scholarly journals Systematics of the Etheostoma cinereum (Teleostei: Percidae) species complex (subgenus Allohistium)

Zootaxa ◽  
2012 ◽  
Vol 3277 (1) ◽  
pp. 43 ◽  
Author(s):  
STEVEN L. POWERS ◽  
BERNARD R. KUHAJDA ◽  
SARAH E. AHLBRAND

We examined geographic variation within the Ashy Darter, Etheostoma cinereum, of the mitochondrially enconded cyto-chrome b gene (cyt b) and nuclear recombination activation gene 1 (RAG1) as well as pigmentation, 6 meristic variables,and 20 morphometric variables for patterns indicative of speciation within the complex. Four geographically disjunct en-tities were identified by at least one of the datasets corresponding to the Cumberland, Duck, Elk, and upper Tennesseeriver systems. Monophyly of cyt b and RAG1 sequences, modal meristic differences, moderate morphometric divergence,and unique pigmentation in specimens from the Cumberland River suggest this entity represents an evolutionary speciesunder many different species concepts and is described herein as Etheostoma maydeni. Other populations exhibit varyingdegrees of divergence in the different datasets and have conflicting relationships in phylogenetic analyses using cyt b andRAG1 sequences, leaving the evolutionary history and taxonomic status of the Duck, Elk and upper Tennessee populations unclear.

2021 ◽  
Vol 28 (2) ◽  
pp. 73-88
Author(s):  
Halime Koç ◽  
Bilal Kutrup ◽  
Ufuk Bülbül ◽  
Muammer Kurnaz

The spiny-tailed lizard, which has a series of taxonomic revisions, is one of the most common lizard species in Turkey. In this study, sequence data derived from three microsatellite loci (Du215, Du281, and Du323), two mitochondrial (16S rRNA and Cyt-b) genes and combined data were used to evaluate the taxonomic status of Darevskia rudis and Darevskia bithynica with new samples from all subspecies populations in Turkey. Our results indicated that the genetic variations of microsatellite loci were not specific to populations within species, and only minor differences separated D. rudis and D. bithynica populations. Furthermore, the markers we used for phylogenetic analyses (NJ, ML, MP, and BI) produced topologically similar trees based on 16S rRNA and Cyt-b while the combined data produced conflicting trees with the separate gene analyses. Finally, the basal relationships among the populations in Turkish populations D. rudis and D. bithynica were not resolved with this dataset, and we found a hard polytomy at the basis of the phylogeny.


Zootaxa ◽  
2020 ◽  
Vol 4834 (3) ◽  
pp. 365-406
Author(s):  
JUAN C. CUSI ◽  
GIUSSEPE GAGLIARDI-URRUTIA ◽  
ISABELA CARVALHO BRCKO ◽  
DAVID B. WAKE ◽  
RUDOLF VON MAY

We examine the phylogenetic relationships among salamanders of the genus Bolitoglossa (Eladinea) distributed in the Amazonian basin of northern Peru and southern Ecuador and assess species diversity based on morphological and phylogenetic analyses. We infer a molecular phylogeny using sequences from two mitochondrial (Cytb, 16S) and two nuclear genes (RAG–1, POMC). We find two well-supported subclades, one including [B. altamazonica + B. peruviana] + B. awajun sp. n., and the other including Bolitoglossa sp. Ituxi + Bolitoglossa sp. Jurúa. Ecuadorian lineages form divergent clades from the Peruvian lineages. Accordingly, Ecuadorian populations previously assigned to Bolitoglossa peruviana sensu lato are treated as members of a Bolitoglossa equatoriana species complex. A newly defined Bolitoglossa altamazonica species complex contains only populations from the Amazonian rainforest of Peru. Maximum likelihood and Bayesian Inference analyses confirm the phylogenetic placement of B. altamazonica and B. peruviana, and support recognition of a related new species of Bolitoglossa. The uncorrected genetic distances between the new species and B. altamazonica are 6.5% for Cytb and 4.9% for 16S; and the uncorrected genetic distances between the new species and B. peruviana are 8.0% for Cytb and 3.9% for 16S. Additionally, analyses of nuclear gene sequences show no haplotype sharing between the new species and closely related species. The new species is distinguished from its congeners by a combination of the following morphological characters: (1) Standard length mean 37.7 mm in males (range 32.0–42.2; n=5) and 41.4 mm in females (range 34.9–48.2; n=6); (2) in life, dorsal coloration uniformly brown with a dark brown triangular marking between the eyes or some irregular light cream spots or patches on the head, back and flanks; (3) iris pale golden; (4) in preservative, dark brown venter with cream mottlings or moderate-sized blotches on the gular region, belly, cloacal region and tail; (5) tips of third finger and third toe protuberant and pointed with nearly complete webbing on the hands and feet; (6) 11–26 maxillary teeth and 8–24 vomerine teeth. Given that the syntypes of B. altamazonica are lost, we designate a neotype for B. altamazonica from Allpahuayo Mishana National Reserve, Loreto department, Peru. Newly collected specimens from ~30 km NE from Moyobamba (type locality of B. peruviana) provide a better understanding of B. peruviana and enable us to show that it is the sister taxon of B. altamazonica. The new species is known from pre-montane forests in Cordillera Escalera Regional Conservation Area, Cordillera Azul National Park and Shucshuyacu, San Martin department, Peru at 485–1311 m elevation,  ~75 km SE from Moyobamba. Bolitoglossa awajun sp. n. is the fourth endemic species of salamander from Peru. 


