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Mapalo MA, Wolfe JM, Ortega-Hernández J. Cretaceous amber inclusions illuminate the evolutionary origin of tardigrades. Commun Biol 2024; 7:953. [PMID: 39107512 PMCID: PMC11303527 DOI: 10.1038/s42003-024-06643-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
Tardigrades are a diverse phylum of microscopic invertebrates widely known for their extreme survival capabilities. Molecular clocks suggest that tardigrades diverged from other panarthropods before the Cambrian, but their fossil record is extremely sparse. Only the fossil tardigrades Milnesium swolenskyi (Late Cretaceous) and Paradoryphoribius chronocaribbeus (Miocene) have resolved taxonomic positions, restricting the availability of calibration points for estimating for the origin of this phylum. Here, we revise two crown-group tardigrades from Canadian Cretaceous-aged amber using confocal fluorescence microscopy, revealing critical morphological characters that resolve their taxonomic positions. Formal morphological redescription of Beorn leggi reveals that it features Hypsibius-type claws. We also describe Aerobius dactylus gen. et sp. nov. based on its unique combination of claw characters. Phylogenetic analyses indicate that Beo. leggi and Aer. dactylus belong to the eutardigrade superfamily Hypsibioidea, adding a critical fossil calibration point to investigate tardigrade origins. Our molecular clock estimates suggest an early Paleozoic diversification of crown-group Tardigrada and highlight the importance of Beo. leggi as a calibration point that directly impacts estimates of shallow nodes. Our results suggest that independent terrestrialization of eutardigrades and heterotardigrades occurred around the end-Carboniferous and Lower Jurassic, respectively. These estimates also provide minimum ages for convergent acquisition of cryptobiosis.
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Affiliation(s)
- Marc A Mapalo
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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2
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Hurtado-Gómez JP, Vargas-Ramírez M, Iverson JB, Joyce WG, McCranie JR, Paetzold C, Fritz U. Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae). Mol Phylogenet Evol 2024; 197:108083. [PMID: 38679303 DOI: 10.1016/j.ympev.2024.108083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/02/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.
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Affiliation(s)
| | - Mario Vargas-Ramírez
- Grupo Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia; Estación de Biología Tropical Roberto Franco (EBTRF), Universidad Nacional de Colombia, Villavicencio, Colombia
| | - John B Iverson
- Department of Biology, Earlham College, Richmond, IN 47374, USA
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, 1700 Fribourg, Switzerland
| | - James R McCranie
- Smithsonian Research Associate, 10770 SW 164th Street, Miami, FL 33157, USA
| | - Claudia Paetzold
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany.
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3
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Vázquez AA, Chapuis E, Sánchez J, Alda P, Faugère D, Sánchez M, Souq L, López-Soriano J, Quiñonero-Salgado S, Bonel N, Pointier JP, Alba A, Hurtrez-Boussès S. Risk of invasion and disease transmission by the Australasian freshwater snail Orientogalba viridis (Lymnaeidae): a field and experimental study. Parasit Vectors 2024; 17:320. [PMID: 39068485 PMCID: PMC11282605 DOI: 10.1186/s13071-024-06403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/12/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Biological invasions pose risks to the normal functioning of ecosystems by altering the structure and composition of several communities. Molluscs stand out as an extensively studied group given their long history of introduction by either natural or anthropogenic dispersal events. An alien population of the lymnaeid species Orientogalba viridis was first sighted in 2009 in southern Spain. In its native range (Australasian), this species is one of the main intermediate hosts of Fasciola hepatica, a major worldwide trematode parasite largely affecting humans, domestic animals and wildlife. METHODS We collected field populations of O. viridis from its native (Malaysia) and invaded (Spain) ranges. We performed detailed morphoanatomical drawings of the species and screened for natural infection of parasites. Individuals were molecularly characterized using ITS2 for comparison with existing sequences in a fine phylogeography study. We founded experimental populations at two different conditions (tropical, 26 °C and temperate, 21 °C) to study the life-history traits of exposed and non-exposed individuals to different F. hepatica isolates. RESULTS We found a 9% natural prevalence of trematode infection (98% similarity with a sequence of Hypoderaeum conoideum [Echinostomatidae]) in the Spanish field population. The haplotypes of O. viridis found in our study from Spain clustered with Australian haplotypes. Experimental infection with F. hepatica was successful in both experimental conditions but higher in tropical (87% prevalence) than in temperate (73%). Overall lifespan, however, was higher in temperate conditions (mean 32.5 ± 7.4 weeks versus 23.3 ± 6.5) and survivorship remained above 70% during the first 20 weeks. In parasite-exposed populations, life expectancy dropped from an overall 37.75 weeks to 11.35 weeks but still doubled the time for initial cercariae shedding. Cercariae shedding started at day 23 post-exposure and peaked between days 53 and 67 with an average of 106 metacercariae per snail. CONCLUSIONS Whether O. viridis will succeed in Europe is unknown, but the odds are for a scenario in which a major snail host of F. hepatica occupy all available habitats of potential transmission foci, ravelling the epidemiology of fasciolosis. This research provides a comprehensive understanding of O. viridis biology, interactions with parasites and potential implications for disease transmission dynamics, offering valuable insights for further research and surveillance.
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Affiliation(s)
- Antonio A Vázquez
- IHPE, UMR 5244 Université de Perpignan Via Domitia, CNRS, IFREMER, Université de Montpellier, Perpignan, France.
- Laboratorio de Malacología, Instituto de Medicina Tropical Pedro Kourí, Havana, Cuba.
| | - Elodie Chapuis
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
- CREES, Montpellier, France
| | - Jorge Sánchez
- Laboratorio de Malacología, Instituto de Medicina Tropical Pedro Kourí, Havana, Cuba
| | - Pilar Alda
- Genética y Ecología Evolutiva, CERZOS, CONICET-UNS, Bahía Blanca, Buenos Aires, Argentina
| | | | - Mónica Sánchez
- Laboratorio de Malacología, Instituto de Medicina Tropical Pedro Kourí, Havana, Cuba
| | - Léa Souq
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | | | | | - Nicolás Bonel
- Genética y Ecología Evolutiva, CERZOS, CONICET-UNS, Bahía Blanca, Buenos Aires, Argentina
| | - Jean-Pierre Pointier
- PSL Research University, UAR 3278 CNRS-EPHE, CRIOBE Université de Perpignan, Perpignan, France
| | - Annia Alba
- IHPE, UMR 5244 Université de Perpignan Via Domitia, CNRS, IFREMER, Université de Montpellier, Perpignan, France
- Institut ExposUM, Université de Montpellier, Montpellier, France
| | - Sylvie Hurtrez-Boussès
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
- CREES, Montpellier, France
- Département de Biologie-Écologie, Faculté des Sciences, Université de Montpellier, Montpellier, France
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4
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L'Hôte L, Light I, Mattiangeli V, Teasdale MD, Halpin Á, Gourichon L, Key FM, Daly KG. An 8000 years old genome reveals the Neolithic origin of the zoonosis Brucella melitensis. Nat Commun 2024; 15:6132. [PMID: 39033187 PMCID: PMC11271283 DOI: 10.1038/s41467-024-50536-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Brucella melitensis is a major livestock bacterial pathogen and zoonosis, causing disease and infection-related abortions in small ruminants and humans. A considerable burden to animal-based economies today, the presence of Brucella in Neolithic pastoral communities has been hypothesised but we lack direct genomic evidence thus far. We report a 3.45X B. melitensis genome preserved in an ~8000 year old sheep specimen from Menteşe Höyük, Northwest Türkiye, demonstrating that the pathogen had evolved and was circulating in Neolithic livestock. The genome is basal with respect to all known B. melitensis and allows the calibration of the B. melitensis speciation time from the primarily cattle-infecting B. abortus to approximately 9800 years Before Present (BP), coinciding with a period of consolidation and dispersal of livestock economies. We use the basal genome to timestamp evolutionary events in B. melitensis, including pseudogenization events linked to erythritol response, the supposed determinant of the pathogen's placental tropism in goats and sheep. Our data suggest that the development of herd management and multi-species livestock economies in the 11th-9th millennium BP drove speciation and host adaptation of this zoonotic pathogen.
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Affiliation(s)
- Louis L'Hôte
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ian Light
- Max Planck Institute for Infection Biology, Evolutionary Pathogenomics, 10117, Berlin, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Áine Halpin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Felix M Key
- Max Planck Institute for Infection Biology, Evolutionary Pathogenomics, 10117, Berlin, Germany
| | - Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
- School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.
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5
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Wutke S, Blank SM, Boevé JL, Faircloth BC, Koch F, Linnen CR, Malm T, Niu G, Prous M, Schiff NM, Schmidt S, Taeger A, Vilhelmsen L, Wahlberg N, Wei M, Nyman T. Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta). Mol Phylogenet Evol 2024; 199:108144. [PMID: 38972494 DOI: 10.1016/j.ympev.2024.108144] [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: 03/11/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.
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Affiliation(s)
- Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
| | - Stephan M Blank
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Jean-Luc Boevé
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Frank Koch
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Marko Prous
- Museum of Natural History, University of Tartu, Estonia
| | - Nathan M Schiff
- Formerly with the USDA Forest Service, Southern Research Station, Center for Bottomland Hardwoods Research, Stoneville, MS, USA
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Lars Vilhelmsen
- Natural History Museum of Denmark, SCIENCE, University of Copenhagen, Denmark
| | | | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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6
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Sewell TR, van Dorp L, Ghosh PN, Wierzbicki C, Caroe C, Lyakurwa JV, Tonelli E, Bowkett AE, Marsden S, Cunningham AA, Garner TWJ, Gilbert TP, Moyer D, Weldon C, Fisher MC. Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild. Proc Biol Sci 2024; 291:20241157. [PMID: 39081176 PMCID: PMC11289635 DOI: 10.1098/rspb.2024.1157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 06/19/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
Outbreaks of emerging infectious diseases are influenced by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Deterioration in the population of the micro-endemic Tanzanian Kihansi spray toad (Nectophrynoides asperginis) occurred after the construction of a hydropower dam, implicating habitat modification in this species decline. Population recovery followed habitat augmentation; however, a subsequent outbreak of chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) led to the spray toad's extinction in the wild. We show using spatiotemporal surveillance and mitogenome assembly of Bd from archived toad mortalities that the outbreak was caused by invasion of the BdCAPE lineage and not the panzootic lineage BdGPL. Molecular dating reveals an emergence of BdCAPE across southern Africa overlapping with the timing of the spray toad's extinction. That our post-outbreak surveillance of co-occurring amphibian species in the Udzungwa Mountains shows widespread infection by BdCAPE yet no signs of ill-health or decline suggests these other species can tolerate Bd when environments are stable. We conclude that, despite transient success in mitigating the impact caused by dams' construction, invasion by BdCAPE caused the ultimate die-off that led to the extinction of the Kihansi spray toad.
