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Franco FF, Amaral DT, Bonatelli IAS, Meek JB, Moraes EM, Zappi DC, Taylor NP, Eaton DAR. A historical stepping-stone path for an island-colonizing cactus across a submerged "bridge" archipelago. Heredity (Edinb) 2024:10.1038/s41437-024-00683-4. [PMID: 38637723 DOI: 10.1038/s41437-024-00683-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the "bridge" hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.
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Affiliation(s)
- Fernando Faria Franco
- Departamento de Biologia. Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil.
| | - Danilo Trabuco Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
- Programa de Pós Graduação em Biologia Comparada. Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Isabel A S Bonatelli
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas. Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Jared B Meek
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
| | - Evandro Marsola Moraes
- Departamento de Biologia. Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil
| | - Daniela Cristina Zappi
- Programa de Pós Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, PO Box 04457, Brasília, DF, 70910970, Brazil
| | - Nigel Paul Taylor
- Departamento de Biologia. Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil
| | - Deren A R Eaton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
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Amaral DT, Bombonato JR, da Silva Andrade SC, Moraes EM, Franco FF. The genome of a thorny species: comparative genomic analysis among South and North American Cactaceae. Planta 2021; 254:44. [PMID: 34357508 DOI: 10.1007/s00425-021-03690-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
The first South American cactus nuclear genome assembly associated with comparative genomic analyses provides insights into nuclear and plastid genomic features, such as size, transposable elements, and metabolic processes related to cactus development. Here, we assembled the partial genome, plastome, and transcriptome of Cereus fernambucensis (Cereeae, Cactaceae), a representative species of the South American core Cactoideae. We accessed other genomes and transcriptomes available for cactus species to compare the heterozygosity level, genome size, transposable elements, orthologous genes, and plastome structure. These estimates were obtained from the literature or using the same pipeline adopted for C. fermabucensis. In addition to the C. fernambucensis plastome, we also performed de novo plastome assembly of Pachycereus pringlei, Stenocereus thurberi, and Pereskia humboldtii based on the sequences available in public databases. We estimated a genome size of ~ 1.58 Gb for C. fernambucensis, the largest genome among the compared species. The genome heterozygosity was 0.88% in C. fernambucensis but ranged from 0.36 (Carnegiea gigantea) to 17.4% (Lophocereus schottii) in the other taxa. The genome lengths of the studied cacti are constituted by a high amount of transposable elements, ranging from ~ 57 to ~ 67%. Putative satellite DNAs are present in all species, excepting C. gigantea. The plastome of C. fernambucensis was ~ 104 kb, showing events of translocation, inversion, and gene loss. We observed a low number of shared unique orthologs, which may suggest gene duplication events and the simultaneous expression of paralogous genes. We recovered 37 genes that have undergone positive selection along the Cereus branch that are associated with different metabolic processes, such as improving photosynthesis during drought stress and nutrient absorption, which may be related to the adaptation to xeric areas of the Neotropics.
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Affiliation(s)
- Danilo Trabuco Amaral
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
- Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Juliana Rodrigues Bombonato
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
- Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Sónia Cristina da Silva Andrade
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Evandro Marsola Moraes
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
| | - Fernando Faria Franco
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil.
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Tonolli PN, Franco FF, Silva AFG. [Historical construction of the concept of the enzyme and approaches in biology textbooks]. Hist Cienc Saude Manguinhos 2021; 28:727-744. [PMID: 34495114 DOI: 10.1590/s0104-59702021000300006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/18/2019] [Indexed: 06/13/2023]
Abstract
The use of the history and philosophy of science in teaching and learning is commonly neglected, linear, and/or out of context in textbooks. This article investigates whether this also occurs with the concept of enzymes. A brief review of the literature establishes the theoretical foundation to investigate how the concept of enzymes is presented in nine textbooks, following three different lines of analysis. A general lack of interconnection was seen in biochemistry topics, with enzymes usually only presented via the "lock-and-key" model, which does not best represent their complexity. Furthermore, conceptual limitations resulting from a lack of historical contextualization (partial or complete) were also observed.
