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Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals
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Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals

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

Deadline for manuscript submissions: closed (15 April 2023) | Viewed by 21806

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, 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,

Due to the increased importance of knowledge related to the evolution and phylogenetics of mammals, we are launching this Special Issue entitled “Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals”. This Special Issue is focused on all mammalian species (wild and domestic) from all continents (Africa, Asia, Australia, Central America, Europe, North America, and South America) related to the following topics: molecular evolution and karyology (gene duplication, chromosome changes, natural selection detection, neutral evolution detection, etc.); phylogeography and molecular ecology using molecular markers and morphometrics; and phylogenetics using molecular markers and genomics. In this Special Issue, in order to help researchers and readers understand the recent application of different evolutionary methods to mammals, we invite a wide range of paper submissions on molecular evolution, phylogeography, and phylogenetics, including reviews, research papers and other article types.

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

  • chromosomes
  • evolution
  • genomics
  • mammals
  • molecular ecology
  • molecular markers
  • phylogenetics
  • phylogeography

Published Papers (7 papers)

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Research

Jump to: Review

14 pages, 3767 KiB  
Article
Human Population Density Influences Genetic Diversity of Two Rattus Species Worldwide: A Macrogenetic Approach
by Chrystian C. Sosa, Catalina Arenas and Víctor Hugo García-Merchán
Genes 2023, 14(7), 1442; https://doi.org/10.3390/genes14071442 - 14 Jul 2023
Viewed by 2290
Abstract
On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore [...] Read more.
On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species Rattus rattus and Rattus norvegicus. Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (microsatellites, Single Nucleotide Polymorphisms—SNPs-, restrictition site-associated DNA sequencing -RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of R. rattus and R. norvegicus, using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the Rattus species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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14 pages, 1737 KiB  
Article
Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini)
by Jeferson Carneiro, Iracilda Sampaio, José de S. e Silva-Júnior, Antonio Martins-Junior, Izeni Farias, Tomas Hrbek, Jean Boubli and Horacio Schneider
Genes 2023, 14(7), 1309; https://doi.org/10.3390/genes14071309 - 21 Jun 2023
Viewed by 942
Abstract
Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the [...] Read more.
Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support five species of Chiropotes that emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondônia and Tapajós. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins probably determined the speciation events within Chiropotes. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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21 pages, 2998 KiB  
Article
Morphological and Genetics Support for a Hitherto Undescribed Spotted Cat Species (Genus Leopardus; Felidae, Carnivora) from the Southern Colombian Andes
by Manuel Ruiz-García, Myreya Pinedo-Castro and Joseph Mark Shostell
Genes 2023, 14(6), 1266; https://doi.org/10.3390/genes14061266 - 15 Jun 2023
Cited by 2 | Viewed by 8187
Abstract
In 1989, a skin of a small spotted cat, from the Galeras Volcano in southern Colombia (Nariño Department), was donated to the Instituto Alexander von Humboldt (identification, ID 5857) at Villa de Leyva (Boyacá Department, Colombia). Although originally classified as Leopardus tigrinus, [...] Read more.
In 1989, a skin of a small spotted cat, from the Galeras Volcano in southern Colombia (Nariño Department), was donated to the Instituto Alexander von Humboldt (identification, ID 5857) at Villa de Leyva (Boyacá Department, Colombia). Although originally classified as Leopardus tigrinus, its distinctiveness merits a new taxonomic designation. The skin is distinct from all known L. tigrinus holotypes as well as from other Leopardus species. Analysis of the complete mitochondrial genomes from 44 felid specimens (including 18 L. tigrinus and all the current known species of the genus Leopardus), the mtND5 gene from 84 felid specimens (including 30 L. tigrinus and all the species of the genus Leopardus), and six nuclear DNA microsatellites (113 felid specimens of all the current known species of the genus Leopardus) indicate that this specimen does not belong to any previously recognized Leopardus taxon. The mtND5 gene suggests this new lineage (the Nariño cat as we name it) is a sister taxon of Leopardus colocola. The mitogenomic and nuclear DNA microsatellite analyses suggest that this new lineage is the sister taxon to a clade formed by Central American and trans-Andean L. tigrinus + (Leopardus geoffroyi + Leopardus guigna). The temporal split between the ancestor of this new possible species and the most recent ancestor within Leopardus was dated to 1.2–1.9 million years ago. We consider that this new unique lineage is a new species, and we propose the scientific name Leopardus narinensis. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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11 pages, 865 KiB  
Article
Polymorphisms Analysis of BMP15, GDF9 and BMPR1B in Tibetan Cashmere Goat (Capra hircus)
by Tianzeng Song, Yacheng Liu, Renqing Cuomu, Yao Tan, Cuoji A. Wang, Ji De, Xiaohan Cao and Xianyin Zeng
Genes 2023, 14(5), 1102; https://doi.org/10.3390/genes14051102 - 18 May 2023
