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Feature Papers in Phylogeny and Evolution
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Feature Papers in Phylogeny and Evolution

A topical collection in Diversity (ISSN 1424-2818). This collection belongs to the section "Phylogeny and Evolution".

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Editor

Dr. Eric Buffetaut

E-Mail Website
Collection Editor
CNRS (UMR 8538), Laboratoire de Géologie de l’Ecole Normale Supérieure, 24 Rue Lhomond, 75231 Paris, CEDEX 05, France
Interests: vertebrate palaeontology
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

As Diversity is a generalist journal, we hereby invite authors to submit articles outlining the state of the art of some special features concerning phylogeny and evolution, dealing with all aspects of the evolution and phylogeny of organisms, both living and extinct.  

Specialized or local studies will be evaluated only if discussion leads to/illustrates general questions/conclusions relevant to evolution and phylogeny. Both descriptive studies and more theoretical papers are acceptable.

The following list includes some of the topics covered:

  •     Evolutionary biology;
  •     Phylogenetic reconstruction;
  •     Evolution of ecosystems;
  •     Palaeontology;
  •     Palaeobotany;
  •     Micropalaeontology;
  •     Invertebrate palaeontology;
  •     Vertebrate palaeontology;
  •     Palaeobiology;
  •     Fossil record;
  •     Macroevolution;
  •     Molecular phylogeny;
  •     Ancient DNA;
  •     Evolutionary biogeography;
  •     Palaeobiogeography;
  •     Island biogeography;
  •     Extinctions;
  •     Evolution of behavior;
  •     Evolutionary patterns;
  •     Mechanisms of evolution;
  •     Factors of evolutionary change;
  •     Climate change and evolution.

Submissions must represent a starting point for further research and be equally accessible to non-biologists and to specialists in the field.

Dr. Eric Buffetaut
Collection 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 collection 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. Diversity 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 2100 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

  • phylogeny
  • evolution
  • palaeontology
  • DNA
  • molecular phylogeny

Published Papers (9 papers)

