The global freshwater bivalve checklist’s extension: Freshwater occurrences and phylogenetic position of Galatea clams from West Africa (Venerida: Donacidae)

The bivalve genus Galatea Bruguière, 1797 (Venerida: Donacidae) was thought to contain exclusively brackish-water clams, the ranges of which are confined to estuaries and lower tidal parts of large rivers in West Africa. This genus was therefore included to the global freshwater bivalve checklists (Bogan 2013; Graf 2013) as a largely estuarine group. Conversely, a review of published data alongside our field surveys indicate that at least three populations of Galatea spp. largely occur in freshwater environment, i.e. those from the Sanaga (Cameroon), Niger (Nigeria), and Volta (Ghana) rivers. The systematic placement of these populations is unclear, as are the taxonomic status and validity of numerous nominal taxa described in this genus from a variety of localities throughout the Atlantic Coast of Africa (Angola to Senegal). We tentatively assign the populations from Niger and Volta to Galatea paradoxa (Born, 1778), while the Sanaga’s population is considered here as Galatea schwabi (Clench, 1929). However, these taxa do not share clear morphological differences and may belong to a single widespread species. In this study, we present the first DNA sequence data for a Galatea member, i.e. G. schwabi. Our COI phylogeny supports its placement within the family Donacidae suggesting sister relationships between Galatea and Donax Linnaeus, 1758. Most Galatea populations play a vital role for local riparian communities in West Africa as an intensively exploited food source. Furthermore, the clams are heavily threaten by anthropogenic impacts such as dam construction, riverbed substrate mining, and river pollution. The fishing loads and habitat degradation altogether lead to the rapid decreasing of Galatea populations in several water bodies, e.g. the Volta River in Ghana. It is impossible to develop conservation and management plans for these clams due to the lack of reliable species-level taxonomic concept of the genus. It is clear that the Galatea taxonomy and ecology need a thorough revision in the future based on DNA sequences of newly collected samples from all West African rivers, in which these remarkable clams occur.

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Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737541 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ying Zhang ◽

Yupei Zhou ◽

Wei Sun ◽

Lili Zhao ◽

D. Pavlic-Zupanc ◽

...

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Sequence Data ◽

Morphological Characteristics ◽

Taxonomic Status ◽

Morphological Characters ◽

Phylogenetic Position ◽

Type Specimens ◽

Natural Classification ◽

Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

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Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements

10.1101/2021.02.18.430751 ◽

2021 ◽

Author(s):

Sylvia Hofmann ◽

Daniel Jablonski ◽

Spartak Litvinchuk ◽

Rafaqat Masroor ◽

Joachim Schmidt

Keyword(s):

Sequence Data ◽

Gene Tree ◽

Early Miocene ◽

Phylogenetic Position ◽

Published Data ◽

Data Set ◽

Sister Clade ◽

Early Neogene ◽

Warm Temperate ◽

Temperate Climates

AbstractBackgroundThe Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the paleoecological development of Tibet.MethodsWe obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests.ResultsConsistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far north western part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene.

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Squamate relationships based on C-mos nuclear DNA sequences: increased taxon sampling improves bootstrap support

Amphibia-Reptilia ◽

10.1163/15685380152030454 ◽

2001 ◽

Vol 22 (2) ◽

pp. 235-242 ◽

Cited By ~ 25

Author(s):

J.C. Marshall ◽

K.A. Crandall ◽

D.J. Harris

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Sequence Data ◽

Nuclear Gene ◽

Bootstrap Support ◽

Published Data ◽

Robust Estimate ◽

Independent Evidence ◽

Rapid Speciation ◽

Mtdna Sequence

AbstractSequences of the nuclear gene C-mos from 16 new species have been combined with previously published data to produce an analysis of squamate relationships using 56 taxa, considerably more than in previous analyses. Support for many nodes is greatly increased, thus producing a more robust assessment of relationships. Sampling was concentrated within the families Iguanidae and Lacertidae, both of which have poorly supported phylogenies based on mtDNA sequence data. Our analysis supports a robust estimate of relationships within the Iguanidae. Within the Lacertidae relationships are only partially well resolved, and this provides independent evidence for rapid speciation within this family.

