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Yang S, Huang J, Qu Y, Zhang D, Tan Y, Wen S, Song Y. Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae). BMC PLANT BIOLOGY 2024; 24:616. [PMID: 38937691 PMCID: PMC11212351 DOI: 10.1186/s12870-024-05050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known. RESULTS Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively. CONCLUSIONS The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.
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Affiliation(s)
- Shiting Yang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China
| | - Jiepeng Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China
| | - Yaya Qu
- Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Di Zhang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Yunhong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Shujun Wen
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, China.
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China.
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Gabriel H, Rothe LD, Khler J, Rakotomanga S, Edmonds D, Galn P, Glaw F, Lehtinen RM, Rakotoarison A, Vences M. Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species. Zootaxa 2024; 5397:451-485. [PMID: 38221190 DOI: 10.11646/zootaxa.5397.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Indexed: 01/16/2024]
Abstract
The area around the Malagasy village of Andasibe, which includes Analamazaotra-Mantadia National Park as well as other protected areas, is characterized by very species-rich and well-studied communities of animals and plants, but new species are still regularly discovered. Three species of phytotelmic frogs of the subgenus Pandanusicola in the genus Guibemantis are known from this area, G. flavobrunneus, G. liber, and G. pulcher. Further Pandanusicola frogs from this area have been provisionally assigned to G. bicalcaratus or G. albolineatus, pending detailed taxonomic review. During preliminary exploration of the ecology of these specialized frogs that live and reproduce in the leaf axils of Pandanus screw pines, we noticed the syntopic presence of two differently colored and differently sized Pandanusicola in Andasibe that could not be unambiguously assigned to any known species. A genetic screening revealed that these correspond to yet two further species in the area. Based on our data, seven species of Pandanusicola occur in Andasibe and nearby forests: (1) G. liber, the only non-phytotelmic species of the subgenus in the region; (2) G. flavobrunneus which is the largest species and characterized by a diagnostic yellowish brown dorsal pattern; (3) G. pulcher, characterized by translucent-green color with purplish brown spotting not observed in any other species in the area; (4) G. methueni, a brownish species usually lacking contrasted dorsolateral bands that differs from the other species in the area by emitting a characteristic trill-like advertisement call series (rather than clicks or chirps) and according to our data is widespread along Madagascars east coast; as well as three new species: (5) G. ambakoana sp. nov., a brownish species, typically with contrasted incomplete light dorsolateral bands and with single click-like advertisement calls; (6) G. vakoa sp. nov., a species that is equally brownish but lacks contrasted light dorsolateral bands and that has single click-like advertisement calls of very short duration; and (7) G. rianasoa sp. nov., a species that is smaller sized and has less distinct femoral glands than all the others, and emits a short series of soft chirp-like advertisement calls. All these species are genetically highly distinct, with >5% uncorrected pairwise distances in the mitochondrial 16S rRNA gene, and lack of haplotype sharing in two nuclear-encoded genes. The co-occurrence of seven Pandanusicola frogs in a relatively small geographic area is unprecedented in Madagascar and calls for in-depth studies of a possible differentiation in habitat use and life history.
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Affiliation(s)
- Hugh Gabriel
- Zoologisches Institut; Technische Universitt Braunschweig; Mendelssohnstr. 4; 38106 Braunschweig; Germany.
| | - Laila-Denise Rothe
- Zoologisches Institut; Technische Universitt Braunschweig; Mendelssohnstr. 4; 38106 Braunschweig; Germany.
| | - Jrn Khler
- Hessisches Landesmuseum Darmstadt; Friedensplatz 1; 64283 Darmstadt; Germany.
| | - Sandratra Rakotomanga
- Mention Zoologie et Biodiversit Animale; Universit dAntananarivo; BP 906; Antananarivo; 101 Madagascar.
| | - Devin Edmonds
- Illinois Natural History Survey; University of Illinois Urbana-Champaign; USA.
| | - Pedro Galn
- Universidad de A Corua; Facultad de Ciencias; Campus de A Zapateira; s/n; (Grupo de Investigacin en Biologa Evolutiva; GIBE); E-15071 A Corua; Spain.
| | - Frank Glaw
- Zoologische Staatssammlung Mnchen (ZSM-SNSB); Mnchhausenstr. 21; 81247 Mnchen; Germany.
