Molecular Evolution and Conservation of Tropical Biodiversity

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (15 October 2022) | Viewed by 13007

Special Issue Editors

Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução da Universidade Federal de Minas Gerais (UFMG), Belo-Horizonte 31270-010, MG, Brazil
Interests: evolutionary biology; neotropical fauna; animal genetics
Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução da Universidade Federal de Minas Gerais (UFMG), Belo-Horizonte 31270-010, MG, Brazil
Interests: evolutionary biology; neotropical bees; animal genetics

Special Issue Information

Dear Colleagues,

The tropical region encompasses most of the biodiversity worldwide, with ecosystems ranging from rain forests to savannas and grasslands. These ecosystems are distributed in a large variety of landscapes at different altitudes and landscapes. All tropical ecosystems are threatened by direct and indirect human impact, particularly habitat disturbance by fires, intensive land use in agriculture, mining, and large enterprises for power production. Among indirect impacts, human-driven climate change is further enhancing threats to most tropical environments and species, which are not able to adapt to extreme weather conditions in reduced and disturbed habitats. Most worldwide hotspots of biodiversity are also located in the Tropics, where relatively fewer species of native fauna and flora have been deeply investigated by molecular methods and there are still large taxonomic gaps with many cryptic species. The high richness of species and complex biotic interactions in the Tropics in comparison to other climatic regions provide a great challenge to scientists worldwide. Hence, research on systematics, taxonomy, population dynamics, evolution, biogeography, and phylogeography using genomics and other molecular-based approaches is greatly needed to understand this spectacular tropical biodiversity in order to allow an adequate conservation management of species and environments and to recognize their value in maintaining or enhancing quality of life for humans. 

Prof. Dr. Fabrício Rodrigues Dos Santos
Dr. José Eustáquio Santos
Guest Editors

Manuscript Submission Information

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Keywords

  • neotropics
  • molecular

Published Papers (6 papers)

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Editorial

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2 pages, 200 KiB  
Editorial
Molecular Evolution and Conservation of Tropical Biodiversity: A Special Issue
by Fabrício R. Santos and José E. Santos-Júnior
Diversity 2022, 14(10), 784; https://doi.org/10.3390/d14100784 - 21 Sep 2022
Viewed by 846
Abstract
Molecular evolutionary studies provide fundamental evidence to be applied in biodiversity conservation and management [...] Full article
(This article belongs to the Special Issue Molecular Evolution and Conservation of Tropical Biodiversity)