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New species of Moluccan trichaline net-winged beetles, with remarks on the phylogenetic position and distribution of Schizotrichalus (Coleoptera: Lycidae: Metriorrhynchinae)

Zootaxa ◽

10.11646/zootaxa.4623.2.8 ◽

2019 ◽

Vol 4623 (2) ◽

pp. 341-350 ◽

Cited By ~ 3

Author(s):

MATEJ BOCEK ◽

KRISTYNA ADAMKOVA

Keyword(s):

New Species ◽

Dna Sequences ◽

Morphological Traits ◽

New Guinea ◽

Molecular Data ◽

Phylogenetic Position ◽

General Validity ◽

Ancestral Area ◽

Recent Origin ◽

Sister Relationships

The Moluccan net-winged beetle fauna remains poorly studied and here, new species of Schizotrichalus Kleine, 1926 and Eniclases Waterhouse, 1879 are reported from Halmahera. Using morphological traits and cox1 mitochondrial DNA sequences, we propose two new species, Eniclases kusyi sp. nov. and Schizotrichalus halmaherensis sp. nov., and redescribe E. moluccanus Kleine, 1930. New molecular data confirm morphology-based sister relationships between Schizotrichalus and Eniclases and the analysis identifies the combined area of the present-day Halmahera and New Guinea as an ancestral area of these genera. Now, Halmahera and New Guinea are quite similar in respect of the number of trichaline genera. Concerning the size of islands and the recent origin of the nowadays northern Moluccas, these results are unexpected and thus the general validity of this distribution pattern should be confirmed with other groups of beetles.

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Mutations as Missing Data: Inferences on the Ages and Distributions of Nonsynonymous and Synonymous Mutations

Genetics ◽

10.1093/genetics/159.1.401 ◽

2001 ◽

Vol 159 (1) ◽

pp. 401-411

Author(s):

Rasmus Nielsen

Keyword(s):

Missing Data ◽

Dna Sequences ◽

Sequence Data ◽

Published Data ◽

Data Sets ◽

Effective Population ◽

Gene Genealogy ◽

Synonymous Mutations ◽

Dna Sequence Data ◽

Slightly Deleterious Mutations

AbstractThis article describes a new Markov chain Monte Carlo (MCMC) method applicable to DNA sequence data, which treats mutations in the genealogy as missing data. The method facilitates inferences regarding the age and identity of specific mutations while taking the full complexities of the mutational process in DNA sequences into account. We demonstrate the utility of the method in three applications. First, we demonstrate how the method can be used to make inferences regarding population genetical parameters such as θ (the effective population size times the mutation rate). Second, we show how the method can be used to estimate the ages of mutations in finite sites models and for making inferences regarding the distribution and ages of nonsynonymous and synonymous mutations. The method is applied to two previously published data sets and we demonstrate that in one of the data sets the average age of nonsynonymous mutations is significantly lower than the average age of synonymous mutations, suggesting the presence of slightly deleterious mutations. Third, we demonstrate how the method in general can be used to evaluate the posterior distribution of a function of a mapping of mutations on a gene genealogy. This application is useful for evaluating the uncertainty associated with methods that rely on mapping mutations on a phylogeny or a gene genealogy.

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Phylogeny of the water strider genus Aquarius Schellenberg (Heteroptera: Gerridae) based on nuclear and mitochondrial DNA sequences and morphology

Insect Systematics & Evolution ◽

10.1163/187631200x00327 ◽

2000 ◽

Vol 31 (1) ◽

pp. 71-90 ◽

Cited By ~ 26

Author(s):

Nils Møller Andersen ◽

Jakob Damgaard ◽

Felix A.H. Sperling

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Molecular Data ◽

Morphological Data ◽

Published Data ◽

Data Sets ◽

Gene Encoding ◽

Data Set

AbstractWe examined phylogenetic relationships among gerrid water striders of the genus Aquarius Schellenberg using molecular and morphological characters. The molecular data sets included 780 bp sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI), and 515 bp sequence data from the nuclear gene encoding elongation factor I alpha (EF-1α). The morphological data set was a slightly modified version of a previously published data set. We included all 17 known species and one subspecies of Aquarius as well as five species from three related genera, Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Gerris pingreensis, and G. lacustris. Unweighted parsimony analyses of the COI data set gave a single most parsimonious tree (MPT) with a topology quite similar to the morphological tree. Parsimony analyses of the EF-1α data set gave 3 MPT's and a strict consensus of these trees gave a tree with a slightly different topology. A combined analysis of the three data sets gave a single MPT with the same topology as for the morphological data set alone. The phylogeny of Aquarius presented here supports the monophyly of the A. najas, remigis, conformis and paludum species groups as well as previous hypotheses about their relationships. On the other hand, the inclusion of molecular data weakens the support for the monophyly of the genus Aquarius, and questions the specific status of the eastern North American A. nebularis (as separate from A. conformis) and members of the Nearctic A. remigis group. Finally, we discuss the implications of the reconstructed phylogeny in the biogeography and ecological phylogenetics of Aquarius.

