alexa The New Mode of Thought of Vertebrates’ Evolution | OMICS International
ISSN: 2329-9002
Journal of Phylogenetics & Evolutionary Biology
Make the best use of Scientific Research and information from our 700+ peer reviewed, Open Access Journals that operates with the help of 50,000+ Editorial Board Members and esteemed reviewers and 1000+ Scientific associations in Medical, Clinical, Pharmaceutical, Engineering, Technology and Management Fields.
Meet Inspiring Speakers and Experts at our 3000+ Global Conferenceseries Events with over 600+ Conferences, 1200+ Symposiums and 1200+ Workshops on
Medical, Pharma, Engineering, Science, Technology and Business

The New Mode of Thought of Vertebrates’ Evolution

Kupriyanova NS* and Ryskov AP
The Institute of Gene Biology RAS, 34/5, Vavilov Str. Moscow, Russia
Corresponding Author : Kupriyanova NS
The Institute of Gene Biology RAS
34/5, Vavilov Str. Moscow, Russia
Tel: +7 8 499 1359864
Fax: +7 8 499 1354105
E-mail: [email protected]
Received May 27, 2014; Accepted July 15, 2014; Published July 22, 2014
Citation: Kupriyanova NS, Ryskov AP (2014) The New Mode of Thought of Vertebrates’ Evolution. J Phylogen Evolution Biol 2:129. doi:10.4172/2329-9002.1000129
Copyright: © 2014 Kupriyanova NS, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Related article at
DownloadPubmed DownloadScholar Google

Visit for more related articles at Journal of Phylogenetics & Evolutionary Biology

Abstract

Molecular phylogeny of the reptiles does not accept the basal split of squamates into Iguania and Scleroglossa that is in conflict with morphological evidence. The classical phylogeny of living reptiles places turtles at the base of the tree. Analyses of mitochondrial DNA and nuclear genes join crocodilians with turtles and places squamates at the base of the tree. Alignment of the reptiles’ ITS2s with the ITS2 of chordates has shown a high extent of their similarity in ancient conservative regions with Cephalochordate Branchiostoma floridae, and a less extent of similarity with two Tunicata, Saussurea tunicate, and Rinodina tunicate. We have performed also an alignment of ITS2 segments between the two break points coming into play in 5.8S rRNA maturation of Branchiostoma floridae in pairs with orthologs from different vertebrates where it was possible. A similarity for most taxons fluctuates between about 50 and 70%. This molecular analysis coupled with analysis of phylogenetic trees constructed on a basis of manual alignment, allows us to hypothesize that primitive chordates being the nearest relatives of simplest vertebrates represent the real base of the vertebrate phylogenetic tree.

Keywords
Vertebrates; Reptiles; Chordates; Evolutionary relations; Base of the phylogenetic trees
Introduction
The standard view has been that lizard species split at the base of the phylogenetic tree into Iguania (iguanas, chameleons, and relatives) and Scleroglossa (all remaining lizards, including geckos, skinks, monitors, and snakes). In the past decade, molecular phylogenetic’s analyses, have strongly contradicted this view [1]. They concluded that iguanians evolved more recently, locate in the lizard tree close to monitors and Anguimorpha and snakes, and that their supposedly ancestral characteristics arose as the result of re-evolution. Recently obtained morphological data set, analyzed with state-of-the-art phylogenetic methods, has not resolved contradictions between morphological and DNA-based studies [2]. So, we have a conundrum here. The molecular data suggest very limited knowledge of the functional link between structures and lifestyle. Conversely, morphology implies a pattern of molecular evolution that has yet to be explained.
Recently, we published the paper in which two different types of phylogenetic trees were constructed on the basis of the ITS2s primary structures alignment for almost 60 reptiles belonging to different orders, and some other animals [3]. All these ITS2s differ significantly by sizes, and primary structures of functionally neutral regions. So, we used (i) GeneBee Services program [4,5] which had made it possible to carry out synchronous total automated alignment of the group of sequences of any sizes with subsequent construction of the unrooted trees based on this alignment. (ii) The other phylogenetic tree was constructed on the basis of manual alignment with the help of the Bayesian inference method (the MrBayes program) [3].
In both cases the trees were generated by separate clades of Iguania (Iguanidae, Agamidae, Chameleonidae), suborder clades of Crocodilians+Testudines, and Snakes+Lacertidae lizards+Anguimorph lizards. The intermediate clades are formed by Scleroglossa (all remaining lizards, including geckos, and skinks). Analysis of ITS2- based phylogenetic trees coupled with molecular analysis, allows us to hypothesize that chordate Branchiostoma floridae, Saussurea tunicate, and Rinodina tunicate being the nearest relatives to vertebrates can be placed near the base of their total phylogenetic tree.
Phylogeny of the reptiles differs significantly in works of various authors. Morphological classification of Squamata lets to make a proposal about a split of Iguania and Scleroglossa in the late Triassic period [6], and places snakes close to the other limbless forms, Dibamidae and Amphisbaenia. In some other, more recent papers, snakes were considered as the sister taxon of varanids or placed into the Anguimorpha clade, thereby controverting their separation as an individual clade from other Squamata [7-9].
Molecular phylogeny does not accept the basal split of squamates into Iguania and Scleroglossa that is in conflict with morphological evidence [10-13]. Phylogenetic analyses based on the molecular data from a number of nuclear protein coding genes places snakes to the same clade as lacertids and amphisbaenids [14]. Furthermore, recently snakes, anguimorphs, and iguanians were combined in a clade Toxicofera based on a presence of toxin secreting oral glands in their organisms [15]. The position of turtles among amniotes remains in dispute, with morphological and molecular comparisons giving different results [16]. The classical phylogeny of living reptiles places turtles at the base of the tree. Analyses of mitochondrial DNA and 22 nuclear genes join crocodilians with turtles and places squamates at the base of the tree [13,17,18].
 
