Species-level Lineages Research Articles

Discovering cryptic species in the Aspiciliella intermutans complex (Megasporaceae, Ascomycota) - First results using gene concatenation and coalescent-based species tree approaches.

Taxonomic identifications in some groups of lichen-forming fungi have been challenge largely due to the scarcity of taxonomically relevant features and limitations of morphological and chemical characters traditionally used to distinguish closely related taxa. Delineating species boundaries in closely related species or species complexes often requires a range of multisource data sets and comprehensive analytical methods. Here we aim to examine species boundaries in a group of saxicolous lichen forming fungi, the Aspiciliella intermutans complex (Megasporaceae), widespread mainly in the Mediterranean. We gathered DNA sequences of the nuclear ribosomal internal transcribed spacer (nuITS), the nuclear large subunit (nuLSU), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the DNA replication licensing factor MCM7 from 80 samples mostly from Iran, Caucasia, Greece and eastern Europe. We used a combination of phylogenetic strategies and a variety of empirical, sequence-based species delimitation approaches to infer species boundaries in this group. The latter included: the automatic barcode gap discovery (ABGD), the multispecies coalescent approach *BEAST and Bayesian Phylogenetics and Phylogeography (BPP) program. Different species delimitation scenarios were compared using Bayes factors species delimitation analysis. Furthermore, morphological, chemical, ecological and geographical features of the sampled specimens were examined. Our study uncovered cryptic species diversity in A. intermutans and showed that morphology-based taxonomy may be unreliable, underestimating species diversity in this group of lichens. We identified a total of six species-level lineages in the A. intermutans complex using inferences from multiple empirical operational criteria. We found little corroboration between morphological and ecological features with our proposed candidate species, while secondary metabolite data do not corroborate tree topology. The present study on the A. intermutans species-complex indicates that the genus Aspiciliella, as currently circumscribed, is more diverse in Eurasia than previously expected.

Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex.

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens sp. nov. and Mycobacterium attenuatum sp. nov.

Among the species Mycobacterium kansasii, seven subtypes have been previously reported based on the PCR and the restriction fragment length polymorphism of the gene hsp65. Here, we used whole-genome sequencing to refine M. kansasii taxonomy and correct multiple inconsistencies. Average nucleotide identity (ANI) values between M. kansasii subtypes ranged from 88.4 to 94.2 %, lower than the accepted 95-96 % cut-off for species delineation. In addition, Mycobacterium gastri was closer to the M. kansasii subtypes 1, 2, 3, 4 and 5 than M. kansasii subtype 6. The recently described species Mycobacterium persicum shared 99.77 % ANI with M. kansasii subtype 2. Consistent with the ANI results, the digital DNA-DNA hybridization value was below the 70 % threshold for species delineation between subtypes and above it within subtypes as well as between subtype 2 and M. persicum. Furthermore, core-genome phylogeny confirmed the current M. kansasii species to be polyphyletic. Hence, we propose (i) Mycobacterium pseudokansasii sp. nov., replacing subtype 3, with the type strain MK142T(=CCUG 72128T=DSM 107152T), (ii) Mycobacterium innocens sp. nov., replacing subtype 5, with the type strain MK13T (=CCUG 72126T=DSM 107161T), and (iii) Mycobacterium attenuatum sp. nov., replacing subtype 6, with the type strain MK41T(=CCUG 72127T=DSM 107153T). Subtype 4 represents a new species-level lineage based on the genomic data but no strain was available. No genome sequence or strain was available for subtype 7. The proposed nomenclature will facilitate the identification of the most pathogenic subtype 1 as M. kansasii by clinicians while the new species names suggest the attenuated pathogenicity of the other subtypes.