| | - Richard M Lehtinen
- The College of Wooster; Department of Biology; 931 College Mall; Wooster; Ohio; 44691 USA.
| | - Andolalao Rakotoarison
- Mention Agriculture; Universite de lItasy; Faliarivo Ambohidanerana; 118 Soavinandriana Itasy; Madagascar; School for International Training; VN 41A Bis Ankazolava Ambohitsoa; Antananarivo; 101 Madagascar.
| | - Miguel Vences
- Zoologisches Institut; Technische Universitt Braunschweig; Mendelssohnstr. 4; 38106 Braunschweig; Germany.
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Cervantes CR, Montes JR, Rosas U, Arias S. Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae). Mol Phylogenet Evol 2023; 187:107891. [PMID: 37517507 DOI: 10.1016/j.ympev.2023.107891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/15/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M. haageana complex, and we also studied the evolutionary relationships with the remainder of the M. ser. Supertextae species. Our genetic analyses, as well as morphological and ecological evidence, led us to propose that the M. haageana complex is made up of six distinct entities (M. acultzingensis, M. conspicua, M. haageana, M. lanigera, M. meissneri, and M. san-angelensis), mainly as a result of ecological speciation. A recent taxonomic proposal considered these taxa as a single species; therefore, we propose their recognition at the species level. Our results also show a high level of incomplete lineage sorting rather than reticulation, which is especially likely in recently diverged species such as those comprising M. ser. Supertextae. The species hypotheses proposed here may be useful in future extinction risk assessments and conservation strategies.
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Affiliation(s)
- Cristian R Cervantes
- Unidad de Síntesis en Sistemática y Evolución, Instituto de Biología, Circuito Exterior s.n., Ciudad Universitaria, Ciudad de México 04510, México; Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México.
| | - José-Rubén Montes
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
| | - Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
| | - Salvador Arias
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
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Marshall AF, Balloux F, Hemmings N, Brekke P. Systematic review of avian hatching failure and implications for conservation. Biol Rev Camb Philos Soc 2023; 98:807-832. [PMID: 36635252 DOI: 10.1111/brv.12931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 12/21/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023]
Abstract
Avian hatching failure is a widespread phenomenon, affecting around 10% of all eggs that are laid and not lost to predation, damage, or desertion. Our understanding of hatching failure is limited in terms of both its underpinning mechanisms and its occurrence across different populations. It is widely acknowledged that rates of hatching failure are higher in threatened species and in populations maintained in captivity compared to wild, non-threatened species, but these differences have rarely been quantified and any broader patterns remain unexplored. To examine the associations between threat status, management interventions, and hatching failure across populations we conducted a phylogenetically controlled multilevel meta-analysis across 231 studies and 241 species of birds. Our data set included both threatened (Critically Endangered, Endangered, and Vulnerable) and non-threatened (Near Threatened and Least Concern) species across wild and captive populations, as well as 'wild managed' ('free-living') populations. We found the mean overall rate of hatching failure across all populations to be 16.79%, with the hatching failure rate of wild, non-threatened species being 12.40%. We found that populations of threatened species experienced significantly higher mean hatching failure than populations of non-threatened species. Different levels of management were also associated with different rates of hatching failure, with wild populations experiencing the lowest rate of hatching failure, followed by wild managed populations, and populations in captivity experiencing the highest rate. Similarly, populations that were subject to the specific management interventions of artificial incubation, supplementary feeding, and artificial nest provision displayed significantly higher rates of hatching failure than populations without these interventions. The driver of this correlation between hatching failure and management remains unclear, but could be an indirect result of threatened species being more likely to have lower hatching success and also being more likely to be subject to management, indicating that conservation efforts are fittingly being focused towards the species potentially most at risk from extinction. This is the most comprehensive comparative analysis of avian hatching failure that has been conducted to date, and the first to quantify explicitly how threat status and management are associated with the rate of hatching failure in a population. We discuss the implications of our results, focusing on their potential applications to conservation. Although we identified several factors clearly associated with variation in hatching failure, a significant amount of heterogeneity was not explained by our meta-analytical model, indicating that other factors influencing hatching failure were not included here. We discuss what these factors might be and suggest avenues for further research. Finally, we discuss the inconsistency in how hatching failure is defined and reported within the literature, and propose a standardised definition to be used in future studies which will enable better comparison across populations and ensure that the most accurate information is used to support management decisions.
