Molecular Phylogeny and Biogeography of the Tasmanian and New Zealand Mudfishes (Salmoniformes : Galaxiidae)

1997 ◽  
Vol 45 (1) ◽  
pp. 39 ◽  
Author(s):  
J. M. Waters ◽  
R. W. G. White
Keyword(s):  
New Zealand ◽  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Convergent Evolution ◽  
Sequence Data ◽  
Mitochondrial Genes ◽  
Divergence Times ◽  
Marine Dispersal ◽  
Close Phylogenetic Relationship ◽  
Phylogenetic Affinities

The phylogenetic affinities of the diadromous Tasmanian mudfish, Galaxias cleaveri, have long been problematic. Some systematists have suggested that this species is closely related to the morphologically similar but non-diadromous New Zealand mudfish genus, Neochanna, while others argued that the similarities represent convergent evolution. Most recently, the Tasmanian mudfish was allocated to Neochanna on morphological grounds. The current paper presents sequence data from two mitochondrial genes that support this decision, revealing a close phylogenetic relationship between Tasmanian and New Zealand mudfish. Molecular clock calibrations are used to examine hypotheses of mudfish evolution and biogeography. Estimated divergence times are consistent with the suggestion that Neochanna burrowsius and N. apoda were separated by the uplift of New Zealand’s southern Alps about five million years ago. In addition, the divergence of the Tasmanian and New Zealand mudfish appears to postdate the rifting of Gondwana and is best explained by marine dispersal during the Pliocene.

Molecular phylogeny and biogeography of the Tasmanian and New Zealand mudfishes (Salmoniformes : Galaxiidae)

1997 ◽  
Vol 45 (6) ◽  
pp. 671
Author(s):  
J. M. Waters ◽  
R. W. G. White
Keyword(s):  
New Zealand ◽  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Convergent Evolution ◽  
Sequence Data ◽  
Mitochondrial Genes ◽  
Divergence Times ◽  
Marine Dispersal ◽  
Close Phylogenetic Relationship ◽  
Phylogenetic Affinities

The phylogenetic affinities of the diadromous Tasmanian mudfish, Galaxias cleaveri, have long been problematic. Some systematists have suggested that this species is closely related to the morphologically similar but non-diadromous New Zealand mudfish genus, Neochanna, while others argued that the similarities represent convergent evolution. Most recently, the Tasmanian mudfish was allocated to Neochanna on morphological grounds. The current paper presents sequence data from two mitochondrial genes that support this decision, revealing a close phylogenetic relationship between Tasmanian and New Zealand mudfish. Molecular clock calibrations are used to examine hypotheses of mudfish evolution and biogeography. Estimated divergence times are consistent with the suggestion that Neochanna burrowsius and N. apoda were separated by the uplift of New Zealand’s southern Alps about five million years ago. In addition, the divergence of the Tasmanian and New Zealand mudfish appears to postdate the rifting of Gondwana and is best explained by marine dispersal during the Pliocene.

scholarly journals RelTime relaxes the strict molecular clock throughout the phylogeny

2017 ◽  
Author(s):  
Fabia U. Battistuzzi ◽  
Qiqing Tao ◽  
Lance Jones ◽  
Koichiro Tamura ◽  
Sudhir Kumar
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Evolutionary Rates ◽  
Molecular Dating ◽  
Divergence Times ◽  
Similar Time ◽  
Time Estimates ◽  
Theoretical Analyses ◽  
Strict Molecular Clock ◽  
Median Rate

