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

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.

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

PeerJ ◽  
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.

scholarly journals Phylogenetic signal is associated with the degree of variation in root-to-tip distances

2020 ◽  
Author(s):  
Mezzalina Vankan ◽  
Simon Y.W. Ho ◽  
Carolina Pardo-Diaz ◽  
David A. Duchêne
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Phylogenetic Inference ◽  
Genomic Region ◽  
Published Data ◽  
Data Sets ◽  
Gene Trees ◽  
Species Trees ◽  
Data Set

AbstractThe phylogenetic information contained in sequence data is partly determined by the overall rate of nucleotide substitution in the genomic region in question. However, phylogenetic signal is affected by various other factors, such as heterogeneity in substitution rates across lineages. These factors might be able to predict the phylogenetic accuracy of any given gene in a data set. We examined the association between the accuracy of phylogenetic inference across genes and several characteristics of branch lengths in phylogenomic data. In a large number of published data sets, we found that the accuracy of phylogenetic inference from genes was consistently associated with their mean statistical branch support and variation in their gene tree root-to-tip distances, but not with tree length and stemminess. Therefore, a signal of constant evolutionary rates across lineages appears to be beneficial for phylogenetic inference. Identifying the causes of variation in root-to-tip lengths in gene trees also offers a potential way forward to increase congruence in the signal across genes and improve estimates of species trees from phylogenomic data sets.

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

scholarly journals Anchored Hybrid Enrichment-Based Phylogenomics of Leafhoppers and Treehoppers (Hemiptera: Cicadomorpha: Membracoidea)

2017 ◽  
Vol 1 (1) ◽  
pp. 57-72 ◽  
Author(s):  
Christopher H Dietrich ◽  
Julie M Allen ◽  
Alan R Lemmon ◽  
Emily Moriarty Lemmon ◽  
Daniela M Takiya ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Single Gene ◽  
Gene Tree ◽  
Divergence Time ◽  
Data Set ◽  
Nucleotide Sequence Data ◽  
Divergence Time Estimates ◽  
Morphological Criteria ◽  
Anchored Hybrid Enrichment

Abstract A data set comprising DNA sequences from 388 loci and >99,000 aligned nucleotide positions, generated using anchored hybrid enrichment, was used to estimate relationships among 138 leafhoppers and treehoppers representative of all major lineages of Membracoidea, the most diverse superfamily of hemipteran insects. Phylogenetic analysis of the concatenated nucleotide sequence data set using maximum likelihood produced a tree with most branches receiving high support. A separate coalescent gene tree analysis of the same data generally recovered the same strongly supported clades but was less well resolved overall. Several nodes pertaining to relationships among leafhopper subfamilies currently recognized based on morphological criteria were separated by short internodes and received low support. Although various higher taxa were corroborated with improved branch support, relationships among some major lineages of Membracoidea are only somewhat more resolved than previously published phylogenies based on single gene regions or morphology. In agreement with previous studies, the present results indicate that leafhoppers (Cicadellidae) are paraphyletic with respect to the three recognized families of treehoppers (Aetalionidae, Melizoderidae, and Membracidae). Divergence time estimates indicate that most of the poorly resolved divergence events among major leafhopper lineages occurred during the lower to middle Cretaceous and that most modern leafhopper subfamilies, as well as the lineage comprising the three recognized families of treehoppers, also arose during the Cretaceous.

Phylogenetic position of Pelusios williamsi and a critique of current GenBank procedures (Reptilia: Testudines: Pelomedusidae)

2012 ◽  
Vol 33 (1) ◽  
pp. 150-154 ◽  
Author(s):  
Uwe Fritz ◽  
Mario Vargas-Ramírez ◽  
Pavel Široký
Keyword(s):  
Natural History ◽  
Genetic Divergence ◽  
Best Practice ◽  
Nuclear Data ◽  
Phylogenetic Position ◽  
Published Data ◽  
Data Sets ◽  
Natural History Museums ◽  
Data Set ◽  
History Museums

We re-examine the phylogenetic position of Pelusios williamsi by merging new sequences with an earlier published data set of all Pelusios species, except the possibly extinct P. seychellensis, and the nine previously identified lineages of the closely allied genus Pelomedusa (2054 bp mtDNA, 2025 bp nDNA). Furthermore, we include new sequences of Pelusios broadleyi, P. castanoides, P. gabonensis and P. marani. Individual and combined analyses of the mitochondrial and nuclear data sets indicate that P. williamsi is sister to P. castanoides, as predicted by morphology. This provides evidence for the misidentification of GenBank sequences allegedly representing P. williamsi. Such mislabelled GenBank sequences contribute to continued confusion, because only the original submitter can revise their identification; an impractical procedure impeding the rectification of obvious mistakes. We recommend implementing another option for revising taxonomic identifications, paralleling the century-old best practice of natural history museums for new determinations of specimens. Within P. broadleyi, P. gabonensis and P. marani, there is only shallow genetic divergence, while some phylogeographic structuring is present in the wide-ranging species P. castaneus and P. castanoides.

scholarly journals Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona)

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 765-775
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Tandem Repeats ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Maximum Parsimony Analysis ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Data Sets ◽  
Data Set ◽  
Protein Coding

Abstract The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNACys). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets—one combining protein-coding genes and the other combining tRNA genes—strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated.

