Influences of oceanic islands and the Pleistocene on the biogeography and evolution of two groups of Australasian parrots (Aves: Psittaciformes: Eclectus roratus, Trichoglossus haematodus complex). Rapid evolution and implications for taxonomy and conservation

AbstractThe Australasian region is a centre of biodiversity and endemism, mainly based on the tropical climate in combination with the large amount of islands. During the Pleistocene, islands of the Sahul Shelf (Australia, New Guinea, Aru Islands) had been part of the same land mass, while islands within the Wallacea (Lesser Sunda Islands, Moluccas, Sulawesi etc.) remained isolated. We investigated biogeographical avian diversification patterns of two species complexes across the Wallacea and the Sahul Shelf: the Eclectus Parrot Eclectus roratus Wagler, 1832, and the Rainbow Lorikeet Trichoglossus haematodus Linnaeus, 1771. Both species are represented by a large number of described geographical subspecies. We used mitochondrial cytochrome b (cyt b) sequences for phylogenetic and network analysis to detect biogeographic roles of islands and avian diversification patterns. The number of threatened taxa in this region is increasing rapidly and there is an urgent need for (sub-)species conservation in this region. Our study provides first genetic evidence for treating several island taxa as distinct species. In both species complexes similar genetic patterns were detected. Genetic diversification was higher across the islands of the Wallacea than across the islands of the Sahul Shelf. Divergence in E. roratus can be dated back about 1.38 million years ago, whereas in the younger T. haematodus it was 0.80 million years ago. Long distance dispersal was the most likely event for distribution patterns across the Wallacea and Sahul Shelf. The geographic origin of the species-complex Eclectus roratus spp. is supposed to be Wallacean, but for the species-complex Trichoglossus haematodus spp. it is supposed to be non-Wallacean. Trichoglossus euteles, so far considered a distinct species, clearly belongs to the Trichoglossus-haematodus-complex. The only case of sympatry in the complex is the distribution of T. (h.) euteles and T. h. capistratus on Timor, which means a rapid evolution from one ancestor into two distinct species within only 800,000 years. For all other taxa a Checkerboard distribution pattern is present. In this complex, 8 taxa are already treated as separate species (del Hoyo et al. 2014). Based on genetic evidence, the following populations are supported to represent phylogenetic units: (1) N New Guinea (haematodus) incl. Biak (rosenbergii), Bismarck Archipelago (massena), and New Caledonia (deplanchii); (2) Flores (weberi); (3) E Australia (moluccanus) incl. Aru Islands (nigrogularis) and S New Guinea (caeruleiceps); (4) N Australia (rubritorquis); (5) Timor 1st lineage (capistratus) incl. Sumba (fortis); (6) Bali and Lombok (mitchellii); (7) Sumbawa (forsteni); (8) Timor 2nd lineage (euteles). Those 8 phylogenetic units are not identical to the 8 species listed by del Hoyo et al. (2014). Several populations on smaller islands are under decline, a separate species status may lead to a higher conservation status in both species complexes, which are currently listed as “Least Concern”. Eclectus roratus is currently treated as monospecific. Based on genetic evidence, the following populations are suggested being treated as valid species: (1) Sumba (Eclectus cornelia), (2) Tanimbar Islands (E. riedeli), (3) Moluccas (E. roratus), and (4) New Guinea (E. polychloros incl. Aru Islands (E. aruensis), and Solomon Island (E. solomonensis).

Download Full-text

Veterinary Fusarioses within the United States

Journal of Clinical Microbiology ◽

10.1128/jcm.01607-16 ◽

2016 ◽

Vol 54 (11) ◽

pp. 2813-2819 ◽

Cited By ~ 21

Author(s):

Kerry O'Donnell ◽

Deanna A. Sutton ◽

Nathan Wiederhold ◽

Vincent A. R. G. Robert ◽

Pedro W. Crous ◽

...

