scholarly journals Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 38 ◽  
Author(s):  
Dehuai Luo ◽  
Yanping Li ◽  
Qingyuan Zhao ◽  
Lianpeng Zhao ◽  
Arne Ludwig ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Single Copy ◽  
Species Trees ◽  
Degenerate Primers ◽  
Nuclear Markers ◽  
Gene Markers ◽  
Fossil Species ◽  
Living Fossil ◽  
Molecular Clock Model ◽  
Extant Species

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.

The jumping plant-lice of the Neotropical genus Tainarys (Hemiptera: Psylloidea) associated with Anacardiaceae

Zootaxa ◽  
2017 ◽  
Vol 4232 (4) ◽  
pp. 535 ◽  
Author(s):  
DANIEL BURCKHARDT ◽  
DALVA L. QUEIROZ
Keyword(s):  
South America ◽  
Phylogenetic Relationships ◽  
Host Plants ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
South American ◽  
Fossil Species ◽  
Dominican Amber ◽  
Extant Species ◽  
East West

The Neotropical psyllid genus Tainarys Brèthes, 1920 is revised to include 14 extant and one fossil species from Dominican amber. Eight species are described as new, viz. Tainarys aroeira sp. nov., T. atra sp. nov., T. hapla sp. nov., T. myracrodrui sp. nov., T. nigricornis sp. nov., T. didyma sp. nov. and T. orientalis sp. nov. from Brazil, the last two also from Uruguay, as well as T. lozadai sp. nov. from Peru. The fifth instar immatures are described for nine species. †Vicinilura Klimaszewski, 1996, erected for the fossil †V. reposta Klimaszewski, 1996 and previously synonymised with Leurolophus Tuthill, 1942, is synonymised here (syn. nov.) with Tainarys and †V. reposta is transferred to become †Tainarys reposta (Klimaszewski), comb. nov. The descriptions are supplemented by illustrations and keys for the identification of adults and immatures. Phylogenetic relationships between species are investigated with a cladistic analysis using 22 adult and six immature morphological characters. The analysis resulted in a single most parsimonious, fully resolved tree. The fossil species is nested within the genus rather than being the sister taxon of the remainder of species. The extant species are restricted to the subtropical and temperate parts of South America. Three pairs of sister clades display an east‒west South American and one a midwest‒southern Brazilian geographical vicariance. Host plants are confirmed for nine and likely for another four species. They are Astronium, Haplorhus, Myracrodruon, Schinopsis and Schinus (Anacardiaceae). All Tainarys species appear to be oligophagous inducing irregular leaf curls on their hosts. 

scholarly journals Phylogenomics supports a Cenozoic rediversification of the “living fossil” Isoetes

2019 ◽  
Author(s):  
Daniel Wood ◽  
Guillaume Besnard ◽  
David J. Beerling ◽  
Colin P. Osborne ◽  
Pascal-Antoine Christin
Keyword(s):  
Fossil Record ◽  
Molecular Dating ◽  
Rate Variation ◽  
Nuclear Markers ◽  
Living Fossil ◽  
Chloroplast Genomes ◽  
Genome Wide ◽  
Extant Species ◽  
Dating Methods ◽  
Insight Into

AbstractThe fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

scholarly journals Ten genes and two topologies: an exploration of higher relationships in skipper butterflies (Hesperiidae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2653 ◽  
Author(s):  
Ranjit Kumar Sahoo ◽  
Andrew D. Warren ◽  
Niklas Wahlberg ◽  
Andrew V. Z. Brower ◽  
Vladimir A. Lukhtanov ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Gene Markers ◽  
Mitochondrial Markers ◽  
Molecular Dataset

Despite multiple attempts to infer the higher-level phylogenetic relationships of skipper butterflies (Family Hesperiidae), uncertainties in the deep clade relationships persist. The most recent phylogenetic analysis included fewer than 30% of known genera and data from three gene markers. Here we reconstruct the higher-level relationships with a rich sampling of ten nuclear and mitochondrial markers (7,726 bp) from 270 genera and find two distinct but equally plausible topologies among subfamilies at the base of the tree. In one set of analyses, the nuclear markers suggest two contrasting topologies, one of which is supported by the mitochondrial dataset. However, another set of analyses suggests mito-nuclear conflict as the reason for topological incongruence. Neither topology is strongly supported, and we conclude that there is insufficient phylogenetic evidence in the molecular dataset to resolve these relationships. Nevertheless, taking morphological characters into consideration, we suggest that one of the topologies is more likely.