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Affiliation(s)
- Thomas R. Sewell
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution & Environment, UCL Genetics Institute, University College London, LondonWC1E 6BT, UK
| | - Pria N. Ghosh
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
| | - Claudia Wierzbicki
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
- Institute of Zoology, Zoological Society of London, LondonNW1 4RY, UK
| | - Christian Caroe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen1353, Denmark
| | - John V. Lyakurwa
- Department of Zoology and Wildlife Conservation, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Elena Tonelli
- Department of Natural Sciences, Manchester Metropolitan University, ManchesterM1 5GD, UK
| | | | - Stuart Marsden
- Department of Natural Sciences, Manchester Metropolitan University, ManchesterM1 5GD, UK
| | | | - Trenton W. J. Garner
- Institute of Zoology, Zoological Society of London, LondonNW1 4RY, UK
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Tom P. Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen1353, Denmark
| | - David Moyer
- Integrated Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
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7
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Cai M, Song K, Wang R, Wang S, Chen H, Wang H. Tracking intra-species and inter-genus transmission of KPC through global plasmids mining. Cell Rep 2024; 43:114351. [PMID: 38923465 DOI: 10.1016/j.celrep.2024.114351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC) poses a major public health risk. Understanding its transmission dynamics requires examining the epidemiological features of related plasmids. Our study compiled 15,660 blaKPC-positive isolates globally over the past two decades. We found extensive diversity in the genetic background of KPC, with 23 Tn4401-related and 341 non-Tn4401 variants across 163 plasmid types in 14 genera. Intra-K. pneumoniae and cross-genus KPC transmission patterns varied across four distinct periods. In the initial periods, plasmids with narrow host ranges gradually established a survival advantage. In later periods, broad-host-range plasmids became crucial for cross-genera transmission. In total, 61 intra-K. pneumoniae and 66 cross-genus transmission units have been detected. Furthermore, phylogenetic reconstruction dated the origin of KPC transmission back to 1991 and revealed frequent exchanges across countries. Our research highlights the frequent and transient spread events of KPC mediated by plasmids across multiple genera and offers theoretical support for high-risk plasmid monitoring.
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Affiliation(s)
- Meng Cai
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Kaiwen Song
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China; Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China; Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China.
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8
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Morales P, Gajardo F, Valdivieso C, Valladares MA, Di Genova A, Orellana A, Gutiérrez RA, González M, Montecino M, Maass A, Méndez MA, Allende ML. Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes. BMC Genomics 2024; 25:614. [PMID: 38890559 PMCID: PMC11184842 DOI: 10.1186/s12864-024-10416-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
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Affiliation(s)
- Pamela Morales
- Millennium Institute Center for Genome Regulation, Santiago, Chile.
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alex Di Genova
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- DiGenoma-Lab, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- ANID Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Martin Montecino
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, 837001, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Modelamiento Matemático IRL 2807 CNRS, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Universidad de Chile, Santiago, Chile
| | - Marco A Méndez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Ecología Aplicada y Sustentabilidad (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Cape Horn International Center (CHIC), Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Lima RC, de Lima SR, Rocha MS, Dos Anjos HDB, Dantas YCA, Benites IDN, Queiroz CDCS, Fraga EDC, Batista JDS. Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding. JOURNAL OF FISH BIOLOGY 2024; 104:1924-1939. [PMID: 38551122 DOI: 10.1111/jfb.15721] [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: 07/08/2023] [Revised: 12/03/2023] [Accepted: 02/25/2024] [Indexed: 06/27/2024]
Abstract
The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.
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Affiliation(s)
- Renato Corrêia Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Sabrina Rufino de Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Marcelo Salles Rocha
- Coordenação de Ciências Biológicas, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
| | | | | | | | | | - Elmary da Costa Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão (UEMA), Caxias, Brazil
| | - Jacqueline da Silva Batista
- Coordenação de Biodiversidade (COBIO), Laboratório Temático de Biologia Molecular (LTBM), Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
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10
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Grismer LL, Aowphol A, Grismer JL, Aksornneam A, Quah ESH, Murdoch ML, Gregory JJ, Nguyen E, Kaatz A, Bringsøe H, Rujirawan A. A new species of the Cyrtodactyluschauquangensis group (Squamata, Gekkonidae) from the borderlands of extreme northern Thailand. Zookeys 2024; 1203:211-238. [PMID: 38855793 PMCID: PMC11161685 DOI: 10.3897/zookeys.1203.122758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/03/2024] [Indexed: 06/11/2024] Open
Abstract
Phylogenetic and morphological analyses delimit and diagnose, respectively, a new population of a karst-dwelling Cyrtodactylus from extreme northern Thailand. The new species, Cyrtodactylusphamiensis sp. nov., of the chauquangensis group inhabits karst caves and outcroppings and karst vegetation in the vicinity of Pha Mi Village in Chiang Rai Province, Thailand. Within the chauquangensis group, Cyrtodactylusphamiensis sp. nov. is the earliest diverging species of a strongly supported clade composed of the granite-dwelling C.doisuthep and the karst-dwelling sister species Cyrtodactylus sp. 6 and C.erythrops. The nearly continuous karstic habitat between the type locality of Cyrtodactylusphamiensis sp. nov. and its close relatives Cyrtodactylus sp. 6 and C.erythrops, extends for approximately 200 km along the border region of Thailand and the eastern limit of the Shan Plateau of Myanmar. Further exploration of this region, especially the entire eastern ~ 95% of the Shan Plateau, will undoubtably recover new populations whose species status will need evaluation. As in all other countries of Indochina and northern Sundaland, the continual discovery of new karst-dwelling populations of Cyrtodactylus shows no signs of tapering off, even in relatively well-collected areas. This only highlights the conservation priority that these unique karstic landscapes still lack on a large scale across all of Asia.
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Affiliation(s)
- L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, California 92505, USALa Sierra UniversityRiversideUnited States of America
- Department of Herpetology, San Diego Natural History Museum, PO Box 121390, San Diego, California, 92112, USAUniversiti Malaysia SabahKota KinabaluMalaysia
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, MalaysiaSan Diego Natural History MuseumSan DiegoUnited States of America
| | - Anchalee Aowphol
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandKasetsart UniversityBangkokThailand
| | - Jesse L. Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, California 92505, USALa Sierra UniversityRiversideUnited States of America
| | - Akrachai Aksornneam
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandKasetsart UniversityBangkokThailand
| | - Evan S. H. Quah
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, MalaysiaSan Diego Natural History MuseumSan DiegoUnited States of America
- Biodiversity Center, Kasetsart University, Bangkok 10900, ThailandNational University of SingaporeSingaporeSingapore
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, 117377, SingaporeUniversiti Sains MalaysiaPenangMalaysia
| | - Matthew L. Murdoch
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, MalaysiaLa Sierra UniversityCaliforniaUnited States of America
| | - Jeren J. Gregory
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, MalaysiaLa Sierra UniversityCaliforniaUnited States of America
| | - Eddie Nguyen
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, MalaysiaLa Sierra UniversityCaliforniaUnited States of America
| | - Amanda Kaatz
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, MalaysiaLa Sierra UniversityCaliforniaUnited States of America
| | | | - Attapol Rujirawan
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandKasetsart UniversityBangkokThailand
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11
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Dixit NM, Guicking D. Exploring the evolutionary dynamics of myrmecophytism: Perspectives from the Southeast Asian Macaranga ant-plant symbiosis. Mol Phylogenet Evol 2024; 194:108028. [PMID: 38342161 DOI: 10.1016/j.ympev.2024.108028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Myrmecophytic plants utilise defensive services offered by obligate ant partners nesting in their domatia in a novel means of survival in tropical habitats. Although much is known about the ecology of myrmecophytism, there aren't enough empirical examples to demonstrate whether it substantially influences evolutionary patterns in host plant lineages. In this study, we make use of the species-rich Macaranga (Euphorbiaceae) ant-plant symbiosis distributed in the Southeast Asian Sundaland to delve into the evolutionary dynamics of myrmecophytism in host plants. We generated the most comprehensive dated phylogeny of myrmecophytic Macaranga till date using genotyping-by-sequencing (GBS). With this in hand, we traced the evolutionary history of myrmecophytism in Macaranga using parametric biogeography and ancestral state reconstruction. Diversification rate analysis methods were employed to determine if myrmecophytism enhanced diversification rates in the genus. Our results demonstrate that myrmecophytism is labile and easily lost. Ancestral state reconstruction supported a single origin of myrmecophytism in Macaranga ∼18 mya on Borneo followed by multiple losses. Diversification rate analysis methods did not yield sufficient evidence to support the hypothesis that myrmecophytism enhanced diversification rates in Macaranga; we found that topographical features on Borneo may have played a more direct role in the divergence of clades instead. Our study provides evidence that while the acquisition of domatia clearly functions as a key innovation that has enabled host plants to exploit the environment in novel ways, it may not necessarily enhance diversification rates. In fact, we hypothesise that overly specialised cases of myrmecophytism may even be an evolutionary dead end.
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Affiliation(s)
- Nadi M Dixit
- Department of Botany, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany.
| | - Daniela Guicking
- Department of Botany, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany.