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Affiliation(s)
- Paulo Newton Tonolli
- Pesquisador, Centro de Estudos do Genoma Humano e Células-tronco/Instituto de Biociências/Universidade de São Paulo. São Paulo - SP - Brasil
| | - Fernando Faria Franco
- Professor, Departamento de Biologia/Centro de Ciências Humanas e Biológicas/Universidade Federal de São Carlos.Sorocaba - SP - Brasil
| | - Antônio Fernando Gouvêa Silva
- Professor, Departamento de Ciências Humanas e Educação/Centro de Ciências Humanas e Biológicas/Universidade Federal de São Carlos.Sorocaba - SP - Brasil
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Bombonato JR, Bonatelli IAS, Silva GAR, Moraes EM, Zappi DC, Taylor NP, Franco FF. Cross-genera SSR transferability in cacti revealed by a case study using Cereus (Cereeae, Cactaceae). Genet Mol Biol 2019; 42:87-94. [PMID: 30794719 PMCID: PMC6428128 DOI: 10.1590/1678-4685-gmb-2017-0293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/13/2018] [Indexed: 11/22/2022] Open
Abstract
The study of transferability of simple sequence repeats (SSR) among closely
related species is a well-known strategy in population genetics, however
transferability among distinct genera is less common. We tested cross-genera SSR
amplification in the family Cactaceae using a total of 20 heterologous primers
previously developed for the genera Ariocarpus, Echinocactus,
Polaskia and Pilosocereus, in four taxa of the
genus Cereus: C. fernambucensis subsp.
fernambucensis, C. fernambucensis subsp.
sericifer, C. jamacaru and C.
insularis. Nine microsatellite loci were amplified in
Cereus resulting in 35.2% of success in transferability,
which is higher than the average rate of 10% reported in the literature for
cross-genera transferability in eudicots. The genetic variation in the
transferred markers was sufficient to perform standard clustering analysis,
indicating each population as a cohesive genetic cluster. Overall, the amount of
genetic variation found indicates that the transferred SSR markers might be
useful in large-scale population studies within the genus
Cereus.
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Affiliation(s)
- Juliana Rodrigues Bombonato
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil.,Programa de Pós-graduação em Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Evandro Marsola Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
| | - Daniela Cristina Zappi
- Instituto Tecnológico Vale, Museu Paraense Emilio Goeldi, Coord. Botânica, Belém, PA, Brazil
| | - Nigel P Taylor
- Singapore Botanic Gardens (National Parks Board), Singapore, Republic of Singapore
| | - Fernando Faria Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
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Barrios-Leal DY, Franco FF, Silva ECC, Santos CKB, Sene FM, Manfrin MH. Deep intraspecific divergence in Drosophila meridionalis, a cactophilic member of the New World Drosophila repleta group. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Franco FF, Jojima CL, Perez MF, Zappi DC, Taylor N, Moraes EM. The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti. Ecol Evol 2017; 7:9281-9293. [PMID: 29187968 PMCID: PMC5696397 DOI: 10.1002/ece3.3458] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/07/2017] [Accepted: 08/11/2017] [Indexed: 01/15/2023] Open
Abstract
In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS-trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.
