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Guillory WX, de Medeiros Magalhães F, Coelho FEA, Bonatelli IAS, Palma-Silva C, Moraes EM, Garda AA, Burbrink FT, Gehara M. Geoclimatic drivers of diversification in the largest arid and semi-arid environment of the Neotropics: Perspectives from phylogeography. Mol Ecol 2024:e17431. [PMID: 38877815 DOI: 10.1111/mec.17431] [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: 02/06/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.
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Affiliation(s)
- Wilson X Guillory
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey, USA
| | | | | | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York City, New York, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
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2
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Ceríaco LMP, Passos P. Historical natural history collections allow the description of a new and presumably extinct species of dwarf gecko (Squamata: Gekkonidae: Lygodactylus Gray, 1864) from Fernando de Noronha Island, Brazil. AN ACAD BRAS CIENC 2023; 95:e20230222. [PMID: 37878915 DOI: 10.1590/0001-3765202320230222] [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: 03/03/2023] [Accepted: 05/28/2023] [Indexed: 10/27/2023] Open
Abstract
A series of specimens of an unidentified species of the genus Lygodactylus from Fernando de Noronha Island were found in the herpetological collections of the Museu Nacional, Rio de Janeiro (Brazil). No species of this genus were known to occur in the archipelago. A review of the historical reports regarding the herpetofauna of the island failed to provide evidence regarding the presence of the species in the last centuries. Morphological comparisons with the two other species of the genus occurring in South America, L. klugei and L. wetzeli, allowed us to confidently confirm that the Fernando de Noronha population belonged to a putatively new species. Here we describe this population as a new species and discuss its possible extinction causes in the archipelago. We also debate the importance of historical natural history collections to the study of biodiversity.
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Affiliation(s)
- Luis M P Ceríaco
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boavista, s/n, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Paulo Passos
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boavista, s/n, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
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3
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Pourmasumi S, Kounis NG, Naderi M, Hosseinisadat R, Khoradmehr A, Fagheirelahee N, Kouni SN, de Gregorio C, Dousdampanis P, Mplani V, Michalaki MA, Plotas P, Assimakopoulos S, Gogos C, Aidonidis G, Roditis P, Matsas N, Velissaris D, Calogiuri G, Hung MY, Koniari I. Effects of COVID-19 Infection and Vaccination on the Female Reproductive System: A Narrative Review. Balkan Med J 2023; 40:153-164. [PMID: 37114907 PMCID: PMC10175880 DOI: 10.4274/balkanmedj.galenos.2023.2023-3-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Several studies and research papers have been published to elucidate and understand the mechanism of the coronavirus disease 2019 (COVID-19) pandemic and its long-term effects on the human body. COVID-19 affects a number of organs, including the female reproductive system. However, less attention has been given to the effects of COVID-19 on the female reproductive system due to their low morbidity. The results of studies investigating the relationship between COVID-19 infection and ovarian function in women of reproductive age have shown the harmless involvement of COVID-19 infection. Several studies have reported the involvement of COVID-19 infection in oocyte quality, ovarian function, and dysfunctions in the uterine endometrium and the menstrual cycle. The findings of these studies indicate that COVID-19 infection negatively affects the follicular microenvironment and dysregulate ovarian function. Although the COVID-19 pandemic and female reproductive health have been studied in humans and animals, very few studies have examined how COVID-19 affects the female reproductive system. The objective of this review is to summarize the current literature and categorize the effects of COVID-19 on the female reproductive system, including the ovaries, uterus, and hormonal profiles. The effects on oocyte maturation, oxidative stress, which causes chromosomal instability and apoptosis in ovaries, in vitro fertilization cycle, high-quality embryos, premature ovarian insufficiency, ovarian vein thrombosis, hypercoagulable state, women’s menstrual cycle, the hypothalamus-pituitary-ovary axis, and sex hormones, including estrogen, progesterone, and the anti-Müllerian hormone, are discussed in particular.