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12
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Almeida-Silva D, Servino LM, Pontes-Nogueira M, Sawaya RJ. Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae). PeerJ 2024; 12:e17232. [PMID: 38646479 PMCID: PMC11027904 DOI: 10.7717/peerj.17232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
The species richness in the Neotropics has been linked to environmental heterogeneity and a complex geological history. We evaluated which biogeographic processes were associated with the diversification of Monkey tree frogs, an endemic clade from the Neotropics. We tested two competing hypotheses: the diversification of Phyllomedusinae occurred either in a "south-north" or a "north-south" direction in the Neotropics. We also hypothesized that marine introgressions and Andean uplift had a crucial role in promoting their diversification. We used 13 molecular markers in a Bayesian analysis to infer phylogenetic relationships among 57 species of Phyllomedusinae and to estimate their divergence times. We estimated ancestral ranges based on 12 biogeographic units considering the landscape modifications of the Neotropical region. We found that the Phyllomedusinae hypothetical ancestor range was probably widespread throughout South America, from Western Amazon to Southern Atlantic Forest, at 29.5 Mya. The Phyllomedusines' ancestor must have initially diverged through vicariance, generally followed by jump-dispersals and sympatric speciation. Dispersal among areas occurred mostly from Western Amazonia towards Northern Andes and the South American diagonal of dry landscapes, a divergent pattern from both "south-north" and "north-south" diversification hypotheses. Our results revealed a complex diversification process of Monkey tree frogs, occurring simultaneously with the orogeny of Northern Andes and the South American marine introgressions in the last 30 million years.
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Affiliation(s)
- Diego Almeida-Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- Miguel Lillo, Unidad Ejecutora Lillo, San Miguel de Tucumán, Tucumán, Argentina
| | - Leonardo Matheus Servino
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Matheus Pontes-Nogueira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | - Ricardo J. Sawaya
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
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13
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Mills KK, Hildebrandt KPB, Everson KM, Horstmann L, Misarti N, Olson LE. Ancient DNA indicates a century of overhunting did not reduce genetic diversity in Pacific Walruses (Odobenus rosmarus divergens). Sci Rep 2024; 14:8257. [PMID: 38589385 PMCID: PMC11001934 DOI: 10.1038/s41598-024-57414-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Pacific Walruses (Odobenus rosmarus divergens [Illiger 1815]) are gregarious marine mammals considered to be sentinels of the Arctic because of their dependence on sea ice for feeding, molting, and parturition. Like many other marine mammal species, their population sizes were decimated by historical overhunting in the nineteenth and twentieth centuries. Although they have since been protected from nearly all commercial hunting pressure, they now face rapidly accelerating habitat loss as global warming reduces the extent of summer sea ice in the Arctic. To investigate how genetic variation was impacted by overhunting, we obtained mitochondrial DNA sequences from historic Pacific Walrus samples in Alaska that predate the period of overhunting, as well as from extant populations. We found that genetic variation was unchanged over this period, suggesting Pacific Walruses are resilient to genetic attrition in response to reduced population size, and that this may be related to their high vagility and lack of population structure. Although Pacific Walruses will almost certainly continue to decline in number as the planet warms and summer sea ice is further reduced, they may be less susceptible to the ratcheting effects of inbreeding that typically accompany shrinking populations.
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Affiliation(s)
- Kendall K Mills
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA.
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - Kyndall P B Hildebrandt
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA
| | - Kathryn M Everson
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA
- Department of Integrative Biology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, 97331, USA
| | - Lara Horstmann
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Nicole Misarti
- Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Link E Olson
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA
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14
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Porta AO, Giribet G. A new genus of scutigerid centipede from southern South America with the description of two new species and an updated molecular phylogeny of the myriapod order Scutigeromorpha (Myriapoda: Chilopoda). INVERTEBR SYST 2024; 38:IS24006. [PMID: 38744498 DOI: 10.1071/is24006] [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: 01/07/2024] [Accepted: 03/12/2024] [Indexed: 05/16/2024]
Abstract
Scutigeromorph centipedes are conspicuous, yet often ignored myriapods for which little work has been conducted in southern South America. After examining recent and museum collections from Chile and Argentina, two new species of generic uncertainty were identified. A new genus of scutigerid centipede, Edgethreua , is therefore described with two new species, E. chilensis from Central Chile (type species of the genus) and E. goloboffi from Argentinian Patagonia. The new genus is characterised by the presence of scattered setiform bristles with short paired spines and the absence of simple spinulae and spines on all stomatotergites, the presence of a single spine-bristle in the prefemur of the second maxilla, a patch of cuticular ridges and pores surrounding the sensilla of the proximal labral portion of the epipharynx, the morphology of the sensilla of the distal patch of the hypopharynx and the morphology of the female gonopods. A phylogenetic analysis of the new species using two nuclear ribosomal RNA genes (18S and 28S rRNA), two mitochondrial ribosomal RNA genes (12S and 16S rRNA) and the mitochondrial protein-encoding gene cytochrome c oxidase subunit I show that the new genus does not cluster with any other described genus of scutigeromorph represented in molecular phylogenies. The data indicate that the new genus is probably sister group to a clade including the genera Lassophora , Ballonema and the subfamily Thereuoneminae, although one analysis suggests a position as sister group to Scutigerinae. ZooBank: urn:lsid:zoobank.org:pub:A4D453F3-9031-4E21-84C7-87F16C07AD51.
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Affiliation(s)
- Andrés O Porta
- División de Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Avenida Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina; and Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, UBA-CONICET), Pabellón II, Ciudad Universitaria, Buenos Aires, C1428EGA, Argentina; and Departamento de Ciencias Exactas, Universidad Nacional del Oeste, Belgrano 369 C1718, San Antonio de Padua, Buenos Aires, Argentina
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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15
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Jablonski D, Mebert K, Masroor R, Simonov E, Kukushkin O, Abduraupov T, Hofmann S. The Silk roads: phylogeography of Central Asian dice snakes (Serpentes: Natricidae) shaped by rivers in deserts and mountain valleys. Curr Zool 2024; 70:150-162. [PMID: 38726254 PMCID: PMC11078056 DOI: 10.1093/cz/zoad008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/02/2023] [Indexed: 05/12/2024] Open
Abstract
Influenced by rapid changes in climate and landscape features since the Miocene, widely distributed species provide suitable models to study the environmental impact on their evolution and current genetic diversity. The dice snake Natrix tessellata, widely distributed in the Western Palearctic is one such species. We aimed to resolve a detailed phylogeography of N. tessellata with a focus on the Central Asian clade with 4 and the Anatolia clade with 3 mitochondrial lineages, trace their origin, and correlate the environmental changes that affected their distribution through time. The expected time of divergence of both clades began at 3.7 Mya in the Pliocene, reaching lineage differentiation approximately 1 million years later. The genetic diversity in both clades is rich, suggesting different ancestral areas, glacial refugia, demographic changes, and colonization routes. The Caspian lineage is the most widespread lineage in Central Asia, distributed around the Caspian Sea and reaching the foothills of the Hindu Kush Mountains in Afghanistan, and Eastern European lowlands in the west. Its distribution is limited by deserts, mountains, and cold steppe environments. Similarly, Kazakhstan and Uzbekistan lineages followed the Amu Darya and the Syr Darya water systems in Central Asia, with ranges delimited by the large Kyzylkum and Karakum deserts. On the western side, there are several lineages within the Anatolia clade that converged in the central part of the peninsula with 2 being endemic to Western Asia. The distribution of both main clades was affected by expansion from their Pleistocene glacial refugia around the Caspian Sea and in the valleys of Central Asia as well as by environmental changes, mostly through aridification.
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Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Rafaqat Masroor
- Pakistan Museum of Natural History, Shakarparian, Islamabad, Pakistan
| | - Evgeniy Simonov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Oleg Kukushkin
- T. I. Vyazemski Karadag Scientific Station—Nature Reserve—Branch of A.O. Kovalevsky Institute of Biology of the Southern Seas, Theodosia, Crimea
- Zoological Institute of the RAS, Saint Petersbourg, Russia
| | - Timur Abduraupov
- Institute of Zoology, Academy of Sciences of the Republic of Uzbekistan, Yunusabad, Tashkent, Uzbekistan
| | - Sylvia Hofmann
- Museum Koenig Bonn, LIB—Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- UFZ – Helmholtz Centre for Environmental Research, Department of Conservation Biology, Permoserstrasse 15, 04318 Leipzig, Germany
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16
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Ulrich S, Vieira M, Coiro M, Bouchal JM, Geier C, Jacobs BF, Currano ED, Lenz OK, Wilde V, Zetter R, Grímsson F. Origin and Early Evolution of Hydrocharitaceae and the Ancestral Role of Stratiotes. PLANTS (BASEL, SWITZERLAND) 2024; 13:1008. [PMID: 38611537 PMCID: PMC11013807 DOI: 10.3390/plants13071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
The combined morphological features of Stratiotes (Hydrocharitaceae) pollen, observed with light and electron microscopy, make it unique among all angiosperm pollen types and easy to identify. Unfortunately, the plant is (and most likely was) insect-pollinated and produces relatively few pollen grains per flower, contributing to its apparent absence in the paleopalynological record. Here, we present fossil Stratiotes pollen from the Eocene of Germany (Europe) and Kenya (Africa), representing the first reliable pre-Pleistocene pollen records of this genus worldwide and the only fossils of this family discovered so far in Africa. The fossil Stratiotes pollen grains are described and compared to pollen from a single modern species, Stratiotes aloides L. The paleophytogeographic significance and paleoecological aspects of these findings are discussed in relation to the Hydrocharitaceae fossil records and molecular phylogeny, as well as the present-day distribution patterns of its modern genera.
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Affiliation(s)
- Silvia Ulrich
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
- Department of Historical Archaeology, Austrian Archaeological Institute (OeAI), Austrian Academy of Sciences (OeAW), 1010 Vienna, Austria
| | - Manuel Vieira
- Department of Earth Sciences, GeoBioTec, NOVA School of Science and Technology, Campus de Caparica, 2829-516 Caparica, Portugal;
| | - Mario Coiro
- Department of Palaeontology, University of Vienna, 1090 Vienna, Austria
| | - Johannes M. Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Christian Geier
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Bonnie F. Jacobs
- Roy M. Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA;
| | - Ellen D. Currano
- Departments of Botany and Geology & Geophysics, University of Wyoming, Laramie, WY 82071, USA;
| | - Olaf K. Lenz
- Institute of Applied Geosciences, Technical University Darmstadt, 64287 Darmstadt, Germany;
| | - Volker Wilde
- Section Palaeobotany, Division Palaeontology and Historical Geology, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany;
| | - Reinhard Zetter
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Friðgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
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17
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Zhao W, Gao J, Hall D, Andersson BA, Bruxaux J, Tomlinson KW, Drouzas AD, Suyama Y, Wang XR. Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. THE NEW PHYTOLOGIST 2024. [PMID: 38515228 DOI: 10.1111/nph.19694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.