AbstractThe RelTime method estimates divergence times when evolutionary rates vary among lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny, and it performs well in the analysis of empirical and computer simulated datasets in which evolutionary rates are variable. Lozano-Fernandez et al. (2017) found that the application of RelTime to one metazoan dataset (Erwin et al. 2011) produced equal rates for several ancient lineages, which led them to speculate that RelTime imposes a strict molecular clock for deep animal divergences. RelTime does not impose a strict molecular clock. The pattern observed by Lozano-Fernandez et al. (2017) was a result of the use of an option to assign the same rate to lineages in RelTime when the rates are not statistically significantly different. The median rate difference was 5% for many deep metazoan lineages for Erwin et al. (2011) dataset, so the rate equality was not rejected. In fact, RelTime analysis with and without the option to test rate differences produced very similar time estimates. We found that the Bayesian time estimates vary widely depending on the root priors assigned, and that the use of less restrictive priors produce Bayesian divergence times that are concordant with those from RelTime for Erwin et al. (2011) dataset. Therefore, it is prudent to discuss Bayesian estimates obtained under a range of priors in any discourse about molecular dating, including method comparisons.

scholarly journals Evolution of gliding in Southeast Asian geckos and other vertebrates is temporally congruent with dipterocarp forest development

2012 ◽  
Vol 8 (6) ◽  
pp. 994-997 ◽  
Author(s):  
Matthew P. Heinicke ◽  
Eli Greenbaum ◽  
Todd R. Jackman ◽  
Aaron M. Bauer
Keyword(s):  
Tropical Forests ◽  
Molecular Clock ◽  
Temporal Pattern ◽  
Sequence Data ◽  
Southeast Asian ◽  
Vertebrate Evolution ◽  
Divergence Times ◽  
Dipterocarp Forest ◽  
Time Period ◽  
Repeated Evolution

Gliding morphologies occur in diverse vertebrate lineages in Southeast Asian rainforests, including three gecko genera, plus frogs, snakes, agamid lizards and squirrels. It has been hypothesized that repeated evolution of gliding is related to the dominance of Asian rainforest tree floras by dipterocarps. For dipterocarps to have influenced the evolution of gliding in Southeast Asian vertebrates, gliding lineages must have Eocene or later origins. However, divergence times are not known for most lineages. To investigate the temporal pattern of Asian gliding vertebrate evolution, we performed phylogenetic and molecular clock analyses. New sequence data for geckos incorporate exemplars of each gliding genus ( Cosymbotus , Luperosaurus and Ptychozoon ), whereas analyses of other vertebrate lineages use existing sequence data. Stem ages of most gliding vertebrates, including all geckos, cluster in the time period when dipterocarps came to dominate Asian tropical forests. These results demonstrate that a gliding/dipterocarp correlation is temporally viable, and caution against the assumption of early origins for apomorphic taxa.

scholarly journals A new microphthalmic stygobitic Graptodytes Seidlitz from Morocco, with a molecular phylogeny of the genus (Coleoptera, Dytiscidae)

Zootaxa ◽  
2010 ◽  
Vol 2641 (1) ◽  
pp. 1 ◽  
Author(s):  
IGNACIO RIBERA ◽  
ARNAUD FAILLE
Keyword(s):  
Molecular Phylogeny ◽  
Canary Islands ◽  
Molecular Clock ◽  
Late Miocene ◽  
Ventral View ◽  
Mitochondrial Genes ◽  
Phylogenetic Position ◽  
Median Lobe ◽  
High Atlas ◽  
Deep Area

We describe Graptodytes eremitus n.sp. (Coleoptera, Dytiscidae), a depigmented, microphthalmic stygobitic species found in a pool in the deep area of a cave in the High Atlas of Morocco. To establish its phylogenetic position we inferred a molecular phylogeny of the genus Graptodytes Seidlitz, using ca. 1.7 Kb of four mitochondrial genes for 18 of the 23 previously known species and subspecies of the genus. Graptodytes can be separated in three well supported main lineages, 1) the G. flavipes lineage (apex of median lobe narrow in ventral view), 2) the G. granularis lineage (apex of median lobe expanded and strongly asymmetrical in ventral view), and 3) the G. varius lineage (apex of median lobe expanded but symmetrical in ventral view). The G. varius lineage includes the G. aequalis and G. varius groups, the latter including G. eremitus n.sp. as sister to G. delectus Wollaston (Canary Islands) plus the G. varius complex. A molecular clock approach, using a calibration rate of 2.3% divergence/MY for the combined mitochondrial sequence, estimated the origin of the diversification within the genus at ca. 7MY (late Miocene), and the origin of G. eremitus n.sp. at ca. 2 MY (Pliocene-Pleistocene boundary).