Research

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16 pages, 1988 KiB  
Article
Complex Evolutionary History of the South American Fox Genus Lycalopex (Mammalia, Carnivora, Canidae) Inferred from Multiple Mitochondrial and Nuclear Markers
by Marina O. Favarini, Taiz L. L. Simão, Gabriel S. Macedo, Fabrício S. Garcez, Larissa R. Oliveira, Susana Cárdenas-Alayza, Marco Cardeña Mormontoy, Fernando Angulo, Carlos Benhur Kasper, Warren E. Johnson and Eduardo Eizirik
Diversity 2022, 14(8), 642; https://doi.org/10.3390/d14080642 - 11 Aug 2022
Cited by 3 | Viewed by 2426
Abstract
The canid genus Lycalopex comprises six recently diversified South American species whose evolutionary relationships have been remarkably challenging to resolve. We analyzed 6000 bp of mitochondrial DNA (mtDNA) from 55 Lycalopex individuals (L. sechurae = 4, L. culpaeus = 7, L.griseus [...] Read more.
The canid genus Lycalopex comprises six recently diversified South American species whose evolutionary relationships have been remarkably challenging to resolve. We analyzed 6000 bp of mitochondrial DNA (mtDNA) from 55 Lycalopex individuals (L. sechurae = 4, L. culpaeus = 7, L.griseus = 8, L.gymnocercus = 17, L.vetulus = 13 and L. fulvipes = 6), and nine specimens from the closely related species Cerdocyon thous, Chrysocyon brachyurus and Speothos venaticus, to reconstruct their phylogenetic relationships, estimate the support for species-level monophyly, and date their divergences. In addition, we also sequenced seven nuclear segments from the same taxa. Three different phylogenetic approaches converged on the same mitochondrial topology with strong support for most nodes. All species were confirmed to be monophyletic for mtDNA, except for one intriguing case in which two L. vetulus individuals carried L. gymnocercus haplotypes, potentially implying a case of interspecies admixture. L. vetulus was the first species to diverge (ca. 1.2 Mya), followed by L. sechurae and then L. gymnocercus. The most internal group comprised L. griseus and the sister-species L. culpaeus and L. fulvipes, which diverged around 430,000 years ago in southern Argentina or Chile. The analysis of nuclear markers revealed several examples of intra-specific variation coupled with lack of species monophyly, consistent with pervasive incomplete lineage sorting and/or hybridization in this recent radiation. Our results provide robust mitochondrial resolution of this challenging radiation, and illustrate the difficulty of attaining similar success with traditional nuclear markers. Full article
(This article belongs to the Special Issue Molecular Evolution and Conservation of Tropical Biodiversity)
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21 pages, 2822 KiB  
Article
Integrative Phylogeography Reveals Conservation Priorities for the Giant Anteater Myrmecophaga tridactyla in Brazil
by Raphael T. F. Coimbra, Rafael F. Magalhães, Priscila Lemes, Flávia R. Miranda and Fabrício R. Santos
Diversity 2022, 14(7), 542; https://doi.org/10.3390/d14070542 - 05 Jul 2022
Cited by 1 | Viewed by 1743
Abstract
The giant anteater (Myrmecophaga tridactyla) is a strictly myrmecophagous xenarthran species that ranges from Honduras to northern Argentina, occupying various habitats, from grassland and floodplains to forests. According to the IUCN, it is a vulnerable species mainly threatened by poaching, habitat [...] Read more.
The giant anteater (Myrmecophaga tridactyla) is a strictly myrmecophagous xenarthran species that ranges from Honduras to northern Argentina, occupying various habitats, from grassland and floodplains to forests. According to the IUCN, it is a vulnerable species mainly threatened by poaching, habitat loss and fragmentation, and road kills. Here, we investigate the phylogeography, distribution, ecology, and historical demography of Brazilian populations of the giant anteater. We analysed two mitochondrial (mtDNA) and three nuclear (nDNA) markers in 106 individuals from the Cerrado, Pantanal, Atlantic Forest, and Amazon Forest biomes through analyses of population structure and demography, phylogeography, and ecological niche modelling. Two divergent mtDNA clusters were found, one in the Amazon (AM) and another in the Cerrado, Pantanal, and Atlantic Forest biomes (CEPTAF). At the population level, CEPTAF presented higher mtDNA haplotype richness than AM and a unidirectional mtDNA gene flow was identified from AM to CEPTAF, which could be linked to more favourable habitat conditions for the species in Cerrado and Pantanal. Paleodemographic reconstructions with mtDNA and nDNA data indicate a large population expansion of the species starting at the end of the Pleistocene. Finally, the integrative phylogeographic analyses of giant anteater populations reinforce the importance of the Brazilian Cerrado as a priority biome for the species’ conservation. Full article
(This article belongs to the Special Issue Molecular Evolution and Conservation of Tropical Biodiversity)
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16 pages, 2430 KiB  
Article
Phylogenetic Analyses of Cyprinid Species from the Rokel River Basin of Sierra Leone, West Africa: Taxonomic, Biogeographic, and Conservation Implications
by Unisa Conteh Kanu, Cao Liang, Chinedu Charles Nwafor, Jianzhong Shen and E Zhang
Diversity 2022, 14(4), 299; https://doi.org/10.3390/d14040299 - 15 Apr 2022
Cited by 2 | Viewed by 1851