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Affiliation(s)
- Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - David Hall
- Forestry Research Institute of Sweden (Skogforsk), Sävar, SE-91833, Sweden
| | - Bea Angelica Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Kyle W Tomlinson
- Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephant, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, 989-6711, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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18
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Luo Z, McTaggart A, Schwessinger B. Genome biology and evolution of mating-type loci in four cereal rust fungi. PLoS Genet 2024; 20:e1011207. [PMID: 38498573 PMCID: PMC10977897 DOI: 10.1371/journal.pgen.1011207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 03/28/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Permanent heterozygous loci, such as sex- or mating-compatibility regions, often display suppression of recombination and signals of genomic degeneration. In Basidiomycota, two distinct loci confer mating compatibility. These loci encode homeodomain (HD) transcription factors and pheromone receptor (Pra)-ligand allele pairs. To date, an analysis of genome level mating-type (MAT) loci is lacking for obligate biotrophic basidiomycetes in the Pucciniales, an order containing serious agricultural plant pathogens. Here, we focus on four species of Puccinia that infect oat and wheat, including P. coronata f. sp. avenae, P. graminis f. sp. tritici, P. triticina and P. striiformis f. sp. tritici. MAT loci are located on two separate chromosomes supporting previous hypotheses of a tetrapolar mating compatibility system in the Pucciniales. The HD genes are multiallelic in all four species while the PR locus appears biallelic, except for P. graminis f. sp. tritici, which potentially has multiple alleles. HD loci are largely conserved in their macrosynteny, both within and between species, without strong signals of recombination suppression. Regions proximal to the PR locus, however, displayed signs of recombination suppression and genomic degeneration in the three species with a biallelic PR locus. Our observations support a link between recombination suppression, genomic degeneration, and allele diversity of MAT loci that is consistent with recent mathematical modelling and simulations. Finally, we confirm that MAT genes are expressed during the asexual infection cycle, and we propose that this may support regulating nuclear maintenance and pairing during infection and spore formation. Our study provides insights into the evolution of MAT loci of key pathogenic Puccinia species. Understanding mating compatibility can help predict possible combinations of nuclear pairs, generated by sexual reproduction or somatic recombination, and the potential evolution of new virulent isolates of these important plant pathogens.
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Affiliation(s)
- Zhenyan Luo
- Research Biology School, Australian National University, Canberra, ACT, Australia
| | - Alistair McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, Queensland, Australia
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19
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Jackson I, Woodman P, Dowd M, Fibiger L, Cassidy LM. Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts. Mol Biol Evol 2024; 41:msae017. [PMID: 38533900 DOI: 10.1093/molbev/msae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 03/28/2024] Open
Abstract
Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.
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Affiliation(s)
- Iseult Jackson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, Ireland
| | - Peter Woodman
- Department of Archaeology, University College Cork, Cork, Ireland
| | - Marion Dowd
- Faculty of Science, Atlantic Technological University, Sligo, Ireland
| | - Linda Fibiger
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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20
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Rayos AL, Renner MAM, Ho SYW. The Neotropical endemic liverwort subfamily Micropterygioideae had circum-Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous. Ecol Evol 2024; 14:e11066. [PMID: 38435016 PMCID: PMC10909501 DOI: 10.1002/ece3.11066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal-vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157-240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American-Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum-Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present-day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.
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Affiliation(s)
- Antonio L Rayos
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
- Institute of Biological Sciences University of the Philippines Los Baños Los Baños Laguna Philippines
| | - Matthew A M Renner
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
- National Herbarium of New South Wales Royal Botanic Gardens Sydney Sydney New South Wales Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
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21
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Mannen K, Nagata T, Rozenberg A, Konno M, Del Carmen Marín M, Bagherzadeh R, Béjà O, Uchihashi T, Inoue K. Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical Properties in a New Group of Microbial Rhodopsins Homologous to TAT Rhodopsin. J Mol Biol 2024; 436:168331. [PMID: 37898385 DOI: 10.1016/j.jmb.2023.168331] [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: 08/17/2023] [Revised: 10/02/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
TAT rhodopsin, a microbial rhodopsin found in the marine SAR11 bacterium HIMB114, uniquely possesses a Thr-Ala-Thr (TAT) motif in the third transmembrane helix. Because of a low pKa value of the retinal Schiff base (RSB), TAT rhodopsin exhibits both a visible light-absorbing state with the protonated RSB and a UV-absorbing state with the deprotonated RSB at a neutral pH. The UV-absorbing state, in contrast to the visible light-absorbing one, converts to a long-lived photointermediate upon light absorption, implying that TAT rhodopsin functions as a pH-dependent light sensor. Despite detailed biophysical characterization and mechanistic studies on the TAT rhodopsin, it has been unknown whether other proteins with similarly unusual features exist. Here, we identified several new rhodopsin genes homologous to the TAT rhodopsin of HIMB114 (TATHIMB) from metagenomic data. Based on the absorption spectra of expressed proteins from these genes with visible and UV peaks similar to that of TATHIMB, they were classified as Twin-peaked Rhodopsin (TwR) family. TwR genes form a gene cluster with a set of 13 ORFs conserved in subclade IIIa of SAR11 bacteria. A glutamic acid in the second transmembrane helix, Glu54, is conserved in all of the TwRs. We investigated E54Q mutants of two TwRs and revealed that Glu54 plays critical roles in regulating the RSB pKa, oligomer formation, and the efficient photoreaction of the UV-absorbing state. The discovery of novel TwRs enables us to study the universality and individuality of the characteristics revealed so far in the original TATHIMB and contributes to further studies on mechanisms of unique properties of TwRs.
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Affiliation(s)
- Kentaro Mannen
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - María Del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Reza Bagherzadeh
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan; Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Institute for Glyco-core Research, Nagoya University, Nagoya 464-8602, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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22
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Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy Z, Baharuddin B, Bakonyi J, Broders K, Cacciola S, Chang TT, Chi N, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu CH, Garcia L, Hieno A, Ho HH, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira L, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu P, Tomić Z, Tomšovský M, Uematsu S, Webber J, Zeng HC, Zheng FC, Brasier C, Horta Jung M. Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Stud Mycol 2024; 107:251-388. [PMID: 38600961 PMCID: PMC11003442 DOI: 10.3114/sim.2024.107.04] [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: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 04/12/2024] Open
Abstract
During 25 surveys of global Phytophthora diversity, conducted between 1998 and 2020, 43 new species were detected in natural ecosystems and, occasionally, in nurseries and outplantings in Europe, Southeast and East Asia and the Americas. Based on a multigene phylogeny of nine nuclear and four mitochondrial gene regions they were assigned to five of the six known subclades, 2a-c, e and f, of Phytophthora major Clade 2 and the new subclade 2g. The evolutionary history of the Clade appears to have involved the pre-Gondwanan divergence of three extant subclades, 2c, 2e and 2f, all having disjunct natural distributions on separate continents and comprising species with a soilborne and aquatic lifestyle and, in addition, a few partially aerial species in Clade 2c; and the post-Gondwanan evolution of subclades 2a and 2g in Southeast/East Asia and 2b in South America, respectively, from their common ancestor. Species in Clade 2g are soilborne whereas Clade 2b comprises both soil-inhabiting and aerial species. Clade 2a has evolved further towards an aerial lifestyle comprising only species which are predominantly or partially airborne. Based on high nuclear heterozygosity levels ca. 38 % of the taxa in Clades 2a and 2b could be some form of hybrid, and the hybridity may be favoured by an A1/A2 breeding system and an aerial life style. Circumstantial evidence suggests the now 93 described species and informally designated taxa in Clade 2 result from both allopatric non-adaptive and sympatric adaptive radiations. They represent most morphological and physiological characters, breeding systems, lifestyles and forms of host specialism found across the Phytophthora clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single Phytophthora clade highlight a critical lack of information on the scale of the unknown pathogen threats to forests and natural ecosystems, underlining the risk of basing plant biosecurity protocols mainly on lists of named organisms. More surveys in natural ecosystems of yet unsurveyed regions in Africa, Asia, Central and South America are needed to unveil the full diversity of the clade and the factors driving diversity, speciation and adaptation in Phytophthora. Taxonomic novelties: New species: Phytophthora amamensis T. Jung, K. Kageyama, H. Masuya & S. Uematsu, Phytophthora angustata T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, Phytophthora balkanensis I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, Phytophthora borneensis T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora calidophila T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora catenulata T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora celeris T. Jung, L. Oliveira, M. Tarigan & I. Milenković, Phytophthora curvata T. Jung, A. Hieno, H. Masuya & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung, Phytophthora excentrica T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora falcata T. Jung, K. Kageyama, S. Uematsu & M. Horta Jung, Phytophthora fansipanensis T. Jung, N.M. Chi, T. Corcobado & C.M. Brasier, Phytophthora frigidophila T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora furcata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora inclinata N.M. Chi, T. Jung, M. Horta Jung & I. Milenković, Phytophthora indonesiensis T. Jung, M. Tarigan, L. Oliveira & I. Milenković, Phytophthora japonensis T. Jung, A. Hieno, H. Masuya & J.F. Webber, Phytophthora limosa T. Corcobado, T. Majek, M. Ferreira & T. Jung, Phytophthora macroglobulosa H.-C. Zeng, H.-H. Ho, F.-C. Zheng & T. Jung, Phytophthora montana T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multipapillata T. Jung, M. Tarigan, I. Milenković & M. Horta Jung, Phytophthora multiplex T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora nimia T. Jung, H. Masuya, A. Hieno & C.M. Brasier, Phytophthora oblonga T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora obovoidea T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora obturata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora penetrans T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora platani T. Jung, A. Pérez-Sierra, S.O. Cacciola & M. Horta Jung, Phytophthora proliferata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora pseudocapensis T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pseudocitrophthora T. Jung, S.O. Cacciola, J. Bakonyi & M. Horta Jung, Phytophthora pseudofrigida T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora pseudoccultans T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pyriformis T. Jung, Y. Balci, K.D. Boders & M. Horta Jung, Phytophthora sumatera T. Jung, M. Tarigan, M. Junaid & A. Durán, Phytophthora transposita T. Jung, K. Kageyama, C.M. Brasier & H. Masuya, Phytophthora vacuola T. Jung, H. Masuya, K. Kageyama & J.F. Webber, Phytophthora valdiviana T. Jung, E. Sanfuentes von Stowasser, A. Durán & M. Horta Jung, Phytophthora variepedicellata T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora vietnamensis T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora ×australasiatica T. Jung, N.M. Chi, M. Tarigan & M. Horta Jung, Phytophthora ×lusitanica T. Jung, M. Horta Jung, C. Maia & I. Milenković, Phytophthora ×taiwanensis T. Jung, T.-T. Chang, H.-S. Fu & M. Horta Jung. Citation: Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy ZÁ, Baharuddin B, Bakonyi J, Broders KD, Cacciola SO, Chang T-T, Chi NM, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu C-H, Garcia L, Hieno A, Ho H-H, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira LSS, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu PQ, Tomić Z, Tomšovský M, Uematsu S, Webber JF, Zeng H-C, Zheng F-C, Brasier CM, Horta Jung M (2024). Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Studies in Mycology 107: 251-388. doi: 10.3114/sim.2024.107.04.