Our phylogenetic trees constructed on the basis of the ITS2s primary structural alignments revealed a split between Iguania clade and Scleroglossa that is in agreement with morphological classification. True lizards and snakes showed sister relationships, as well as the two other reptilian orders, Crocodilia+Aves, and Testudines. In summary, our phylogenetic trees exhibit specific features deduced or, to the contrary, rejected earlier by other authors. We hypothesize that simplest organisms at the base of the vertebrates’ phylogenetic tree were among simplest chordates.
 
Results and Discussion
The ITS2 of Branchiostoma floridae contains four conservative segments (consensus sequences) similar to those found in all known vertebrates [19-21]. The very first 12 nucleotides of the ITS2 (consensus ‘a’) represent a cis-element for the U3 small nucleolar RNA. Five nucleotides at the 5’-end often incorporate taxon specific substitutions, whereas seven bases at the 3’-end form extremely conservative nucleotide block. The second consensus (‘b’) is the most conservative one, but its functions are unknown until now. The consensuses ‘c’ and ‘d’ contain the regions providing the ITS2 specific cleavages for the 8S and 12S pre-rRNA forming during 5.8S rRNA maturation Table 1.
It is known that at least two conservative break points provide maturation of 5.8S rRNA. Their positions were detected experimentally for X.laevis8S pre-rRNA as(C) 3–5 (N)1–3 AAG(N)3-4A^GA [19,20], and CGGCTGTC^TGTGGA for 12S pre-rRNA [21]. The corresponding sequence for Muridae is different (CGTCCG^TGCGCCGA) [21]. These sequences are present practically in all analyzed vertebrates’ ITS2s, and contain very rare substitutions [3].

The consensus ‘a’ of Branchiostoma floridaeITS2 contains at its 3’- end the same 5’-TCAATCG-3’ sequence as all known vertebrates with the exception of a G→A substitution in one lizard, and one crocodile. At the same time Tunicata Ciona intestinalis contains at the 3’-end of the consensus ‘a’ three substitutions, and two deletions, and Rinudina tunicata has two orthologic substitutions, and one rare insertion upstream 5’-TCAATCG-3’ sequence similar to those in Gallus gallus (Table 1). The consensus ‘b’ is practically identical in all vertebrates (5’- CGCGGCTGGGG-3’) including Branchiostoma floridae. However, in Ciona intestinalis, it involves three substitutions and one deletion, whereas in Rinudina tunicata consensus ‘b’ has only one substitution. The consensuses ‘c’ and ‘d’ are more variable. In the consensus ‘c’ 5’- poly C, central AAG, and 3’-AGA regions can be marked as the most constant, and, possibly, more important ones for 5.8S rRNA maturation, although these elements contain 2-6 substitutions in Branchiostoma floridae, and both Tunicata. In the consensus ‘d’ the most constant role can possibly play 5’-CGG-CTG-TCT-3’ elements. It is necessary to note that consensus‘d’ is especially variable in

 

and Tunicata, where indicated constant element is practically absent Table 1.