Keyword(s):

United States ◽

Dna Sequence ◽

Species Complex ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Distinct Species ◽

The United States ◽

Content Type ◽

Dna Sequence Data ◽

Species Complexes

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67Fusariumstrains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within theFusarium solanispecies complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme,Fusarium keratoplasticum, andFusariumsp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of theF. falciformestrains (12/15) were recovered from equine keratitis infections; however, strains ofF. keratoplasticumandFusariumsp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that theFusarium incarnatum-equisetispecies complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance withinFusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and theFusarium oxysporumspecies complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

Download Full-text

Molecular, chromosomal and morphological characters reveal a new diploid species in the Smilax china complex (Smilacaceae)

Phytotaxa ◽

10.11646/phytotaxa.212.3.2 ◽

2015 ◽

Vol 212 (3) ◽

pp. 199 ◽

Cited By ~ 1

Author(s):

Yunpeng Zhao ◽

Zhongshuai Sun ◽

Yihan Wang ◽

Chengxin Fu

Keyword(s):

Species Complex ◽

Phylogenetic Analyses ◽

Diploid Species ◽

Distinct Species ◽

Morphological Characters ◽

Molecular Data ◽

Eastern Asia ◽

Diploid Population ◽

Species Complexes ◽

Molecular Phylogenetic

The Smilax china complex (Smilacaceae) is a typical mixoploid species complex including five extant diploid taxa with a widespread distribution across eastern Asia. The diploid population (mHB, 2n = 32), which was originally considered to be diploid S. china, together with two newly discovered diploid populations (mZZ and mYXS) is supported here as a distinct species by morphological, karyotypic and molecular data. These three populations present consistent morphological characters of sub-erect stems, rudimentary tendrils and minutely serrulate leaf margins, in which they differ from S. china. Molecular phylogenetic analyses also confirm its monophyly with a closer relationship to the other two erect species S. biflora and S. trinervula in the complex. These three populations are thus proposed to be a clear new diploid species and described with the name of Smilax microdontus Z. S. Sun & C.X. Fu, sp. nov. The discovery of this new species highlights the importance of closer examinations on species complexes by integrating multiple evidence.

Download Full-text

Analysis of the differences between Syntormon pallipes and S. pseudospicatus (Diptera: Dolichopodidae): morphological and molecular data

Zoosystematica Rossica ◽

10.31610/zsr/2019.28.2.305 ◽

2019 ◽

Vol 28 (2) ◽

pp. 305-316

Author(s):

M.A. Chursina ◽

I.Ya. Grichanov

Keyword(s):

Dna Analysis ◽

Distinct Species ◽

Molecular Data ◽

Wing Shape ◽

Morphological Data ◽

12S Rrna ◽

Separate Species ◽

Geometric Morphometric ◽

Geometric Morphometric Analysis ◽

Morphological And Molecular Data

The recent catalogues of the family Dolichopodidae considered Syntormon pallipes (Fabricius, 1794) and S. pseudospicatus Strobl, 1899 as separate species. In this study, we used three approaches to estimate the significance of differences between the two species: molecular analysis (COI and 12S rRNA sequences), analysis of leg colour characters and geometric morphometric analysis of wing shape. The morphological data confirmed the absence of significant differences between S. pallipes and S. pseudospicatus found in the DNA analysis. Significant differences in the wing shape of two species have not been revealed. Hence, according to our data, there is no reason to consider S. pseudospicatus as a distinct species.

Download Full-text

Redescription of Orthopristis ruber and Orthopristis scapularis (Haemulidae: Perciformes), with a hybridization zone off the Atlantic coast of South America

Zootaxa ◽

10.11646/zootaxa.4576.1.5 ◽

2019 ◽

Vol 4576 (1) ◽

pp. 109 ◽

Cited By ~ 1

Author(s):

ALEXANDRE PIRES MARCENIUK ◽

RODRIGO ANTUNES CAIRES ◽

LEONARDO MACHADO ◽

NAJILA NOLIE CATARINE DANTAS CERQUEIRA ◽

RAYLA ROBERTA M. DE S. SERRA ◽

...