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Affiliation(s)
- Ashleigh F Marshall
- Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London, NW1 4RY, UK
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Nicola Hemmings
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London, NW1 4RY, UK
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Bertolani R, Cesari M, Giovannini I, Rebecchi L, Guidetti R, Kaczmarek Ł, Pilato G. The Macrobiotus persimilis-polonicus complex (Eutardigrada, Macrobiotidae), another example of problematic species identification, with the description of four new species. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00599-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence. PLoS One 2022; 17:e0263764. [PMID: 35358210 PMCID: PMC8970393 DOI: 10.1371/journal.pone.0263764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.
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Belluardo F, Quirós DD, Lobón-Rovira J, Rosa GM, Rasoazanany M, Andreone F, Crottini A. Uncovering the herpetological diversity of small forest fragments in south-eastern Madagascar (Haute Matsiatra). ZOOSYST EVOL 2021. [DOI: 10.3897/zse.97.63936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Madagascar has historically suffered from high fragmentation of forested habitats, often leading to biodiversity loss. Neverthless, forest fragments still retain high levels of biological diversity. The Haute Matsiatra Region (south-eastern Madagascar) hosts the renowned Andringitra National Park and several surrounding isolated forest fragments embedded in a matrix of human-dominated landscape. During a herpetological survey conducted in the Region, we visited a total of 25 sites. We applied a molecular taxonomic approach to identify the collected material and generate new reference sequences to improve the molecular identification of Malagasy herpetofauna. We identified a total of 28 amphibian and 38 squamate taxa and provided a systematic account for each one of them. Nine of the identified taxa are candidate species, amongst which one was newly identified. We extended the known distributional range of 21 taxa (nine amphibians and 12 squamates). Although the largest forest fragments hold a higher number of species, we also detected a relatively high herpetological diversity in small patches. Our results highlight the importance of investigating small forest fragments to contribute to a better understanding of the patterns of diversity and distribution of the amphibians and reptiles of Madagascar.
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Ortega-Andrade HM, Rodes Blanco M, Cisneros-Heredia DF, Guerra Arévalo N, López de Vargas-Machuca KG, Sánchez-Nivicela JC, Armijos-Ojeda D, Cáceres Andrade JF, Reyes-Puig C, Quezada Riera AB, Székely P, Rojas Soto OR, Székely D, Guayasamin JM, Siavichay Pesántez FR, Amador L, Betancourt R, Ramírez-Jaramillo SM, Timbe-Borja B, Gómez Laporta M, Webster Bernal JF, Oyagata Cachimuel LA, Chávez Jácome D, Posse V, Valle-Piñuela C, Padilla Jiménez D, Reyes-Puig JP, Terán-Valdez A, Coloma LA, Pérez Lara MB, Carvajal-Endara S, Urgilés M, Yánez Muñoz MH. Red List assessment of amphibian species of Ecuador: A multidimensional approach for their conservation. PLoS One 2021; 16:e0251027. [PMID: 33956885 PMCID: PMC8101765 DOI: 10.1371/journal.pone.0251027] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/19/2021] [Indexed: 12/26/2022] Open
Abstract
Ecuador is one of the most biodiverse countries in the world, but faces severe pressures and threats to its natural ecosystems. Numerous species have declined and require to be objectively evaluated and quantified, as a step towards the development of conservation strategies. Herein, we present an updated National Red List Assessment for amphibian species of Ecuador, with one of the most detailed and complete coverages for any Ecuadorian taxonomic group to date. Based on standardized methodologies that integrate taxonomic work, spatial analyses, and ecological niche modeling, we assessed the extinction risk and identified the main threats for all Ecuadorian native amphibians (635 species), using the IUCN Red List Categories and Criteria. Our evaluation reveals that 57% (363 species) are categorized as Threatened, 12% (78 species) as Near Threatened, 4% (26 species) as Data Deficient, and 27% (168 species) as Least Concern. Our assessment almost doubles the number of threatened species in comparison with previous evaluations. In addition to habitat loss, the expansion of the agricultural/cattle raising frontier and other anthropogenic threats (roads, human settlements, and mining/oil activities) amplify the incidence of other pressures as relevant predictors of ecological integrity. Potential synergic effects with climate change and emergent diseases (apparently responsible for the sudden declines), had particular importance amongst the threats sustained by Ecuadorian amphibians. Most threatened species are distributed in montane forests and paramo habitats of the Andes, with nearly 10% of them occurring outside the National System of Protected Areas of the Ecuadorian government. Based on our results, we recommend the following actions: (i) An increase of the National System of Protected Areas to include threatened species. (ii) Supporting the ex/in-situ conservation programs to protect species considered like Critically Endangered and Endangered. (iii) Focalizing research efforts towards the description of new species, as well as species currently categorized as Data Deficient (DD) that may turn out to be threatened. The implementation of the described actions is challenging, but urgent, given the current conservation crisis faced by amphibians.
