Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.Peer reviewe

The (non) accuracy of mitochondrial genomes for family-level phylogenetics in Erebidae (Lepidoptera)

The use of molecular data to study the evolutionary history of organisms has revolutionized the field of systematics. Now with the appearance of high throughput sequencing (HTS) technologies, more and more genetic sequence data are available. One of the important sources of genetic data for phylogenetic analyses has been mitochondrial DNA. The limitations of mitochondrial DNA for the study of phylogenetic relationships have been thoroughly explored in the age of single locus phylogenetic studies. Now with the appearance of genomic scale data, increasing number of mitochondrial genomes are available, leading to an increasing number of mitophylogenomic studies. Here, we assemble 47 mitochondrial genomes using whole genome Illumina short reads from representatives of the family Erebidae (Lepidoptera), in order to evaluate the accuracy of mitochondrial genome application in resolving deep phylogenetic relationships. We find that mitogenomes are inadequate for resolving subfamily-level relationships in Erebidae, but given good taxon sampling, we see its potential in resolving lower level phylogenetic relationships.Peer reviewe

A new species of the genus Capoeta Valenciennes, 1842 from the Caspian Sea basin in Iran (Teleostei, Cyprinidae)

A new species of algae-scraping cyprinid of the genus Capoeta Valenciennes, 1842 is described from the Kheyroud River, located in the southern part of the Caspian Sea basin in Iran. The species differs from other members of this genus by a combination of the following characters: one pair of barbels; predorsal length equal to postdorsal length; maxillary barbel slightly smaller than eye¿s horizontal diameter and reach to posterior margin of orbit; intranasal length slightly shorter than snout length; lateral line with 46¿54 scales; 7¿9 scales between dorsal-fin origin and lateral line, and 6¿7 scales between anal-fin origin and lateral line.This research was funded by Tehran University and the Spanish Ministry of Economy and Competitiveness (project number CGL2016-75262-P).Peer Reviewe

A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies

Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondria) (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1 alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hubner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenee is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of "slender-bodied Oenochrominae" that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenee, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively.Peer reviewe

Phylogenetic relationships of freshwater fishes of the genus Capoeta (Actinopterygii, Cyprinidae) in Iran

The Middle East contains a great diversity of Capoeta species, but their taxonomy remains poorly described. We used mitochondrial history to examine diversity of the algae‐scraping cyprinid Capoeta in Iran, applying the species‐delimiting approaches General Mixed Yule‐Coalescent (GMYC) and Poisson Tree Process (PTP) as well as haplotype network analyses. Using the BEAST program, we also examined temporal divergence patterns of Capoeta. The monophyly of the genus and the existence of three previously described main clades (Mesopotamian, Anatolian‐Iranian, and Aralo‐Caspian) were confirmed. However, the phylogeny proposed novel taxonomic findings within Capoeta. Results of GMYC, bPTP, and phylogenetic analyses were similar and suggested that species diversity in Iran is currently underestimated. At least four candidate species, Capoeta sp4, Capoeta sp5, Capoeta sp6, and Capoeta sp7, are awaiting description. Capoeta capoeta comprises a species complex with distinct genetic lineages. The divergence times of the three main Capoeta clades are estimated to have occurred around 15.6–12.4 Mya, consistent with a Mio‐Pleistocene origin of the diversity of Capoeta in Iran. The changes in Caspian Sea levels associated with climate fluctuations and geomorphological events such as the uplift of the Zagros and Alborz Mountains may account for the complex speciation patterns in Capoeta in Iran.Spanish Ministry of Economy and Competitiveness, (Grant/Award Number: “CGL2013-41375-P”).Peer Reviewe

Glyptothorax vatandousti, a new species of torrent catfish from the upper Karkheh drainage in Iran (Teleostei: Sisoridae)

