Special Issue "Evolutionary Genetics of Reptiles and Amphibians"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 July 2019

Special Issue Editors

Guest Editor
Prof. Dr. Sebastian Steinfartz

Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Germany
Website | E-Mail
Interests: ecology; evolution; genetics
Guest Editor
Prof. Dr. Jonathon Marshall

Department of Zoology, Weber State University, Ogden, UT, USA
Website | E-Mail
Interests: species delimitation; evolutionary genetics
Guest Editor
Dr. Katharina Wollenberg Valero

Department of Biological and Marine Sciences, University of Hull, UK
Website | E-Mail
Interests: evolutionary and functional genomics of climate stress and -adaptation

Special Issue Information

Dear Colleagues,

Despite being divided into two distinct taxonomic classes of vertebrates, amphibians and reptiles have been classically lumped together under the science of Herpetology due to their creeping and crawling movements. Indeed, both groups are fundamentally different regarding their general biology and environmental demands. Still, amphibian and reptile research has been integrated by the herpetological community in a very successful way, in which scientists often work in parallel on amphibian and reptile systems to address major scientific questions. During the 7th World Congress of Herpetology in Canada, we organised a symposium entitled “Speciation in amphibians and reptiles: from patterns to processes and mechanisms” to bring together leading herpetologists and integrate their research on crucial evolutionary topics. Since then, especially the field of Genomics has undergone a rapid expansion. With this Special Issue, we aim to summarize research on the evolutionary genetics of amphibians and reptiles. We invite studies that use genetic and genomic approaches to unravel basic questions of evolutionary biology on different taxonomic levels of amphibians and reptiles. Therefore, we invite submissions on speciation research, local adaptation, phenotypic plasticity, and also conservation-related issues, such as infectious diseases based in a detailed genetic or genomic framework. Manuscripts submitted to this Special Issue are guaranteed to have a quick and fair review process. Potential topics for the Special Issue include, but are not limited to:

  • Evolutionary systematics
  • Patterns and mechanisms of speciation
  • Local adaptation
  • Phenotypic plasticity and epigenetics
  • Gene expression
  • Genetics of emerging infectious diseases
  • Diversity and genetics of microbiota

We aim to reward the best paper published in the Special Issue with a publication fee waiver. Authors that would like to participate for this option should submit the following pre-submission material to one of the Guest Editors before 1 January 2019: a cover letter reasoning why their study is outstanding, an abstract, and a conceptual and methodological outline (not longer than one page) of the manuscript that will be submitted.

Dr. Sebastian Steinfartz
Prof. Dr. Jonathon Marshall
Dr. Katharina Wollenberg Valero
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • herpetofauna
  • evolutionary genetics and genomics
  • systematics
  • speciation
  • adaptation
  • epigenetics
  • infectious diseases

Published Papers (5 papers)

