Multigene Data Research Articles

Molecular phylogeny of Trictenotomidae (Coleoptera: Tenebrionoidea): insights into species validation and biogeography of genus Autocrates

Abstract Trictenotomidae, one of the most charismatic and enigmatic groups of beetles, known for their large size and distinctive mandibles, is widely distributed throughout tropical and subtropical Asia. New species are continually being discovered, and the known range of the group has been expanded considerably by the discovery of Autocrates maqueti Drumont in the Korean Peninsula, ~2,000 km from its previously known distribution in the Chinese mainland highlands. A comprehensively sampled multigene phylogenetic tree of Trictenotomidae, including all six species of Autocrates and five species of Trictenotoma, was reconstructed using multigene data. Using the resulting phylogeny, we performed divergence time estimation, biogeographical assessments, and molecular species delimitation. All six known species of the genus Autocrates were found to be valid in all four molecular species delimitation scenarios, indicating the need for further taxonomic research on these poorly understood taxa. The A. maqueti population in South Korea forms a genetically distinct clade in all genetic analyses, suggesting that it is a natural distribution rather than a result of anthropogenically driven spread. The Korean A. maqueti population is likely to have been isolated since ~1.8 Mya, when the Yellow Sea was still a landmass, highlighting the need for targeted conservation measures in South Korea.

Validating a molecular clock for nudibranchs-No fossils to the rescue.

Time calibrated phylogenies are typically reconstructed with fossil information but for soft-bodied marine invertebrates that lack hard parts, a fossil record is lacking. In these cases, biogeographic calibrations or the rates of divergence for related taxa are often used. Although nudibranch phylogenies have advanced with the input of molecular data, no study has derived a divergence rate for this diverse group of invertebrates. Here, we use an updated closure date for the Isthmus of Panama (2.8 Ma) to derive the first divergence rates for chromodorid nudibranchs using multigene data from a geminate pair with broad phylogeographic sampling. Examining the species Chromolaichma sedna (Marcus & Marcus, 1967), we uncover deep divergences among eastern Pacific and western Atlantic clades and we erect a new species designation for the latter (Chromolaichma hemera sp. nov.). Next, we discover extensive phylogeographic structure within C. hemera sp. nov. sensu lato, thereby refuting the hypothesis of a recent introduction. Lastly, we derive divergence rates for mitochondrial and nuclear loci that exceed known rates for other gastropods and we highlight significant rate heterogeneity both among markers and taxa. Together, these findings improve understanding of nudibranch systematics and provide rates useful to apply to divergence scenarios in this diverse group.

Phylogenetic Structure Revealed through Combining DNA Barcodes with Multi-Gene Data for Agrodiaetus Blue Butterflies (Lepidoptera, Lycaenidae).

The need for multi-gene analysis in evolutionary and taxonomic studies is generally accepted. However, the sequencing of multiple genes is not always possible. For various reasons, short mitochondrial DNA barcodes are the only source of molecular information for some species in many genera, although multi-locus data are available for other species of the same genera. In particular, such situation exists in the species-rich butterfly subgenus Polyommatus (Agrodiaetus). Here, we analyzed the partitioning of this subgenus into species groups by using three data sets. The first data set was represented by short mitochondrial DNA barcodes for all analyzed samples. The second and third data sets were represented by a combination of short mitochondrial DNA barcodes for part of the taxa with longer mitochondrial sequences COI + tRNA-Leu + COII (data set 2) and with longer mitochondrial COI + tRNA-Leu + COII and nuclear 5.8S rDNA + ITS2 + 28S rDNA sequences (data set 3) for the remaining species. We showed that the DNA barcoding approach (data set 1) failed to reveal the phylogenetic structure, resulting in numerous polytomies in the tree obtained. Combined analysis of the mitochondrial and nuclear sequences (data sets 2 and 3) revealed the species groups and the position within these species groups, even for the taxa for which only short DNA barcodes were available.