Genetic and morphological variations of the lichenized fungus Steinera intricata (Arctomiaceae, Lecanoromycetes) from southern South America to Antarctic Peninsula

Steinera (Arctomiaceae, Lecanoromycetes) is an Austral genus of lichenized fungi that form symbiotic associations with cyanobacteria, producing small and inconspicuous thalli. Most species of Steinera present a high degree of endemism restricted to sub-Antarctic islands except S. intricata which occurs from southern South America to the Antarctic Peninsula and presents remarkable phenotypic variation along its distribution range. In this study, an integrative approach was used to explore the extent of intraspecific diversity of S. intricata throughout its distribution. Morphological and anatomical descriptions and the phylogenetic analyses of three genomic regions were performed with specimens collected from seven Antarctic islands and in the Tierra del Fuego National Park (Argentina). Genetic data revealed species-level lineages are not associated with the differences observed in the thalli shape, which probably are related to distinct microhabitats and substrates as well as to the development stage. Molecular clock analyses estimated that S. intricata originated at about 0.24 Myr and that the diversification of the Antarctic lineages occurred at about 0.16 Myr. This study revealed that there is probably an unknown diversity of new members of Steinera in southern South America and that the evolutionary history of these cyanolichens may contribute to the understanding of the phylogeographic connections between members of the Austral-Antarctic flora.

The hills are alive with geckos! A radiation of a dozen species on sky islands across peninsular India (Squamata: Gekkonidae, Hemiphyllodactylus) with the description of three new species

Sky Islands are high-elevation environments that are separated by warmer, low elevations, forming natural patches of unique montane habitat that often persist through changing climates. Peninsular India was ancestrally forested and has gradually become more arid since at least the Oligocene, and open landscapes have dominated since the middle-late Miocene. Mesic forests today are largely restricted to coastal mountains and some other montane habitats. A mitochondrial phylogeny and fossil-calibrated timetree of Indian Hemiphyllodactylus reveal an Indochinese origin and an endemic radiation with 12 species-level lineages, where a single species was known, that diversified in the Oligocene-Miocene across montane forest habitats in the Eastern Ghats and south India. The phylogeny also suggests the discontinuous Eastern Ghats mountain range encompasses two distinct biogeographic entities: north and south of the Pennar/Krishna-Godavari River basins. This study highlights the deep history of the region and the importance of montane habitats as islands of unique biodiversity that have persisted through millions of years of changing climates. We describe three new species: Hemiphyllodactylus arakuensis sp. nov., H. jnana sp. nov. and H. kolliensis sp. nov. from montane habitats above 1000 m. The montane habitats of these species are emerging hotspots of reptile endemism, and this study emphasizes the need for systematic biodiversity inventory across India to uncover basic patterns of diversity and distribution.

The reduced limbed lizards of the genus Bachia (Reptilia, Squamata, Gymnophthalmidae); biogeography, cryptic diversity, and morphological convergence in the eastern Caribbean

The phylogenetic and systematic relationships of the reduced limbed lizards of the genus Bachia are poorly understood. Here, we investigate the eastern Caribbean Bachia assigned to the B. heteropa and B. flavescens groups, whose members are characterized by a band of hexagonal or quadrangular scales on the dorsum, respectively. The polytypic Bachia heteropa is redefined, and the previous subspecies in the Grenadines (Bachia heteropa alleni) and Trinidad (B. h. trinitatis) are demonstrated to be species-level lineages. One new species of hex-scaled Bachia was formerly assigned intergrade status between B. heteropa and Bachia trinitatis. Here, it is described as a new species from Caripito, Venezuela. Bachia h. heteropa, B. h. lineata, and B. h. marcelae are elevated to species status. The Tobago species formerly considered a member of the Bachia flavescens species group is described as a new species. In this paper, we increase the number of species in the genus Bachia from 25 to 31 with the description of two new species and the elevation of four previously described species from the synonymy of Bachia heteropa. This work will greatly improve the understanding of the systematics and evolution of Bachia in the eastern Caribbean.