Cited by 2 | Viewed by 1409
Abstract
The Tibetan cashmere goat is a prolific goat breed in China. In sheep breeds, natural mutations have demonstrated that the transforming growth factor beta (TGF-β) super family ligands, such as growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15 [...] Read more.
The Tibetan cashmere goat is a prolific goat breed in China. In sheep breeds, natural mutations have demonstrated that the transforming growth factor beta (TGF-β) super family ligands, such as growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15) and their type I receptor (bone morphogenetic protein receptor (BMPR1B), are essential for ovulation and increasing litter size. In this study, 216 female Tibetan cashmere goats were sampled, and candidate genes with fecundity traits were detected via restriction fragment length polymorphism (RFLP) and sequenced. Four polymorphic loci were found in specific amplification fragments of BMP15 and GDF9. Two SNP sites of the BMP15 gene were discovered, namely G732A and C805G. The G732A mutation did not cause the change in amino acids, and the frequencies of each genotype were 0.695 for the GG type, 0.282 for the GA type and 0.023 for the AA type. The C805G mutation caused amino acids to change from glutamine to glutamate. The genotype frequencies were 0.620 for the CC type, 0.320 for the CG type and 0.320 for the CG type. For the GG type 0.060, the G3 and G4 mutations of the GDF9 gene were all homozygous mutations. Two known SNP sites, C719T and G1189A, were detected in the Tibetan cashmere goat GDF9 gene, of which the C719T mutation caused a change of alanine to valine, with a genotype frequency of 0.944 for the CC type and 0.056 for the CT type, whereas no TT type was found. The G1189A mutation caused valine to become isoleucine, and the frequencies of each genotype were 0.579 for the GG type, 0.305 for the GA type and 0.116 for the AA type; G1, B2, B3, B4, FecXH, FecXI, FecXL, G2, G5, G6, G7, G8, FecGE, FecTT and FecB mutations were not found in Tibetan cashmere goats. The results of this study provide a data basis for future studies of BMP15, GDF9 and BMPR1B gene mutations in goats. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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13 pages, 6041 KiB  
Communication
Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication
by Shantanu Kundu, Manokaran Kamalakannan, Tanoy Mukherjee, Dhriti Banerjee and Hyun-Woo Kim
Genes 2023, 14(3), 765; https://doi.org/10.3390/genes14030765 - 21 Mar 2023
Viewed by 1648
Abstract
The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. [...] Read more.
The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42–53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km2), of which the majority (171 km2) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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11 pages, 4255 KiB  
Article
Polymorphisms and mRNA Expression Levels of IGF-1, FGF5, and KAP 1.4 in Tibetan Cashmere Goats
by Tianzeng Song, Yao Tan, Renqing Cuomu, Yacheng Liu, Gui Ba, Langda Suo, Yujiang Wu, Xiaohan Cao and Xianyin Zeng
Genes 2023, 14(3), 711; https://doi.org/10.3390/genes14030711 - 14 Mar 2023
Cited by 1 | Viewed by 1100
Abstract
The Tibetan cashmere goat is a precious breed in China and its cashmere is widely used in clothing and textiles. The genes IGF-1, FGF5, and KAP 1.4 have been shown to be crucial regulators of cashmere growth. In this study, we [...] Read more.
The Tibetan cashmere goat is a precious breed in China and its cashmere is widely used in clothing and textiles. The genes IGF-1, FGF5, and KAP 1.4 have been shown to be crucial regulators of cashmere growth. In this study, we examined mRNA expression levels of these three genes and detected IGF-1, FGF5, and KAP 1.4 SNP loci in the Tibetan cashmere goat. After amplification and sequence alignment of the genes IGF-1, FGF5, and KAP 1.4 among 206 Tibetan cashmere goats, two new SNP loci were detected in gene KAP 1.4, while no SNP loci were found in amplified fragments of genes IGF-1 and FGF5. The expression levels of gene IGF-1 in Baingoin and Nyima counties were significantly higher than in other counties (p < 0.05). Moreover, the expression level of gene FGF5 in Gêrzê was significantly higher than in Rutog. The expression levels of mRNA in KAP 1.4 showed significant variation among seven counties. There were no significant differences in mRNA expression levels of IGF-1, FGF5, and KAP 1.4 in Tibetan cashmere goats when analysed by sex. The gene IGF-1 was slightly up-regulated in one to five-year-old cashmere goats, except in those that were 4 years old. The mRNA expression levels of FGF5 in one and two-year-old cashmere goats was lower compared with those in three to five-year-old cashmere goats. KAP 1.4 was up-regulated across one to five-year-old cashmere goats. In this study, SNP detection and mRNA expression analysis of IGF-1, FGF5, and KAP 1.4 genes was able to add data to genetic evolutionary analysis. Further studies should be carried out in SNPs to detect other fragments in genes IGF-1 and FGF5, as well as signal pathways and gene functions in protein levels of genes IGF-1, FGF5, and KAP 1.4 in the Tibetan cashmere goat. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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Review

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17 pages, 5100 KiB  
Review
Being a Dog: A Review of the Domestication Process
by Domenico Tancredi and Irene Cardinali
Genes 2023, 14(5), 992; https://doi.org/10.3390/genes14050992 - 27 Apr 2023
Cited by 2 | Viewed by 5537
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A “multiphase” view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic [...] Read more.
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A “multiphase” view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev’s foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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