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Affiliation(s)
- T. Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
| | - I. Milenković
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Belgrade, Faculty of Forestry, 11030 Belgrade, Serbia
| | - Y. Balci
- USDA-APHIS Plant Protection and Quarantine, 4700 River Road, Riverdale, Maryland, 20737 USA
| | - J. Janoušek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - T. Kudláček
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Greifswald, Institute for Mathematics and Computer Science & Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Z.Á. Nagy
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - B. Baharuddin
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - J. Bakonyi
- HUN-REN Centre for Agricultural Research, Plant Protection Institute, ELKH, 1022 Budapest, Hungary
| | - K.D. Broders
- Smithsonian Tropical Research Institute, Apartado Panamá, República de Panamá
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, 61604, USA
| | - S.O. Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - T.-T. Chang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - N.M. Chi
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - T. Corcobado
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Cravador
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, University of Algarve, 8005-130 Faro, Portugal
| | - B. Đorđević
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Durán
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - M. Ferreira
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - C.-H. Fu
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - L. Garcia
- Universidad Nacional Agraria, Carretera Norte, Managua 11065, Nicaragua
| | - A. Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - H.-H. Ho
- Department of Biology, State University of New York, New Paltz, New York 12561, USA
| | - C. Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| | - M. Junaid
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - K. Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - T. Kuswinanti
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - C. Maia
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
| | - T. Májek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - H. Masuya
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, 305-8687, Japan
| | - G. Magnano di San Lio
- University Mediterranea of Reggio Calabria, Department of Agriculture, 89124 Reggio Calabria, Italy
| | | | - N. Nasri
- The United Graduate School of Agricultural Science, Ehime University, Matsuyama, 790-8566, Japan
| | - L.S.S. Oliveira
- Research and Development, Bracell, Alagoinhas, Bahia 48030-300, Brazil
| | - A. Pane
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - A. Pérez-Sierra
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - A. Rosmana
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - E. Sanfuentes von Stowasser
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de Biotecnología, Universidad de Concepción, 4030000 Concepción, Chile
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39A, 07100 Sassari, Italy
| | - R. Singh
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Z. Stanivuković
- University of Banja Luka, Faculty of Forestry, 78000 Banja Luka, Bosnia and Herzegovina
| | - M. Tarigan
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - P.Q. Thu
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - Z. Tomić
- Center for Plant Protection, Croatian Agency for Agriculture and Food, 10000 Zagreb, Croatia
| | - M. Tomšovský
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - S. Uematsu
- Laboratory of Molecular and Cellular Biology, Dept. of Bioregulation and Bio-interaction, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - J.F. Webber
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - H.-C. Zeng
- The Institute of Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
| | - F.-C. Zheng
- College of Environment and Plant Protection, Hainan University, Baodoa Xincun, Danzhou City, Hainan 571737, China
| | - C.M. Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - M. Horta Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
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23
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Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
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Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
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24
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Hu J, Zhao J, Sui X, Zhu R, He D. Across the highest mountain on earth: discordant phylogeographic patterns and recent dispersal of Tibetan stone loaches (Triplophysa) in the Himalayas. JOURNAL OF FISH BIOLOGY 2024; 104:374-386. [PMID: 36571395 DOI: 10.1111/jfb.15296] [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: 10/23/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Phylogeographic congruence among co-distributed taxa is regarded as an inherent inference to vicariance events. Nonetheless, incongruent patterns of contemporary lineage divergence among taxa indicated that species differ in their response to common past events. To investigate the role of past events, ecological traits and lineage diversification time in shaping the contemporary phylogeographic patterns, comparative analyses were conducted for Tibetan stone loaches in the Himalayas using three gene markers and two ecological traits (depth of caudal peduncle in their length and presence/absence of posterior chamber of the air bladder). By a thorough sampling in two flanks of the Himalayas, the authors detected that phylogenetic breaks were spatially discordant and divergences of populations were also temporally asynchronous in co-distributed loaches. Estimated divergence time using fossil-calibrated node dating indicated that the Tibetan stone loaches colonised into the south flank of the Himalayas until the Pleistocene. The demographic expansions were also disconcerted between populations in north and south flanks, or east and west Himalayas. Ongoing gene flows between populations in north and south sides implied that the Himalayas do not strictly impede dispersal of cold-adapted species. The results highlight that the quaternary climatic oscillation, in conjunction with ecological traits and lineage diversification time, shaped contemporary phylogenetic patterns of stone loaches in the Himalayas and provide new insights into the biodiversity and composition of species in the Himalayas and surrounding region.
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Affiliation(s)
- Jiaxin Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoyun Sui
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ren Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Dekui He
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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25
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Dowle EJ, Trewick SA, Morgan-Richards M. Fossil-calibrated phylogenies of Southern cave wētā show dispersal and extinction confound biogeographic signal. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231118. [PMID: 38356874 PMCID: PMC10864783 DOI: 10.1098/rsos.231118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
The biota of continents and islands are commonly considered to have a source-sink relationship, but small islands can harbour distinctive taxa. The distribution of four monotypic genera of Orthoptera on young subantarctic islands indicates a role for long-distance dispersal and extinction. Phylogenetic relationships were inferred from whole mtDNA genomes and nuclear sequences (45S cassette; four histones). We used a fossil and one palaeogeographic event to calibrate molecular clock analysis. We confirm that neither the Australian nor Aotearoa-New Zealand Rhaphidophoridae faunas are monophyletic. The radiation of Macropathinae may have begun in the late Jurassic, but trans-oceanic dispersal is required to explain the current distribution of some lineages within this subfamily. Dating the most recent common ancestor of seven island endemic species with their nearest mainland relative suggests that each existed long before their island home was available. Time estimates from our fossil-calibrated molecular clock analysis suggest several lineages have not been detected on mainland New Zealand, Australia, or elsewhere most probably due to their extinction, providing evidence that patterns of extinction, which are not consistently linked to range size or lineage age, confound biogeographic signal.
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Affiliation(s)
- Eddy J. Dowle
- Department of Anatomy, University of Otago, 9016 Dunedin, New Zealand
| | - Steven A. Trewick
- Ecology, School of Natural Sciences, Massey University Manawatū, Private Bag 11 222, Palmerston North 4410, New Zealand
| | - Mary Morgan-Richards
- Ecology, School of Natural Sciences, Massey University Manawatū, Private Bag 11 222, Palmerston North 4410, New Zealand
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26
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Delicado D, Hauffe T, Wilke T. Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae). Cladistics 2024; 40:82-96. [PMID: 37712584 DOI: 10.1111/cla.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
The fifth mass extinction event (MEE) at the Cretaceous-Palaeogene (K-Pg) boundary 66 million years ago (Ma) led to massive species loss but also triggered the diversification of higher taxa. Five models have been proposed depending on whether this diversification occurred before, during or after the K-Pg boundary and the rate of species accumulation. While the effects of the K-Pg MEE on vertebrate evolution are relatively well understood, the impact on invertebrates, particularly in freshwater ecosystems, remains controversial. One example is the hyperdiverse Hydrobiidae-the most species-rich family of freshwater gastropods. Whereas some studies place its origin in the Jurassic or even Carboniferous, most fossil records postdate the K-Pg event. We therefore used robustly time-calibrated multi-locus phylogenies of >400 species representing >100 hydrobiid genera to unravel its evolutionary history and patterns of diversification. We found that the family started diversifying shortly after the K-Pg boundary (∼60 Ma; 95% highest posterior density 52-69 Ma). Lineage richness gradually increased to the present and phylogenetic diversity until ∼25 Ma. These findings suggest that diversification was not initially driven by ecological opportunity. Combining the two criteria of timing and rate of diversification, a soft-explosive diversification model of aquatic vertebrates best fits the patterns observed. We also show that most higher hydrobiid taxa (i.e. subfamilies) diversified from the Middle Oligocene to Middle Miocene (i.e. 12-28 Ma). Two of the 15 major clades delimited are described here as new subfamilies (i.e. Bullaregiinae n. subfam. and Pontobelgrandiellinae n. subfam.), whose members are restricted to subterranean waters. Our results are an important contribution to understanding how the fifth MEE has shaped evolution and patterns of biodiversity in continental aquatic systems. Given the high extinction risks faced by many hydrobiids today, they also emphasise the need to study the biodiversity of vulnerable ecosystems.
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Affiliation(s)
- Diana Delicado
- Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392, Giessen, Germany
| | - Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Thomas Wilke
- Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392, Giessen, Germany
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27
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Rowe AG, Bataille CP, Baleka S, Combs EA, Crass BA, Fisher DC, Ghosh S, Holmes CE, Krasinski KE, Lanoë F, Murchie TJ, Poinar H, Potter B, Rasic JT, Reuther J, Smith GM, Spaleta KJ, Wygal BT, Wooller MJ. A female woolly mammoth's lifetime movements end in an ancient Alaskan hunter-gatherer camp. SCIENCE ADVANCES 2024; 10:eadk0818. [PMID: 38232155 DOI: 10.1126/sciadv.adk0818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
Woolly mammoths in mainland Alaska overlapped with the region's first people for at least a millennium. However, it is unclear how mammoths used the space shared with people. Here, we use detailed isotopic analyses of a female mammoth tusk found in a 14,000-year-old archaeological site to show that she moved ~1000 kilometers from northwestern Canada to inhabit an area with the highest density of early archaeological sites in interior Alaska until her death. DNA from the tusk and other local contemporaneous archaeological mammoth remains revealed that multiple mammoth herds congregated in this region. Early Alaskans seem to have structured their settlements partly based on mammoth prevalence and made use of mammoths for raw materials and likely food.