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Research

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Open AccessArticle
Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella
Received: 6 February 2019 / Revised: 9 April 2019 / Accepted: 15 April 2019 / Published: 23 April 2019
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Abstract
Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantella madagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first [...] Read more.
Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantella madagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantella aurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantella crocea + Mantella milotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)
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Open AccessArticle
Shedding Light on a Secretive Tertiary Urodelean Relict: Hynobiid Salamanders (Paradactylodon persicus s.l.) from Iran, Illuminated by Phylogeographic, Developmental, and Transcriptomic Data
Received: 17 March 2019 / Revised: 10 April 2019 / Accepted: 11 April 2019 / Published: 18 April 2019
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Abstract
The Hyrcanian Forests present a unique Tertiary relict ecosystem, covering the northern Elburz and Talysh Ranges (Iran, Azerbaijan), a poorly investigated, unique biodiversity hotspot with many cryptic species. Since the 1970s, two nominal species of Urodela, Hynobiidae, Batrachuperus (later: Paradactylodon) have been [...] Read more.
The Hyrcanian Forests present a unique Tertiary relict ecosystem, covering the northern Elburz and Talysh Ranges (Iran, Azerbaijan), a poorly investigated, unique biodiversity hotspot with many cryptic species. Since the 1970s, two nominal species of Urodela, Hynobiidae, Batrachuperus (later: Paradactylodon) have been described: Paradactylodon persicus from northwestern and P. gorganensis from northeastern Iran. Although P. gorganensis has been involved in studies on phylogeny and development, there is little data on the phylogeography, systematics, and development of the genus throughout the Hyrcanian Forests; genome-wide resources have been entirely missing. Given the huge genome size of hynobiids, making whole genome sequencing hardly affordable, we aimed to publish the first transcriptomic resources for Paradactylodon from an embryo and a larva (9.17 Gb RNA sequences; assembled to 78,918 unigenes). We also listed 32 genes involved in vertebrate sexual development and sex determination. Photographic documentation of the development from egg sacs across several embryonal and larval stages until metamorphosis enabled, for the first time, comparison of the ontogeny with that of other hynobiids and new histological and transcriptomic insights into early gonads and timing of their differentiation. Transcriptomes from central Elburz, next-generation sequencing (NGS) libraries of archival DNA of topotypic P. persicus, and GenBank-sequences of eastern P. gorganensis allowed phylogenetic analysis with three mitochondrial genomes, supplemented by PCR-amplified mtDNA-fragments from 17 museum specimens, documenting <2% uncorrected intraspecific genetic distance. Our data suggest that these rare salamanders belong to a single species P. persicus s.l. Humankind has a great responsibility to protect this species and the unique biodiversity of the Hyrcanian Forest ecosystems. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)
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Open AccessArticle
Evolutionary Insights of the ZW Sex Chromosomes in Snakes: A New Chapter Added by the Amazonian Puffing Snakes of the Genus Spilotes
Received: 4 January 2019 / Revised: 12 March 2019 / Accepted: 31 March 2019 / Published: 9 April 2019
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Abstract
Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process [...] Read more.
Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and trends for sex chromosomes in two Amazonian Puffer Snakes (S. pulllatus and S. sulphureus). We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches. The karyotype of S. sulphureus (presented here for the first time) exhibits a 2n = 36, similar to that previously described in S. pullatus. Both species have highly differentiated ZZ/ZW sex chromosomes, where the W chromosome is highly heterochromatic in S. pullatus but euchromatic in S. sulphureus. Both W chromosomes are homologous between these species as revealed by cross-species comparative genomic hybridization, even with heterogeneous distributions of several repetitive sequences across their genomes, including on the Z and on the W chromosomes. Our study provides evidence that W chromosomes in these two species have shared ancestry. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)
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Open AccessArticle
Satellite DNA Mapping in Pseudis fusca (Hylidae, Pseudinae) Provides New Insights into Sex Chromosome Evolution in Paradoxical Frogs
Received: 24 December 2018 / Revised: 31 January 2019 / Accepted: 8 February 2019 / Published: 19 February 2019
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Abstract
In the frog genus Pseudis, previous works found a sex-linked heteromorphism of the PcP190 satellite DNA in the nucleolus organizer region (NOR)-bearing chromosome pairs of Pseudis bolbodactyla and Pseudis tocantins, which possess a ZZ/ZW sex determination system. A pericentromeric inversion was [...] Read more.
In the frog genus Pseudis, previous works found a sex-linked heteromorphism of the PcP190 satellite DNA in the nucleolus organizer region (NOR)-bearing chromosome pairs of Pseudis bolbodactyla and Pseudis tocantins, which possess a ZZ/ZW sex determination system. A pericentromeric inversion was inferred to have occurred during W chromosome evolution, moving a chromosomal cluster enriched by the PcP190 from the short arm (as observed in P. bolbodactyla) to the NOR-bearing long arm (as observed in P. tocantins). However, whether such an inversion happened in P. tocantins or in the common ancestor of Pseudis fusca and P. tocantins remained unclear. To assess this question, we mapped PcP190 in the karyotype of P. fusca from three distinct localities. Southern blotting was used to compare males and females. The mitochondrial H1 fragment (which contains the 12S ribosomal RNA (rRNA), tRNAval, and 16S rRNA genes) and cytochrome b gene were partially sequenced, and a species tree was inferred to guide our analysis. Pseudis fusca specimens were placed together as the sister group of P. tocantins, but based on genetic distance, one of the analyzed populations is probably an undescribed species. A cluster of PcP190, located in the long arm of chromosome 7, is sex linked in this putative new species but not in the remaining P. fusca. We could infer that the pericentromeric inversion that moved the PcP190 site to the NOR-bearing chromosome arm (long arm) occurred in the common ancestor of P. fusca, the putative undescribed species, and P. tocantins. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)
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Open AccessTechnical Note
Development and Validation of Sex-Specific Markers in Pelodiscus Sinensis Using Restriction Site-Associated DNA Sequencing
Received: 7 March 2019 / Revised: 3 April 2019 / Accepted: 10 April 2019 / Published: 15 April 2019
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Abstract
The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, Pelodiscus sinensis, is an economically important aquatic species that shows significant male sexual dimorphism, with a large body size, faster growth, a thick [...] Read more.
The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, Pelodiscus sinensis, is an economically important aquatic species that shows significant male sexual dimorphism, with a large body size, faster growth, a thick and wide calipash, and lower body fat. In this study, ten male and ten female turtles were subjected to restriction site-associated DNA sequencing (RAD-seq) using the Hi-Seq 4000 sequencing platform to isolate female-specific DNA fragments. We identified 5967 bp and 6532 bp fragments using genome walking. Three female-specific markers designed from these two fragments were confirmed to separate the sexes of Pelodiscus sinensis perfectly. One of the female-specific markers showed dosage association in female and male individuals. Individuals from different populations (n = 296) were used to validate that the female-specific markers could identify the genetic sex of Pelodiscus sinensis with 100% accuracy. The results of the present study demonstrated that RAD-seq was useful to develop sex-related markers in animals, and verified that the sex determination system of Pelodiscus sinensis belonged to the ZZ/ZW heterogametic system. Importantly, the developed markers could lead to a method for sex-controlled breeding in the Chinese soft-shelled turtle. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Reptiles and Amphibians)
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