Further insights into the phylogeny of facultative parasitic ciliates associated with tetrahymenosis (Ciliophora, Oligohymenophorea) based on multigene data.

Tetrahymenosis, caused by about 10 Tetrahymena species, is an emerging problem inflicting a significant economic loss on the aquaculture industry worldwide. However, in the order Tetrahymenida, there are many unresolved evolutionary relationships among taxa. Here we report 21 new sequences, including SSU-rRNA, ITS1-5.8S-ITS2 rRNA and LSU-rRNA, genes of 10 facultative parasitic Tetrahymena associated with tetrahymenosis, and conduct phylogenetic analyses based on each individual gene and a three-gene concatenated dataset. The main findings are: (1) All the parasitic and facultative parasitic species cluster in borealis group. (2) With the addition of new sequences, Tetrahymena is still divided into three groups, namely the "borealis group", the "australis group," and the "paravorax group." (3) the cluster pattern of all the newly sequenced facultative parasitic Tetrahymena species shows that members of the "borealis" group may be more susceptible to parasitism. (4) phylogeny based on concatenated genes show that T. pyriformis, T. setosa, and T. leucophrys have close relationship.

Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid.

The euglenids are a species-rich group of flagellates with varying modes of nutrition that can be found in diverse habitats. Phagotrophic members of this group gave rise to phototrophs and hold the key to understanding the evolution of euglenids as a whole, including the evolution of complex morphological characters like the euglenid pellicle. Yet to understand the evolution of these characters, a comprehensive sampling of molecular data is needed to correlate morphological and molecular data, and to estimate a basic phylogenetic backbone of the group. While the availability of SSU rDNA and, more recently, multigene data from phagotrophic euglenids has improved, several "orphan" taxa remain without any molecular data whatsoever. Dolium sedentarium is one such taxon: It is a rarely-observed phagotrophic euglenid that inhabits tropical benthic environments and is one of few known sessile euglenids. Based on morphological characters, it has been thought of as part of the earliest branch of euglenids, the Petalomonadida. We report the first molecular sequencing data for Dolium using single-cell transcriptomics, adding another small piece in the puzzle of euglenid evolution. Both SSU rDNA and multigene phylogenies confirm it as a solitary branch within Petalomonadida.

Taxonomic revision ofIsochelesStimpson, 1858 andLoxopagurusForest, 1964 (Decapoda: Anomura: Diogenidae) using morphological and multigene data, with the description of a new Eastern Pacific species

AbstractThe genera IsochelesStimpson, 1858 and LoxopagurusForest, 1964 are endemic to America and occur in tropical and subtropical waters. There are five species of Isocheles, two of them are found in the Western Atlantic (I. sawayaiForest & de Saint Laurent, 1968 and I. wurdemanniStimpson 1859) and three in the Eastern Pacific (I. pilosus (Holmes, 1900), I. pacificusBouvier, 1907, and I. aequimanus (Dana, 1852)). Loxopagurus is a monotypic genus and occurs only in southeastern South America. These two genera are morphologically similar, with differences in shape and size of chelae. The published information on the taxonomy of these genera is scant, and there have been some recent doubts about their phylogenetic relationship. Our study aimed to elucidate the phylogenetic relationship of Isocheles and Loxopagurus and evaluate their taxonomic validity and contextualization in Diogenidae Ortmann, 1892. We performed an integrative analysis using multigene data (16S rRNA, COI, and H3) and a detailed morphological evaluation, including redescriptions, seeking characters that allow the clear identification of these species. The type specimens of I. aequimanus, I. pilosus, and L. loxochelis (Moreira, 1901) were lost and errors are common regarding the identification of the species of Isocheles. Characters that clearly delimit these species, such as the ornamentation and shape of the chelipeds and the number of teeth on the second article of the antenna, were stated. The morphological and molecular analyses corroborated the taxonomical validity of Isocheles and Loxopagurus as two distinct genera based on the differences of the shield and chelipeds, on the topology of the trees, and on the genetic divergence inferred from three molecular markers. We also verified that the five amplified species of Isocheles constitute five distinct clades and described a new species of Isocheles, using both molecular and morphological differences from congeners. An identification key for Isocheles is proposed. Although the type material of two out of the five species of Isocheles and the holotype of Loxopagurus loxochelis were lost, the designation of neotypes is not recommended in these cases.