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Affiliation(s)
- Soheila Pourmasumi
- Social Determinants of Health Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
- Clinical Research Development Unit, Ali-Ibn Abi-Talib Hospital, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Nicholas G. Kounis
- Department of Internal Medicine, Division of Cardiology, University of Patras Medical School, Patras, Greece
| | - Monavar Naderi
- Knowledge and Information Science, Vice Chancellor for Science and Technology, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Robabe Hosseinisadat
- Department of Obstetrics and Gynecology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Niloofar Fagheirelahee
- Department of Anatomy, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | | | - Cesare de Gregorio
- Department of Clinical and Experimental Medicine, University of Messina Medical School, Messina, Italy
| | | | - Virginia Mplani
- Intensive Care Unit, Patras University Hospital, Patras, Greece
| | - Marina A. Michalaki
- Department of Internal Medicine, Division of Endocrinology, Fculty of Health Sciences, University of Patras, Patras, Greece
| | | | - Stelios Assimakopoulos
- Department of Internal Medicine, Division of Infectious Diseases, University of Patras Medical School, Patras, Greece
| | - Christos Gogos
- COVID-19 Unit, Papageorgiou General Hospital, Thessaloniki, Greece
| | | | - Pavlos Roditis
- Department of Cardiology, Mamatsio Kozanis General Hospital, Kozani, Greece
| | | | | | - Gianfranco Calogiuri
- Pneumonology Department, Civil Hospital “Ninetto Melli”, Pietro Vernoti, Brindisi, Italy
- Department of Internal Medicine, Immunology and Infectious Diseases, Section of Allergology and Clinical Immunology, University of Bari Medical School, Bari, Italy
| | - Ming-Yow Hung
- Division of Cardiology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Division of Cardiology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Taipei Heart Institute, Taipei Medical University, Taipei, Taiwan
| | - Ioanna Koniari
- Departmentof Cardiology, Liverpool Heart and Chest Hospital, Liverpool, UK
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4
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Porto CR, Fazolato CP, Marques R, Batalha-Filho H, Napoli MF, Garda AA, de Carvalho MLS, de Campos Fernandes FM. Unravelling the cryptic diversity and evolution of the dwarf swamp frog Pseudopaludicola mystacalis (Anura, Leptodactylidae) in open habitats of South America. AMPHIBIA-REPTILIA 2022. [DOI: 10.1163/15685381-bja10099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Many studies on the diversity of the South American biota support the role of ecological and geological events as main drivers of species diversification. For many groups, geomorphological events are the key drivers of diversification, while the influence of Pleistocene climate oscillations is prominent for others. To precisely indicate which events were key for the development of the astonishing biodiversity in South America, studies on widely distributed species are paramount. One such species, the dwarf swamp frog Pseudopaludicola mystacalis (Leptodactylidae, Leiuperinae), is widely distributed in open habitats of South America and we herein investigate population differentiation and diversification in this species across its geographic range. We sequenced a 1374 bp mtDNA fragment from 64 specimens across 25 localities. We used population assignment and species delimitation methods to assess genetic structure and lineage limits across the species distribution. We estimated, for each lineage, intraspecific diversity, divergence times, and demographic histories. Our results recovered ten lineages with up to 5% of genetic divergence among them. Diversification occurred mainly during the Tertiary, suggesting that Miocene-Pliocene topographic events had a major influence on the diversification of P. mystacalis. Pleistocene climatic oscillations also played a role on evolutionary history of P. mystacalis, causing demographic changes in one lineage.