A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny

Zootaxa ◽  
2009 ◽  
Vol 2211 (1) ◽  
pp. 1-35 ◽  
Author(s):  
MATTHEW P. HEINICKE ◽  
WILLIAM E. DUELLMAN ◽  
LINDA TRUEB ◽  
D. BRUCE MEANS ◽  
ROSS D. MacCULLOCH ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Mitochondrial Genes ◽  
Direct Development ◽  
Morphological Evidence ◽  
New Family ◽  
Close Phylogenetic Relationship ◽  
Basal Clade ◽  
Relationship Of ◽  
A New Species

Three frogs of a new species found in cloud forests on two nearby mountains in Guyana were included in a molecular phylogeny of 17 nuclear and mitochondrial genes (10,739 aligned sites) that revealed that their closest relative is Terrarana (Brachycephalidae, Craugastoridae, Eleutherodactylidae, and Strabomantidae) and their next-closest relative is Hemiphractidae (marsupial frogs). We place these frogs in a new family, genus, and species which is strongly supported as the basal clade within Terrarana: Ceuthomantidae n. fam., Ceuthomantis smaragdinus n. gen, n. sp. Morphological evidence supports the placement of two other species from the Guiana Highlands, Pristimantis aracamuni (BarrioAmorós & Molina) and P. cavernibardus (Myers & Donnelly), in the new family and genus. This close phylogenetic relationship of terraranans and marsupial frogs, nearly all of which have direct development, supports an hypothesis that direct development evolved early in the evolution of this huge clade (~1000 species), for which we propose the unranked taxonomic epithet Orthobatrachia.

scholarly journals A molecular phylogeny of Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) based on 12 protein-coding mitochondrial genes and RAG1 gene analysis

2019 ◽  
Author(s):  
Yurong Du ◽  
Ting Wang ◽  
Delin Qi ◽  
Desheng Qi ◽  
Weilin Li ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Sister Group ◽  
Mitochondrial Genes ◽  
Tibet Plateau ◽  
Divergence Times ◽  
Protein Coding ◽  
Rag1 Gene ◽  
The Times

AbstractThe ever-increasing interest in the investigation of origin and speciation of schizothoracine fishes can be dated to 20th century. However, molecular phylogeny of Schizothoracinae and their phylogenetic relationships, as well as the divergence times still remain controversial. In this study, two DNA sets consisting of 12 protein-coding mitochondrial genes from 254 individuals and RAG1 gene from 106 individuals were used to reconstruct the phylogenetic relationships and calculate the divergence times among the subfamily schizothoracinae. Our results indicated that both of the data sets supported a non-monophyletic relationship due to involving of species of Barbinae. However, the phylogenetic relationships based on mtDNA genes were more reliable than that inferred from RAG1 gene. The highly specialized grade formed a monophyletic group, together with Ptychobarbus as a sister group of Diptychus and Gymnodiptychus, which was belonging to specialized grade, indicating that Ptychobarbus may be transition species to involve to highly specialized schizothoracianae. In addition, the primitive grade clustered with Percocypris pingi, a species of Barbinae. Based on mtDNA gene, the speciation time of Schizothoracinae was 66 Ma, and the divergence time of the primitive grade and Percocypris pingi was 64 Ma. The speciation times of the three grades Schizothoracinae were 57 Ma, 51 Ma and 43 Ma, respectively; and the divergence time of specialized and highly specialized grade was 46 Ma. The divergence times of three grades were not consistent with the three stages of uplift of Qinghai-Tibet Plateau, which is older than the times.

