scholarly journals Phylogenetic Relationships of Micronesian White-Eyes Based on Mitochondrial Sequence Data

The Auk ◽  
2000 ◽  
Vol 117 (2) ◽  
pp. 355-365 ◽  
Author(s):  
Beth Slikas ◽  
Isaac B. Jones ◽  
Scott R. Derrickson ◽  
Robert C. Fleischer
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Species ◽  
Additional Species ◽  
Data Set ◽  
Mitochondrial Sequence ◽  
Sister Relationships ◽  
Optimal Trees

Abstract Using mitochondrial sequence data, we estimated phylogenetic relationships and genetic divergence among selected species of white-eyes (Zosteropidae). We focused on taxa endemic to islands in Micronesia, specifically Zosterops conspicillatus, Z. semperi, Z. hypolais, Rukia oleaginea, and Cleptornis marchei. We also included in our data set five additional species of Zosterops from the Indo-Australian region and three species from Africa, as well as additional passerine outgroups. Our mitochondrial sequence data revealed substantial genetic divergence (5.7 to 7.3%) among Z. conspicillatus, Z. semperi, and Z. hypolais, three taxa that formerly were treated as a single species. In addition, a sequence divergence of 6.5 ± SE of 1.7% was found between the population of Z. conspicillatus from Rota and “conspecific” populations on Guam, Tinian, and Saipan. The distinctiveness of the Rota population suggests that this taxon should be recognized as a distinct species, a result that bears on the conservation of this population because it has been declining dramatically in recent years. All optimal trees based on analysis of the mitochondrial sequence data place Rukia oleaginea within the genus Zosterops. In all optimal trees, Cleptornis marchei positions as the sister taxon to a clade including all other zosteropids included in this study. The trees based on our data strongly contradict the traditional classification of Cleptornis as a honeyeater (family Meliphagidae). Our data cannot resolve with any confidence the sister relationships of the insular endemic white-eyes, although the optimal trees suggest multiple colonizations of Micronesia by more than one white-eye lineage.

Genetic divergence and geographic diversification in Nautilus

Paleobiology ◽  
1995 ◽  
Vol 21 (2) ◽  
pp. 220-228 ◽  
Author(s):  
Charles G. Wray ◽  
Neil H. Landman ◽  
W. Bruce Saunders ◽  
James Bonacum
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Distinct Species ◽  
Morphological Characters ◽  
Geographic Diversification ◽  
Isolated Populations ◽  
Systematic Analysis

Despite exhaustive investigation of present-day Nautilus, the phylogenetic relationships of the five or six recognized species within this genus remain unclear. Mitochondrial and nuclear DNA sequence data plus a suite of morphological characters are used to investigate phylogenetic relationships. Systematic analysis of the morphological variation fails to characterize described species as independent lineages. However, DNA sequence analysis indicates that there are three geographically distinct clades consisting of western Pacific, eastern Australian/Papua-New Guinean, and western Australian/Indonesian forms. The morphologically and genetically distinct species Nautilus scrobiculatus falls outside the three geographically recognized assemblages. Members of the genus Nautilus also exhibit low levels of sequence divergence. All these data suggest that Nautilus is currently undergoing diversification, which may have begun only several million years ago. These data also suggest that some of the morphological features used to define Nautilus species may simply represent fixed variations in isolated populations within the same species.

Another new Cyrtodactylus (Squamata: Gekkonidae) from Guwahati, Assam, India

Zootaxa ◽  
2020 ◽  
Vol 4732 (3) ◽  
pp. 375-392
Author(s):  
JAYADITYA PURKAYASTHA ◽  
MADHURIMA DAS ◽  
SANATH CHANDRA BOHRA ◽  
AARON M. BAUER ◽  
ISHAN AGARWAL
Keyword(s):  
New Species ◽  
Additional Data ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Northeast India ◽  
The State ◽  
Colour Pattern ◽  
Mitochondrial Sequence ◽  
Guwahati City ◽  
A New Species

We describe a new species of Cyrtodactylus from Guwahati city in the state of Assam, India and provide additional data on the recently described Cyrtodactylus guwahatiensis. Cyrtodactylus urbanus sp. nov. falls in the newly defined khasiensis group within the Indo-Burma clade of Cyrtodactylus and is the poorly supported sister taxon to Cyrtodactylus khasiensis. The new species differs from other members of the khasiensis group in mitochondrial sequence data (12.5–17.1 % uncorrected pairwise ND2 sequence divergence) as well as aspects of morphology including the number and arrangement of precloacal pores in males, the number of mid-ventral scales and paravertebral tubercles, and colour pattern. This is the second Cyrtodactylus endemic to the Guwahati region, the fourth from Assam and the twelfth from Northeast India. 