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Affiliation(s)
- Fernando Faria Franco
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Cecília Leiko Jojima
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Manolo Fernandez Perez
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Daniela Cristina Zappi
- Museu Paraense Emilio GoeldiCoord. Botânica/Instituto Tecnológico ValeBelém do ParáBrazil
| | | | - Evandro Marsola Moraes
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
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Franco FF, Silva ECC, Barrios-Leal DY, Sene FM, Manfrin MH. The Calibrated Phylogeny of the Drosophila fasciola Subgroup (D. repleta Group Wasserman) Indicates Neogene Diversification of Its Internal Branches. Neotrop Entomol 2017; 46:537-545. [PMID: 28144910 DOI: 10.1007/s13744-017-0484-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/06/2017] [Indexed: 06/06/2023]
Abstract
The species of the Drosophila fasciola subgroup Wasserman represent the dominant section of the Drosophila repleta group Wasserman in the American rainforests and have a broad geographical distribution in the New World. However, despite of its wide range, the D. fasciola subgroup is one of the most overlooked D. repleta subgroups. Here, we report a molecular phylogenetic analysis focused on the D. fasciola subgroup using two mitochondrial [cytochrome oxidase subunit I (COI), cytochrome oxidase subunit II (COII)] and two nuclear [elongation factor-1alpha F1 (EF-alphaF1) and transformer (tra)] genes. Overall, we found that this subgroup is a monophyletic taxon, subdivided into two main internal branches: named Fas1 and Fas2 clades. The diversification of these clades is estimated to have begun in the middle Miocene, around 12 Ma [95% high posterior density (HPD) 9.0-15 Ma], and might be associated with the colonization of South America by Central America populations after the closure of Isthmus of Panama due to the temporal congruence between these events. The terminal branches had their origins estimated to be in the Pliocene or the Plio-Pleistocene transition. For the later estimates, both the geomorphological influences and the climatic oscillations of the Pleistocene may have played a role in shaping the diversification of the D. fasciola group.
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Affiliation(s)
- F F Franco
- Depto de Biologia, Centro de Ciências Humanas e Biológicas, Univ Federal de São Carlos, Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brasil.
| | - E C C Silva
- Secretaria do Meio Ambiente do Estado de São Paulo, São Paulo, Brasil
| | - D Y Barrios-Leal
- Pós-Graduação do Depto de Genética-Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, São Paulo, Brasil
| | - F M Sene
- Pós-Graduação do Depto de Genética-Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, São Paulo, Brasil
- Depto de Biologia-Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brasil
| | - M H Manfrin
- Pós-Graduação do Depto de Genética-Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, São Paulo, Brasil
- Depto de Biologia-Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brasil
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Bonatti V, Simões ZLP, Franco FF, Francoy TM. Evidence of at least two evolutionary lineages in Melipona subnitida (Apidae, Meliponini) suggested by mtDNA variability and geometric morphometrics of forewings. Naturwissenschaften 2014; 101:17-24. [DOI: 10.1007/s00114-013-1123-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 11/28/2022]
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Franco FF, Sene FM, Manfrin MH. Low satellite DNA variability in natural populations of Drosophila antonietae involved in different evolutionary events. J Hered 2010; 101:650-6. [PMID: 20497968 DOI: 10.1093/jhered/esq056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Drosophila antonietae is a cactophilic species that is found in the mesophilic forest of the Paraná-Paraguay river basin and in the dunes of the South Atlantic coast of Brazil. Although the genetic structure of the Paraná-Paraguay river basin populations has already been established, the relationship between these populations and those on the Atlantic coast is controversial. In this study, we compared 33 repetitive units of pBuM-2 satellite DNA isolated from individuals from 8 populations of D. antonietae in these geographic regions, including some populations found within a contact zone with the closely related D. serido. The pBuM-2 sequences showed low interpopulational variability. This result was interpreted as a consequence of both gene flow among the populations and unequal crossing over promoting homogenization of the tandem arrays. The results presented here, together with those of previous studies, highlight the use of pBuM-2 for solving taxonomic conflicts within the D. buzzatii species cluster.
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Affiliation(s)
- Fernando Faria Franco
- Campus de Sorocaba, Universidade Federal de São Carlos, CEP 18052-780 Sorocaba, Brazil.
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Franco FF, Silva-Bernardi ECC, Sene FM, Hasson ER, Manfrin MH. Intra- and interspecific divergence in the nuclear sequences of the clock gene period in species of the Drosophila buzzatii cluster. J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2010.00564.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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