hypocrealean fungi (Ascomycota) was compared in forest stands in Eastern Costa Rica representing three stages of succession: 1–2, 25–27 yr old, and an old growth forest. Species diversity in a second‐growth forest fragment surrounded by timber plantations and second‐growth forest was also compared to that of a stand surrounded by old growth forest. The results show that the overall diversity of hypocrealean fungi was inversely proportional to the age of the forest stand, and each family showed different successional trends. Clavicipitaceae was more diverse in the old‐growth forest and was positively related to the age of the forest stand. Nectriaceae was highly diverse in the 1‐ to 2‐yr‐old stand and less diverse in the old‐growth stand. Saprobic and plant pathogenic fungal species were more diverse in the 1‐ to 2‐yr‐old stand and their diversity was inversely proportional to the age of the forest stand. The diversity of insect pathogens was positively related to the age of the forest stand. The 20‐ to 22‐yr‐old forest fragment had the lowest number of species overall. Based on the data gathered in this study, hypocrealean fungal species diversity is related to the successional stage and fragmentation of tropical forest.     

Homology Assessment of the Boundary Tissue in Fruiting Bodies of the Lichen Family Sphaerophoraceae (Lecanorales, Ascomycota)

Abstract: The ascoma ontogeny of the family Sphaerophoraceae is reviewed. The development of the boundary tissue in Leifidium tenerum is described and compared with similar structures in some other mazaediate representatives of the family ( Sphaerophorus globosus, Bunodophoron dodgei and B. diplotypum ), and with the non-mazaedia-producing genera Austropeltum and Neophyllis. The dominant structure in the base of mature ascomata in all genera is a boundary tissue forming the border between ascomatal ("generative") and thalline ("vegetative") tissue. In the mazaedia-forming genera, the boundary tissue is composed of two layers. The upper layer is a zone of ascogenous hyphae, homologous to similar zones in Neophyllis and Austropeltum. The lower layer is a pseudoparenchymatic and often strongly pigmented zone formed by generative tissue, homologous to a zone of generative tissue present in Neophyllis but lacking in Austropeltum.     

Population Evidence of Cryptic Species and Geographical Structure in the Cosmopolitan Ectomycorrhizal Fungus, Tricholoma scalpturatum

Tricholoma scalpturatum is an ectomycorrhizal fungus that forms symbioses with roots of diverse trees and shrubs. It is commonly encountered in a wide range of habitats, across temperate ecosystems. A previous study has revealed a high genetic diversity at a local scale, and ruderal abilities. To examine genetic structure at a large geographical scale, a total of 164 basidiocarps were collected from 30 populations located in Western Europe, from Spain to Scandinavia. These samples were analyzed by three molecular methods with different levels of resolution: inter-simple sequence repeats (ISSRs), restriction fragment length polymorphisms (RFLPs) in the rDNA internal transcribed spacer (ITS), and ITS sequence analysis. Considerable genetic variation was found, and the morphospecies was separated into two genetic groups that were distinct from each other. The ISSR data and the relatively low percentage value (96%) of shared sequence polymorphisms in the ITS between isolates from the two groups, strongly suggest cryptic species and long-lasting separation. No geographical exclusion was detected for these two widely distributed taxa. However, high estimates of population differentiation were observed in each group, including between populations less than a few kilometers apart. This result provides evidence for limited gene flow and/or founding effects. It also indicates that T. scalpturatum does not constitute a random mating population, and the hypothesis of endemism cannot be excluded for this cosmopolitan wind-dispersed fungus.     

Phylogeography and Cryptic Species Diversity of Paramesotriton caudopunctatus Species Group(Salamandridae: Paramesotriton) in Guizhou,China

The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary relationships and divergence-time of members of this species group as a whole remain unexplored. In this study, we report the sequencing of one protein coding mitochondrial gene fragment(ND2) and one nuclear gene(POMC), and use a combination of phylogenetic analyses and coalescent simulations to explore the cryptic diversity and evolutionary history of the P. caudopunctatus species group. Phylogenetic relationships revealed that the P. caudopunctatus species group is composed of two major groups, i. e., East Clade and Western-South Clade. The divergence-time and ancestral area estimation suggested that the P. caudopunctatus species group likely originated in the Doupeng Mountains in Guizhou, China at 12.34 Ma(95% HPD: 8.30–14.73), and intraspecific divergence began at about 2.17 Ma(95% HPD: 1.39–2.97). This timing coincides with the orogenesis of the Miaoling Mountains during the Late Miocene to early Pleistocene. The delimitation of species in the P. caudopunctatus species group supports the existence of the currently identified species, and consensus was confirmed across methods for the existence of least to two cryptic species within what has been traditionally considered to be P. caudopunctatus species group. This study is of significance for understanding the species formation, dispersal, and diversity of the tailed amphibians in the karst mountains ecosystem of Guizhou and the role of the Miaoling Mountains as a geographical barrier to species dispersal.     

