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Sgarlata GM, Rasolondraibe E, Salmona J, Le Pors B, Ralantoharijaona T, Rakotonanahary A, Jan F, Manzi S, Iribar A, Zaonarivelo JR, Volasoa Andriaholinirina N, Rasoloharijaona S, Chikhi L. The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species. Mol Phylogenet Evol 2024; 193:107997. [PMID: 38128795 DOI: 10.1016/j.ympev.2023.107997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.
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Affiliation(s)
| | - Emmanuel Rasolondraibe
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Jordi Salmona
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Barbara Le Pors
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Tantely Ralantoharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Ando Rakotonanahary
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Fabien Jan
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Amaia Iribar
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - John Rigobert Zaonarivelo
- Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, 201 Antsiranana, Madagascar.
| | | | - Solofonirina Rasoloharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
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Sgarlata GM, Salmona J, Le Pors B, Rasolondraibe E, Jan F, Ralantoharijaona T, Rakotonanahary A, Randriamaroson J, Marques AJ, Aleixo-Pais I, de Zoeten T, Ousseni DSA, Knoop SB, Teixeira H, Gabillaud V, Miller A, Ibouroi MT, Rasoloharijaona S, Zaonarivelo JR, Andriaholinirina NV, Chikhi L. Genetic and morphological diversity of mouse lemurs (Microcebus spp.) in northern Madagascar: The discovery of a putative new species? Am J Primatol 2019; 81:e23070. [PMID: 31808195 DOI: 10.1002/ajp.23070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/20/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Tropical forests harbor extremely high levels of biological diversity and are quickly disappearing. Despite the increasingly recognized high rate of habitat loss, it is expected that new species will be discovered as more effort is put to document tropical biodiversity. Exploring under-studied regions is particularly urgent if we consider the rapid changes in habitat due to anthropogenic activities. Madagascar is known for its extraordinary biological diversity and endemicity. It is also threatened by habitat loss and fragmentation. It holds more than 100 endemic primate species (lemurs). Among these, Microcebus (mouse lemurs) is one of the more diverse genera. We sampled mouse lemurs from several sites across northern Madagascar, including forests never sampled before. We obtained morphological data from 99 Microcebus individuals; we extracted DNA from tissue samples of 42 individuals and amplified two mitochondrial loci (cytb and cox2) commonly used for species identification. Our findings update the distribution of three species (Microcebus tavaratra, Microcebus arnholdi, and Microcebus mamiratra), including a major increase in the distribution area of M. arnholdi. We also report the discovery of a new Microcebus lineage genetically related to M. arnholdi. Several complementary approaches suggest that the newly identified Microcebus lineage might correspond to a new putative species, to be confirmed or rejected with additional data. In addition, morphological analyses showed (a) clear phenotypic differences between M. tavaratra and M. arnholdi, but no clear differences between the new Microcebus lineage and the sister species M. arnholdi; and (b) a significant correlation between climatic variables and morphology, suggesting a possible relationship between species identity, morphology, and environment. By integrating morphological, climatic, genetic, and spatial data of two northern Microcebus species, we show that the spatial distribution of forest-dwelling species may be used as a proxy to reconstruct the past spatial changes in forest cover and vegetation type.
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Affiliation(s)
| | - Jordi Salmona
- Instituto Gulbenkian de Ciênca, Oeiras, Portugal.,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), IRD, CNRS, UPS, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | | | - Emmanuel Rasolondraibe
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Fabien Jan
- Instituto Gulbenkian de Ciênca, Oeiras, Portugal
| | - Tantely Ralantoharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Ando Rakotonanahary
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Jacquis Randriamaroson
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | | | - Isa Aleixo-Pais
- Instituto Gulbenkian de Ciênca, Oeiras, Portugal.,Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Centre for Research in Anthropology (CRIA-FCSH/NOVA), Lisbon, Portugal
| | | | - Dhurham Said Ali Ousseni
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | | | - Helena Teixeira
- Instituto Gulbenkian de Ciênca, Oeiras, Portugal.,Institute of Zoology, University of Veterinary Medicine Hanover, Hanover, Germany
| | | | - Alex Miller
- Instituto Gulbenkian de Ciênca, Oeiras, Portugal.,School of Human Sciences, The University of Western Australia, Crawley, Australia
| | - Mohamed Thani Ibouroi
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.,Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, Antsiranana, Madagascar.,Institut des Sciences et Industrie du Vivant et de l'environnement, AgroParisTech, Paris, France
| | - Solofonirina Rasoloharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - John Rigobert Zaonarivelo
- Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, Antsiranana, Madagascar
| | | | - Lounès Chikhi
- Instituto Gulbenkian de Ciênca, Oeiras, Portugal.,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), IRD, CNRS, UPS, Université de Toulouse Midi-Pyrénées, Toulouse, France
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