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2024

Jump to: 2023, 2022

11 pages, 1660 KiB  
Article
Phylogeographic Relationships Reveal the Origin of an Introduced Population of the Dalmatian Algyroides (Reptilia: Lacertidae) into Southern Italy
by Elisavet-Aspasia Toli, Dimitra Sergiadou, Piero Carlino, Anastasios Bounas, Miguel A. Carretero, Riccardo Castiglia, D. James Harris, Chrysoula Papadaki, Olivier S. G. Pauwels, Lidija Leković and Konstantinos Sotiropoulos
Diversity 2024, 16(7), 406; https://doi.org/10.3390/d16070406 - 14 Jul 2024
Viewed by 789
Abstract
The genetic structure and dispersal dynamics of reptile populations are profoundly influenced by natural processes and human activities. While natural dispersal is shaped by species’ characteristics and paleogeographical features, human-mediated translocations have become increasingly prevalent, posing ecological challenges. Mitochondrial genetic markers have been [...] Read more.
The genetic structure and dispersal dynamics of reptile populations are profoundly influenced by natural processes and human activities. While natural dispersal is shaped by species’ characteristics and paleogeographical features, human-mediated translocations have become increasingly prevalent, posing ecological challenges. Mitochondrial genetic markers have been pivotal in untangling invasion pathways for various species. Our study focuses on the Dalmatian Algyroides, Algyroides nigropunctatus (Duméril & Bibron, 1839), a lizard species endemic to the Balkan Peninsula, where recent observations in the Apulian region of Italy suggest an introduced population. Genetic analyses employing two mtDNA markers (16S and ND4 genes) elucidate the phylogenetic relationships of the Dalmatian Algyroides and trace the geographic origin of the introduced population. Our findings reveal areas in western Greece and southwestern Albania as the most probable areas of the source population, while we identify two previously undetected geographical lineages in the native range, highlighting the complex evolutionary history of the species in the region. Additionally, indications of potential glacial refugia and post-glacial dispersal patterns shed more light on the species’ demographic dynamics. Full article
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21 pages, 3288 KiB  
Article
Relic Vergilius Oak (Quercus virgiliana Ten.) Trees Could Preserve Microhabitats of Pannonian Forest–Steppe Vegetation
by Sándor Bordács, Beáta Pintér, Csaba Horváth, Lajos Benedek and Márta Ladányi
Diversity 2024, 16(7), 401; https://doi.org/10.3390/d16070401 - 12 Jul 2024
Viewed by 1183
Abstract
In the framework of an ongoing gene conservation programme in the Tolna Hills Region, Hungary, a total of 41 site plots were selected on agricultural land that had recently been used as grassland, meadow or vineyard. Aims of our study were (i) to [...] Read more.
In the framework of an ongoing gene conservation programme in the Tolna Hills Region, Hungary, a total of 41 site plots were selected on agricultural land that had recently been used as grassland, meadow or vineyard. Aims of our study were (i) to test the taxonomic status of relic oak trees growing out of forested lands; (ii) to verify the origin of relic trees whether they regenerated by sprouts and suckers or by seeds in order to estimate their age and origin (nativeness); (iii) to test their microhabitats to see if forest-specific plant and fungal species were presented; (iv) and to test species to see if their presence linked to any forest vegetation in the past. Furthermore, the land-use type did not show a significant effect on the abundance of woody, dicot herbaceous, or monocot herbaceous plants recorded on sites based on maps from 1941 or earlier. The follow-up univariate ANOVA revealed a significant direct effect of recent land-use type (of 2022) on monocot herbaceous plants (F(3,33) = 5.21, p < 0.01). Additionally, a significant but weaker effect was observed on woody plants (F(3,33) = 3.22, p < 0.05). The overall past effect of land-use type showed a significantly high positive correlation between the abundance of woody plants and the number of times the maps showed forest or forest boundary land-use types (R = 0.46, p < 0.01). The plots have likely preserved and sustained the microhabitats of the native forest vegetation that was once distributed in the region. The site plots of relic oak trees, considered as flagstone habitats, create opportunities for gene flow, not only for the species with dispersal or discontinuous distribution, but also for the Vergilius oak populations. Therefore, relic trees and their microhabitats might have an important role in the mating system of various species and might also be valuable resources for genetic conservation programmes. Full article