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Affiliation(s)
- H. Mauricio Ortega-Andrade
- Grupo de Biogeografía y Ecología Espacial, Universidad Regional Amazónica Ikiam, Tena, Ecuador
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- * E-mail:
| | - Marina Rodes Blanco
- Grupo de Biogeografía y Ecología Espacial, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | - Diego F. Cisneros-Heredia
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Instituto de Diversidad Biológica Tropical iBIOTROP, Museo de Zoología & Laboratorio de Zoología Terrestre, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Nereida Guerra Arévalo
- Grupo de Biogeografía y Ecología Espacial, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | | | - Juan C. Sánchez-Nivicela
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Instituto de Diversidad Biológica Tropical iBIOTROP, Museo de Zoología & Laboratorio de Zoología Terrestre, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Grupo de Investigación Evolución y Ecología de Fauna Neotropical, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Diego Armijos-Ojeda
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Carolina Reyes-Puig
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Instituto de Diversidad Biológica Tropical iBIOTROP, Museo de Zoología & Laboratorio de Zoología Terrestre, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | | | - Paul Székely
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Diana Székely
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto Biósfera USFQ, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Luis Amador
- Instituto de Ciencias Ambientales y Evolutivas, Doctorado en Ciencias m. Ecología y Evolución, Universidad Austral de Chile, Valdivia, Chile
| | | | | | | | | | | | | | - Daniel Chávez Jácome
- Instituto de Ciencias Ambientales y Evolutivas, Doctorado en Ciencias m. Ecología y Evolución, Universidad Austral de Chile, Valdivia, Chile
| | - Valentina Posse
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | | | - Juan Pablo Reyes-Puig
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Fundación Ecominga/Fundación Oscar Efrén Reyes, Baños, Ecuador
| | - Andrea Terán-Valdez
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Quito, Ecuador
| | - Luis A. Coloma
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Quito, Ecuador
| | | | - Sofía Carvajal-Endara
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Quito, Ecuador
| | - Miguel Urgilés
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
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Cordier JM, Rojas-Soto O, Semhan R, Abdala CS, Nori J. Out of sight, out of mind: Phylogenetic and taxonomic gaps imply great underestimations of the species’ vulnerability to global climate change. Perspect Ecol Conserv 2021. [DOI: 10.1016/j.pecon.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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'Barcode fishing' for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species. Sci Rep 2020; 10:19109. [PMID: 33154397 PMCID: PMC7644772 DOI: 10.1038/s41598-020-75431-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/28/2020] [Indexed: 11/08/2022] Open
Abstract
Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne d'Ambre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d'Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this 'barcode fishing' approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.