More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae)

2018 ◽  
Vol 32 (2) ◽  
pp. 448 ◽  
Author(s):  
Mun Hua Tan ◽  
Han Ming Gan ◽  
Gavin Dally ◽  
Suzanne Horner ◽  
Paula A. Rodríguez Moreno ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Large Scale ◽  
Mitochondrial Gene ◽  
Lower Triassic ◽  
Molecular Data ◽  
Systematic Position ◽  
Fossil Species ◽  
Living Fossil ◽  
Extant Species ◽  
Complete Mitogenome

Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.

scholarly journals A Recent species of <i>Frambocythere</i> Colin, 1980 (Ostracoda, Crustacea) from a cave in South Korea; the first extant representative of a genus thought extinct since the Eocene

2012 ◽  
Vol 31 (2) ◽  
pp. 131-138 ◽  
Author(s):  
Robin J. Smith ◽  
Jimin Lee ◽  
Yong Geun Choi ◽  
Cheon Young Chang ◽  
Jean-Paul Colin
Keyword(s):  
South Korea ◽  
Lower Cretaceous ◽  
Middle Eocene ◽  
Paris Basin ◽  
Fossil Species ◽  
Living Fossil ◽  
Extant Species ◽  
Living Species ◽  
Recent Species ◽  
Stratigraphic Range

Abstract. The non-marine ostracod genus Frambocythere Colin, 1980 (Limnocytheridae, Timiriaseviinae) had a previously known stratigraphical range from the Albian (Lower Cretaceous) through to the Lutetian (middle Eocene). However, during surveys of Seongryu Cave in Uljin-gun Province, South Korea, specimens of an extant species of Frambocythere were recovered. This extends the stratigraphic range of the genus by more than 40 million years to the present, and the species is, therefore, considered to be a relict ‘living fossil’. This newly described species is most similar in morphology to Frambocythere gr. tumiensis (Helmdach, 1978), reported from Thanetian (Paleocene) deposits of the Paris Basin. The living species was found in the hypogean realm, in contrast to the fossil species, which were all epigean. It is hypothesized that, like the genus Kovalevskiella Klein, 1963, which belongs to the same lineage, Frambocythere migrated from epigean to hypogean habitats.

Integration of molecular, bioacoustical and morphological data reveals two new cryptic species of Pelodytes (Anura, Pelodytidae) from the Iberian Peninsula

Zootaxa ◽  
2017 ◽  
Vol 4243 (1) ◽  
pp. 1 ◽  
Author(s):  
JESÚS DÍAZ-RODRÍGUEZ ◽  
MARCELO GEHARA ◽  
RAFAEL MÁRQUEZ ◽  
MIGUEL VENCES ◽  
HELENA GONÇALVES ◽  
...  
Keyword(s):  
Iberian Peninsula ◽  
Western Europe ◽  
Relative Size ◽  
Morphological Data ◽  
Genetic Admixture ◽  
Species Discrimination ◽  
Rrna Gene ◽  
Species Trees ◽  
Nuclear Markers ◽  
Extant Species

Parsley frogs (Pelodytes) comprise the only genus in the family Pelodytidae, an ancient anuran lineage that split from their closest relatives over 140 million years ago. Pelodytes is a Palearctic group restricted to Western Eurasia including three extant species: the eastern species P. caucasicus, endemic to the Caucasus area, and two closely related species inhabiting Western Europe: the Iberian endemic P. ibericus and the more widespread P. punctatus. Previous studies based on mitochondrial and nuclear DNA markers have revealed the existence of two additional lineages of Parsley frogs in the Iberian Peninsula, which have been flagged as candidate species. Here, we integrate novel molecular, morphological and bioacoustical data to assess the differentiation of the four western Parsley frog lineages. Species trees and Bayesian population assignment analyses based on nuclear markers confirm previous studies and concordantly delineate four parapatric lineages with narrow hybrid zones. Mitochondrial divergence is low (< 2% pairwise distances in the 16S rRNA gene), in line with previously reported low mitochondrial substitution rates in non-neobatrachian frogs. Based on concordance between mitochondrial and nuclear markers, we conclude that four species of Parsley frogs occur in Western Europe: Pelodytes punctatus, distributed from northern Italy to northeastern Spain; Pelodytes ibericus, inhabiting southern Spain and southern Portugal; Pelodytes atlanticus sp. nov., from the Portuguese Atlantic coast; and Pelodytes hespericus sp. nov., occurring in central and eastern Spain. However, bioacoustical and morphological differentiation of these species is low, with no obvious and qualitative diagnostic characters allowing full species discrimination. Differences in the relative size of metacarpal tubercles exist but this character is variable. Pelodytes ibericus and Pelodytes atlanticus are smaller than the other two species, and P. ibericus has shorter limbs and various distinctive osteological characters. Bioacoustically, the pattern by which two different note types are combined in advertisement calls separates P. hespericus from the remaining species. Despite these differences, we emphasize that the taxonomic status of all four western Parsley frogs requires additional investigation, especially the patterns of genetic admixture across contact zones. While a status of separate species best conforms to the currently available data, alternative hypotheses are also discussed. 