Six new species of the Cyrtodactylus intermedius complex (Squamata: Gekkonidae) from the Cardamom Mountains and associated highlands of Southeast Asia

An integrative taxonomic analysis using color pattern, morphology, and 1449 base pairs of the ND2 mitochondrial gene and its five flanking tRNAs demonstrated that eight species-level lineages occur within the Cyrtodactylus intermedius complex (Cyrtodactylus intermedius sensu stricto, C. phuquocensis and related populations) of the Cardamom mountains and associated highlands that have a sequence divergence ranging 3.4-8.9%. Additionally, each lineage is discretely diagnosable from one another based on morphology and color pattern and most occur in specific geographic regions (upland areas, karst formations or islands) that prevent or greatly restrict interpopulation gene flow. Six of these lineages were masquerading under the nomen C. intermedius and are described as the following: Cyrtodactylus auralensis sp. nov. endemic to Phnom Aural, the highest mountain in Cambodia; C. bokorensis sp. nov. endemic to the Bokor Plateau, Cambodia; C. cardamomensis sp. nov. from the main block of the Cardamom mountains; C. thylacodactylus sp. nov. endemic to Phnom Dalai the northernmost peak of the Cardamom mountains; C. laangensis sp. nov. endemic to the Phnom Laang karst formation, Cambodia; and C. septimontium sp. nov. from the Bảy Núi Hills of southwest Vietnam.

Two new, sympatric and semi-cryptic species ofSulzbacheromyces(Lichenized Basidiomycota, Lepidostromatales) from the Chocó Biogeographic Region in Colombia

Nuclear ribosomal internal transcribed spacer (ITS) region is well-established as universal DNA barcode marker for Fungi. Here we examined the utility of DNA barcoding for delimiting species in lichenized Basidiomycota from Colombia, focusing on the genus Sulzbacheromyces (Lepidostromatales). The topology of the best-scoring maximum likelihood tree based on ITS data shows eight separate, well-supported lineages within Sulzbacheromyces, including the six already known species S. caatingae from Brazil, S. miomboensis De Kesel & Ertz from Africa, and S. bicolor, S. fossicola, S. sinensis, and S. yunnanensis from Asia. In addition, two further, sympatric and semi-cryptic species from the Choco Biogeographic Region, one of the most diverse regions of the world, are recognized: S. chocoensis Coca, Lucking & Moncada sp. nov and S. tutunendo Coca, Lucking & Moncada sp. nov. Both form separate, strongly supported species-level lineages, but differ morphologically from each other and from S. caatingae in minor details only, which are best assessed with fresh material in the field.

Does Population Structure Predict the Rate of Speciation? A Comparative Test across Australia's Most Diverse Vertebrate Radiation.

Population divergence is the first step in allopatric speciation, as has long been recognized in both theoretical models of speciation and empirical explorations of natural systems. All else being equal, lineages with substantial population differentiation should form new species more quickly than lineages that maintain range-wide genetic cohesion through high levels of gene flow. However, there have been few direct tests of the extent to which population differentiation predicts speciation rates as measured on phylogenetic trees. Here, we explicitly test the links between organismal traits, population-level processes, and phylogenetic speciation rates across a diverse clade of Australian lizards that shows remarkable variation in speciation rate. Using genome-wide double digest restriction site-associated DNA data from 892 individuals, we generated a comparative data set on isolation by distance and population differentiation across 104 putative species-level lineages (operational taxonomic units). We find that species show substantial variation in the extent of population differentiation, and this variation is predicted by organismal traits that are thought to be proxies for dispersal and deme size. However, variation in population structure does not predict variation in speciation rate. Our results suggest that population differentiation is not the rate-limiting step in species formation and that other ecological and historical factors are primary determinants of speciation rates at macroevolutionary scales.

An integrative perspective into diversity in Acarospora (Acarosporaceae, Ascomycota), including a new species from the Great Basin, U.S.A.

A broad range of morphological variation is known to occur within the lichen-forming fungal genus Acarospora (Acarosporaceae, Ascomycota). In this study, we investigated the relationships of a number of interesting Acarospora collections from western North America using morphological, chemical and molecular sequence data. Our results revealed patterns of apparent convergence of some morphologies traditionally considered a single taxon, coupled with a striking range of morphological disparity within other lineages. Based on the results of this study, a species of lichen-forming fungi, Acarospora tintickiana sp. nov., is formally described as new to science, occurring on hard limestone substrates in the Great Basin of western North America. Furthermore, a number of additional candidate species are recognized and merit additional research before formal taxonomic recognition. This study highlights the importance of implementing an integrative taxonomic approach, incorporating a broad range of data, including molecular sequence data, for diagnosing evolutionarily independent species-level lineages in lichen-forming fungi.