Keyword(s):

South America ◽

Nuclear Dna ◽

Atlantic Coast ◽

Morphological Characteristics ◽

Distinct Species ◽

Valid Species ◽

Brazilian Coast ◽

Northern Coast ◽

Western Atlantic ◽

Coloration Patterns

The genus Orthopristis includes seven valid species, three from the western Atlantic and five from eastern Pacific, while the available identification guides and taxonomic keys incorrectly recognize Orthopristis ruber as the only valid species found on the Atlantic coast of South America. Efforts to expand the inventory of fish species from the northern coast of Brazil led to the identification of two distinct species of Orthopristis from Atlantic South America, based on the analysis of coloration patterns and meristic data, as well as DNA. In the present study, the limits of Orthopristis ruber are reviewed, while Orthopristis scapularis is recognized as a valid species for the northern and northeastern coasts of South America. Based on intermediate morphological characteristics and nuclear DNA markers, a hybrid zone was identified off the state of Espírito Santo, on the eastern Brazilian coast. Additionally, considerations are made on the diversity and biogeography of the coastal marine and estuarine fishes found on the Brazilian coast.

Download Full-text

Disentangling Species Delineation and Guiding Conservation of Endangered Magnolias in Veracruz, Mexico

Plants ◽

10.3390/plants10040673 ◽

2021 ◽

Vol 10 (4) ◽

pp. 673

Author(s):

Fabián Augusto Aldaba Aldaba Núñez ◽

Emily Veltjen ◽

Esteban Manuel Martínez Martínez Salas ◽

Marie-Stéphanie Samain

Keyword(s):

Conservation Status ◽

Full Range ◽

Genetic Evidence ◽

Primary Forest ◽

Volcanic Area ◽

Conservation Units ◽

Separate Species ◽

Representative Sampling ◽

Conservation Projects ◽

Very High

The Mexican state of Veracruz has suffered very high deforestation rates in the last few decades, and despite the establishment of protected areas and conservation projects, primary forest is now mainly persisting in mostly small, scattered, fragmented remnants. New species of Magnolia section Talauma in this state have been described with little to no reference to the already existing ones, potentially resulting in over-splitting, obscuring their taxonomic delineation and conservation status, and consequently conservation programs. To study the conservation units and their genetic diversity, we here employ 15 microsatellite markers on a highly representative sampling of 254 individuals of what are presumed to be five Magnolia species. The results support at least three species and maximum five main conservation units. We propose downgrading the latter to four, given morphological, ecological, demographical, and geographical considerations. Two out of the three sympatrically occurring species in the rainforest in the Los Tuxtlas volcanic area have weak genetic evidence to be considered separate species. Similarly, the individuals in the Sierra de Zongolica in central Veracruz, who bear a very high morphological and genetic similarity to Magnolia mexicana, have weak genetic evidence to be recognised as a separate species. Nonetheless, the individuals could be identified as Magnolia decastroi based on morphology, and further research including the full range of this species is recommended.

Download Full-text

Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

Genome Biology and Evolution ◽

10.1093/gbe/evab020 ◽

2021 ◽

Author(s):

Anna Lavecchia ◽

Matteo Chiara ◽

Caterina De Virgilio ◽

Caterina Manzari ◽

Carlo Pazzani ◽

...

Keyword(s):

Comparative Genomics ◽

Species Complex ◽

Large Scale ◽

Genomic Sequence ◽

Bacterial Species ◽

Taxonomic Revision ◽

Distinct Species ◽

The Novel ◽

Staphylococcus Cohnii ◽

Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Download Full-text

The taxonomic history of Indo-Papuan groundsnakes, genus Stegonotus Duméril et al., 1854 (Colubridae), with some taxonomic revisions and the designation of a neotype for S. parvus (Meyer, 1874)

Zootaxa ◽

10.11646/zootaxa.4512.1.1 ◽

2018 ◽

Vol 4512 (1) ◽

pp. 1

Author(s):

CHRISTINE M. KAISER ◽

HINRICH KAISER ◽

MARK O’SHEA

Keyword(s):