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12 pages, 11137 KiB  
Communication
Stratigraphic Reassessment of the Mexican Chasmosaurine Coahuilaceratops magnacuerna as the First Diagnostic Dinosaur Remains from the Cerro Huerta Formation (Lower Maastrichtian) Supporting the Southern Origin of the Triceratopsini
by Daniela Barrera Guevara, Belinda Espinosa Chávez, Claudia Inés Serrano Brañas, Claudio de León Dávila, Daniel Posada Martinez, Elizabeth Freedman Fowler and Denver Fowler
Diversity 2024, 16(7), 390; https://doi.org/10.3390/d16070390 - 8 Jul 2024
Cited by 1 | Viewed by 4202
Abstract
Very few remains of ceratopsid dinosaurs have been recovered so far from the Difunta Group of Coahuila, Mexico. The enigmatic chasmosaurine Coahuilaceratops magnacuerna was previously described on the basis of two partial skulls purportedly derived from the Cerro del Pueblo Formation (~73–72.5 Ma?). On [...] Read more.
Very few remains of ceratopsid dinosaurs have been recovered so far from the Difunta Group of Coahuila, Mexico. The enigmatic chasmosaurine Coahuilaceratops magnacuerna was previously described on the basis of two partial skulls purportedly derived from the Cerro del Pueblo Formation (~73–72.5 Ma?). On the basis of a new measured section and lithological identification of the host rock, we reassign Coahuilaceratops to the overlying Cerro Huerta Formation (~71.5–70.5 Ma?). Thus, we formally assign the first dinosaur taxon to the Cerro Huerta Formation. This reassignment is more consistent with the relatively derived phylogenetic position of Coahuilaceratops, with implications for the southern Laramidia hypothesis concerning the origin of the Triceratopsini. Full article
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15 pages, 2691 KiB  
Article
Comparative Genomics of Limosilactobacillus pontis Strains: Niche-Specific Variations and Adaptations
by Xueyan Lei, Qing Liu, Weicheng Li, Yu Li, Lixia Zhao and Wenjun Liu
Diversity 2024, 16(7), 380; https://doi.org/10.3390/d16070380 - 29 Jun 2024
Viewed by 781
Abstract
Limosilactobacillus pontis (L. pontis) is a species of lactic acid bacteria (LAB) found in various products, including fermented milk, sourdough, and broiler chickens’ gastrointestinal tracts. However, the evolutionary strategies and genomic features of the species remain unknown, which limits its application. [...] Read more.
Limosilactobacillus pontis (L. pontis) is a species of lactic acid bacteria (LAB) found in various products, including fermented milk, sourdough, and broiler chickens’ gastrointestinal tracts. However, the evolutionary strategies and genomic features of the species remain unknown, which limits its application. In this study, whole-genome sequencing was carried out to investigate the genomic characteristics and evolutionary strategies of L. pontis, combined with a comparative genomic approach, providing the necessary theoretical basis for its application. The genomic sequences in this study included three published genomic sequences and two strains isolated from fermented milk in our lab in Inner Mongolia, China. The mean genome size of the five L. pontis strains was 1.70 Mb, and the mean DNA G + C content was 53.06%. L. pontis was a species with higher G + C content in LAB. The phylogenetic evolutionary tree for the core genes showed that the strains from the same sources were aggregated into a cluster. There were some differences in the genomic information and phylogenetic relationships amongst L. pontis from different sources. An analysis of the annotation results identified differences in the functional genes, carbohydrate-active enzymes, and bacteriocins amongst different isolated strains, which were related to the environment. L. pontis was rich in glycosyltransferases, especially in strains isolated from fermented milk, indicating that they had higher sugar synthesis abilities. It is worth mentioning that only the L. pontis strains isolated in our laboratory identified the bacteriocin operon, which may increase its application potential. The genomic characteristics and evolutionary process of L. pontis were analyzed by comparative genomics, and this study explored the differences in the functional genes amongst the strains, aiming to provide new insights into the genetic characteristics and niche adaptations of L. pontis. Full article
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2023