MycoKeys ◽  
2018 ◽  
Vol 32 ◽  
pp. 25-48 ◽  
Author(s):  
Shi-Liang Liu ◽  
Karen K. Nakasone ◽  
Sheng-Hua Wu ◽  
Shuang-Hui He ◽  
Yu-Cheng Dai

Eleven taxa ofLopharias.s.,Dendrodontia,DentocorticiumandFuscocerrenain Polyporales are included in the phylogenetic analyses of nuc rDNA ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S) and RNA polymerase II second-largest subunit (rpb2) sequences. New speciesLophariaresupinataandL.sinensisare described and illustrated.Lophariaresupinata, from south-eastern China, is closely related toL.ayresii, andL.sinensis, from northern China, is related toL.cinerascensandL.mirabilis.Lophariamirabilisspecimens from temperate to tropical areas with varied hymenophore configurations all cluster together in a fully supported clade.DendrodontiaandFuscocerrenaare shown to be synonyms ofDentocorticium, which is phylogenetically related toLopharia. Four new combinations,Dentocorticiumbicolor,D.hyphopaxillosum,D.portoricenseandD.taiwanianum, are proposed. Revised generic descriptions ofLophariaandDentocorticiumare provided with keys to the six accepted species in each genus. A list of all names inLophariaandDentocorticiumare presented with their current taxonomic status. Type specimens ofDentocorticiumbrasilienseandD.irregularewere examined and determined to be later synonyms ofPunctulariasubhepaticaandDiplomitoporusdaedaleiformis, respectively.Corticioid fungi, dendrohyphidia, species complex, wood-inhabiting fungi


2020 ◽  
Vol 101 (4) ◽  
pp. 1117-1132
Author(s):  
M Ángel Léon-Tapia ◽  
Jesús A Fernández ◽  
Yessica Rico ◽  
F A Cervantes ◽  
Alejandro Espinosa de los Monteros

Abstract The Peromyscus maniculatus species complex is one of the most widespread group of small mammals in North America. However, the taxonomy and phylogenetic relationships among its constituent taxa remain unclear. As part of a revision of Peromyscus specimens from the highlands of the Trans-Mexican Volcanic Belt in central Mexico, we identified five individuals collected in 1968 that differed externally from other Peromyscus specimens, although morphologically similar to P. labecula and P. melanotis, both latter in the P. maniculatus species complex. Based on cranial measurements and mitochondrial DNA sequences, we aimed to more accurately determine the phylogenetic relationships and the taxonomic status of these individuals. Molecular phylogenetic analyses showed that the specimens formed a monophyletic clade sister to the P. maniculatus species complex. Pairwise genetic distances between those specimens and other species within the P. maniculatus species complex were greater than 7.91%. In addition, morphological analyses clearly distinguished the test specimens from P. melanotis and P. labecula. Based on the results of our molecular and morphological analyses, we conclude that these specimens represent an undescribed species of the P. maniculatus species complex, which we describe herein.


2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.


2020 ◽  
Vol 66 (3-4) ◽  
pp. 151-179
Author(s):  
L. Lee Grismer ◽  
L. Wood Perry ◽  
Marta S. Grismer ◽  
Evan S.H. Quah ◽  
Myint Kyaw Thura ◽  
...  

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain non-monophyletic lineages. This is especially true at the species level where small amounts of gene flow may not preclude the evolution of localized adaptions in different geographic areas while underpinning the paraphyletic nature of each population with respect to the other. We illustrate this point by examining genetic and morphological variation among three putatively allopatric populations of the granite-dwelling Bent-toed Gecko Cyrtodactylus aequalis from hilly regions in southeastern Myanmar. In the absence of molecular phylogenetic inference, a compelling argument for three morphologically diagnosable species could be marshaled. However, when basing the morphological analyses of geographic variation on a molecular phylogeny, there is a more compelling argument that only one species should be recognized. We are cognizant of the fact however, that when dealing with rare species or specimens for which no molecular data are possible, judicious morphological analyses are the only option—and the desired option given the current worldwide biodiversity crisis.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.


Plant Disease ◽  
2021 ◽  
pp. PDIS-06-20-1290
Author(s):  
Juliana S. Baggio ◽  
Bruna B. Forcelini ◽  
Nan-Yi Wang ◽  
Rafaela G. Ruschel ◽  
James C. Mertely ◽  
...  

Pestalotiopsis-like species have been reported affecting strawberry worldwide. Recently, severe and unprecedented outbreaks have been reported in Florida commercial fields where leaf, fruit, petiole, crown, and root symptoms were observed, and yield was severely affected. The taxonomic status of the fungus is confusing because it has gone through multiple reclassifications over the years. Morphological characteristics, phylogenetic analyses, and pathogenicity tests were evaluated for strawberry isolates recovered from diseased plants in Florida. Phylogenetic analyses derived from the combined internal transcribed spacer, β-tub, and tef1 regions demonstrated that although there was low genetic diversity among the strawberry isolates, there was a clear separation of the isolates in two groups. The first group included isolates recovered over a period of several years, which was identified as Neopestalotiopsis rosae. Most isolates recovered during the recent outbreaks were genetically different and may belong to a new species. On potato dextrose agar, both groups produced white, circular, and cottony colonies. From the bottom, colonies were white to pale yellow for Neopestalotiopsis sp. and pale luteous to orange for N. rosae. Spores for both groups were five-celled with three median versicolored cells. Mycelial growth and spore production were higher for the new Neopestalotiopsis sp. isolates. Isolates from both groups were pathogenic to strawberry roots and crowns. However, the new Neopestalotiopsis sp. proved more aggressive in fruit and leaf inoculation tests, confirming observations from the recent outbreaks in commercial strawberry fields in Florida.


Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.


2020 ◽  
Vol 49 (4) ◽  
pp. 427-439 ◽  
Author(s):  
Fatemeh Ghorbani ◽  
Mansour Aliabadian ◽  
Ruiying Zhang ◽  
Martin Irestedt ◽  
Yan Hao ◽  
...  

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