Abstract
The Rokel River (RR) basin is one of the most neglected ichthyofaunal basins, despite the potential for undetected diversity and high levels of endemism. Data on the molecular phylogeny of freshwater fish from this river are rare. Morphological features alone are inadequate for [...] Read more.
The Rokel River (RR) basin is one of the most neglected ichthyofaunal basins, despite the potential for undetected diversity and high levels of endemism. Data on the molecular phylogeny of freshwater fish from this river are rare. Morphological features alone are inadequate for precise species identification. Here, a phylogenetic analysis performed based on the mtDNA Cytb gene for eleven cyprinid fish from the RR basin recovered eleven distinct lineages. The same was also observed for two of our species delineation analyses, of which four are identical to six morphospecies, one is of taxonomic uncertainty, and the rest are currently unrecognized. The disjunct distribution found here in some cyprinid species from the RR basin and their sister species suggests that this river had a past complex historical inter-basin connection exchange with the nearby river basins of the Zaire and lower Guinean ecoregions. The unrecognized diversity observed from cyprinid species of this area may have significant implications for the conservation of biodiversity. Full article
(This article belongs to the Special Issue Molecular Evolution and Conservation of Tropical Biodiversity)
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17 pages, 3155 KiB  
Article
Biogeography and Diversification of Bumblebees (Hymenoptera: Apidae), with Emphasis on Neotropical Species
by José Eustáquio Santos Júnior, Paul H. Williams, Cayo A. Rocha Dias, Fernando A. Silveira, Pierre Faux, Raphael T. F. Coimbra, Davidson P. Campos and Fabrício Rodrigues Santos
Diversity 2022, 14(4), 238; https://doi.org/10.3390/d14040238 - 25 Mar 2022
Cited by 6 | Viewed by 2723
Abstract
A detailed phylogeny of bumblebees is urgently needed to understand speciation and biogeographic diversification in the Neotropical region. We sequenced autosomal and mtDNA loci from nine Brazilian bumblebee species and compiled it with the data already available to obtain highly resolved phylogenetic trees [...] Read more.
A detailed phylogeny of bumblebees is urgently needed to understand speciation and biogeographic diversification in the Neotropical region. We sequenced autosomal and mtDNA loci from nine Brazilian bumblebee species and compiled it with the data already available to obtain highly resolved phylogenetic trees with fossil-calibrated dates. The ancestral Bombus lineage was estimated to diversify between 47.08 and 34.27 million years ago (Ma) in the Holarctic region, but largely restricted to the eastern Old World. The Neotropical region was initially colonized in the Late Miocene, where bumblebee diversification was shown to be consistent with geologic and climatic events of the Late Cenozoic. Neotropical bumblebees likely originated from Nearctic lineages, which dispersed towards South America after 29 Ma. Full article
(This article belongs to the Special Issue Molecular Evolution and Conservation of Tropical Biodiversity)
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17 pages, 2339 KiB  
Article
Phylogeography of Hypomasticus copelandii (Teleostei, Anostomidae) Reveals Distinct Genetic Lineages along Atlantic Coastal Drainages of Eastern Brazil
by Izabela S. Mendes, Bruno F. Melo, Júnio S. Damasceno, Daniel F. Teixeira and Daniel C. Carvalho
Diversity 2022, 14(1), 29; https://doi.org/10.3390/d14010029 - 04 Jan 2022
Cited by 4 | Viewed by 2434
Abstract
Hypomasticus copelandii is a Neotropical freshwater fish widely distributed across coastal drainages of southeastern Brazil, a highly impacted region of South America. The interspecific phylogenetic relationships within the genus and the taxonomic status of the species remain uncertain. Using two mitochondrial and one [...] Read more.
Hypomasticus copelandii is a Neotropical freshwater fish widely distributed across coastal drainages of southeastern Brazil, a highly impacted region of South America. The interspecific phylogenetic relationships within the genus and the taxonomic status of the species remain uncertain. Using two mitochondrial and one nuclear locus, we performed a phylogenetic, species delimitation, and time-calibrated analyses to test the hypothesis that H. copelandii is a species complex currently delimited by different Atlantic coastal systems. Results indicate that H. copelandii presents two well-delimited genetic lineages: one in the northern drainages of the Jucuruçu, Mucuri and Doce rivers, and the other in the southern region represented by the Paraíba do Sul River Basin. The time-calibrated phylogeny indicated a split between the two genetic lineages at around 2.8 million years ago (Ma), which might be related to headwater capture events during the Plio-Pleistocene. The discovery of a distinct genetic lineage for H. copelandii suggests distinct management plans for the northern and southern drainages. Such hidden diversity within the H. copelandii provides useful information for taxonomy and conservation across a severely impacted region of Brazil. Full article
(This article belongs to the Special Issue Molecular Evolution and Conservation of Tropical Biodiversity)
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