Glyptothorax vatandousti, new species, from the upper Karkheh drainage, a tributary of the Iranian Tigris, is distinguished from its congeners in the Persian Gulf basin by having the flank with a fine, pale-brown mottled pattern overlaid by small and large, blackish or dark-brown blotches, deep caudal-peduncle (its depth 1.1–1.3 times in length), and without, or with a pale-brown triangle-shaped blotch in front of dorsal-fin origin

Ichthyofauna from iranian freshwater : Annotated checklist, diagnosis, taxonomy, distribution and conservation assessment

This is an annotated checklist of all the recognized and named taxa of freshwater fishes in Iran. It documents recent changes and controversies in the nomenclature and includes primary synonyms updated from the Jouladeh-Roudbar et al. (2015b) checklist. We provide an updated comprehensive listing of taxonomy, diagnostic and meristic characters, names, and conservation status, including detailed distribution maps. We strive to record the most recent justified taxonomic assignment in a hierarchical framework, providing annotations, including alternative possible arrangements, for some proposed changes. We provide common English and Persian names, and detail distributional data for all taxa, listing occurrence by basins, including indications of native, endemic, and translocated populations. We used the IUCN Red List Categories and Criteria for classifying species at high risk of global extinction. This checklist consists of 274 recognized species in 100 genera, 33 families, 20 orders and 3 classes. We also report and confirm for the first time the presence of seven species from Iran’s basins: Aphanius kruppi, Capoeta kaput, Luciobarbus conocephalus, Oxynoemacheilus veyselorum, O. gyndes, O. hanae and Squalius latus. The confirmed freshwater fishes of Iran comprise 264 species in 97 genera, 33 families, 20 orders and 3 classes. The 241 endemic and native fish species can be divided into the following conservation statuses: 1 Extinct in the Wild (EW), 17 Critically Endangered (CR), 12 Endangered (EN), 15 Vulnerable (VU), 9 Near Threatened (NT), 148 Least Concern (LC) and 39 Data Deficient (DD). Forty-four fish species (18.3% of the 241 species listed) are officially regarded as globally Threatened (Critically Endangered [CR], Endangered [EN], or Vulnerable [VU]). These numbers and percentages of Threatened species have increased since the last checklist

Three new species of algae-scraping cyprinid from Tigris River drainage in Iran (Teleostei: Cyprinidae).

Traditionally small-scale populations of Capoeta in the Tigris River drainage are identified as Capoeta damascina. The recent finding revealed that some populations of small-scaled C. damascina species group are not identified as any described species. We examined these populations and the results showed that there are pronounced differences between them in morphological and molecular characters. Therefore based on differences found, here we describe three new small-scaled Capoeta species from Zohreh, Tireh and Gamasiab Rivers, Tigris River drainage, Iran.This research was funded by University of Tehran and the Spanish Ministry of Economy and Competitiveness (project number CGL2016-75262-P).Peer Reviewe

The Phylogenetic Placement of an Enigmatic Moth Egybolis Vaillantina Based on Museomics

Here, we present multi-locus sequencing results from the enigmatic Afrotropical monotypic genus Egybolis Boisduval (occurring in East- and South Africa—previously placed in the subfamily Catocalinae, Noctuidae). Model-based phylogenetic analysis places Egybolis within a strongly supported clade comprising four Old World Tropical genera Cocytia Boisduval, Avatha Walker, Anereuthina Hübner, and Serrodes Guenée from the family Erebidae, subfamily Erebinae. Hence, we propose to formally assign the monotypic genus Egybolis to the subfamily Erebinae and the tribe Cocytiini. Timing of divergence analysis reveals the late Oligocene origin around 25 million years ago (Ma) for the tribe Cocytiini, and an early Miocene ( ~21 Ma) for the split between Cocytia and Egybolis

Barbus urmianus, a synonym of Barbus cyri (Teleostei: Cyprinidae)

Barbus urmianus, from the upper Mahabad River in Lake Urmia basin, was distinguished from B. cyri based on several morphological characters. Our analysis demonstrated very small molecular (COI) differences between both species and mostly overlapping or identic morphological character states. Therefore, Barbus urmianus is treated as a junior synonymof B. cyri