Phylogenetic position, systematic status, and divergence time of the Procarididea (Crustacea: Decapoda)

The Yenyuan stream salamander (Batrachuperus yenyuanensis) has been previously evaluated with regards to phylogeny, population genetics, and hematology, but genomic information is sparse due to the giant genome size of salamanders which contain highly repetitive sequences, thus resulting in the lack of a complete reference genome. This study evaluates the encoding genetic sequences and provides the first transcriptome assembly of Yenyuan stream salamander based on mixed samples from the liver, spermary, muscle and spleen tissues. Using this transcriptome assembly and available encoding sequences from other vertebrates, the gene families, phylogenetic status, and species divergence time were compared or estimated. A total of 13,750 encoding sequences were successfully obtained from the transcriptome assembly of Yenyuan stream salamander, estimated to contain 40.1% of the unigenes represented in tetrapod databases. A total of 88.79% of these genes could be annotated to a biological function by current databases. Through gene family clustering, we found multiple possible isoforms of the Scribble gene—whose function is related to regeneration—based on sequence similarity. Meanwhile, we constructed a robust phylogenetic tree based on 56 single-copy orthologues, which indicates that based on phylogenetic position, the Yenyuan stream salamander presents the closest relationship with the Chinese giant salamander (Andrias davidianus) of the investigated vertebrates. Based on the fossil-calibrated phylogeny, we estimated that the lineage divergence between the ancestral Yenyuan stream salamander and the Chinese giant salamander may have occurred during the Cretaceous period (~78.4 million years ago). In conclusion, this study not only provides a candidate gene that is valuable for exploring the remarkable capacity of regeneration in the future, but also gives an interesting insight into the understanding of Yenyuan stream salamander by this first transcriptome assembly.

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Phylogenetic relationships among Callosciurus squirrels in the Indochina Peninsula: phylogenetic position of C. pygerythrus from Myanmar

Acta Zoologica Academiae Scientiarum Hungaricae ◽

10.17109/azh.67.1.87.2021 ◽

2021 ◽

Vol 67 (1) ◽

pp. 87-98

Author(s):

Tatsuo Oshida ◽

Wynn Than ◽

Thida Oo ◽

Khin Yu Yu Swe ◽

Hiroaki Saito ◽

...

Keyword(s):

Cytochrome B ◽

Phylogenetic Relationships ◽

Divergence Time ◽

Divergence Times ◽

Phylogenetic Position ◽

Mitochondrial Cytochrome ◽

Indochina Peninsula ◽

Mitochondrial Cytochrome B ◽

Global Cooling ◽

Mitochondrial Cytochrome B Gene

The phylogenetic relationships among seven Callosciurus species from the Indochina Peninsula, including the C. honkhoaiensis which is endemic to Hon Khoai Island, were studied using complete mitochondrial cytochrome b gene sequences (1140 bases). We primarily focused on the phylogenetic position of C. pygerythrus, which is distributed in the western part of the peninsula. We identified two main lineages: 1) C. caniceps, C. honkhoaiensis, C. inornatus, C. phayrei and C. pygerythrus, and 2) C. erythraeus and C. finlaysonii. Estimated divergence time between the two lineages was at the junction of the Zanclean and Piacenzian in the Pliocene. Within the first linage, the divergence time of sub-lineages corresponded to the Pliocene-Pleistocene boundary, although phylogenetic relationships were unclear. These two divergence times estimated in the present study correspond to episodes of global cooling, suggesting that climate may have contributed to the divergence of these Callosciurus squirrels.

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Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time

Zootaxa ◽

10.11646/zootaxa.3664.3.2 ◽

2013 ◽

Vol 3664 (3) ◽

pp. 312 ◽

Cited By ~ 3

Author(s):

LAUREN M. CHAN ◽

JAMES W. ARCHIE ◽

ANNE D. YODER ◽

LEE A. FITZGERALD

Keyword(s):

Divergence Time ◽

Systematic Status

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LAUREN M. CHAN, JAMES W. ARCHIE, ANNE D. YODER & LEE A. FITZGERALD (2013) Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time. Zootaxa, 3664(3), 312–320.

Zootaxa ◽

10.11646/zootaxa.3686.1.8 ◽

2013 ◽

Vol 3686 (1) ◽

pp. 99

Author(s):

LAUREN M. CHAN ◽

JAMES W. ARCHIE ◽

ANNE D. YODER ◽

LEE A. FITZGERALD

Keyword(s):

Divergence Time ◽

Systematic Status

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Phylogenetic position of Neotropical Bursera-specialist mistletoes: the evolution of deciduousness and succulent leaves in Psittacanthus (Loranthaceae)

Botanical Sciences ◽

10.17129/botsci.1961 ◽

2018 ◽

Vol 96 (3) ◽

pp. 443 ◽

Cited By ~ 2

Author(s):