Note on the genus Nemania (Xylariaceae) - first records and a new species of the genus from Iran.

In a survey of xylarialean fungi in northern Iran, some specimens attributable to the genus Nemania were collected, cultured and sequenced. Morphological evidence and phylogenetic analyses of a combined ITS, LSU, RPB2 and TUB2 gene dataset confirmed the presence of Nemaniadiffusa and N.serpens in Iran for the first time. Furthermore, the new species N.hyrcana, which shows similarities to N.subaenea and its putative synonym N.plumbea, but significantly differs from the latter in its DNA sequences, was encountered. All species are illustrated, described and discussed. In the phylogenetic analyses, for the first time, the overlooked ex-type ITS sequences of the neotype of the generic type, N.serpens and that of the holotype of N.prava, were added to a multi-gene matrix of Nemania. This revealed that the two accessions of N.serpens (HAST 235 and CBS 679.86), for which multigene data are available in GenBank, are misidentified, while the Iranian accession of N.serpens has an almost identical ITS sequence to the neotype, confirming its morphological species identification. The two previously accepted species of Euepixylon, E.udum and E.sphaeriostomum, are embedded within Nemania and are revealed as close relatives of N.serpens, supporting the inclusion of Euepixylon in Nemania.

Insights into the phylogeny of the ciliate of class Colpodea based on multigene data.

In the class Colpodea, there are many unresolved evolutionary relationships among taxa. Here, we report 30 new sequences including SSU‐rRNA, ITS1‐5.8S‐ ITS2 rRNA, and the mitochondrial small subunit ribosomal RNA (mtSSU‐rRNA) genes of five colpodeans, and conduct phylogenetic analyses based on each individual gene and a two‐gene concatenated dataset. For the first time, multi‐genes were used to analyze phylogenetic relationships in the class Colpodea. The main findings are: (1) SSU‐rRNA, ITS1‐5.8S‐ ITS2 rRNA, and mtSSU‐rRNA gene sequences of C. reniformis and C. grandis are provided for the first time, and these two species group into the clade including C. inflata, C. lucida, C. cucullus, and C. henneguyi; (2) clustering pattern and morphological similarity indicate that Bresslauides discoideus has a close relation with Colpodidae spp.; (3) Emarginatophrya genus diagnosis is improved to be ‘Hausmanniellidae with sharply shortened and isometric leftmost 1‐4 ciliary rows’ and Colpoda elliotti is transferred to Emarginatophrya; (4) the genus Colpoda is still non‐monophyletic with the addition of 10 populations from five Colpoda species sequences, but there are only two Colpoda groups left based on the present work: Group I comprises C. inflata, C. lucida, C. cucullus, C. henneguyi, C. reniformis, and C. grandis, Group II comprises C. maupasi and C. ecaudata, and the presence of diagonal grooves and the way the vestibular opens might be the two key features that differentiates Colpoda species groups; (5) a close molecular relationship, and highly similar merotelokinetal mode, somatic ciliary pattern, and basic organization of the oral apparatus with P. steinii suggests Bromeliothrix metopoides should be temporarily assigned to Colpodidae.