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Affiliation(s)
- Clara Ribeiro Porto
- Universidade Federal da Bahia, Programa de Pós-Graduação em Genética e Biodiversidade, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Cecil Pergentino Fazolato
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Ricardo Marques
- Universidade do Estado de Mato Grosso, 78690-000, Nova Xavantina, Mato Grosso, Brazil
| | - Henrique Batalha-Filho
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Marcelo Felgueiras Napoli
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Adrian Antonio Garda
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Botânica e Zoologia, Avenida Senador Salgado Filho, S/N, Lagoa Nova, 59078-900, Natal, RN, Brazil
| | - Maria Luiza Silveira de Carvalho
- Universidade Federal da Bahia, Programa de Pós-Graduação em Genética e Biodiversidade, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Flora Maria de Campos Fernandes
- Universidade Federal da Bahia, Programa de Pós-Graduação em Genética e Biodiversidade, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
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5
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Mittan CS, Zamudio KR, Thomé MTC, Camurugi F, Colli GR, Garda AA, Haddad CFB, Prado CPA. Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group. Mol Phylogenet Evol 2022; 175:107579. [PMID: 35835425 DOI: 10.1016/j.ympev.2022.107579] [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: 10/22/2021] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Despite extensive research on biodiversity in Neotropical forests, biodiversity in seasonally dry, open biomes in South America has been underestimated until recently. We leverage a widespread group, Boana albopunctata, to uncover cryptic lineages and investigate the timing of diversification in Neotropical anurans with a focus on dry diagonal biomes (Cerrado, Caatinga and Chaco) and the ecotone between Amazonia and the Cerrado. We inferred a multilocus phylogeny of the B. albopunctata species group that includes 15 of 18 described species, recovered two cryptic species, and reconstructed the timing of diversification among species distributed across multiple South American biomes. One new potential species (B. aff. steinbachi), sampled in the Amazonian state of Acre, clustered within the B. calcara-fasciata species complex and is close to B. steinbachi. A second putative new species (B. aff. multifasciata), sampled in the Amazonia-Cerrado ecotone, is closely related to B. multifasciata. Lastly, we place a recently identified Cerrado lineage (B. aff. albopuncata) into the B. albopunctata species group phylogeny for the first time. Our ancestral range reconstruction showed that species in the B. albopuctata group likely dispersed from Amazonia-Cerrado into the dry-diagonal and Atlantic Forest. Intraspecies demography showed, for both B. raniceps and B. albopunctata, signs of rapid expansion across the dry diagonal. Similarly, for one clade of B. multifasciata, our analyses support an invasion of the Cerrado from Amazonia, followed by a rapid expansion across the open diagonal biomes. Thus, our study recovers several recent divergences along the Amazonia-Cerrado ecotone in northern Brazil. Tectonic uplift and erosion in the late Miocene and climate oscillations in the Pleistocene corresponded with estimated divergence times in the dry diagonal and Amazonia-Cerrado ecotone. Our study highlights the importance of these threatened open formations in the generation of biodiversity in the Neotropics.
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Affiliation(s)
- Cinnamon S Mittan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - M Tereza C Thomé
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Adrian A Garda
- Laboratório de Anfíbios e Répteis, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Cynthia P A Prado
- Departamento de Morfologia e Fisiologia Animal, Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
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6
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A New Species of Proceratophrys (Anura: Odontophrynidae) from Boqueirão da Onça, Northern Bahia State, Brazil. J HERPETOL 2022. [DOI: 10.1670/20-070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Gippner S, Travers SL, Scherz MD, Colston TJ, Lyra ML, Mohan AV, Multzsch M, Nielsen SV, Rancilhac L, Glaw F, Bauer AM, Vences M. A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation. Mol Phylogenet Evol 2021; 165:107311. [PMID: 34530117 DOI: 10.1016/j.ympev.2021.107311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/22/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35-22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches.