Phylogenetic Relationships among Members of the Coregoninae Inferred from Direct Sequencing of PCR-Amplified Mitochondrial DNA

1993 ◽  
Vol 50 (10) ◽  
pp. 2112-2118 ◽  
Author(s):  
S. Fournier Lockwood ◽  
Robert E. Dillinger Jr. ◽  
Tim P. Birt ◽  
John M. Green ◽  
Thomas P. Snyder
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Direct Sequencing ◽  
Cladistic Analysis ◽  
Sequence Divergence ◽  
Amino Acid Replacement ◽  
Mitochondrial Cytochrome B ◽  
Mtdna Sequence ◽  
Polymerase Chain

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for eight members of the Coregoninae (Salmonidae) from North America in an effort to elucidate phylogenetic relationships in the subfamily. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Direct estimates of mitochondrial DNA (mtDNA) sequence divergence among taxa ranged from 0.0% between Arctic cisco (Coregonus autumnalis) from the Mackenzie River, Canada, and cisco (C. artedi) from the Laurentian Great Lakes to 5.8% between the inconnu (Stenodus leucichthys) and the round whitefish (Prosopium cylindraceum). As has been noted in other fish species and vertebrates in general, third position silent substitutions predominated over any other type of nucleotide change. No amino acid replacement substitutions were found among any of the eight taxa examined. Comparison of mtDNA sequence divergence estimates from this and other studies suggests that the radiation of the genera within the Coregoninae occurred relatively recently (2–6 million yr B.P.). Cladistic analysis of the mtDNA sequence data yields a hypothesis of relationships that supports previous genetic and morphological classifications of coregonines.

scholarly journals Plastome data reveal multiple geographic origins of Quercus Group Ilex

2015 ◽  
Author(s):  
Marco Cosimo Simeone ◽  
Guido W Grimm ◽  
Alessio Papini ◽  
Federico Vessella ◽  
Simone Cardoni ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Sequence Divergence ◽  
Geographic Area ◽  
Geographic Region ◽  
Tectonic Activity ◽  
Lineage Sorting ◽  
Distribution Ranges

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK-matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. Main plastid haplotypes shared by distinct oak lineages from the same geographic region and high plastid diversity in members of Group Ilex are indicative for a polyphyletic origin of their plastomes. The results suggest that incomplete lineage sorting and repeated phases of unidirectional introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

Phylogenetic position of the fish genera Lobotes, Datnioides and Hapalogenys, with a reappraisal of acanthuriform composition and relationships based on adult and larval morphology

Zootaxa ◽  
2019 ◽  
Vol 4680 (1) ◽  
pp. 1-81 ◽  
Author(s):  
ANTHONY C. GILL ◽  
JEFFREY M. LEIS
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Item Analysis ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Larval Morphology ◽  
Tooth Replacement ◽  
Optimal Trees

Lobotes, Datnioides and Hapalogenys are assigned to a newly defined Acanthuriformes on the basis of their pattern of tooth replacement (termed posterolateral tooth replacement), where new teeth form at the posterolateral ends of series. Posterolateral tooth replacement is shown to be a synamorphy of the order. The order is expanded to include Chaetodontidae, Pomacanthidae, Drepaneidae, Ephippidae, Leiognathidae, Antigonia, Scatophagidae and Capros, along with the more traditional members, Siganidae, Luvaridae, Zanclidae and Acanthuridae. Three-item analysis of 63 adult and larval morphological characters yields two optimal trees that differ only in the relative positions of Capros and Siganidae. The intersection tree of the two optimal trees is: (((Hapalogenys (Datnioides, Lobotidae)) (Pomacanthidae (Drepaneidae (Chaetodontidae (Ephippidae (Leiognathidae (Scatophagidae (Antigonia (Siganidae, Capros (Luvaridae (Zanclidae, Acanthuridae)))))))))))). This cladogram is compared with recent phylogenies based on analyses of sequence data, and few differences are found once the weakly-supported interior nodes of the latter are collapsed. Aside from expansion of the Acanthuriformes, the following classification changes are proposed in order to reflect the phylogenetic relationships: redefinition of the Lobotidae to include Lobotes, Datnioides and Hapalogenys; separate families for Antigonia and Capros (Antigoniidae and Caproidae, respectively); continued recognition of Drepaneidae (often considered a synonym of Ephippidae). The larvae of Capros aper are illustrated to show features overlooked in earlier descriptions. 