Jump to: 2024, 2022

15 pages, 2822 KiB  
Article
The Characterization and Phylogenetic Implications of the Mitochondrial Genomes of Antheminia varicornis and Carpocoris purpureipennis (Hemiptera: Pentatomidae)
by Ying Wang, Ruijuan Yang, Xiuxiu Zhu, Chenguang Zheng and Wenjun Bu
Diversity 2023, 15(12), 1209; https://doi.org/10.3390/d15121209 - 9 Dec 2023
Cited by 1 | Viewed by 1720
Abstract
The mitochondrial genome (mitogenome) has been widely used for structural comparisons and phylogenetic analyses of Hemiptera groups at different taxonomic levels. However, little is known about the mitogenomic characteristics of species from Antheminia and Carpocoris, two morphologically similar genera in the Pentatomidae [...] Read more.
The mitochondrial genome (mitogenome) has been widely used for structural comparisons and phylogenetic analyses of Hemiptera groups at different taxonomic levels. However, little is known about the mitogenomic characteristics of species from Antheminia and Carpocoris, two morphologically similar genera in the Pentatomidae family, and their phylogenetic relationships need to be further confirmed. In this study, the mitogenomes of Antheminia varicornis (Jakovlev, 1874) and Carpocoris purpureipennis (De Geer, 1773) were sequenced and analyzed. Coupled with previously published mitogenomes of Pentatomidae, we performed a phylogenetic analysis. The mitogenomes of A. varicornis and C. purpureipennis are conserved in terms of genomic structure, base composition, codon usage, and tRNA secondary structure. Each mitogenome contains the typical 37 genes and a control region and all genes are arranged in the same order as in the ancestral insect mitogenome. Nucleotide composition is highly biased with the third codon in PCGs displaying the highest A + T content. Phylogenetic analysis strongly supports the sister relationship between A. varicornis and C. purpureipennis. The phylogenetic trees show a strong support for the monophyly of Asopinae and Phyllocephalinae, while the monophyly of Pentatominae and Podopinae was rejected. Our study enriches the mitochondrial genome database of the genera Antheminia and Carpocoris and provides a valuable resource for further phylogenetic and evolutionary analyses of the Pentatomidae. Full article
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32 pages, 19074 KiB  
Article
A New Basal Neornithischian Dinosaur from the Phu Kradung Formation (Upper Jurassic) of Northeastern Thailand
by Sita Manitkoon, Uthumporn Deesri, Bouziane Khalloufi, Thanit Nonsrirach, Varavudh Suteethorn, Phornphen Chanthasit, Wansiri Boonla and Eric Buffetaut
Diversity 2023, 15(7), 851; https://doi.org/10.3390/d15070851 - 13 Jul 2023
Cited by 3 | Viewed by 12480
Abstract
An exceptional articulated skeleton of a new basal neornithischian dinosaur, Minimocursor phunoiensis gen. et sp. nov., was discovered in the Late Jurassic Phu Kradung Formation at the Phu Noi locality, Kalasin Province, Thailand, a highly productive non-marine fossil vertebrate locality of the Khorat [...] Read more.
An exceptional articulated skeleton of a new basal neornithischian dinosaur, Minimocursor phunoiensis gen. et sp. nov., was discovered in the Late Jurassic Phu Kradung Formation at the Phu Noi locality, Kalasin Province, Thailand, a highly productive non-marine fossil vertebrate locality of the Khorat Plateau. It is one of the best-preserved dinosaurs ever found in Southeast Asia. Minimocursor phunoiensis gen. et sp. nov. shows a combination of both plesiomorphic and apomorphic characters resembling those of Late Jurassic to Early Cretaceous small-bodied ornithischians from China: a low subtriangular boss is projected laterally on the surface of the jugal, the brevis shelf of the ilium is visible in lateral view along its entire length, a distinct supraacetabular flange is present on the pubic peduncle of the ilium, the prepubis tip extends beyond the distal end of the preacetabular process of the ilium, and the manus digit formula is ?-3-4-3-2. The phylogenetic analysis shows that this dinosaur is among the most basal neornithischians. This study provides a better understanding of the early evolution and taxonomic diversity of ornithischians in Southeast Asia. Full article
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18 pages, 4221 KiB  
Article
A New Enigmatic Teleost Fish from the Mid-Cretaceous of Lebanon
by Tamara El Hossny and Lionel Cavin
Diversity 2023, 15(7), 839; https://doi.org/10.3390/d15070839 - 8 Jul 2023
Cited by 3 | Viewed by 3135
Abstract
Teleosts form the largest clade among the extant actinopterygians, some extinct forms of which are still poorly positioned in the phylogeny. The Tselfatiiformes and Araripichthyidae are such examples. A newly discovered genus and species from the Cenomanian of Haqel, Lebanon, is described, and [...] Read more.
Teleosts form the largest clade among the extant actinopterygians, some extinct forms of which are still poorly positioned in the phylogeny. The Tselfatiiformes and Araripichthyidae are such examples. A newly discovered genus and species from the Cenomanian of Haqel, Lebanon, is described, and its systematic affinities are discussed. It shares several characteristics (deep and compressed body with elongated and high dorsal and anal fins, edentulous maxilla, and sinusoidal vertebral column) with both the Tselfatiiformes and Araripichthys, making it difficult to place within the teleosts. It shares with Abisaadichthys, among the tselfatiiforms’ family Protobramidae, an autogenous retroarticular, and with Araripichthys premaxillae with a long ascending process, well-developed maxillary articular condyle and two supramaxillae. Moreover, it shows some unique characteristics (a thin maxilla with two large supramaxillae, fused articular and angular bones, mandibular sensory canal opening on the external side of the anguloarticular, first dorsal pterygiophore having the same enlarged semi-circular plate as the first anal pterygiophore) justifying its generic status. Comments on some of the protobramids are presented, and the necessity for phylogenetic analysis to place the Tselfatiiformes, Araripichthys and Ypsiloichthys within the teleosts is outlined. Full article
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2022