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Nori J, Loyola R, Villalobos F. Priority areas for conservation of and research focused on terrestrial vertebrates. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1281-1291. [PMID: 32009235 DOI: 10.1111/cobi.13476] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Effective conservation policies require comprehensive knowledge of biodiversity. However, knowledge shortfalls still remain, hindering possibilities to improve decision making and built such policies. During the last 2 decades, conservationists have made great efforts to allocate resources as efficiently as possible but have rarely considered the idea that if research investments are also strategically allocated, it would likely fill knowledge gaps while simultaneously improving conservation actions. Therefore, prioritizing areas where both conservation and research actions could be conducted becomes a critical endeavor that can further maximize return on investment. We used Zonation, a conservation planning tool and geographical distributions of amphibians, birds, mammals, and reptiles to suggest and compare priority areas for conservation and research of terrestrial vertebrates worldwide. We also evaluated the degree of human disturbance in both types of priority areas by describing the value of the human footprint index within such areas. The spatial concordance between priority conservation and research areas was low: 0.36% of the world's land area. In these areas, we found it would be possible to protect almost half of the currently threatened species and to gather information on nearly 42% of data-deficient (DD) species. We also found that 6199 protected areas worldwide are located in such places, although only 35% of them have strict conservation purposes. Areas of consensus between conservation and research areas represent an opportunity for simultaneously conserving and acquiring knowledge of threatened and DD species of vertebrates. Although the picture is not the most encouraging, joint conservation and research efforts are possible and should be fostered to save vertebrate species from our own ignorance and extinction.
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Affiliation(s)
- Javier Nori
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas, y Naturales, Centro de Zoología Aplicada, Rondeau 798, Córdoba, 5000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Av Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Rafael Loyola
- Laboratório de Biogeografia da Conservação, Departamento de Ecologia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- Fundação Brasileira para o Desenvolvimento Sustentável, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabricio Villalobos
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología A.C., Xalapa, Veracruz, Mexico
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Martinsson S, Klinth M, Erséus C. Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation. BMC Evol Biol 2020; 20:116. [PMID: 32928097 PMCID: PMC7488859 DOI: 10.1186/s12862-020-01678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. RESULTS A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. CONCLUSION We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.
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Affiliation(s)
- Svante Martinsson
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.
| | - Mårten Klinth
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Christer Erséus
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
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Rancilhac L, Bruy T, Scherz MD, Pereira EA, Preick M, Straube N, Lyra ML, Ohler A, Streicher JW, Andreone F, Crottini A, Hutter CR, Randrianantoandro JC, Rakotoarison A, Glaw F, Hofreiter M, Vences M. Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus). J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1748243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Teddy Bruy
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Mark D. Scherz
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Elvis Almeida Pereira
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
- Programa de Pós-Graduação em Biologia Animal, Departamento de Biologia Animal, Laboratório de Herpetologia, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Michaela Preick
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nicolas Straube
- Department of Natural History, University Museum of Bergen, Bergen, Norway
| | - Mariana L. Lyra
- Depto de Zoologia, Instituto de Biologia, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Annemarie Ohler
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Jeffrey W. Streicher
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK
| | - Franco Andreone
- Sezione zoologia, Museo Regionale di Scienze Naturali, Torino, Italy
| | - Angelica Crottini
- Cibio, Research Centre in Biodiversity, Genetics and Evolution, InBio, Universidade do Porto, Vairão, Portugal
| | - Carl R. Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Andolalao Rakotoarison
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, Antananarivo, Madagascar
| | - Frank Glaw
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
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Multilocus phylogeny of Paratelmatobiinae (Anura: Leptodactylidae) reveals strong spatial structure and previously unknown diversity in the Atlantic Forest hotspot. Mol Phylogenet Evol 2020; 148:106819. [PMID: 32289449 DOI: 10.1016/j.ympev.2020.106819] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 02/15/2020] [Accepted: 04/01/2020] [Indexed: 11/21/2022]
Abstract
The Brazilian Atlantic Forest harbors high levels of anuran diversity and endemism, including several taxa restricted to small geographic ranges. Here, we provide a multilocus phylogeny for Paratelmatobiinae, a leptodactylid subfamily composed of small-ranged species distributed in the Brazilian Atlantic Forest and in the campo rupestre ecosystem. We performed Bayesian inference and maximum likelihood analyses using three mitochondrial and five nuclear markers, and a matrix comprising a broad taxonomic sampling. We then delimitated independently evolving lineages within the group. We recovered Paratelmatobiinae and each of its four genera as monophyletic and robustly supported. Five putatively new species included in our analyses were unambiguously supported in the phylogenetic trees and delimitation analyses. We also recovered other deeply divergent and geographically structured lineages within the four genera of Paratelmatobiinae. Our estimation of divergence times indicates that diversification in the subfamily began in the Eocene and continued until the Pleistocene. We discuss possible scenarios of diversification for the four genera of Paratelmatobiinae, and outline the implications of our findings for taxonomy and conservation.
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