Stictonectes rebeccae sp. n. from the Iberian Peninsula, with notes on its phylogenetic position (Coleoptera, Dytiscidae)

Zootaxa ◽  
2012 ◽  
Vol 3188 (1) ◽  
pp. 42
Author(s):  
DAVID T. BILTON
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Iberian Peninsula ◽  
Late Pleistocene ◽  
Molecular Clock ◽  
Mitochondrial Genes ◽  
Phylogenetic Position

Stictonetes rebeccae sp. n. (Coleoptera, Dytiscidae) is described from central and northwestern Iberia. The new species isclose morphologically to Stictonectes epipleuricus (Seidlitz, 1887), widespread in Iberia and adjacent areas of southernFrance, and Stictonectes occidentalis Fresneda & Fery, 1990, endemic to the extreme southwest of Portugal and Spain.Characters on which the three species can be distinguished are presented and discussed; the apex of the male parameresbeing particularly diagnostic. A molecular phylogeny based on fragments of two mitochondrial genes places S. rebeccaesp.n. sister to S. occidentalis. These two taxa are entirely allopatric, and according to molecular clock estimations divergedduring the late Pleistocene. S. rebeccae sp. n. is broadly sympatric with S. epipleuricus, although to date the two taxa havenot been collected in the same localities. A lectotype of S. epipleuricus is designated from the collection in the Zoologische Staatssammlung, Munich.

Sugarcane moth borers (Lepidoptera: Noctuidae and Pyraloidea): phylogenetics constructed using COII and 16S mitochondrial partial gene sequences

2004 ◽  
Vol 94 (5) ◽  
pp. 457-464 ◽  
Author(s):  
C.L. Lange ◽  
K.D. Scott ◽  
G.C. Graham ◽  
M.N. Sallam ◽  
P.G. Allsopp
Keyword(s):  
Molecular Phylogeny ◽  
Sequence Data ◽  
Sugar Industry ◽  
Economic Loss ◽  
Mitochondrial Genes ◽  
The Other ◽  
Diverse Group ◽  
Sugarcane Moth Borers ◽  
The Individual ◽  
Lepidoptera Noctuidae

AbstractSugarcane moth borers are a diverse group of species occurring in several genera, but predominately within the Noctuidae and Pyraloidea. They cause economic loss in sugarcane and other crops through damage to stems and stalks by larval boring. Partial sequence data from two mitochondrial genes, COII and 16S, were used to construct a molecular phylogeny based on 26 species from ten genera and six tribes. The Noctuidae were found to be monophyletic, providing molecular support for the taxonomy within this subfamily. However, the Pyraloidea are paraphyletic, with the noctuids splitting Galleriinae and Schoenobiinae from the Crambinae. This supports the separation of the Pyralidae and Crambinae, but does not support the concept of the incorporation of the Schoenobiinae in the Crambidae. Of the three crambine genera examined, Diatraea was monophyletic, Chilo paraphyletic, and Eoreuma was basal to the other two genera. Within the Noctuidae, Sesamia and Bathytricha were monophyletic, with Busseola basal to Bathytricha. Many species in this study (both noctuids and pyraloids) had different biotypes within collection localities and across their distribution; however the individual biotypes were not phylogenetically informative. These data highlight the need for taxonomic revisions at all taxon levels and provide a basis for the development of DNA-based diagnostics for rapidly identifying many species at any developmental stage. This ability is vital, as the species are an incursion threat to Australia and have the potential to cause significant losses to the sugar industry.

A revised circumscription for Siphonolejeunea and a new species from New Zealand

2020 ◽  
Author(s):  
Matt A. M. Renner ◽  
Peter J. de Lange
Keyword(s):  
New Species ◽  
New Zealand ◽  
Molecular Phylogeny ◽  
Sequence Data ◽  
New Combinations ◽  
Key To Species ◽  
Chloroplast Markers ◽  
A New Species ◽  
Significant Conflict