Three new cribrimorph bryozoans (order Cheilostomatida) from the early Miocene of Argentina, with a discussion on spinocystal shield morphologies

2021 ◽  
pp. 1-15
Author(s):  
Juan López-Gappa ◽  
Leandro M. Pérez ◽  
Ana C.S. Almeida ◽  
Débora Iturra ◽  
Dennis P. Gordon ◽  
...  
Keyword(s):  
Type Species ◽  
Systematic Position ◽  
Early Miocene ◽  
Morphological Data ◽  
Fossil Species ◽  
Extant Species ◽  
The Family ◽  
Subjective Synonym

Abstract Bryozoans with calcified frontal shields formed by the fusion of costae, collectively constituting a spinocyst, are traditionally assigned to the family Cribrilinidae. Today, this family is regarded as nonmonophyletic. In the Argentine Cenozoic, cribrilinids were until recently represented by only two fossil species from the Paleocene of Patagonia. This study describes the first fossil representatives of Jolietina and Parafigularia: J. victoria n. sp. and P. pigafettai n. sp., respectively. A fossil species of Figularia, F. elcanoi n. sp., is also described. The material comes from the early Miocene of the Monte León and Chenque formations (Patagonia, Argentina). For comparison, we also provide redescriptions of the remaining extant species of Jolietina: J. latimarginata (Busk, 1884) and J. pulchra Canu and Bassler, 1928a. The systematic position of some species previously assigned to Figularia is here discussed. Costafigularia n. gen. is erected, with Figularia pulcherrima Tilbrook, Hayward, and Gordon, 2001 as type species. Two species previously assigned to Figularia are here transferred to Costafigularia, resulting in C. jucunda n. comb. and C. tahitiensis n. comb. One species of Figularia is reassigned to Vitrimurella, resulting in V. ampla n. comb. The family Vitrimurellidae is here reassigned to the superfamily Cribrilinoidea. The subgenus Juxtacribrilina is elevated to genus rank. Inferusia is regarded as a subjective synonym of Parafigularia. Parafigularia darwini Moyano, 2011 is synonymized with I. taylori Kuklinski and Barnes, 2009, resulting in Parafigularia taylori n. comb. Morphological data suggest that these genera comprise different lineages, and a discussion on the disparities among cribrilinid (sensu lato) spinocysts is provided. UUID: http://zoobank.org/215957d3-064b-47e2-9090-d0309f6c9cd8

A new species of Lonchodryinus (Hymenoptera, Dryinidae) from Upper Eocene Baltic amber

Zootaxa ◽  
2021 ◽  
Vol 5020 (2) ◽  
pp. 328-336
Author(s):  
MASSIMO OLMI ◽  
DMITRY V. VASILENKO ◽  
LEONARDO CAPRADOSSI ◽  
EVGENY E. PERKOVSKY ◽  
ADALGISA GUGLIELMINO
Keyword(s):  
New Species ◽  
Fore Wing ◽  
Baltic Amber ◽  
Upper Eocene ◽  
Fossil Species ◽  
Extant Species ◽  
A New Species

Lonchodryinus groehni sp. nov. (Hymenoptera: Chrysidoidea: Dryinidae) is described from Baltic amber. The new species is close to L. balticus Olmi & Guglielmino, 2012, but it can be distinguished for the different OPL/POL ratio and 2r-rs&Rs vein of the fore wing. A key to the fossil species of Lonchodryinus and a comparison with the extant species L. ruficornis (Dalman, 1818) are presented.  

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