A multilocus assessment of nuclear and mitochondrial sequence data elucidates phylogenetic relationships among European spirlins (Alburnoides, Cyprinidae)

2016 ◽  
Vol 94 ◽  
pp. 479-491 ◽  
Author(s):  
Soňa Stierandová ◽  
Jasna Vukić ◽  
Ekaterina D. Vasil’eva ◽  
Stamatis Zogaris ◽  
Spase Shumka ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Sequence

scholarly journals Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)

Genome ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 169-182 ◽  
Author(s):  
Robert G. Young ◽  
Cathryn L. Abbott ◽  
Thomas W. Therriault ◽  
Sarah J. Adamowicz
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Graphical Method ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Threshold Value ◽  
Quantitative Comparison ◽  
Data Set ◽  
Pairwise Sequence Divergence ◽  
Marine Realm

DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value. With these thresholds, and using a newly generated planktonic marine data set, we quantify the degree of concordance using a bidirectional analysis and discuss different analytical methods for sequence-based species delimitation (e.g., BIN, ABGD, jMOTU, UPARSE, Mothur, PTP, and GMYC). Our results support a COI-5P threshold between 2.1% and 2.6% p-distance across methods for these crustacean taxa, yielding molecular groupings largely concordant with traditional, morphologically defined species. The adoption of internal methods for clustering verification enables rapid biodiversity studies and the exploration of unknown faunas using DNA barcoding. The approaches taken here for concordance assessment also provide a more quantitative comparison of clustering results (as contrasted with “success/failure” of barcoding), and we recommend their further consideration for barcoding studies.

Phylogenetic relationships among the Lorisoidea as indicated by craniodental morphology and mitochondrial sequence data

2006 ◽  
Vol 69 (1) ◽  
pp. 6-15 ◽  
Author(s):  
Judith C. Masters ◽  
Michele Boniotto ◽  
Sergio Crovella ◽  
Christian Roos ◽  
Luca Pozzi ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Sequence

scholarly journals Molecular data suggest that Heteromys irroratus bulleri should be recognized as a species-level taxon

Therya ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 139-148
Author(s):  
Maria A. Gutiérrez-Costa ◽  
Francisco X. González-Cózatl ◽  
María Magdalena Ramírez-Martínez, ◽  
Luis Ignacio Iñiguez-Dávalos ◽  
Duke S. Rogers
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Conservation Status ◽  
Biosphere Reserve ◽  
Genetic Distances ◽  
Species Level ◽  
Cranial Measurements ◽  
Sierra De Manantlán ◽  
Pocket Mouse

Recent collecting surveys in the Sierra de Manantlán Biosphere Reserve, Jalisco (México), uncovered the existence of a new population of the Mexican spiny pocket mouse, Heteromys irroratus.  Because the subspecies H. i. bulleri and H. i. jaliscensis occur nearby, our objective was to properly determine the taxonomic identity of the novel sample.  Also, we evaluate its distinctiveness, both in terms of genetic divergence and phylogenetic placement, relative to other members of H. irroratus.  Preliminary, we compared external and cranial measurements of recently collected individuals to those reported for representatives of the subspecies of H. irroratus occurring close by.  In addition, we examined levels of genetic differentiation and phylogenetic relationships, based on sequence data of the Cytochrome b, among this population and other members of H. irroratus, including an individual from Sierra de Juanacatlán, Jalisco, the type locality of H. i. bulleri. Phylogenetic relationships were estimated using Maximum Likelihood and Bayesian Inference methods and levels of genetic divergence were assessed employing Kimura-2-parameters genetic distances.  Samples from Sierra de Manantlán and Sierra de Juanacatlán were grouped together in a well-supported haplogroup and genetic distances between them were lower than < 1.02 %.  Our phylogenetic hypothesis shows that H. i. bulleri represents the sister group to all other samples of H. irroratus but that, genetically, is a very divergent lineage.  Distances values between H. i. bulleri to any of the other groups were > 10.05 %.  Comparison of external and cranial measurements showed that, in average, individuals from Sierra de Manantlán are larger than those of H. i. jaliscensis, but more similar in size to H. i. bulleri.  Our results show that the new population of the Mexican spiny pocket mouse from Sierra de Manantlán belongs to H. i. bulleri.  In addition, the phylogenetic separation and the high levels of genetic divergence of H. i. bulleri, relative to other members of H. irroratus, suggest that the first should be recognized as a species-level taxon.  Considering the scarce collecting records of H. i. bulleri and the known area of occurrence, that is very restricted, this taxon may warrant special conservation status.

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