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Affiliation(s)
- Sven Gippner
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany; State Natural History Museum of Braunschweig, Pockelsstr. 10, 38106 Braunschweig, Germany
| | - Scott L Travers
- Department of Biological Sciences, Rutgers University-Newark, 195 University Avenue, Newark, NJ 07102, USA
| | - Mark D Scherz
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Timothy J Colston
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP CEP13506-900, Brazil
| | - Ashwini V Mohan
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Malte Multzsch
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Stuart V Nielsen
- Santa Fe College, 3000 NW 83rd St., Gainesville, FL 32606, USA; Florida Museum of Natural History, Division of Herpetology, 1659 Museum Road - Dickinson Hall, Gainesville, FL 32611, USA
| | - Loïs Rancilhac
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Miguel Vences
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
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8
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Lobon-Rovira J, Bauer A. Bone-by-bone: A detailed skull description of the White-headed dwarf gecko Lygodactylus picturatus (Peters, 1870). AFR J HERPETOL 2021. [DOI: 10.1080/21564574.2021.1980120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Javier Lobon-Rovira
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Aaron Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, Villanova, United States
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9
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Ceron K, Mângia S, Guedes TB, Alvares DJ, Neves MO, De Toledo Moroti M, Torello N, Borges-Martins M, Ferreira VL, Santana DJ. Ecological Niche Explains the Sympatric Occurrence of Lined Ground Snakes of the Genus Lygophis (Serpentes, Dipsadidae) in the South American Dry Diagonal. HERPETOLOGICA 2021. [DOI: 10.1655/herpetologica-d-20-00056.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Fonseca EM, Colli GR, Werneck FP, Carstens BC. Phylogeographic model selection using convolutional neural networks. Mol Ecol Resour 2021; 21:2661-2675. [PMID: 33973350 DOI: 10.1111/1755-0998.13427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 11/26/2022]
Abstract
The discipline of phylogeography has evolved rapidly in terms of the analytical toolkit used to analyse large genomic data sets. Despite substantial advances, analytical tools that could potentially address the challenges posed by increased model complexity have not been fully explored. For example, deep learning techniques are underutilized for phylogeographic model selection. In non-model organisms, the lack of information about their ecology and evolution can lead to uncertainty about which demographic models are appropriate. Here, we assess the utility of convolutional neural networks (CNNs) for assessing demographic models in South American lizards in the genus Norops. Three demographic scenarios (constant, expansion, and bottleneck) were considered for each of four inferred population-level lineages, and we found that the overall model accuracy was higher than 98% for all lineages. We then evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among the four lineages, identifying a single model with an estimated overall accuracy of 87% when using CNNs. The inferred demography of the lizard system suggests that gene flow between non-sister populations and changes in effective population sizes through time, probably in response to Pleistocene climatic oscillations, have shaped genetic diversity in this system. Approximate Bayesian computation (ABC) was applied to provide a comparison to the performance of CNNs. ABC was unable to identify a single model among the larger set of 26 models in the subsequent analysis. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer's toolkit.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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11
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Fonseca EM, Duckett DJ, Carstens BC. P2C2M.GMYC: An R package for assessing the utility of the Generalized Mixed Yule Coalescent model. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emanuel M. Fonseca
- Department of Evolution, Ecology, & Organismal Biology The Ohio State University Columbus OH USA
| | - Drew J. Duckett
- Department of Evolution, Ecology, & Organismal Biology The Ohio State University Columbus OH USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology, & Organismal Biology The Ohio State University Columbus OH USA
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12
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Magalhães FDM, Lyra ML, de Carvalho TR, Baldo D, Brusquetti F, Burella P, Colli GR, Gehara MC, Giaretta AA, Haddad CF, Langone JA, López JA, Napoli MF, Santana DJ, de Sá RO, Garda AA. Taxonomic Review of South American Butter Frogs: Phylogeny, Geographic Patterns, and Species Delimitation in the Leptodactylus latrans Species Group (Anura: Leptodactylidae). HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/0733-1347-31.4.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Felipe de M. Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
| | - Mariana L. Lyra
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Thiago R. de Carvalho
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Diego Baldo
- Instituto de Biología Subtropical (IBS, CONICET-UNaM), Laboratorio de Genética Evolutiva, Facultad de Ciencias Exactas, Universidad Nacional de Misiones, CP N3300LQF, Posadas, Misiones, Argentina
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay (IIBP), Del Escudo 1607, CP 1425 Asunción, Paraguay
| | - Pamela Burella
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Guarino R. Colli
- Departamento de Zoologia, Universidade de Brasília (UNB), CEP 70910-900, Brasília, Distrito Federal, Brazil
| | - Marcelo C. Gehara
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, 07102, USA
| | - Ariovaldo A. Giaretta
- Laboratório de Taxonomia e Sistemática de Anuros Neotropicais (LTSAN), Instituto de Ciências Exatas e Naturais do Pontal (ICENP), Universidade Federal de Uberlândia (UFU), Ituiutaba, Minas Gerais, Brazil