Understanding the diversity and phylogenetic placements of New Zealand amphipods within a global context

ABSTRACT Amphipods are an ecologically diverse group of crustaceans. Due to the limited number of fossil data and common morphological homoplasy, molecular data can be very useful to understand their evolutionary relationships and history. However, despite their global distribution and an increasing number of phylogenetic studies, molecular data from the Southern Hemisphere is considerably limited. Here, I report multigene data (18S, 28S, and COI) of New Zealand endemic freshwater families as well as some other marine taxa. Also, I report two new species/genera that have not been described yet. Phylogenetic analyses were conducted including major amphipod groups to understand phylogenetic placements of New Zealand amphipods. Based on the ML and Bayesian trees, Paracallipe, Paraleptamphopus, and the two unknown species belong to the eusiroids/iphimedioids clade; Parorchestia and a talitrid species clearly belong to talitroids; Paracorophium and Monocorophium were placed within corophiids; Themisto belongs to physosomatans; Josephosella was closely related to other hadzoids. The present study suggests that the Southern and Northern Hemisphere freshwater amphipods are likely to have originated from different marine ancestors. Molecular data from other regions in the Southern Hemisphere will be highly valuable for understanding the phylogeographic histories of amphipods that have shaped the current diversity and distribution.

Phylogenetic position of Trichomycterus astromycterus (Siluriformes: Trichomycteridae), an enigmatic trichomycterid from eastern Brazil, inferred from molecular data.

Recently in this journal, a new trichomycterine from eastern Brazil, Trichomycterus astromycterus, was described and considered possibly related to the Chilean Bullockia maldonadoi due to morphological similarities. Subsequently, osteological data supported T. astromycterus in the subgenus Psammocambeva of Trichomycterus, from eastern Brazil. Phylogenetic analyses, performed here, using a multigene data set for a broad trichomycterine sample, corroborate T. astromycterus as a member of Psammocambeva, reinforcing the importance of molecular data for inferring trichomycterine relationships but showing that osteological data alone may infer correctly phylogenetic placements when using broad comparative databases.

Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences

In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution.

Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]

Insights into the phylogeny of three systematically controversial subfamilies of urostylid ciliates based on rDNA

AbstractThe family Pseudokeronopsidae Borror & Wicklow, 1983 has an extensive history of iterative revisions regarding phylogenetic relationships of its members and some related taxa from the order Urostylida. The accumulation of morphological and multigene data has provided the opportunity to gain a more comprehensive understanding of their systematic and evolutionary relationship. We conducted phylogenetic analyses of multiple molecular markers and predicted secondary structures of SSU rRNA and ITS regions by adding 14 new sequences. The results demonstrate that: (1) all the present phylogenetic analyses support the transfer of the subfamily Thigmokeronopsinae from the family Pseudokeronopsidae to the family Urostylidae; (2) the monophyly of two subfamilies Pseudokeronopsinae and Nothoholostichinae is substantiated with high support values of the SSU rDNA, LSU rDNA and the concatenated rDNA loci; (3) the monophyly of Pseudokeronopsidae is substantiated of the LSU rDNA only, and the AU tests do not reject the possibilities of Anteholosticha pulchra in this family; (4) phylogenetic trees based on the ITS region do not support the monophylies of the Pseudokeronopsidae and Nothoholostichinae, but the AU tests do not reject their possibilities; and (5) even though Pseudokeronopsis is morphologically well‐defined, it is very likely a paraphyletic genus in which both Antiokeronopsis and Uroleptopsis could be included. Moreover, this study reveals that the V2 and V4 regions of the SSU rRNA molecule are rather conserved at genus level and could be used to distinguish different subfamilies and families. Although they are less stable than the Watson–Crick complementarities, the GU appositions often occur in the ITS transcripts, which are much more variable at genus level than the V2 and V4 regions of the SSU rRNA molecule.