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Affiliation(s)
- Audrey G Rowe
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
- Department of Marine Biology, University of Alaska Fairbanks, AK, USA
| | - Clement P Bataille
- Department of Earth and Environmental Sciences, University of Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ontario, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | | | - Barbara A Crass
- University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Daniel C Fisher
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
| | - Sambit Ghosh
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
| | - Charles E Holmes
- Department of Anthropology, University of Alaska Fairbanks, AK, USA
| | | | - François Lanoë
- Bureau of Applied Research in Anthropology, University of Arizona, Tucson, AZ, USA
| | - Tyler J Murchie
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Departments of Biochemistry and Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ben Potter
- Department of Anthropology, University of Alaska Fairbanks, AK, USA
| | | | - Joshua Reuther
- University of Alaska Museum of the North, Fairbanks, AK, USA
- Department of Anthropology, University of Alaska Fairbanks, AK, USA
| | - Gerad M Smith
- Department of Anthropology and Geography, University of Alaska Anchorage, AK, USA
| | - Karen J Spaleta
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
| | - Brian T Wygal
- Department of Anthropology, Adelphi University, Garden City, NY, USA
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
- Department of Marine Biology, University of Alaska Fairbanks, AK, USA
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28
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Esquivel Gomez LR, Weber A, Kocher A, Kühnert D. Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2. Sci Rep 2024; 14:541. [PMID: 38177346 PMCID: PMC10766966 DOI: 10.1038/s41598-023-50952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
SARS-CoV-2 can infect human cells through the recognition of the human angiotensin-converting enzyme 2 receptor. This affinity is given by six amino acid residues located in the variable loop of the receptor binding domain (RBD) within the Spike protein. Genetic recombination involving bat and pangolin Sarbecoviruses, and natural selection have been proposed as possible explanations for the acquisition of the variable loop and these amino acid residues. In this study we employed Bayesian phylogenetics to jointly reconstruct the phylogeny of the RBD among human, bat and pangolin Sarbecoviruses and detect recombination events affecting this region of the genome. A recombination event involving RaTG13, the closest relative of SARS-CoV-2 that lacks five of the six residues, and an unsampled Sarbecovirus lineage was detected. This result suggests that the variable loop of the RBD didn't have a recombinant origin and the key amino acid residues were likely present in the common ancestor of SARS-CoV-2 and RaTG13, with the latter losing five of them probably as the result of recombination.
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Affiliation(s)
- Luis Roger Esquivel Gomez
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany.
| | - Ariane Weber
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany.
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29
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Magalhães RF, K S Ramos E, Bandeira LN, Ferreira JS, Werneck FP, Anciães M, Bruschi DP. Integrative species delimitation uncovers hidden diversity within the Pithecopus hypochondrialis species complex (Hylidae, Phyllomedusinae) and its phylogeography reveals Plio-Pleistocene connectivity among Neotropical savannas. Mol Phylogenet Evol 2024; 190:107959. [PMID: 37918682 DOI: 10.1016/j.ympev.2023.107959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Despite their limited vagility and pronounced habitat heterogeneity in the tropics, many anuran species have unexpectedly extensive geographic ranges. One prominent example of this phenomenon is Pithecopus hypochondrialis, which is found in the Cerrado, Guianan savanna, and Llanos domains, as well as isolated tracts of savanna and open habitat within the Amazon Forest. The present study employs an integrative species delimitation approach to test the hypothesis that P. hypochondrialis is in fact a species complex. We also reconstruct the relationships among the lineages delimited here and other Pithecopus species. In this study, we employ Ecological Niche Modelling (ENM) and spatiotemporal phylogeographic reconstruction approaches to evaluate a multitude of scenarios of connectivity across the Neotropical savannas. We identified three divergent lineages, two of which have been described previously. The lineages were allocated to a lowland Pithecopus clade, although the relationships among these lineages are weakly supported. Both the ENM and the phylogeographic reconstruction highlight the occurrence of periods of connectivity among the Neotropical savannas over the course of the Pliocene and Pleistocene epochs. These processes extended from eastern Amazonia to the northern coast of Brazil. The findings of the present study highlight the presence of hidden diversity within P. hypochondrialis, and reinforce the need for a comprehensive taxonomic review. These findings also indicate intricate and highly dynamic patterns of connectivity across the Neotropical savannas that date back to the Pliocene.
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Affiliation(s)
- Rafael F Magalhães
- Department of Natural Sciences, Universidade Federal de São João del-Rei, Campus Dom Bosco, Praça Dom Helvécio, 70, São João del-Rei, MG 36301-160, Brazil; Postgraduate Programme in Zoology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG 31270-010, Brazil.
| | - Elisa K S Ramos
- Faculty of Philosophy and Natural Sciences, Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, Basel 4056, Switzerland.
| | - Lucas N Bandeira
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Johnny S Ferreira
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
| | - Fernanda P Werneck
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Marina Anciães
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Daniel P Bruschi
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
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30
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Winn JC, Maduna SN, Bester-van der Merwe AE. A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae. Genomics 2024; 116:110771. [PMID: 38147941 DOI: 10.1016/j.ygeno.2023.110771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023]
Abstract
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.
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Affiliation(s)
- Jessica C Winn
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa
| | - Simo N Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa.
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31
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Bickerstaff JRM, Jordal BH, Riegler M. Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia. Heredity (Edinb) 2024; 132:43-53. [PMID: 37949964 PMCID: PMC10798974 DOI: 10.1038/s41437-023-00659-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Sympatric lineages of inbreeding species provide an excellent opportunity to investigate species divergence patterns and processes. Many ambrosia beetle lineages (Curculionidae: Scolytinae) reproduce by predominant inbreeding through sib mating in nests excavated in woody plant parts wherein they cultivate symbiotic ambrosia fungi as their sole source of nutrition. The Xyleborini ambrosia beetle species Cnestus solidus and Cnestus pseudosolidus are sympatrically distributed across eastern Australia and have overlapping morphological variation. Using multilocus sequencing analysis of individuals collected from 19 sites spanning their sympatric distribution, we assessed their phylogenetic relationships, taxonomic status and microbial symbionts. We found no genetic differentiation between individuals morphologically identified as C. solidus and C. pseudosolidus confirming previous suggestions that C. pseudosolidus is synonymous to C. solidus. However, within C. solidus we unexpectedly discovered the sympatric coexistence of two morphologically indistinguishable but genetically distinct lineages with small nuclear yet large mitochondrial divergence. At all sites except one, individuals of both lineages carried the same primary fungal symbiont, a new Ambrosiella species, indicating that fungal symbiont differentiation may not be involved in lineage divergence. One strain of the maternally inherited bacterial endosymbiont Wolbachia was found at high prevalence in individuals of the more common lineage but not in the other, suggesting that it may influence host fitness. Our data suggest that the two Australian Cnestus lineages diverged allopatrically, and one lineage then acquired Wolbachia. Predominant inbreeding and Wolbachia infection may have reinforced reproductive barriers between these two lineages after their secondary contact contributing to their current sympatric distribution.
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Affiliation(s)
- James R M Bickerstaff
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia.
| | - Bjarte H Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, NO-5020, Bergen, Norway
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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32
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Núñez-Flores M, Solórzano A, Avaria-Llautureo J, Gomez-Uchida D, López-González PJ. Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum. Mol Phylogenet Evol 2024; 190:107945. [PMID: 37863452 DOI: 10.1016/j.ympev.2023.107945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.
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Affiliation(s)
- Mónica Núñez-Flores
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca, Chile; Laboratorio Ecología de Abejas, Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile.
| | - Andrés Solórzano
- Escuela de Geología, Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile
| | | | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution, and Conservation Laboratory (GEECLAB), Department of Zoology, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Pablo J López-González
- Biodiversidad y Ecología Acuática. Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Reina Mercedes 6, 41012 Sevilla, Spain
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Németh A, Mizsei E, Laczkó L, Czabán D, Hegyeli Z, Lengyel S, Csorba G, Sramkó G. Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group. Mol Phylogenet Evol 2024; 190:107958. [PMID: 37914032 DOI: 10.1016/j.ympev.2023.107958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
Species delimitation is a powerful approach to assist taxonomic decisions in challenging taxa where species boundaries are hard to establish. European taxa of the blind mole rats (genus Nannospalax) display small morphological differences and complex chromosomal evolution at a shallow evolutionary divergence level. Previous analyses led to the recognition of 25 'forms' in their distribution area. We provide a comprehensive framework to improve knowledge on the evolutionary history and revise the taxonomy of European blind mole rats based on samples from all but three of the 25 forms. We sequenced two nuclear-encoded genetic regions and the whole mitochondrial cytochrome b gene for phylogenetic tree reconstructions using concatenation and coalescence-based species-tree estimations. The phylogenetic analyses confirmed that Aegean N. insularis belongs to N. superspecies xanthodon, and that it represents the second known species of this superspecies in Europe. Mainland taxa reached Europe from Asia Minor in two colonisation events corresponding to two superspecies-level taxa: N. superspecies monticola (taxon established herewith) reached Europe c. 2.1 million years ago (Mya) and was followed by N. superspecies leucodon (re-defined herewith) c. 1.5 Mya. Species delimitation allowed the clarification of the taxonomic contents of the above superspecies. N. superspecies monticola contains three species geographically confined to the western periphery of the distribution of blind mole rats, whereas N. superspecies leucodon is more speciose with six species and several additional subspecies. The observed geographic pattern hints at a robust peripatric speciation process and rapid chromosomal evolution. The present treatment is thus regarded as the minimum taxonomic content of each lineage, which can be further refined based on other sources of information such as karyological traits, crossbreeding experiments, etc. The species delimitation models also allowed the recognition of a hitherto unnamed blind mole rat taxon from Albania, described here as a new subspecies.