| | - Célio F.B. Haddad
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - José A. Langone
- Departamento de Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, CP 11.000, Montevideo, Uruguay
| | - Javier A. López
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Marcelo F. Napoli
- Laboratório de Taxonomia e História Natural de Anfíbios (AMPHIBIA), Museu de História Natural, Instituto de Biologia, Universidade Federal da Bahia (UFBA), CEP 40170–115, Salvador, Bahia, Brazil
| | - Diego J. Santana
- Mapinguari – Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis, Universidade Federal de Mato Grosso do Sul (UFMS), CEP 79002-970 Campo Grande, Mato Grosso, Brazil
| | - Rafael O. de Sá
- Department of Biology, University of Richmond, Richmond, Virginia, 23173, USA
| | - Adrian A. Garda
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
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13
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Corbett EC, Bravo GA, Schunck F, Naka LN, Silveira LF, Edwards SV. Evidence for the Pleistocene Arc Hypothesis from genome-wide SNPs in a Neotropical dry forest specialist, the Rufous-fronted Thornbird (Furnariidae: Phacellodomus rufifrons). Mol Ecol 2020; 29:4457-4472. [PMID: 32974981 DOI: 10.1111/mec.15640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022]
Abstract
South American dry forests have a complex and poorly understood biogeographic history. Based on the fragmented distribution of many Neotropical dry forest species, it has been suggested that this biome was more widely distributed and contiguous under drier climate conditions in the Pleistocene. To test this scenario, known as the Pleistocene Arc Hypothesis, we studied the phylogeography of the Rufous-fronted Thornbird (Phacellodomus rufifrons), a widespread dry forest bird with a disjunct distribution closely matching that of the biome itself. We sequenced mtDNA and used ddRADseq to sample 7,167 genome-wide single-nucleotide polymorphisms from 74 P. rufifrons individuals across its range. We found low genetic differentiation over two prominent geographic breaks - particularly across a 1,000 km gap between populations in Bolivia and Northern Peru. Using demographic analyses of the joint site frequency spectrum, we found evidence of recent divergence without subsequent gene flow across those breaks. By contrast, parapatric morphologically distinct populations in northeastern Brazil show high genetic divergence with evidence of recent gene flow. These results, in combination with our paleoclimate species distribution modelling, support the idea that currently disjunct patches of dry forest were more connected in the recent past, probably during the Middle and Late Pleistocene. This notion fits the major predictions of the Pleistocene Arc Hypothesis and illustrates the importance of comprehensive genomic and geographic sampling for examining biogeographic and evolutionary questions in complex ecosystems like Neotropical dry forests.
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Affiliation(s)
- Eamon C Corbett
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,Department of Biological Sciences & Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Fabio Schunck
- Seção de Aves, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Luciano N Naka
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Luís F Silveira
- Seção de Aves, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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14
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Mângia S, Oliveira EF, Santana DJ, Koroiva R, Paiva F, Garda AA. Revising the taxonomy of
Proceratophrys
Miranda‐Ribeiro, 1920 (Anura: Odontophrynidae) from the Brazilian semiarid Caatinga: Morphology, calls and molecules support a single widespread species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah Mângia
- Departamento de Sistemática e Ecologia Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Universidade Federal da Paraı́ba João Pessoa Brazil
| | - Eliana Faria Oliveira
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Diego José Santana
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Ricardo Koroiva
- Laboratório de Citotaxonomia e Insetos Aquáticos Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Fernando Paiva
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
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15
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Lanna FM, Gehara M, Werneck FP, Fonseca EM, Colli GR, Sites JW, Rodrigues MT, Garda AA. Dwarf geckos and giant rivers: the role of the São Francisco River in the evolution of Lygodactylus klugei (Squamata: Gekkonidae) in the semi-arid Caatinga of north-eastern Brazil. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Species diversification can be strongly influenced by geomorphological features, such as mountains, valleys and rivers. Rivers can act as hard or soft barriers to gene flow depending on their size, speed of flow, historical dynamics and regional topographical characteristics. The São Francisco River (SFR) is the largest perennial river in the Caatinga biome in north-eastern Brazil and has been considered a barrier to gene flow and dispersal. Herein, we evaluated the role of the SFR on the evolution of Lygodactylus klugei, a small gecko from the Caatinga. Using a single-locus species delimitation method (generalized mixed Yule coalescent), we defined lineages (haploclades). Subsequently, we evaluated the role of the SFR in structuring genetic diversity in this species using a multilocus approach to quantify migration across margins. We also evaluated genetic structure based on nuclear markers, testing the number of populations found through an assignment test (STRUCTURE) across the species distribution. We recovered two mitochondrial lineages structured with respect to the SFR, but only a single population was inferred from nuclear markers. Given that we detected an influence of the SFR only on mitochondrial markers, we suggest that the current river course has acted as a relatively recent geographical barrier for L. klugei, for ~450 000 years.