A phylogenetic assessment of Pholiota and the new genus Pyrrhulomyces

ABSTRACT Multigene data sets were assembled to evaluate the phylogeny of species attributed to the genus Pholiota sensu A.H. Sm. & Hesler. This effort included generation of just more than 200 new sequences from 19 type collections of Pholiota and recent samples from East Asia. Phylogenetic analyses reinforced the autonomous phylogenetic positions of pholiotoid taxa in the genera Flammula (Hymenogastraceae) and Kuehneromyces (Strophariaceae). Samples of Pholiota astragalina from diverse geographic regions split into two species-level lineages but occupied an isolated phylogenetic position apart from Pholiota sensu stricto. The new genus Pyrrhulomyces is described to accommodate P. astragalina and a new cryptic species from the Southern Appalachians, Pyrrhulomyces amariceps. Pyrrhulomyces is distinguished from other genera of Strophariaceae by the blackening basidiomata with a bitter taste, smooth basidiospores without a germ pore under light microscopy, presence of pleurochrysocystidia, an ixocutis, rugulose spore ornamentation under scanning electron microscope (SEM), and association with late stages of conifer wood decay. Pholiota subochracea was found to be sister to a clade containing samples of Hypholoma and Bogbodia, but this portion of the Strophariaceae will require further taxon and gene sampling to resolve relationships between these three taxa. Pholiota sensu stricto comprised at least two major groups, but several residual poorly placed lineages were also noted depending on the data set analyzed. New combinations are made in the genera Flammula, Kuehneromyces, and Stropharia for three species of Pholiota—P. abieticola, P. obscura, and P. scabella, respectively, based on molecular annotation of type collections. Overall, 20 new synonymies are proposed, mostly in Pholiota. Illustrations of Pyrrhulomyces are provided along with a key to genera of Strophariaceae and Hymenogastraceae.

Further insights into the phylogeny of peniculid ciliates (Ciliophora, Oligohymenophorea) based on multigene data

Peniculids comprise a large order of ciliated protists in Class Oligohymenophorea having many unresolved evolutionary relationships. Herein, we report 27 new sequences, including 18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA and the mitochondrial cox1 genes of eight peniculids. We conducted phylogenetic analyses based on each these markers and on a four-gene concatenated data set (18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA, and cox1 gene). The main findings are: 1) subclass Peniculia and family Parameciidae are monophyletic, with genus Frontonia remaining non-monophyletic; 2) Urocentrids have traditionally been regarded as a family, multi-gene analyses support the rank of Urocentrida and consistently recovers this order as sister to Peniculida, and Urocentrida and Peniculida comprise subclass Peniculia in agreement with Lynn’s (2008) classification; 3) discrepancies between multiple-gene phylogenies, and conflicts with morphologic data regarding genus Frontonia necessitate expansion and revision of species diagnoses and we propose consideration of Group III of Frontonia (including F. didieri, F. ocularis, F. anatolica, F. pusilla and F. elegans) as incertae sedis in Peniculida; 4) multi-gene analyses of Parameciidae support five previously established subgenera. Paramecium buetschlii is placed in subgenus Chloroparamecium, and P. chlorelligerum into subgenus Viridoparamecium.

Genetic Evidence for a Mixed Composition of the Genus Myoxocephalus (Cottoidei: Cottidae) Necessitates Generic Realignment.

Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.

Phylogeny and evolution of unique skull morphologies in dietary specialist African shovel-snouted snakes (Lamprophiidae:Prosymna)

AbstractProsymna is a specialized African snake genus lacking close relatives. The evolutionary relationships and history within Prosymna are poorly understood. Here we assembled a multi-gene data set including representatives for 11 of 16 species to investigate the phylogenetic relationships of this group. Our analyses support the monophyly of Prosymna and are congruent with species groups previously recognized on the basis of external morphology. Divergences among extant Prosymna began in the mid-Cenozoic, with the earliest divergence splitting northern from southern lineages. High-resolution computed tomography scans confirm that a specialized skull morphology is found across the genus and was probably present in the common ancestor of Prosymna. This specialization is exemplified by dentition featuring reduced anterior but greatly enlarged, blade-like posterior maxillary teeth and an unusually high degree of fusion of cranial bones. One species, P. visseri, has a hammer-like maxilla unlike that of any other known snake. Evidence for oophagy in Prosymna and the possible roles of morphological specializations in egg-slitting or egg-crushing feeding mechanisms are discussed.

