scholarly journals Stock mislabelling and its impact on phylogenomic analysis in the Drosophila nasuta subgroup/species complex

2019 ◽  
Author(s):  
Peter J. Waddell ◽  
Jeremy Wang ◽  
Corbin D. Jones
Keyword(s):  
Species Complex ◽  
De Novo ◽  
Short Note ◽  
Species Group ◽  
Phylogenomic Analysis ◽  
Genome Study ◽  
Drosophila Nasuta

AbstractIn the course of our 28 de novo genome study of the nasuta-subgroup of the immigrans species group, we have come to suspect that several stocks acquired from the major stock centers may have either been mislabeled or mixed up in other ways. This is a short note to indicate which stocks these are, how they were diagnosed, and how an alignment and assembly free (AFAF) phylogenomic analysis sheds further light on what probably occurred.

Heteroplasmy due to coexistence of mtCOI haplotypes from different lineages of theThrips tabacicryptic species group

2017 ◽  
Vol 107 (4) ◽  
pp. 534-542 ◽  
Author(s):  
S.J. Gawande ◽  
S. Anandhan ◽  
A.A. Ingle ◽  
Alana Jacobson ◽  
R. Asokan
Keyword(s):  
Flow Cytometry ◽  
Mitochondrial Dna ◽  
Real Time Pcr ◽  
Copy Number ◽  
Species Complex ◽  
Species Group ◽  
Thrips Tabaci ◽  
Mitochondrial Cytochrome ◽  
Quantitative Real Time Pcr ◽  
Putative Species

AbstractHeteroplasmy is the existence of multiple mitochondrial DNA haplotypes within the cell. Although the number of reports of heteroplasmy is increasing for arthropods, the occurrence, number of variants, and origins are not well studied. In this research, the occurrence of heteroplasmy was investigated inThrips tabaci, a putative species complex whose lineages can be distinguished by their mitochondrial DNA haplotypes. The results from this study showed that heteroplasmy was due to the occurrence of mitochondrial cytochrome oxydase I (mtCOI) haplotypes from two differentT. tabacilineages. An assay using flow cytometry and quantitative real-time PCR was then used to quantify the per cell copy number of the two mtCOI haplotypes present in individuals exhibiting heteroplasmy from nine geographically distant populations in India. All of theT. tabaciindividuals in this study were found to exhibit heteroplasmy, and in every individual the per cell copy number of mtCOI from lineage 3 comprised 75–98% of the haplotypes detected and was variable among individuals tested. There was no evidence to suggest that the presense of lineage-specific haplotypes was due to nuclear introgression; however, further studies are needed to investigate nuclear introgression and paternal leakage during rare interbreeding between individuals from lineages 2 and 3.

A revision of the Myopsalta crucifera (Ashton) species group (Hemiptera: Cicadidae: Cicadettini) with 14 new species from mainland Australia

Zootaxa ◽  
2017 ◽  
Vol 4340 (1) ◽  
pp. 1
Author(s):  
LINDSAY W. POPPLE
Keyword(s):  
New Species ◽  
Species Complex ◽  
Species Group ◽  
Undescribed Species ◽  
Key To Species ◽  
Species Groups ◽  
Song Types

The genus Myopsalta Moulds is distributed throughout much of Australia. Previous studies have associated several undescribed species with the Myopsalta crucifera (Ashton) species complex. The present study informally divides the cicadas in the genus Myopsalta into two species groups. It provides a revision of the M. crucifera species group, which includes redescriptions of M. crucifera s. str. and M. mackinlayi (Distant). The identity of the latter species is further refined and attributed to material formerly presented under the name Myopsalta atrata (Goding & Froggatt). In addition to the redescriptions, 14 new species belonging to the M. crucifera species group are described, including M. albiventris n. sp., M. bassiana n. sp., M. chrysopedia n. sp., M. gordoni n. sp., M. leona n. sp., M. longicauda n. sp., M. majurae n. sp., M. melanobasis n. sp., M. parvula n. sp., M. platyptera n. sp., M. riverina n. sp., M. septa n. sp., M. umbra n. sp. and M. xerograsidia n. sp. A key to species in the genus Myopsalta is provided. Standard morphological descriptions and descriptions of calling songs unique to each species are included along with a discussion on different song types in the M. crucifera species group. 