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Affiliation(s)
- Flávia M Lanna
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, USA
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
| | - Marcelo Gehara
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Emanuel M Fonseca
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, USA
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Jack W Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
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16
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Magalhaes ILF, Neves DM, Santos FR, Vidigal THDA, Brescovit AD, Santos AJ. Phylogeny of Neotropical Sicarius sand spiders suggests frequent transitions from deserts to dry forests despite antique, broad-scale niche conservatism. Mol Phylogenet Evol 2019; 140:106569. [PMID: 31362083 DOI: 10.1016/j.ympev.2019.106569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 07/03/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022]
Abstract
Phylogenetic niche conservatism (PNC) shapes the distribution of organisms by constraining lineages to particular climatic conditions. Conversely, if areas with similar climates are geographically isolated, diversification may also be limited by dispersal. Neotropical xeric habitats provide an ideal system to test the relative roles of climate and geography on diversification, as they occur in disjunct areas with similar biotas. Sicariinae sand spiders are intimately associated with these xeric environments, particularly seasonally dry tropical forests (SDTFs) and subtropical deserts/scrublands in Africa (Hexophthalma) and the Neotropics (Sicarius). We explore the role of PNC, geography and biome shifts in their evolution and timing of diversification. We estimated a time-calibrated, total-evidence phylogeny of Sicariinae, and used published distribution records to estimate climatic niche and biome occupancy. Topologies were used for estimating ancestral niches and biome shifts. We used variation partitioning methods to test the relative importance of climate and spatially autocorrelated factors in explaining the spatial variation in phylogenetic structure of Sicarius across the Neotropics. Neotropical Sicarius are ancient and split from their African sister-group around 90 (57-131) million years ago. Most speciation events took place in the Miocene. Sicariinae records can be separated in two groups corresponding to temperate/dry and tropical/seasonally dry climates. The ancestral climatic niche of Sicariinae are temperate/dry areas, with 2-3 shifts to tropical/seasonally dry areas in Sicarius. Similarly, ancestral biomes occupied by the group are temperate and dry (deserts, Mediterranean scrub, temperate grasslands), with 2-3 shifts to tropical, seasonally dry forests and grasslands. Most of the variation in phylogenetic structure is explained by long-distance dispersal limitation that is independent of the measured climatic conditions. Sicariinae have an ancient association to arid lands, suggesting that PNC prevented them from colonizing mesic habitats. However, niches are labile at a smaller scale, with several shifts from deserts to SDTFs. This suggests that PNC and long-distance dispersal limitation played major roles in confining lineages to isolated areas of SDTF/desert over evolutionary history, although shifts between xeric biomes occurred whenever geographical opportunities were presented.
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Affiliation(s)
- I L F Magalhaes
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina; Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil.
| | - D M Neves
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA; Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - F R Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - T H D A Vidigal
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - A D Brescovit
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, São Paulo, Brazil
| | - A J Santos
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
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