Andrés Ernesto Ortiz-Rodriguez ◽

Eydi Yanina Guerrero ◽

Juan Francisco Ornelas

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary History ◽

Morphological Evolution ◽

Divergence Time ◽

Molecular Dating ◽

Phylogenetic Position ◽

Long Time ◽

History Of ◽

Nuclear Its ◽

Divergence Timing

Background: The phylogenetic relationships of the Bursera-host specialist Psittacanthus nudus, P. palmeri and P. sonorae (Loranthaceae) remain uncertain. These mistletoe species exhibit morphological and phenological innovations probably related to their dry habitats, so that determining their phylogenetic position is key to the understanding of factors associated with the morphological evolution within Psittacanthus.Questions: (1) Is the evolution of some morphological innovations in the Bursera-host specialists associated with the ecological conditions linked to host diversification? (2) Does time of diversification in both lineages coincide?Study species: Fourteen species of Psittacanthus.Methods: Sequences of nuclear (ITS) and plastid (trnL-trnF) markers are analyzed with Bayesian inference, maximum likelihood and maximum parsimony methods, and molecular dating under a Bayesian approach estimated to elucidate the phylogenetic position and divergence timing of the Bursera-host specialists.Results: The Bursera-host specialists form a strongly supported clade, named here the ‘Bursera group’. The divergence time for the Bursera-host specialists was estimated at 7.89 Ma. Interestingly, phylogenetic relationships between P. nudus and P. palmeri, as currently circumscribed, were not fully resolved, making P. palmeri paraphyletic.Conclusions: Based on these results, the plants collected by type locality of P. nudus in Honduras should be named P. palmeri. The seasonal deciduousness of P. palmeri (including P. nudus) and morphology of P. sonorae (small size, fleshy leaves) are clearly adaptations to dry ecosystems where these species have lived for a long time. In parallel, the evolutionary history of these mistletoes seems to be correlated with the evolutionary history and diversification patterns of Bursera.

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Divergence time analyses suggest a Miocene origin of the narrow Amazonian endemic rheophytic Ceratolejeunea temnantha (Spruce) Reiner-Drehwald (Porellales, Lejeuneaceae)

Bryophyte Diversity and Evolution ◽

10.11646/bde.40.2.4 ◽

2018 ◽

Vol 40 (2) ◽

pp. 55

Author(s):

ADRIEL M. SIERRA ◽

JULIA BECHTELER ◽

DOMINGOS CARDOSO ◽

CHARLES E. ZARTMAN ◽

JUAN CARLOS VILLARREAL

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Original Description ◽

Phylogenetic Position ◽

Ecological Niches ◽

Divergence Time Estimates ◽

Potential Habitat ◽

The North ◽

Time Estimates ◽

Rio Negro

The recent rediscovery of the rheophytic endemic Ceratolejeunea temnantha ~130 years after its original description, on the upper Rio Negro in the Brazilian Amazon, has enabled the assessment of its enigmatic phylogenetic position, estimates of its divergence time, and updates on its distribution and potential habitat threats. Phylogenetic analyses strongly supported its placement in the genus Ceratolejeunea in a geographically disparate clade including a Madagascar endemic C. saroltae and two Neotropical taxa, C. confusa and C. caducifolia. Divergence time estimates date the clade’s stem age to the late Miocene (8.92 [HPD: 12.39–6.04] Ma) offering further evidence that the evolution of rheophytes in northern South America is correlated with the expansion of cryptogams into novel ecological niches promoted by dramatic landscape changes during the Miocene. Major geomorphological and hydrological transformations contributing to such diversification are most likely the changing dynamics of the inundated mega lake system to the establishment of the Amazon River due to the Andean orogeny and the subsequent cessation of marine influences in the north-western portion of the Basin. Until recently, this rheophyte of seasonally inundated black-water forests was only known from its type collection from the Rio Negro near São Gabriel da Cachoeira (Brazil) as described by Richard Spruce in 1884. These new collections extend the distribution of this rare narrow endemic to the middle Rio Uaupés, a tributary of the upper Rio Negro near the Columbian border.

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Insights into the lower torso in late Miocene hominoidOreopithecus bambolii

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1911896116 ◽

2019 ◽

Vol 117 (1) ◽

pp. 278-284 ◽

Cited By ~ 2

Author(s):

Ashley S. Hammond ◽

Lorenzo Rook ◽

Alisha D. Anaya ◽

Elisabetta Cioppi ◽

Loïc Costeur ◽

...

Keyword(s):

Divergence Time ◽

Lumbar Vertebrae ◽

Great Apes ◽

Locomotor Behavior ◽

Phylogenetic Position ◽

Lumbar Region ◽

Anterior Inferior Iliac Spine ◽

Early Hominin ◽

Pelvic Stabilization ◽

Intense Debate

Oreopithecus bambolii(8.3–6.7 million years old) is the latest known hominoid from Europe, dating to approximately the divergence time of thePan-hominin lineages. Despite being the most complete nonhominin hominoid in the fossil record, theO. bamboliiskeleton IGF 11778 has been, for decades, at the center of intense debate regarding the species’ locomotor behavior, phylogenetic position, insular paleoenvironment, and utility as a model for early hominin anatomy. Here we investigate features of the IGF 11778 pelvis and lumbar region based on torso preparations and supplemented by otherO. bamboliimaterial. We correct several crucial interpretations relating to the IGF 11778 anterior inferior iliac spine and lumbar vertebrae structure and identifications. We find that features of the early homininArdipithecus ramidustorso that are argued to have permitted both lordosis and pelvic stabilization during upright walking are not present inO. bambolii. However,O. bamboliialso lacks the complete reorganization for torso stiffness seen in extant great apes (i.e., living members of the Hominidae), and is more similar to large hylobatids in certain aspects of torso form. We discuss the major implications of theO. bamboliilower torso anatomy and howO. bamboliiinforms scenarios of hominoid evolution.