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Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species

ZooKeys ◽

10.3897/zookeys.932.48532 ◽

2020 ◽

Vol 932 ◽

pp. 27-74 ◽

Cited By ~ 1

Author(s):

Avery S. Hatch ◽

Haebin Liew ◽

Stéphane Hourdez ◽

Greg W. Rouse

Keyword(s):

Pacific Ocean ◽

Atlantic Ocean ◽

Dna Sequences ◽

Deep Sea ◽

Gulf Of California ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Type Locality ◽

Phylogenetic Position ◽

28S Rrna

Polynoidae Kinberg, 1856 has five branchiate genera: Branchipolynoe Pettibone, 1984, Branchinotogluma Pettibone, 1985, Branchiplicatus Pettibone, 1985, Peinaleopolynoe Desbruyères & Laubier, 1988, and Thermopolynoe Miura, 1994, all native to deep-sea, chemosynthetic-based habitats. Of these, Peinaleopolynoe has two accepted species; Peinaleopolynoe sillardi Desbruyères & Laubier, 1988 (Atlantic Ocean) and Peinaleopolynoe santacatalina Pettibone, 1993 (East Pacific Ocean). The goal of this study was to assess the phylogenetic position of Peinaleopolynoe, utilizing DNA sequences from a broad sampling of deep-sea polynoids. Representatives from all five branchiate genera were included, several species of which were sampled from near the type localities; Branchinotogluma sandersi Pettibone, 1985 from the Galápagos Rift (E/V “Nautilus”); Peinaleopolynoe sillardi from organic remains in the Atlantic Ocean; Peinaleopolynoe santacatalina from a whalefall off southern California (R/V “Western Flyer”) and Thermopolynoe branchiata Miura, 1994 from Lau Back-Arc Basin in the western Pacific (R/V “Melville”). Phylogenetic analyses were conducted using mitochondrial (COI, 16S rRNA, and CytB) and nuclear (18S rRNA, 28S rRNA, and H3) genes. The analyses revealed four new Peinaleopolynoe species from the Pacific Ocean that are formally described here: Peinaleopolynoe orphanae Hatch & Rouse, sp. nov., type locality Pescadero Basin in the Gulf of California, Mexico (R/V “Western Flyer”); Peinaleopolynoe elvisi Hatch & Rouse, sp. nov. and Peinaleopolynoe goffrediae Hatch & Rouse, sp. nov., both with a type locality in Monterey Canyon off California (R/V “Western Flyer”) and Peinaleopolynoe mineoi Hatch & Rouse, sp. nov. from Costa Rica methane seeps (R/V “Falkor”). In addition to DNA sequence data, the monophyly of Peinaleopolynoe is supported by the presence of ventral papillae on segments 12–15. The results also demonstrated the paraphyly of Branchinotogluma and Lepidonotopodium Pettibone, 1983 and taxonomic revision of these genera is required. We apply the subfamily name Lepidonotopodinae Pettibone 1983, for the clade comprised of Branchipolynoe, Branchinotogluma, Bathykurila, Branchiplicatus, Lepidonotopodium, Levensteiniella Pettibone, 1985, Thermopolynoe, and Peinaleopolynoe.

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Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements

PeerJ ◽

10.7717/peerj.11793 ◽

2021 ◽

Vol 9 ◽

pp. e11793

Author(s):

Sylvia Hofmann ◽

Daniel Jablonski ◽

Spartak N. Litvinchuk ◽

Rafaqat Masroor ◽

Joachim Schmidt

Keyword(s):

Sequence Data ◽

Gene Tree ◽

Early Miocene ◽

Phylogenetic Position ◽

Published Data ◽

Northwestern Part ◽

Data Set ◽

Early Neogene ◽

Warm Temperate ◽

Temperate Climates

Background The Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the potential paleoecological development of Tibet. Methods We obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests. Results Consistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya, although a basal position of Allopaa to the genus Nanorana cannot be entirely excluded. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far northwestern part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene. They contradict prevalent geological models of a highly uplifted late Paleogene proto-Plateau.