Furthermore, we have performed an alignment of the ITS2 variable segment localized between ‘c’ and ‘d’, namely between the two break points coming into play in 5.8S rRNA maturation for Branchiostoma floridae, in pairs with its orthologs from different vertebrate classes (Supplement 1). For most taxons similarity is fixed at the level of about 50-70% Table 2. Corresponding part of the ITS2s of the two Tunicata reveals substantially less similarity with the region implicated in 5.8S rRNA maturation in vertebrates, and its position can be only roughly estimated (Table 1).
We have obtained unexpected result on comparison of the two Bayesian trees differing only by presence or absence of Cephalochordata and Tunicata ITS2 among sequences implicated in the Bayesian trees construction Figures 1 and 2. We see that clade Iguanidae changes its position on phylogenetic tree becoming tightly coupled with Cephalochordata, and Tunicata. Furthermore, fishes, and amphibians occupy a middle position between Iguanidae and Acrodonts. The upper part of the tree stays unchanged in these conditions. It is difficult to explain this phenomenon with an exception of the only proposal that primary structures of Iguanidae, Cephalochordata, and Tunicata ITS2s are most similar to each other.
So, we hypothesize that “the base of the tree” is possibly misused termini, but all vertebrates’ classes started their evolution almost simultaneously from a group of primitive chordates. They could probably form hybrids in the beginning of radiation, but rather soon they have formed individual branches. A time of formation of discrete branches, and rate of evolution in different taxons could be significantly different. Higher rates of molecular evolution in iguanians and snakes [22] for an example suggest that the genes in these taxa are not evolving like those in other lizard lineages,
In a recent paper a phylogenomic dataset based on 248 nuclear genes for 16 vertebrate taxa including turtles, caimans, lizards, and a lungfish were obtained to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches unambiguously support turtles as a sister group to birds and crocodiles [15]. It is intriguing that conclusions inferred from analysis of all our trees are in a full agreement with the conclusions made in this paper. Besides of it our results show that a branch leading to mammals’ line starts among turtles in spite of their vigorous subsequent diversification. It is not appropriate now to discuss this result without of supplementary data.
Acknowledgements
This study was supported by the Russian Foundation for Basic Research (project no. 13-04-00544-а), and the Presidium of Russian Academy of Sciences Programs “Living Nature” and “Molecular and Cell Biology”.
References






















 

Tables and Figures at a glance

image   image
Table 1   Table 2

 

Figures at a glance

image   image
Figure 1   Figure 2
Select your language of interest to view the total content in your interested language
Post your comment

Share This Article

Relevant Topics

Recommended Conferences

Article Usage

  • Total views: 11729
  • [From(publication date):
    November-2014 - Dec 13, 2017]
  • Breakdown by view type
  • HTML page views : 7936
  • PDF downloads : 3793
 

Post your comment

captcha   Reload  Can't read the image? click here to refresh

Peer Reviewed Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

Agri & Aquaculture Journals

Dr. Krish

[email protected]

1-702-714-7001Extn: 9040

Biochemistry Journals

Datta A

[email protected]

1-702-714-7001Extn: 9037

Business & Management Journals

Ronald

[email protected]

1-702-714-7001Extn: 9042

Chemistry Journals

Gabriel Shaw

[email protected]

1-702-714-7001Extn: 9040

Clinical Journals

Datta A

[email protected]

1-702-714-7001Extn: 9037

Engineering Journals

James Franklin

[email protected]

1-702-714-7001Extn: 9042

Food & Nutrition Journals

Katie Wilson

[email protected]

1-702-714-7001Extn: 9042

General Science

Andrea Jason

[email protected]

1-702-714-7001Extn: 9043

Genetics & Molecular Biology Journals

Anna Melissa

[email protected]

1-702-714-7001Extn: 9006

Immunology & Microbiology Journals

David Gorantl

[email protected]

1-702-714-7001Extn: 9014

Materials Science Journals

Rachle Green

[email protected]

1-702-714-7001Extn: 9039

Nursing & Health Care Journals

Stephanie Skinner

[email protected]

1-702-714-7001Extn: 9039

Medical Journals

Nimmi Anna

[email protected]

1-702-714-7001Extn: 9038

Neuroscience & Psychology Journals

Nathan T

[email protected]

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

Ann Jose

[email protected]

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

[email protected]

1-702-714-7001Extn: 9042

 
© 2008- 2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version