The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota).

Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen-forming fungal genus Stereocaulon provides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282 Stereocaulon specimens, collected in diverse habitats worldwide, using the algal ITS rDNA and actin gene sequences and fungal ITS rDNA sequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genus Asterochloris (Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera, Vulcanochloris and Chloroidium, were also found. We used variation-partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts and vice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species-level lineages. We demonstrated that species-level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity-tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.

A preliminary molecular phylogeny shows Japanese and Austrian populations of the red mite Balaustium murorum (Acari: Trombidiformes: Erythraeidae) to be closely related

The red mite Balaustium murorum (Hermann) inhabits the Western Palaearctic realm and is well adapted to man-made structures. In Japan, B. murorum had been reported more frequently after the 1980s. A molecular phylogeny based on the nuclear 18S rRNA and mitochondrial COI genes, and including B. murorum individuals from Japan and Austria and representatives of related species from Japan showed four Balaustium species-level lineages in Japan (B. murorum, Balaustium sp. 1, Balaustium sp. 2, Balaustium sp. 3). The B. murorum lineage shared identical 18S sequence and COI haplotype with the Austrian population. Balaustium sp. 1 was detected from the Tokyo and Misaki area (Honshu Island) and was the sister group to B. murorum; the other two lineages inhabited coastal environments of Erimo, Hokkaido Island (Balaustium sp. 2) and Ainan, Shikoku Island (Balaustium sp. 3). The high genetic distances among these four lineages indicate that each lineage is a distinct species, with three of the lineages representing undescribed species. Our results are compatible with the conclusion that B. murorum was introduced to Japan from Europe, although our study did not resolve the polarity or timing of migration events.

Multiple, Distinct Intercontinental Lineages but Isolation of Australian Populations in a Cosmopolitan Lichen-Forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota).

Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.

Fusarium oligoseptatum sp. nov., a mycosymbiont of the ambrosia beetle Euwallacea validus in the Eastern U.S. and typification of F. ambrosium.

Fusarium oligoseptatum sp. nov. was isolated from the invasive Asian ambrosia beetle Euwallacea validis (Coleoptera, Scolytinae, Xyleborini) and from the galleries that females had constructed in dying Ailanthus altissima (tree-of-heaven) symptomatic for Verticillium wilt in south-central Pennsylvania, USA. This ambrosia fungus was cultivated by Euwallacea validis as the primary source of nutrition together with a second symbiont, Raffaelea subfusca . Female beetles transport their fungal symbionts within and from their natal galleries in paired pre-oral mycangia. Fusarium oligoseptatum was distinguished phenotypically from the 11 other known members of the Ambrosia Fusarium Clade (AFC) by uniquely producing mostly 1-2 septate clavate sporodochial conidia that were swollen apically. Phylogenetic analysis of multilocus DNA sequence data resolved F. oligoseptatum as a genealogically exclusive species-level lineage but evolutionary relationships with other members of the AFC were unresolved. Published studies have shown that F. oligoseptatum can be identified via phylogenetic analysis of multilocus DNA sequence data or a PCR multiplex assay employing species-specific oligonucleotide primers. In addition, to provide nomenclatural stability, an epitype was prepared from an authentic strain of F. ambrosium that was originally isolated from a gallery constructed in Chinese tea (Camellia sinensis ) by E. fornicatus in India, together with its lectotypification based on a published illustration.

Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent.

The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent (MSC) to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the MSC model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across data sets. Posterior predictive tests find the poorest model performance in data sets that were hypothesized to be impacted by model violations. We also show that while the inferences assuming the MSC are robust to minor model violations, such inferences can be biased under some biologically plausible scenarios. Taken together, these results suggest that researchers can identify individual data sets in which species delimitation under the MSC is likely to be problematic, thereby highlighting the cases where additional lines of evidence to identify species boundaries are particularly important to collect. Our study supports a growing body of work highlighting the importance of model checking in phylogenetics, and the usefulness of tailoring tests of model fit to assess the reliability of particular inferences. [Populations structure, gene flow, demographic changes, posterior prediction, simulation, genetics.].