New Guinea ◽

Molecular Data ◽

The Philippines ◽

Morphological Data ◽

Valid Species ◽

Museum Specimens ◽

Type Specimens ◽

History Of ◽

Original Species ◽

Species Specific

Since its conceptualization in 1854, 29 species of the colubrid genus Stegonotus have been recognized or described, of which 15 (admiraltiensis, batjanensis, borneensis, cucullatus, derooijae, diehli, florensis, guentheri, iridis, heterurus, melanolabiatus, modestus, muelleri, parvus, poechi) are still considered valid today. Original species descriptions for the members of this genus were published in Dutch, English, French, German, and Italian and, perhaps as a consequence of these polyglot origins, there has been a considerable amount of confusion over which species names should be applied to which populations of Stegonotus throughout its range across Borneo, the Philippines, Wallacea, New Guinea, Australia, and associated archipelagos. In addition, the terminology used to notate characteristics in the descriptions of these forms was not uniform and may have added to the taxonomic confusion. In this paper, we trace in detail the history of the type specimens, the species, and the synonyms currently associated with the genus Stegonotus and provide a basic, species-specific listing of their characteristics, derived from our examination of over 1500 museum specimens. Based on our data, we are able to limit the distribution of S. modestus to the islands of Ambon, Buru, and Seram in the central Moluccas of Indonesian Wallacea. We correct the type locality of S. cucullatus to the Manokwari area on the Bird’s Head Peninsula of West Papua, Indonesian New Guinea and designate a neotype for S. parvus, a species likely to be a regional endemic in the Schouten Archipelago of Cenderawasih Bay (formerly Geelvink Bay), Indonesian New Guinea. We unequivocally identify and explain the problematic localities of the type specimens of S. muelleri and Lycodon muelleri, which currently reside in the same specimen jar. We remove L. aruensis and L. lividum from the synonymy of S. modestus and recognize them as S. aruensis n. comb. and S. lividus n. comb., respectively. We remove S. keyensis and Zamenophis australis from the synonymy of S. cucullatus and recognize them as S. keyensis n. comb. and S. australis n. comb., respectively. We further remove S. reticulatus from the synonymy of S. cucullatus, S. dorsalis from the synonymy of S. diehli, and S. sutteri from the synonymy of S. florensis. We designate lectotypes for S. guentheri, S. heterurus, S. lividus, and S. reticulatus. Lastly, we introduce S. poechi, a valid species not mentioned in the scientific literature since its description in 1924. This brings the diversity in the genus Stegonotus to 22 species. We also caution that in a complex group of organisms like Stegonotus any rush to taxonomic judgment on the basis of molecular and incomplete morphological data sets may perpetuate errors and introduce incongruities. Only through the careful work of connecting type material with museum specimens and molecular data can the taxonomy and nomenclature of complex taxa be stabilized.

Download Full-text

Biodiversity Inventory and Distribution of Metriorrhynchina Net-Winged Beetles (Coleoptera: Lycidae), with the Identification of Generic Ranges

Insects ◽

10.3390/insects11100710 ◽

2020 ◽

Vol 11 (10) ◽

pp. 710

Author(s):

Ladislav Bocak ◽

Michal Motyka ◽

Dominik Kusy ◽

Renata Bilkova

Keyword(s):