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Affiliation(s)
- Attila Németh
- Department of Nature Conservation, Zoology and Game Management, University of Debrecen, Böszörményi u. 138, H-4032 Debrecen, Hungary; BirdLife Hungary - Hungarian Ornithological and Nature Conservation Society, Költő u. 21, H-1121 Budapest, Hungary
| | - Edvárd Mizsei
- Department of Ecology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; DRI Conservation Ecology Research Group, Centre for Ecological Research, Hungarian Academy of Sciences, Bem tér 18/C, H-4026 Debrecen, Hungary
| | - Levente Laczkó
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, H-4032 Debrecen, Hungary
| | | | - Zsolt Hegyeli
- Milvus Group Bird and Nature Protection Association, Crinului St. 22, 540343 Târgu Mureş, Romania
| | - Szabolcs Lengyel
- DRI Conservation Ecology Research Group, Centre for Ecological Research, Hungarian Academy of Sciences, Bem tér 18/C, H-4026 Debrecen, Hungary
| | - Gábor Csorba
- Hungarian Natural History Museum, Baross u. 13, H-1088 Budapest, Hungary.
| | - Gábor Sramkó
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, H-4032 Debrecen, Hungary
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Guimarães Fabreti L, Höhna S. Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors. Syst Biol 2023; 72:1418-1432. [PMID: 37455495 DOI: 10.1093/sysbio/syad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/02/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
Model selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough not to overfit. In phylogenetics, the most common model selection scenario concerns selecting an adequate substitution and partition model for sequence evolution to infer a phylogenetic tree. Previously, several studies showed that substitution model under-parameterization can bias phylogenetic studies. Here, we explored the impact of substitution model over-parameterization in a Bayesian statistical framework. We performed simulations under the simplest substitution model, the Jukes-Cantor model, and compare posterior estimates of phylogenetic tree topologies and tree length under the true model to the most complex model, the $\text{GTR}+\Gamma+\text{I}$ substitution model, including over-splitting the data into additional subsets (i.e., applying partitioned models). We explored 4 choices of prior distributions: the default substitution model priors of MrBayes, BEAST2, and RevBayes and a newly devised prior choice (Tame). Our results show that Bayesian inference of phylogeny is robust to substitution model over-parameterization and over-partitioning but only under our new prior settings. All 3 current default priors introduced biases for the estimated tree length. We conclude that substitution and partition model selection are superfluous steps in Bayesian phylogenetic inference pipelines if well-behaved prior distributions are applied and more effort should focus on more complex and biologically realistic substitution models.
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Affiliation(s)
- Luiza Guimarães Fabreti
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Sebastian Höhna
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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Chan KO, Mulcahy DG, Anuar S. The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex). Syst Biol 2023; 72:1209-1219. [PMID: 37478480 DOI: 10.1093/sysbio/syad043] [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: 03/06/2023] [Revised: 05/19/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiates the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
| | - Daniel G Mulcahy
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Shahrul Anuar
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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36
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Vieira FM, Pereira FB, Ribeiro LB, Oliveira JB, Silva DCN, Muniz-Pereira LC, Felix-Nascimento G. Oswaldocruzia franciscoensis n. sp. (Nematoda: Molineidae) in Leptodactylus macrosternum Miranda-Ribeiro, 1926 (Anura: Leptodactylidae) from Caatinga morphoclimatic domain, Brazil: morphological and molecular characterisation. J Helminthol 2023; 97:e104. [PMID: 38148677 DOI: 10.1017/s0022149x23000858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
A new species of Oswaldocruzia Travassos, 1917 (Nematoda, Molineidae), parasite of Leptodactylus macrosternum Miranda-Ribeiro, 1926 (Anura: Leptodactylidae), from Caatinga morphoclimatic domain, Brazil, is described based on morphological and molecular data. Oswaldocruzia franciscoensis n. sp. is characterised by an anterior extremity with a cephalic vesicle divided into two portions, a body covered by cuticular longitudinal ridges, and cervical alae. Males of the new species have caudal bursa of type I with a 2-1-2 pattern, spicules divided into a shoe, bifurcated fork, and blade with two unequal branches, in which the longer branch bifurcates at its distal portion end and the smaller branch with three distal processes, each with distal bifurcations. Females have didelphic and amphidelphic uteri, an ovijector divided into vestibule, anterior and posterior sphincters, and anterior and posterior infundibula. The new species differs from its Neotropical congeners that have caudal bursa of type I, based on the presence of cervical alae and by having a spicular blade distally divided into two unequal branches, with the longer branch bifurcating at its distal portion and smaller branch with three distal processes, each distally bifurcated. The partial 18S rDNA sequence generated for Oswaldocruzia franciscoensis n. sp. is the first of a representative belonging to this genus in the Neotropical region.
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Affiliation(s)
- F M Vieira
- Campus de Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), Rodovia BR-407, KM 12 Lote 543 S/n Projeto de Irrigação Nilo Coelho, Petrolina, 56300-000, Brazil
| | - F B Pereira
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Bloco L4 sala 252, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG31270-901, Brazil
| | - L B Ribeiro
- Campus de Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), Rodovia BR-407, KM 12 Lote 543 S/n Projeto de Irrigação Nilo Coelho, Petrolina, 56300-000, Brazil
| | - J B Oliveira
- Laboratório de Parasitologia, Universidade Federal Rural de Pernambuco (UFRPE), Rua Dom Manoel de Medeiros s/nº, Recife CEP 52051-360, Brazil
| | - D C N Silva
- Campus de Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), Rodovia BR-407, KM 12 Lote 543 S/n Projeto de Irrigação Nilo Coelho, Petrolina, 56300-000, Brazil
| | - L C Muniz-Pereira
- Laboratório de Helmintos Parasitos de Vertebrados, Instituto Oswaldo Cruz, FIOCRUZ. Av. Brasil 4365, Rio de Janeiro CEP 21040-900, Brazil
| | - G Felix-Nascimento
- Campus de Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), Rodovia BR-407, KM 12 Lote 543 S/n Projeto de Irrigação Nilo Coelho, Petrolina, 56300-000, Brazil
- Laboratório de Anatomia dos Animais Domésticos e Silvestres (LAADS), Universidade Federal do Vale do São Francisco (UNIVASF), Rodovia BR-407, Km. 12 Lote 543 s/n Projeto de Irrigação Nilo Coelho, Petrolina, Pernambuco56300-000, Brazil
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Polotan FGM, Salazar CRP, Morito HLE, Abulencia MFB, Pantoni RAR, Mercado ES, Hué S, Ditangco RA. Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018. Virus Evol 2023; 9:vead073. [PMID: 38131006 PMCID: PMC10735293 DOI: 10.1093/ve/vead073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The Philippines has had a rapidly growing human immunodeficiency virus (HIV) epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing the history of HIV-1 CRF01_AE transmissions in the Philippines through molecular epidemiology. Partial polymerase sequences (n = 1144) collected between 2008 and 2018 from three island groups were collated from the Research Institute for Tropical Medicine drug resistance genotyping database. Estimation of the time to the most recent common ancestor (tMRCA), effective reproductive number (Re), effective viral population size (Ne), relative migration rates, and geographic spread of CRF01_AE was performed with BEAST. Re and Ne were compared between CRF01_AE and B. Most CRF01_AE sequences formed a single clade with a tMRCA of June 1996 [95 per cent highest posterior density (HPD): December 1991, October 1999]. An increasing CRF01_AE Ne was observed from the tMRCA to 2013. The CRF01_AE Re reached peaks of 2.46 [95 per cent HPD: 1.76, 3.27] in 2007 and 2.52 [95 per cent HPD: 1.83, 3.34] in 2015. A decrease of CRF01_AE Re occurred in the intervening years of 2007 to 2011, reaching as low as 1.43 [95 per cent HPD: 1.06, 1.90] in 2011, followed by a rebound. The CRF01_AE epidemic most likely started in Luzon and then spread to the other island groups of the country. Both CRF01_AE and Subtype B exhibited similar patterns of Re fluctuation over time. These results characterize the subtype-specific phylodynamic history of the largest CRF01_AE cluster in the Philippines, which contextualizes and may inform past, present, and future public health measures toward controlling the HIV epidemic in the Philippines.
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Affiliation(s)
- Francisco Gerardo M Polotan
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Carl Raymund P Salazar
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6700 EH, The Netherlands
| | - Hannah Leah E Morito
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Miguel Francisco B Abulencia
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Roslind Anne R Pantoni
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Edelwisa S Mercado
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Stéphane Hué
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
| | - Rossana A Ditangco
- AIDS Research Group, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
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Carter JE, Sporre MA, Eytan RI. Phylogenetic review of the comb-tooth blenny genus Hypleurochilus in the northwest Atlantic and Gulf of Mexico. Mol Phylogenet Evol 2023; 189:107933. [PMID: 37769827 DOI: 10.1016/j.ympev.2023.107933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
As some of the smallest vertebrates, yet largest producers of consumed reef biomass, cryptobenthic reef fishes serve a disproportionate role in reef ecosystems and are one of the most poorly understood groups of fish. The blenny genera Hypleurochilus and Parablennius are currently considered paraphyletic and the interrelationships of Parablennius have been the focus of recent phylogenetic studies. However, the interrelationships of Hypleurochilus remain understudied. This genus is transatlantically distributed and comprises 11 species with a convoluted taxonomic history. In this study, relationships for ten Hypleurochilus species are resolved using multi-locus nuclear and mtDNA sequence data, morphological data, and mined COI barcode data. Mitochondrial and nuclear sequence data from 61 individuals collected from the western Atlantic and northern Gulf of Mexico (N. GoM) delimit seven species into a temperate clade, a tropical clade, and a third distinct lineage. This lineage, herein referred to as H. cf. aequipinnis, may represent a species of Hypleurochilus whose range has expanded into the N. GoM. Inclusion of publicly available COI sequence for an additional three species provides further phylogenetic resolution. H. bananensis forms a new eastern Atlantic clade with H. cf. aequipinnis, providing further evidence for a western Atlantic range expansion. Single marker COI delimitation was unable to elucidate the relationships between H. springeri/H. pseudoaequipinnis and between H. multifilis/H. caudovittatus due to incomplete lineage sorting. Mitochondrial data are also unable to accurately resolve the placement of H. bermudensis. However, a comprehensive approach using multi-locus phylogenetic and species delimitation methods was able to resolve these relationships. While mining publicly available sequence data allowed for the inclusion of an increased number of species in the analysis and a more comprehensive phylogeny, it was not without drawbacks, as a handful of sequences are potentially mis-identified. Overall, we find that the recent divergence of some species within this genus and potential introgression events confound the results of single locus delimitation methods, yet a combination of single and multi-locus analyses has allowed for insights into the biogeography of this genus and uncovered a potential transatlantic range expansion.