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

2020 ◽  
Vol 35 ◽  
pp. 144-158
Author(s):  
Alexander V. Kondakov ◽  
Ekaterina S. Konopleva ◽  
Abiona J. Adesanya ◽  
Yulia V. Bespalaya ◽  
Jean J. Braun ◽  
...  
Keyword(s):  
West Africa ◽  
Dna Sequences ◽  
Sequence Data ◽  
Anthropogenic Impacts ◽  
Phylogenetic Position ◽  
Published Data ◽  
Freshwater Bivalve ◽  
Freshwater Environment ◽  
Widespread Species ◽  
Sister Relationships

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.

scholarly journals Mitochondrial cob and cox1 Genes and Editing of the Corresponding mRNAs in Dinophysis acuminata from Narragansett Bay, with Special Reference to the Phylogenetic Position of the Genus Dinophysis

2007 ◽  
Vol 74 (5) ◽  
pp. 1546-1554 ◽  
Author(s):  
Huan Zhang ◽  
Debashish Bhattacharya ◽  
Lucie Maranda ◽  
Senjie Lin
Keyword(s):  
Flow Cytometry ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
Narragansett Bay ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Data Set ◽  
Specific Pcr ◽  
Dinophysis Acuminata ◽  
Unbiased Test

ABSTRACT Dinophysis acuminata cells were isolated from Narragansett Bay water samples in June 2005 using flow cytometry. Dinoflagellate-specific PCR primers were used to isolate small-subunit rRNA (18S rRNA), mitochondrial cytochrome b (cob), and cytochrome c oxidase I (cox1) genes and the encoded cDNAs. Maximum-likelihood analysis of a concatenated data set of ribosomal DNA and cDNA sequences of cob and cox1 showed that D. acuminata was sister to Gonyaulacoids, but without strong bootstrap support. The approximately unbiased test could not reject alternative positions of D. acuminata. To gain better resolution, mRNA editing of cob and cox1 was inferred for D. acuminata and 13 other dinoflagellate species. The location and type of editing as well as the distribution pattern in D. acuminata were generally similar to those in other dinoflagellates except for two edited sites that are unique to this species. Bayesian analyses of a matrix that recorded the location and type of editing, and of a matrix that included the protein sequences of COB and COX1 with the editing data yielded tree topologies similar to the three-gene tree but again failed to resolve the phylogenetic position of D. acuminata. However, the density of edited sites in the D. acuminata mitochondrial genes, consistent with phylogenetic trees, indicated that Dinophysis is a derived dinoflagellate lineage, diverging after other lineages such as Oxyrrhis, Amphidinium, and Symbiodinium. We demonstrate that dinoflagellate-specific PCR coupled with flow cytometry can be a useful tool to analyze genes and their transcripts from a natural dinoflagellate population.

Serpulidae (Annelida, Polychaeta) from Patton-Murray Seamounts, Gulf of Alaska, North Pacific Ocean

Zootaxa ◽  
2010 ◽  
Vol 2665 (1) ◽  
pp. 51 ◽  
Author(s):  
ELENA K. KUPRIYANOVA ◽  
EIJIROH NISHI
Keyword(s):  
Sequence Data ◽  
North Pacific Ocean ◽  
Gulf Of Alaska ◽  
Sister Group ◽  
Maximum Parsimony Analysis ◽  
Phylogenetic Position ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The North

A collection of Serpulidae (Annelida, Polychaeta) from the Patton-Murray Seamounts, Gulf of Alaska, USA contained three species Apomatus voightae n. sp., Bathyvermilia eliasoni n. comb., and Hyalopomatus biformis (Hartman, 1960). Apomatus voightae n. sp. differed from all other Apomatus spp. and from all known serpulid species by very unusual flat and ribbon-like branchial radioles as well by details of chaetal structure. Vermiliopsis eliasoni Zibrowius (1970) previously known from Atlantic and Mediterranean, was transferred to the genus Bathyvermilia Zibrowius, 1973. Hyalopomatus biformis is a deep-sea species distributed in the north-eastern Pacific from Alaska to California, USA. All serpulids were described in detail and their chaetal structure elucidated with the help of scanning electron microscopy. Molecular sequence data (18S rDNA) were aligned to a recently published serpulid data set and maximum parsimony analysis was performed to examine the phylogenetic position of the species and confirm their identification. Hyalopomatus biformis formed a sister group with Laminatubus alvini, Apomatus voightae n. sp. formed a sister group with Apomatus globifer, and Bathyvermilia eliasoni formed a weakly supported polytomy with Chitinopoma serrula, Protula tubularia and Apomatus spp. We briefly discussed biogeographic affinities of the serpulids from the PattonMurray Seamounts in the light of seamount ecology and biogeography.

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

2000 ◽  
Vol 31 (1) ◽  
pp. 71-90 ◽  
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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