Genetic diversity and photobiont associations in selected taxa of the Tephromela atra group (Lecanorales, lichenised Ascomycota)

Mycobiont and photobiont genetic diversity was investigated in four taxa of the Tephromela atra complex, which differ in ecology and substratum preference (from siliceous rocks, limestone to bark), and are differently interpreted by taxonomists. Phylogenetic analyses were performed using mycobiont nuclear ITS, beta tubulin and homologous polyketide synthase gene (PKS) sequences obtained from freshly collected material sampled from the Mediterranean region to the Southern Alps. The silicicolous samples from the Alps form a basal lineage of the entire complex, and despite the morphological similarity, they do not form a monophyletic group with the Mediterranean samples. No resolution was found among the calcicolous and the silicicolous taxa from Mediterranean habitats, which are traditionally segregated at variety or species level. The epiphytic taxon, although nested with the other ecotypes, splits in two well-supported lineages. Among the four taxa, Tephromela grumosa is the only morphologically, chemically and genetically distinct taxon. However, it is also nested in the large T. atra complex. Phylogenetic analysis of photobionts ITS sequences revealed that thalli from the Mediterranean region are associated with two distinct lineages of Trebouxia, but the lineages are not correlated with substrate or mycobiont phenotype. The thalli from the Alps are exclusively associated with T. simplex, suggesting a protracted isolation from the other lineages.     

Exploring Species Level Taxonomy and Species Delimitation Methods in the Facultatively Self-Fertilizing Land Snail Genus Rumina (Gastropoda: Pulmonata)

Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected.     

Morphology and Molecules Reveal Unexpected Cryptic Diversity in the Enigmatic Genus Sinobirma Bryk, 1944 (Lepidoptera: Saturniidae)

The wild silkmoth genus Sinobirma Bryk, 1944 is a poorly known monotypic taxon from the eastern end of the Himalaya Range. It was convincingly proposed to be closely related to some members of an exclusively Afro-tropical group of Saturniidae, but its biogeographical and evolutionary history remains enigmatic. After examining recently collected material from Tibet, northern India, and northeastern Myanmar, we realized that this unique species, S. malaisei Bryk, 1944 only known so far from a few specimens and from a very restricted area near the border between north-eastern Myanmar and the Yunnan province of China, may in fact belong to a group of closely related cryptic species. In this work, we combined morphological comparative study, DNA barcoding, and the sequences of a nuclear marker (D2 expansion segment of the 28S rRNA gene) to unequivocally delimit three distinct species in the genus Sinobirma, of which two are described as new to science: S. myanmarensis sp. n. and S. bouyeri sp. n. An informative DNA barcode sequence was obtained from the female holotype of S. malaisei—collected in 1934—ensuring the proper assignation of this name to the newly collected and studied specimens. Our findings represent another example of the potential of coupling traditional taxonomy and DNA barcoding for revealing and solving difficult cases of cryptic diversity. This approach is now being generalized to the world fauna of Saturniidae, with the participation of most of the taxonomists studying these moths.     

Cryptic Diversity and Venom Glands in Western Atlantic Clingfishes of the Genus Acyrtus (Teleostei: Gobiesocidae)

Examination of genetic data (mitochondrial cytochrome c oxidase I) for western Atlantic clingfishes revealed two distinct lineages within a group of individuals originally identified as Acyrtus artius. Subsequent investigation of preserved voucher specimens was conducted to reconcile the genetic data and the existing classification, which is based on morphology. In addition to discovering that one of the genetic lineages is an undescribed species, which we describe as Acyrtus lanthanum, new species, we found that the nominal species Acyrtus artius has a putative venom gland associated with the subopercle that has been overlooked since the species was described nearly 60 years ago. The new species lacks the subopercular gland as does Acyrtus rubiginosus, but one is present in the related Arcos nudus. Venom glands have not been reported previously for the Gobiesocidae, and the venom gland described herein for Acyrtus and Arcos represents the first example in teleost fishes of a venom gland associated with the subopercle.