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Salix transect of Europe: records of willow-associated weevils (Coleoptera: Curculionoidea) from Greece to Arctic Norway, with insights from DNA barcoding

Biodiversity Data Journal ◽

10.3897/bdj.8.e52881 ◽

2020 ◽

Vol 8 ◽

Author(s):

Roy Canty ◽

Enrico Ruzzier ◽

Quentin Cronk ◽

Diana Percy

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Sequence Data ◽

Size Variation ◽

Common Species ◽

Widespread Species ◽

Dna Sequence Data ◽

Geographic Clustering ◽

Site Variation ◽

The Mean

Curculionid beetles associated with willow (Salix spp.) were surveyed at 42 sites across Europe, from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N). DNA sequence data provide additional verification of identifications and geographic clustering. In all, 73 curculionid species were collected from willows, of which seven were particularly abundant. The most widespread species were: Acalyptus carpini Fabricius, 1793 at 15 sites; Tachyerges stigma Germar, 1821 at 13 sites; Phyllobius oblongus (Linnaeus, 1758) at 11 sites; Phyllobius maculicornis Germar, 1824 at 10 sites; and Archarius salicivorus (Paykull, 1792), Melanapion minimum (Herbst, 1797), and Phyllobius cf. pyri (Linnaeus, 1758) all at nine sites. The mean number of curculionid species collected on willow at each site was 5.5 (range 0-14). Compared to chrysomelids, curculionids were richer in species but the species had relatively low average abundance. Widespread curculionid species appear to have scattered and patchy observed distributions with limited geographical structuring in our data. However, deeper sampling (e.g. over multiple seasons and years), would give a better indication of distribution, and may increase apparent geographical structuring. There is some site-to-site variation in colour in a few taxa, but little notable size variation. DNA barcoding, performed on some of the more common species, provides clear species clusters and definitive separation of the taxonomically more challenging species, as well as some interesting geographic insights. Our northernmost sample of Phyllobius oblongus is unique in clustering with Canadian samples of this species. On the other hand, our samples of Acalyptus carpini cluster with European samples and are distinct from a separate Canadian cluster of this species. We provide the first available DNA sequences for Phyllobius thalassinus Gyllenhal, 1834 (Hungary).

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A novel Arabidopsis phyllosphere resident Protomyces sp. and a re-examination of genus Protomyces based on genome sequence data

10.1101/2019.12.13.875955 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kai Wang ◽

Timo Sipilä ◽

Kirk Overmyer

Keyword(s):

Dna Sequences ◽

Plant Pathogens ◽

Sequence Data ◽

Carbon Assimilation ◽

Morphological Characteristics ◽

Nuclear Gene ◽

Molecular Data ◽

Rapid Identification ◽

Phylogenetic Position ◽

Culture Collections

ABSTRACTProtomyces is a genus of yeast-like fungi that is currently defined as plant pathogens of only the Umbelliferae (Apiaceae) and Compositae (Asteraceae) family plants. Many Protomyces species have been proposed; however, there is a lack of molecular data and available specimens for Protomyces spp., just over ten species are officially accepted and only six species are preserved and available in public culture collections for examination. Phylogenetic relationships and species boundaries within this genus remain largely controversial. Recently, we isolated Protomyces strains from wild Arabidopsis thaliana (Arabidopsis), a Brassicaceae family plant only distantly related to the accepted Protomyces hosts. We have previously sequenced the genomes of all the currently public available Protomyces species, together with a strain (SC29) we isolated from the Arabidopsis phyllosphere. Genome-wide phylogenetic analysis suggests that SC29 occupies a unique phylogenetic position in the genus Protomyces. The SC29 genome has low average nucleotide identity values in comparison with other species genomes. As physiological evidence, SC29 has morphological characteristics and carbon assimilation patterns that distinguish it from the other six Protomyces species. Analysis with several nuclear gene phylogenetic markers further confirms SC29 as a novel Protomyces species and suggests the act1 gene DNA sequences can be used together with ITS sequences for the rapid identification of Protomyces species. In our previous study, SC29 could persist on the Arabidopsis phyllosphere in both short term laboratory and overwinter outdoor garden experiments and Protomyces spp. (or OTUs) were found in the Arabidopsis phyllosphere at multiple sites in both Finland and Germany. We conclude that SC29 is a novel Protomyces species isolated from Arabidopsis and propose the name of Protomyces arabidopsidicola sp. nov. Additionally, the genus Protomyces may not be strictly associated with only Compositae or Umbelliferae family host plants, as evidenced by SC29 and Protomyces strains previously isolated from plants in other families. The merging of two Protomyces species found to have high genomic similarity (P. inouyei and P. lactucaedebilis) is also proposed.

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