scholarly journals Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

ABSTRACTThe Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

scholarly journals The speciation history of the Drosophila nasuta complex

2006 ◽  
Vol 88 (1) ◽  
pp. 13-26 ◽  
Author(s):  
DORIS BACHTROG
Keyword(s):  
Genetic Differentiation ◽  
Population Genetic ◽  
Species Group ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Genetic Analyses ◽  
Nucleotide Variability ◽  
Drosophila Nasuta ◽  
Population Genetic Analyses

The Drosophila nasuta subgroup of the immigrans species group is widely distributed throughout the South-East Asian region, consisting of morphologically similar species with varying degrees of reproductive isolation. Here, I report nucleotide variability data for five X-linked and two mtDNA loci in eight taxa from the nasuta subgroup, with deeper sampling from D. albomicans and its sister species D. nasuta. Phylogenetic relationships among these species vary among different genomic regions, and levels of genetic differentiation suggest that this species group diversified only about one million years ago. D. albomicans and D. nasuta share nucleotide polymorphisms and are distinguished by relatively few fixed differences. Patterns of genetic differentiation between this species pair are compatible with a simple isolation model with no gene flow. Nucleotide variability levels of species in the nasuta group are comparable to those in members of the melanogaster and pseudoobscura species groups, indicating effective population sizes on the order of several million. Population genetic analyses reveal that summaries of the frequency distribution of neutral polymorphisms in both D. albomicans and D. nasuta generally fit the assumptions of the standard neutral model. D. albomicans is of particular interest for evolutionary studies because of its recently formed neo-sex chromosomes, and our phylogenetic and population genetic analyses suggest that it might be an ideal model to study the very early stages of Y chromosome evolution.

Revision of the taxonomy and distribution of the Neotropical Copris incertus species complex (Coleoptera: Scarabaeidae: Scarabaeinae)

2018 ◽  
Vol 150 (5) ◽  
pp. 539-577 ◽  
Author(s):  
James D.G. Darling ◽  
François Génier
Keyword(s):  
New Species ◽  
Costa Rica ◽  
Species Distribution ◽  
Male Genitalia ◽  
Species Complex ◽  
New World ◽  
Species Group ◽  
Distribution Maps ◽  
Multiple Species ◽  
A New Species

AbstractCopris incertus Say, 1835 (Coleoptera: Scarabaeidae: Scarabaeinae: Coprini) has been described as a New World coprophagous scarab distributed from Mexico to Ecuador with large discontinuities in its range between the Yucatán province and Costa Rica. The C. incertus species complex of the Copris minutus (Drury, 1773) species group consists of C. incertus, Copris laeviceps Harold, 1869, and Copris lugubris Boheman, 1858. Based on external morphology and male genitalia, we discovered that multiple species have been classified as C. incertus. Of these species, five are new: Copris amazonicusnew species, Copris brevicornisnew species, Copris davidinew species, Copris moroninew species, and Copris susanaenew species. Herein, we revise the organisation of the C. incertus species complex and propose a new species complex, the C. laeviceps species complex, which includes: C. davidi, Copris igualensis Warner, 1990, and C. laeviceps, formerly included in the C. incertus species complex. We provide an identification key along with species distribution maps, images of habitus, and diagnostic characters.

scholarly journals A new Gonatocerus (Hymenoptera: Mymaridae) from Argentina, with taxonomic notes and molecular data on the G. tuberculifemur species complex

Zootaxa ◽  
2008 ◽  
Vol 1949 (1) ◽  
pp. 1-29 ◽  
Author(s):  
SERGUEI V. TRIAPITSYN ◽  
GUILLERMO A. LOGARZO ◽  
JESSE H. DE LEÓN ◽  
EDUARDO G. VIRLA
Keyword(s):  
New Species ◽  
Species Complex ◽  
Reciprocal Cross ◽  
Molecular Data ◽  
Species Group ◽  
Host Association ◽  
Cross Breeding ◽  
Association Data ◽  
Distinguishing Features ◽  
Distinct Taxon

