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New Phylogenetic and Phylogeography Insights in Animals Using Genes, Genomics,...
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New Phylogenetic and Phylogeography Insights in Animals Using Genes, Genomics, Chromosomes, and Morphological Traits

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

Deadline for manuscript submissions: 25 January 2025 | Viewed by 1085

Special Issue Editor

Dr. Manuel Ruiz-Garcia

E-Mail Website
Guest Editor
Laboratory of Molecular Population Genetics and Evolutionary Biology, Department of Biology, Faculty of Science, Pontificia Universidad Javeriana, Cra 7A No 43-82, Bogotá, Colombia
Interests: chromosomes; evolution; genomics; mammals; molecular ecology; molecular markers; phylogenetics; phylogeography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Phylogenetics and phylogeographical studies are essential to understand the complete biodiversity we observe in the world. Initially, morphological traits were used to carry out this task. However, over the last decades, with the arrival of new technologies, the use of chromosome procedures, molecular markers and genomics has assisted in adequately describing phylogenetic relationships among the organisms of determined taxa or groups, and phylogeographic spatial patterns, due to their closest neutral evolutionary dynamics. Many of these contributions have helped discover new taxa or species which were not recognized by scientists until now. In other words, these studies have discovered hidden biodiversity, which is essential to undertake adequate conservation programs to try to preserve any lifeform. It is noteworthy to try to use various data (molecular, metagenomics, chromosomal, reproductive, immunological, ecological, ethological, morphological ones) to obtain integrative and more precise phylogenetic and phylogeography results to discover the fascinating world of the hidden animal biodiversity. For this reason, I invite you to participle in this Special Issue to show your studies on phylogenetics and phylogeography with whichever species of animals you study.

Dr. Manuel Ruiz-Garcia
Guest Editor

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 submissions that pass pre-check are 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 2600 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

  • animals
  • chromosomal evolution
  • DNA
  • population genetics
  • mitochondrial genome evolution
  • morphological evolution
  • neutral and selective evolution
  • nuclear genome evolution
  • phylogenetics
  • phylogeography

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Published Papers (1 paper)

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Research

40 pages, 4795 KiB  
Article
New Insights into the Molecular Evolution of Tapirus pinchaque (Tapiridae, Perissodactyla) and the Rise and Fall of Tapirus kabomani as a Full Species
by Manuel Ruiz-García, Armando Castellanos, Franz Kaston, Myreya Pinedo-Castro and Joseph Mark Shostell
Genes 2024, 15(12), 1537; https://doi.org/10.3390/genes15121537 - 28 Nov 2024
Viewed by 805
Abstract
Large wild mammals are extremely important in their respective ecological communities and are frequently considered to be emblematic. This is the case of the different tapir species, the largest terrestrial mammals from the Neotropics. Despite their large size and being objects of interest [...] Read more.
Large wild mammals are extremely important in their respective ecological communities and are frequently considered to be emblematic. This is the case of the different tapir species, the largest terrestrial mammals from the Neotropics. Despite their large size and being objects of interest for many naturalists, the field still lacks critical genetics and systematics information about tapir species. In the current work, we analyzed four molecular datasets (mitogenomes, and three nuclear genes, RAG 1-2, IRBP, and BRCA1) of two South American tapirs: the Andean tapir (Tapirus pinchaque) and the alleged new species of tapir, Tapirus kabomani. We derived four main findings. (1) Our molecular phylogenetic analyses showed T. pinchaque as the youngest tapir branch in Neotropics and a sister species of Tapirus terrestris. This contradicts the traditional morphological observations of renowned zoologists and paleontologists, who considered T. pinchaque as the oldest Neotropical tapir. (2) Our data does not support that the alleged T. kabomani is a full species. Rather, it is a specific group within T. terrestris. (3) T. pinchaque is the Neotropical tapir species which yielded the lowest levels of genetic diversity (both for mitochondrial and nuclear data). (4) The spatial genetic structure for T. pinchaque shows differences depending on the type of molecular marker used. With mitogenomes, the spatial structure is relatively weak, whereas with two nuclear genes (RAG 1-2 and IRBP), the spatial structure is highly significant. Curiously, for the other nuclear gene (BRCA1), the spatial structure is practically nonexistent. In any case, the northernmost population of T. pinchaque we studied (Los Nevados National Park in Colombia) was in a peripatric situation and was the most genetically differentiated. This is important for the adequate conservation of this population. (5) T. pinchaque showed clear evidence of population expansion during the last part of the Pleistocene, a period during which the dryness and glacial cold extinguished many large mammals in the Americas. However, T. pinchaque survived and spread throughout the Northern Andes. Full article
(This article belongs to the Special Issue New Phylogenetic and Phylogeography Insights in Animals Using Genes, Genomics, Chromosomes, and Morphological Traits)
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