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A new section and species of Agaricus subgenus Pseudochitonia from Thailand

MycoKeys ◽

10.3897/mycokeys.40.26918 ◽

2018 ◽

Vol 40 ◽

pp. 53-67 ◽

Cited By ~ 4

Author(s):

Mao-Qiang He ◽

Boontiya Chuankid ◽

Kevin D. Hyde ◽

Ratchadawan Cheewangkoon ◽

Rui-Lin Zhao

Keyword(s):

Gene Sequence ◽

Sequence Data ◽

Divergence Time ◽

Morphological Characteristics ◽

Phylogenetic Position ◽

Its Sequence ◽

Large Species ◽

Monophyletic Clade ◽

A New Species ◽

Gene Sequence Data

A large species diversity has recently been discovered in the genus Agaricus. Six subgenera and 23 sections are now recognised. In this study, three specimens collected from Thailand, formed a monophyletic clade in subgenus Pseudochitonia, based on analyses of ITS sequence data. Further analyses, based on multi-gene sequence data (ITS, LSU, tef1-α), using BEAST, revealed that this clade originated 26.7 Ma. According to their distinct morphological characteristics, phylogenetic position and relatively old divergence time, a new section Cymbiformes is proposed and this section is represented by a new species A.angusticystidiatus. This new section is characterised by the strong iodoform odour of basidiomes and cymbiform basidiospores. Descriptions, colour photographs and illustrations are presented.

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New Material of Paleocene-Eocene Pellornis (Aves: Gruiformes) Clarifies the Pattern and Timing of the Extant Gruiform Radiation

Diversity ◽

10.3390/d11070102 ◽

2019 ◽

Vol 11 (7) ◽

pp. 102 ◽

Cited By ~ 6

Author(s):

Grace Musser ◽

Daniel T. Ksepka ◽

Daniel J. Field

Keyword(s):

Mass Extinction ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Phylogenetic Position ◽

Postcranial Skeleton ◽

Holotype Specimen ◽

New Information ◽

Mechanical Preparation ◽

New Material ◽

Early Radiation

Pellornis mikkelseni is an early gruiform from the latest Paleocene-earliest Eocene Fur Formation of Denmark. At approximately 54 million years old, it is among the earliest clear records of the Gruiformes. The holotype specimen, and only material thus far recognised, was originally considered to comprise a partial postcranial skeleton. However, additional mechanical preparation of the nodule containing the holotype revealed that the skeleton is nearly complete and includes a well-preserved skull. In addition to extracting new information from the holotype, we identify and describe two additional specimens of P. mikkelseni which reveal further morphological details of the skeleton. Together, these specimens show that P. mikkelseni possessed a schizorhinal skull and shared many features with the well-known Paleogene Messelornithidae (“Messel rails”). To reassess the phylogenetic position of P. mikkelseni, we modified an existing morphological dataset by adding 20 characters, four extant gruiform taxa, six extinct gruiform taxa, and novel scorings based on the holotype and referred specimens. Phylogenetic analyses recover a clade containing P. mikkelseni, Messelornis, Songzia and crown Ralloidea, supporting P. mikkelseni as a crown gruiform. The phylogenetic position of P. mikkelseni illustrates that some recent divergence time analyses have underestimated the age of crown Gruiformes. Our results suggest a Paleocene origin for this important clade, bolstering evidence for a rapid early radiation of Neoaves following the end-Cretaceous mass extinction.

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Systematic status of the rare Himalayan wolf snake Lycodon mackinnoni Wall, 1906 (Serpentes: Colubridae)

Zootaxa ◽

10.11646/zootaxa.4966.3.3 ◽

2021 ◽

Vol 4966 (3) ◽

pp. 305-320

Author(s):

SWATI NAWANI ◽

V. DEEPAK ◽

KUMUDANI BALA GAUTAM ◽

SANDEEP KUMAR GUPTA ◽

BITUPAN BORUAH ◽

...

Keyword(s):

Natural History ◽

Phylogenetic Relationship ◽

Western Himalaya ◽

Original Description ◽

Type Locality ◽

Type Material ◽

Phylogenetic Position ◽

Morphological Description ◽

Systematic Status ◽

History Information

Lycodon mackinnoni is a poorly known Himalayan endemic snake known from Western Himalaya. Since the original description of L. mackinnoni almost 112 years ago, this species was not reported from its type locality and its phylogenetic position remain unknown. We herein, provide detail morphological description, comparison with type material, phylogenetic relationship with its congeners and new natural history information.

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