Gonatocerus deleoni Triapitsyn, Logarzo & Virla sp. n., reared from sentinel eggs of Tapajosa rubromarginata (Signoret) (Cicadellidae: Cicadellinae: Proconiini) on citrus plants, a new member of the ater species group of Gonatocerus Nees (Mymaridae), is described from the state of Mendoza, Argentina. Taxonomic notes and host association data are provided to help differentiate this new species from the morphologically similar but genetically distinct taxon, G. tuberculifemur (Ogloblin). The female of the latter is redescribed and the male is newly described. Gonatocerus deleoni, G. tuberculifemur, and three forms (different molecular clades) comprise the G. tuberculifemur complex. These forms are identified but not formally described because of lack of morphologically distinguishing features. The taxonomic conclusions are supported by molecular data, and by results of reciprocal cross-breeding experiments between most of them.

scholarly journals Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group

ZooKeys ◽  
2018 ◽  
Vol 751 ◽  
pp. 1-40 ◽  
Author(s):  
Alice Laciny ◽  
Herbert Zettel ◽  
Alexey Kopchinskiy ◽  
Carina Pretzer ◽  
Anna Pal ◽  
...  
Keyword(s):  
Species Complex ◽  
Mandibular Gland ◽  
Species Group ◽  
The Philippines ◽  
Species Level ◽  
Model Species ◽  
Species Identity ◽  
Taxonomic Description ◽  
Biological Studies ◽  
Taxonomic Changes

A taxonomic description of all castes of Colobopsisexplodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on “exploding ants” in Southeast Asia. The new species is a member of the Colobopsiscylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsissaundersi (Emery, 1889) (formerly Camponotussaundersi). The COCY species group is known under its vernacular name “exploding ants” for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsisexplodens Laciny & Zettel, sp. n. and Colobopsisbadia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C.explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C.badia, a lectotype from Singapore is designated. The following taxonomic changes within the C.saundersi complex are proposed: Colobopsissolenobia (Menozzi, 1926), syn. n. and Colobopsistrieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsiscorallina Roger, 1863, a common endemic species of the Philippines. Colobopsissaginata Stitz, 1925, stat. n., hitherto a subspecies of C.badia, is raised to species level.

Review of some species groups of the genus Oospila Warren, with descriptions of nine new species (Lepidoptera: Geometridae: Geometrinae)

Zootaxa ◽  
2018 ◽  
Vol 4497 (2) ◽  
pp. 151 ◽  
Author(s):  
AARE LINDT ◽  
AXEL HAUSMANN ◽  
JAAN VIIDALEPP
Keyword(s):  
New Species ◽  
Costa Rica ◽  
Species Complex ◽  
French Guiana ◽  
Species Group ◽  
New Subspecies ◽  
Wing Patterns ◽  
Species Groups ◽  
Males And Females

The Neotropical geometrine genus Oospila Warren, 1897 includes seventy-nine species and was revised by Cook & Scoble (1995). The genus is distinctive in having a row of raised abdominal crests, which are composed of specialized, erect, metallic shining scales. This paper focuses on the integrative morphological and molecular delimitation of the smallest Oospila species. The wing patterns and genitalia structures of males and females are illustrated. Cook & Scoble (1995) distinguished 13 species groups within Oospila. We discuss the species of the Oospila flavilimes species group, the O. stigma species group and O. miccularia species group below, and separate the O. arpata species complex into a group of its own. Nine new species and two new subspecies are described in this paper: O. cristae sp. n. from Ecuador, O. falcata sp. n. from French Guiana, O. pallidaria boliviensis subsp. n. from Bolivia, and O. loreenae sp. n. from Bolivia (flavilimes species group), O. ehakernae sp. n. from Costa Rica, O. similiplaga bolarpata subsp. n. from Bolivia (arpata species group), O. brehmi sp. n. and O. bifida sp. n. both from Bolivia, O. moseri sp. n. from Brazil, O. absaloni sp. n. and O. pipa sp. n. both from Ecuador (miccularia species group). Oospila similiplaga (Warren) (stat. nov.) is raised here from synonymy with O. arpata (Schaus) and O. imula (Dognin) from synonymy with O. miccularia (Guenée), respectively. Oospila agnetaforslundae nom. nov. is proposed as a replacement name for Oospila marginata Schaus, 1912 (nec Oospila marginata Warren, 1897), raising it to species rank from synonymy of Oospila permagna (Warren, 1909). With this paper, the number of Neotropical Oospila species is raised to 88. 

scholarly journals Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome

2020 ◽  
Vol 10 (3) ◽  
pp. 891-897 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

The Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193 Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromeres, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

Sign in / Sign up

Export Citation Format

Share Document