A molecular phylogeny to test the monophyly of Nephelolejeunea by using previously published nrITS, rbcL and trnL–F sequence data demonstrated that Nephelolejeunea is paraphyletic with respect to Siphonolejeunea. Nephelolejeunea and Siphonolejeunea are, therefore, merged and, as the latter name has priority, new combinations in Siphonolejeunea are made for 10 species. The valid publication of the name Austrolejeunea is re-evaluated and we conclude that both Siphonolejeunea subgenus Austrolejeunea and Siphonolejeunea olgae were validly published in 1963. Siphonolejeunea bidentata is reported as new for New Zealand on the basis of a collection from the Wairarapa, a new species, Siphonolejeunea raharahanehemiae, is described on the basis of recent collections from Te Paki, where it grows on the twigs of Metrosideros bartlettii (Myrtaceae), and we provide a revised key to species of Siphonolejeunea. The significant conflict in signal between nrITS and chloroplast markers associated with the relationships of Cololejeunea angustiflora, which chloroplast sequence data suggest may not be grouped with the rest of Cololejeunea, is another interesting result from the phylogeny. The relationships of Cololejeunea angustiflora and its allies warrant further investigation.

scholarly journals Phylogenetic Relationships of the Red-Bellied Grackle (Icteridae: Hypopyrrhus Pyrohypogaster) Inferred From Mitochondrial DNA Sequence Data

The Condor ◽  
2004 ◽  
Vol 106 (3) ◽  
pp. 664-670 ◽  
Author(s):  
Carlos Daniel Cadena ◽  
Andrés M. Cuervo ◽  
Scott M. Lanyon
Keyword(s):  
New World ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Mitochondrial Genes ◽  
Morphological Data ◽  
South American ◽  
South American Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities

Abstract The phylogenetic affinities of the Red-bellied Grackle (Hypopyrrhus pyrohypogaster), a Colombian endemic and the only member of this genus, are enigmatic. Based on phylogenetic analyses of sequences from the cytochrome b and ND2 mitochondrial genes, we present a first hypothesis on the systematic position of Hypopyrrhus. In so doing, we complete the sampling at the genus level for a published phylogeny of New World blackbirds (Johnson and Lanyon 1999). Hypopyrrhus belongs in a clade composed of mostly South American species within the grackles and allies assemblage, one of the five main lineages in the Icteridae. Within this lineage, Hypopyrrhus is consistently placed in a clade with Gymnomystax mexicanus and Lampropsar tanagrinus, but parsimony and maximum-likelihood reconstructions do not agree on which of these species is its sister taxon. Vocal and morphological data suggest that Hypopyrrhus and Gymnomystax are likely sister taxa. The addition of Hypopyrrhus does not cause major topological changes to Johnson and Lanyon's (1999) phylogeny of the grackles and allies; thus, the conclusions of evolutionary studies that used this phylogeny as a baseline remain largely unaltered. Relaciones Filogenéticas de Hypopyrrhus pyrohypogaster (Icteridae) Inferidas a Partir de Secuencias de ADN Mitocondrial Resumen. Las afinidades filogenéticas de Hypopyrrhus pyrohypogaster, el único miembro de este género endémico de Colombia, son enigmáticas. En este estudio establecemos la posición sistemática de Hypopyrrhus con base en análisis filogenéticos de secuencias de los genes mitocondriales citocromo b y ND2. Además, completamos el muestreo a nivel genérico para una filogenia del grupo publicada por Johnson y Lanyon (1999). Hypopyrrhus pertenece a un clado compuesto principalmente por especies suramericanas dentro del grupo de los changos y chamones, uno de los cinco clados principales de los Icteridae. Dentro de este grupo, Hypopyrrhus se ubica consistentemente en un clado junto con Gymnomystax mexicanus y Lampropsar tanagrinus, pero las reconstrucciones de parsimonia y máxima verosimilitud se contradicen en cuanto a cuál de estas especies es su taxón hermano. Datos de vocalizaciones y morfología sugieren que Hypopyrrhus y Gymnomystax son probablemente géneros hermanos. La incorporación de Hypopyrrhus a la filogenia de Johnson y Lanyon (1989) no causó cambios topoló gicos importantes, por lo que las conclusiones de los estudios evolutivos que usaron esta filogenia como base no fueron alteradas.

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