Thalassotalea litorea sp. nov., isolated from seashore sand.

A novel Gram-stain-negative, aerobic and rod-shaped marine bacterium, designated strain HMF4135T, was isolated from a sand sample which was collected from the seashore of the South Sea, Republic of Korea. It required NaCl for growth and exhibited optimal growth at 30 °C, with 2 % (w/v) NaCl and at pH 7-8. Cellular fatty acids were dominated by C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c and C12 : 0 3-OH. The predominant isoprenoid quinone was ubiquinone-8 (Q-8). Polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain HMF4135T formed a distinct species-level lineage within the genus Thalassotalea of the class Gammaproteobacteria and was most closely related to Thalassotalea ponticola GJSW-36T (96.4 % similarity). Based on the distinctive phenotypic characteristics and phylogenetic analysis, it is concluded that strain HMF4135T represents a novel species of the genus Thalassotalea, for which the name Thalassotalea litorea sp. nov. is proposed. The type strain is HMF4135T (=KCTC 52154T=NBRC 112672T).

Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards.

Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.

Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales)

BackgroundThe aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU).ResultsResults of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area.ConclusionsFour intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.

Life history, patchy distribution, and patchy taxonomy in a shallow-water invertebrate (Mollusca: Polyplacophora: Lepidopleurida)

Things without names are difficult to rationalise, and so species that go without names are difficult to conserve or protect. This is a case study in resolving conflicts in historical taxonomy and ‘real’ species (identifiable and evolutionarily relevant groupings) using an approach including population genetics, natural history, and pragmatism. We report the observation that populations of a shallow-water chiton species from Washington and British Columbia demonstrate extremely high site fidelity and patchy distribution. Their limited dispersal potential and isolation could be explained by a brooding life history. This stands in direct contrast with the supposedly wide distribution of this “species”, Leptochiton rugatus (Carpenter in Pilsbry, 1892) sensu lato, from the Sea of Japan to Baja California. But this lineage has previously been suggested to comprise several cryptic species. Indeed, a haplotype network analysis using 61 individual sequences of the cytochrome oxidase c subunit I gene for L. rugatus s.l. revealed four discrete clusters which correspond to different parts of the geographic range. We infer these to represent four distinct species, at least two of which are likely novel. Leptochiton rugatus sensu stricto is herein reinterpreted as restricted to California and Baja California, and the new name L. cascadiensis sp. nov. is established for the lineage with a distribution in the Cascadia coastal bioregion from the panhandle of Alaska to Oregon. There are minor morphological differences among these species in the L. rugatus species complex, but genetic data or morphological observations alone would not have been sufficient to definitively recognise these groups as species-level lineages. The observation that different species within the complex may have different life history strategies provides important support for interpreting different populations as genuinely separate species.

New species of Tulasnella associated with terrestrial orchids in Australia

Recent studies using sequence data from eight sequence loci and coalescent-based species delimitation methods have revealed several species-level lineages of Tulasnella associated with the orchid genera Arthrochilus, Caleana, Chiloglottis, and Drakaea in Australia. Here we formally describe three of those species, Tulasnella prima, T. secunda, and T. warcupii spp. nov, as well as an additional Tulasnella species associated with Chiloglottis growing in Sphagnum, T sphagneti sp. nov. Species were identified by phylogenetic analyses of the ITS with up to 1.3 % sequence divergence within taxa and a minimum of 7.6 % intraspecific divergence. These new Tulasnella (Tulasnellaceae, Cantharellales) species are currently only known from orchid hosts, with each fungal species showing a strong relationship with an orchid genus. In this study, T. prima and T. sphagneti associate with Chiloglottis, while T. secunda associates with Drakaea and Caleana, and T. warcupii associates with Arthrochilus oreophilus.