Jump to: 2024, 2023

18 pages, 4242 KiB  
Article
Characterization of Two New Apodemus Mitogenomes (Rodentia: Muridae) and Mitochondrial Phylogeny of Muridae
by Di Wu, Lizhi Zhou, Jiezhong Xue, Qiliang Xia and Lei Meng
Diversity 2022, 14(12), 1089; https://doi.org/10.3390/d14121089 - 9 Dec 2022
Cited by 3 | Viewed by 2461
Abstract
Apodemus is the most common small rodent species in the Palearctic realm and an ideal species for biogeographical research and understanding environmental changes. Elucidating phylogenetic relationships will help us better understand species adaptation and genetic evolution. Due to its stable structure, maternal inheritance, [...] Read more.
Apodemus is the most common small rodent species in the Palearctic realm and an ideal species for biogeographical research and understanding environmental changes. Elucidating phylogenetic relationships will help us better understand species adaptation and genetic evolution. Due to its stable structure, maternal inheritance, and rapid evolution, the mitogenome has become a hot spot for taxonomic and evolutionary studies. In this research, we determined the mitochondrial genome of Apodemus agrarius ningpoensis and Apodemus draco draco and studied the phylogeny of Muridae using ML and BI trees based on all known complete mitogenomes. The mitochondrial genome of Apodemus agrarius ningpoensis was 16,262 bp, whereas that of Apodemus draco draco was 16,222 bp, and both encoded 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Analysis of base composition showed a clear A-T preference. All tRNAs except tRNASer and tRNALys formed a typical trilobal structure. All protein-coding genes contained T- and TAA as stop codons. Phylogeny analysis revealed two main branches in the Muridae family. Apodemus agrarius ningpoensis formed sister species with Apodemus chevrieri, whereas Apodemus draco draco with Apodemus latronum. Our findings provide theoretical basis for future studies focusing on the mitogenome evolution of Apodemus. Full article
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17 pages, 1554 KiB  
Article
Phylogenetic Reconstruction of the Rainforest Lineage Fontainea Heckel (Euphorbiaceae) Based on Chloroplast DNA Sequences and Reduced-Representation SNP Markers
by Aaron J. Brunton, Robert W. Lamont, Gabriel C. Conroy, Samantha Yap, Maurizio Rossetto, Alyce Taylor-Brown, Laurent Maggia, Paul W. Reddell and Steven M. Ogbourne
Diversity 2022, 14(9), 725; https://doi.org/10.3390/d14090725 - 1 Sep 2022
Cited by 6 | Viewed by 3298
Abstract
Fontainea is a plant genus with nine recognised species that occur across the tropical and subtropical rainforests of Australia, Papua New Guinea, New Caledonia, and Vanuatu. One of these species is cultivated commercially as the source of a cancer therapeutic, and several other [...] Read more.
Fontainea is a plant genus with nine recognised species that occur across the tropical and subtropical rainforests of Australia, Papua New Guinea, New Caledonia, and Vanuatu. One of these species is cultivated commercially as the source of a cancer therapeutic, and several other species are under threat of extinction. Despite this, the phylogenetic relationships of the genus have not been explored. Our study assessed the phylogeny of seven Fontainea taxa from the Australian and Pacific Island complex using chloroplast DNA sequence data and reduced-representation genome sequencing. Maximum-likelihood and consensus network trees were used to infer the topology of phylogenetic relationships between species, which highlighted three distinct lineages and a number of sister species. Our results indicated that the geographically disjunct species Fontainea venosa and F. pancheri formed a sister group at the earliest position of divergence for the genus. The data also revealed that the vulnerable Fontainea australis and the critically endangered F. oraria form a sister subclade with evidence of some shared plastid genotypes. Generally, our phylogenetic reconstruction supports the modern taxonomical nomenclature. However, we suggest further accessions across several species may support improved genetic distinctions between the sister groups of Fontainea within the genus. Full article
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