Molecular Characterization of a Fungal Ketide Synthase Gene Among Swainsonine-Producing Alternaria Species in the USA

Locoweeds are toxic leguminous plants in Astragalus and Oxytropis genera that contain fungal endophytes of Alternaria section Undifilum species. These fungi produce swainsonine, an alkaloid α-mannosidase inhibitor that causes a neurological syndrome, locoism in grazing animals. A SWN gene cluster has been identified in many swainsonine-producing fungi. The swnK gene, which is an essential component of the swainsonine biosynthetic pathway, encodes a polyketide synthase-nonribosomal peptide synthase (PKS-NRPS). To determine if swnK was conserved among Alternaria section Undifilum endophytes of locoweed, the sequence of the KS region of swnK was compared between various swainsonine-producing fungi. The internal transcribed spacer (ITS), andglyceraldehyde-3-phosphate dehydrogenase (GPD)regions from the same fungi were also assessed. Sequences were examined at the nucleotide and protein levels. Alternaria oxytropis, A. fulva, A. cinerea, and Alternaria sp. from Swainsona species produced distinct clades for all multigene data sets. swnK-KS sequence did not differ among fungi isolated from Astragalus mollissimus varieties or A. lentiginosus varieties. The swnK-KS amino acid sequence was essentially identical among all swainsonine-producing Alternaria sp. Two low swainsonine-producing fungi, Alternaria bornmuelleri and A. gansuense, clustered together, as did non-pathogen Alternaria endophytes. The swnK-KS sequence comparisons were effective in identifying swainsonine production capability and differentiating among swainsonine-producing fungal species.

Repetitive DNA Profiles Reveal Evidence of Rapid Genome Evolution and Reflect Species Boundaries in Ground Beetles.

Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification, but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multigene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution. [Bembidion; Carabidae; copy number variation profiles; rapid genome evolution; ribosomal DNA; species delimitation.].

Multigene phylogeny reveals convergent evolution in small interstitial catfishes from the Amazon and Atlantic forests (Siluriformes: Trichomycteridae)

AbstractInterstitial trichomycterid catfishes of the Glanapteryginae and Sarcoglanidinae with uncommon morphology have been known for long time from taxa endemic to the Amazon. In most recent decades, two genera, Listrura and Microcambeva, respectively, placed in Glanapteryginae and Sarcoglanidinae on the basis of morphological characters, have been described from the Atlantic Forest of eastern South America, about 1,500 km from the area inhabited by those Amazon taxa. Herein, we first test the phylogenetic positioning of Listrura and Microcambeva using a multigene data set, including two nuclear and three mitochondrial genes for nine species of Listrura and Microcambeva and 11 species representing all closely related subfamilies (TSVSG‐clade), as well as five used as outgroups. The phylogenetic analyses generated a robust tree with high support values in all nodes, where monophyly of Glanapteryginae and Sarcoglanidinae is refuted. In contrast, Listrura and Microcambeva form a highly supported clade, herein formally described as a new subfamily, sister to a clade containing taxa representing the Glanapteryginae, Sarcoglanidinae, Stegophilinae, Tridentinae and Vandelliinae. This study also indicates that Microcambeva and Listrura exhibit divergent evolutionary trends in ecological and morphological attributes. Species of Microcambeva inhabit patches of loose sand and possess morphological traits that were convergently acquired by Amazon sand‐dwelling sarcoglanidines, including loss of body pigmentation and long maxilla. Species of Listrura live burrowed inside small stretches of dense leaf litter and have morphological traits that were convergently acquired by Amazon glanapterygines inhabiting leaf litter bottom rivers, including elongate body, with numerous vertebrae and loss or reduction of all fins.