Solomon Islands ◽

New Guinea ◽

The Philippines ◽

Species Level ◽

Valid Species ◽

Distribution Data ◽

Generic Level ◽

Biodiversity Inventory ◽

Australian Continent ◽

Northern Edge

We reviewed the species-level classification of Metriorrhynchina net-winged beetles to make the group accessible for further studies. Altogether, 876 valid species are listed in a checklist along with known synonyms, combinations, and distribution data. The compilation of geographic distribution showed that Metriorrhynchina is distributed mainly in the Australian region with very high diversity in the islands at the northern edge of the Australian craton, i.e., in the Moluccas and New Guinea (54 and 423 spp. respectively). The neighboring northern part of the Australian continent houses a majority of known Australian species (112 spp.) and the diversity of net-winged beetles gradually decreases to the south (43 spp.). The fauna of Sulawesi is highly endemic at the generic level (4 of 10 genera, 67 of 84 spp.). Less Metriorrhynchina occur in the Solomon Islands and Oceania (in total 22 spp.). The Oriental Metriorrhynchina fauna consists of a few genera and a limited number of species, and most of these are known from the Philippines (51 of 94 Oriental spp.). We identified a high species level turn-over between all neighboring landmasses. The genus-level endemism is high in Sulawesi (4 genera) and New Guinea (11 genera), but only a single genus is endemic to Australia. During the compilation of the checklist, we identified some homonyms, and we propose the following replacement names and a new synonym: Metriorrhynchus pseudobasalis, nom. nov. for M. basalis Lea, 1921 nec M. basalis Bourgeois, 1911; Metriorrhynchus pseudofunestus, nom. nov. for M. funestus Lea, 1921 nec M. funestus (Guérin-Méneville, 1838), Trichalus pseudoternatensis, nom. nov. for T. ternatensis Kleine, 1930 nec T. ternatensis Bourgeois, 1900, Procautires subparallelus, nom. nov. for P. parallelus (Pic, 1926) nec P. parallelus (Bourgeois, 1883), and Cautires pseudocorporaali, nom. nov. for C. corporaali (Pic, 1921: 12), (formerly Odontocerus and Cladophorus) nec C. corporaali (Pic, 1921) (formerly Bulenides, later Cautires). Diatrichalus biroi Kleine, 1943, syn. nov. is proposed as a junior subjective synonym of D. subarcuatithorax (Pic, 1926). Altogether, 161 new combinations are proposed, and 47 species earlier placed in Xylobanus Waterhouse, 1879 transferred from Cautirina to Metriorrhynchina incertae sedis. The study clarifies the taxonomy of Metriorrhynchini and should serve as a restarting point for further taxonomic, evolutionary, and biogeographic studies.

Download Full-text

Optimal markers for the identification ofColletotrichumspecies

10.1101/659177 ◽

2019 ◽

Cited By ~ 2

Author(s):

Willie Anderson dos Santos Vieira ◽

Priscila Alves Bezerra ◽

Anthony Carlos da Silva ◽

Josiene Silva Veloso ◽

Marcos Paz Saraiva Câmara ◽

...

Keyword(s):

Molecular Markers ◽

Species Complex ◽

Plant Pathogens ◽

Phylogenetic Signal ◽

Intergenic Spacer ◽

Internal Transcribed Spacers ◽

Type Locus ◽

Phylogenetic Studies ◽

Fungal Plant Pathogens ◽

Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

Download Full-text

Toward a comprehensive taxonomic revision of the “hirculus” group of American Onthophagus Latreille, 1802 (Coleoptera, Scarabaeidae, Scarabaeinae)

European Journal of Taxonomy ◽

10.5852/ejt.2018.432 ◽

2018 ◽

Cited By ~ 3

Author(s):

Michele Rossini ◽

Fernando Z. Vaz-de-Mello ◽

Mario Zunino

Keyword(s):

Geographic Distribution ◽

General Scheme ◽

Taxonomic Revision ◽

Junior Synonym ◽

Valid Species ◽

Species Complexes ◽

Scarab Beetles

The taxonomy of the American Onthophagus Latreille, 1802 included in the “hirculus” group is revised, and a study of their morphology allows for the delineation of five species-complexes. Herein, we provide a diagnosis of the “hirculus” group, an illustrated key to the complexes, along with a descriptive overview of their taxonomy and geographic distribution. Onthophagus hirculus Mannerheim, 1829 is considered to be a junior synonym of O. hircus Billberg, 1815, which is here demonstrated to be a valid species name. Thus, the “hirculus” group is here renamed the “hircus” group. Furthermore, a general scheme of the genital organs of American Onthophagus is provided, including names of different anatomical parts and a brief discussion on the need for nomenclatural stability for the genitalia of scarab beetles.

Download Full-text