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Affiliation(s)
- Joshua E Carter
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States.
| | - Megan A Sporre
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
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de Carvalho Ruthner Batista HB, Vieira LFP, Kawai JGC, de Oliveira Fahl W, Barboza CM, Achkar S, de Novaes Oliveira R, Brandão PE, Carnieli Junior P. Dispersion and diversification of Lyssavirus rabies transmitted from haematophagous bats Desmodus rotundus: a phylogeographical study. Virus Genes 2023; 59:817-822. [PMID: 37796410 DOI: 10.1007/s11262-023-02030-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023]
Abstract
Rabies is worldwide zoonosis caused by Lyssavirus rabies (RABV) a RNA negative sense virus with low level of fidelity during replication cycle. Nucleoprotein of RABV is the most conserved between all five proteins of the virus and is the most used gene for phylogenetic and phylogeographic studies. Despite of rabies been very important in Public Health concern, it demands continuous prophylactic care for herbivores with economic interest, such as cattle and horses. The main transmitter of RABV for these animals in Brazil is the hematophagous bats Desmodus rotundus. The aim of this study was to determine the dispersion over time and space of RABV transmitted by D. rotundus. Samples of RABV from the State of São Paulo (SP), Southeast Brazil isolated from the central nervous system (CNS) of cattle, were submitted to RNA extraction, RT-PCR, sequencing and phylogeographic analyzes with BEAST (Bayesian Evolutionary Analysis Sampling Trees) v 2.5 software. Was possible to identify high rate of diversification in starts sublineages of RABV what are correlated with a behavior of D. rotundus, the main transmitter of rabies to cattle. This study also highlights the importance of continuous monitoring of genetic lineages of RABV in Brazil.
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Laroche RA, Duran DP, Lee CTA, Godwin W, Roman SJ, Herrmann DP, Egan SP. A genomic test of subspecies in the Eunota togata species group (Coleoptera: Cicindelidae): Morphology masks evolutionary relationships and taxonomy. Mol Phylogenet Evol 2023; 189:107937. [PMID: 37797795 DOI: 10.1016/j.ympev.2023.107937] [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: 11/20/2022] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
Most of the world's biodiversity is described primarily or exclusively using morphological traits that may not always reflect the true evolutionary units. Accurate taxonomy is critical for conservation efforts and re-evaluation of traditional taxonomy may often be warranted since species and subspecies are frequently the focus of conservation and faunistic studies. Here, we test comprehensive taxonomic hypotheses of morphologically defined subspecies in the tiger beetle, Eunota togata (LaFerté-Sénectère, 1841). The four recognized subspecies were delineated based mainly on the dorsal coloration and extent of white markings termed maculations. We combine inferences from mtDNA genealogies and genome-wide multilocus data to elucidate the evolutionary relationships within the group and assess the taxonomic implications. Three of the four subspecific taxa delineated by morphology were not supported by the genomic or mtDNA data. In fact, the species-level diversity in this group was underestimated, as E. togata was found to represent three well-supported distinct species in all genetic analyses. Emerging from these analyses, we also document an intriguing example of convergent evolution in lighter colored E. togata adapting to similar white saline backgrounds. Our collective work underscores the importance of using molecular methods to reevaluate morphological based taxonomy for species and subspecies delimitation and conservation.
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Affiliation(s)
- Robert A Laroche
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Daniel P Duran
- Department of Environmental Science, Rowan University, Glassboro, NJ 08028, USA.
| | - Cin-Ty A Lee
- Department of Earth, Environmental & Planetary Science, Rice University, Houston, TX 77005, USA
| | - William Godwin
- Sam Houston State Natural History Collection, Huntsville, TX 77320, USA
| | | | | | - Scott P Egan
- Department of BioSciences, Rice University, Houston, TX 77005, USA
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41
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Ni X, Chen Y, Deng G, Fu C. Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China. Genes (Basel) 2023; 14:2146. [PMID: 38136969 PMCID: PMC10743038 DOI: 10.3390/genes14122146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.
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Affiliation(s)
| | | | | | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.N.); (Y.C.); (G.D.)
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Collobert G, Perez-Lamarque B, Dubuisson JY, Martos F. Gains and losses of the epiphytic lifestyle in epidendroid orchids: review and new analyses of succulence traits. ANNALS OF BOTANY 2023; 132:787-800. [PMID: 37777476 PMCID: PMC10799982 DOI: 10.1093/aob/mcad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND AND AIMS Epiphytism has evolved repeatedly in plants and has resulted in a considerable number of species with original characteristics. Because water supply is generally erratic compared to that in soils, succulent forms in particular are widespread in epiphytic species. However, succulent organs also exist in terrestrial plants, and the question of the concomitant evolution of epiphytism and succulence has received little attention, not even in the epidendroid orchids, which account for 67.6 % of vascular epiphytes. METHODS We built a new time-calibrated phylogenetic tree of Epidendroideae with 203 genera treated in genus Orchidacearum, from which we reconstructed the evolution of epiphytism as well as traits related to water scarcity (stem and leaf succulence and the number of velamen layers), while testing for the correlated evolution between the two. Furthermore, we estimated the ancestral geographical ranges to evaluate the palaeoclimatic context in which epiphytism evolved. KEY RESULTS Epiphytism evolved at least three times: 39.0 million years ago (Mya) in the common ancestor of the Malaxideae and Cymbidieae that probably ranged from the Neotropics to Southeast Asia and Australia, 11.5 Mya in the Arethuseae in Southeast Asia and Australia, and 7.1 Mya in the neotropical Sobralieae, and it was notably lost in the Malaxidiinae, Collabieae, Calypsoeae, Bletiinae and Eulophiinae. Stem succulence is inferred to have evolved once, in a terrestrial ancestor at least 4.1 Mya before the emergence of epiphytic lineages. If lost, stem succulence was almost systematically replaced by leaf succulence in epiphytic lineages. CONCLUSIONS Epiphytism may have evolved in seasonally dry forests during the Eocene climatic cooling, among stem-succulent terrestrial orchids. Our results suggest that the emergence of stem succulence in early epidendroids was a key innovation in the evolution of epiphytism, facilitating the colonization of epiphytic environments that later led to the greatest diversification of epiphytic orchids.
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Affiliation(s)
- Géromine Collobert
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Benoît Perez-Lamarque
- Institut de Biologie de l’ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, 75005 Paris, France
| | - Jean-Yves Dubuisson
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
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43
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Stenhouse GE, Keddy KH, Bengtsson RJ, Hall N, Smith AM, Thomas J, Iturriza-Gómara M, Baker KS. The genomic epidemiology of shigellosis in South Africa. Nat Commun 2023; 14:7715. [PMID: 38001075 PMCID: PMC10673971 DOI: 10.1038/s41467-023-43345-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.
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Affiliation(s)
- George E Stenhouse
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
| | | | - Rebecca J Bengtsson
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Miren Iturriza-Gómara
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Kate S Baker
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
- Department of Genetics, University of Cambridge, CB23EH, Cambridge, UK.
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Poofery J, Ngamprasertwong T, Narapakdeesakul D, Arnuphapprasert A, Nugraheni YR, Thanee S, Asada M, Kaneko O, Kaewthamasorn M. Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species. Sci Rep 2023; 13:20258. [PMID: 37985797 PMCID: PMC10662395 DOI: 10.1038/s41598-023-45551-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023] Open
Abstract
In recent phylogenetic studies, bat Polychromophilus and ungulate Plasmodium, two relatively understudied haemosporidian parasites within the Apicomplexa phylum, have often been overlooked. Instead, the focus has been primarily on haemosporidian parasites in primates, rodents, and birds. Several phylogenetic analyses of bat Polychromophilus have relied on limited datasets and short informative DNA sequences. As a result of these inherent limitations, the substantiation of their evolutionary stance has encountered a diminished degree of robust validation. This study successfully obtained complete mitochondrial genome sequences from 11 Polychromophilus parasites originating from Hipposideros gentilis and Myotis siligoensis bats for the first time. Additionally, the authors have sequenced the apicoplast caseinolytic protease C genes from Polychromophilus murinus and a potentially new Polychromophilus species. These mitochondrial genomes range in length from 5994 to 6001 bp and consist of three protein-coding genes (PCGs), seven small subunit ribosomal RNA genes (SSU rRNA), 12 large subunit ribosomal RNA genes (LSU rRNA), and seven miscellaneous RNA genes. Phylogenetic analyses using Bayesian Inference and Maximum Likelihood methods indicated robust support for the grouping of ungulate Plasmodium and bat Polychromophilus in a single clade separate from other Plasmodium spp., confirming previous reports, albeit with stronger evidence in this study. The divergence between Polychromophilus in bats and Plasmodium in ungulates occurred approximately 29.61 to 55.77 million years ago (Mya), with a node age estimated at 40.63 Mya. These findings highlight that the genus Plasmodium, which includes species found in ungulates, birds, reptiles, and other mammals, does not form a monophyletic group. By incorporating Polychromophilus in bats and Plasmodium in ungulates, this study contributes significantly to understanding the phylogenetic relationships within the Haemosporida order. It provides valuable insights into the evolutionary history and interconnections among these diverse parasites, thereby expanding knowledge in this field.
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Affiliation(s)
- Juthathip Poofery
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Duriyang Narapakdeesakul
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Pathobiology Graduate Program, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Apinya Arnuphapprasert
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Yudhi Ratna Nugraheni
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Sleman, Indonesia
| | - Suchansa Thanee
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Masahito Asada
- Research Unit for Global Infection Control, National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Morakot Kaewthamasorn
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
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45
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Ramírez JP, Reeder TW, Spasojevic MJ. Extinction debt and functional traits mediate community saturation over large spatiotemporal scales. J Anim Ecol 2023; 92:2228-2239. [PMID: 37786361 DOI: 10.1111/1365-2656.14009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Determining if ecological communities are saturated (have a limit to the number of species they can support) has important implications for understanding community assembly, species invasions, and climate change. However, previous studies have generally been limited to short time frames that overlook extinction debt and have not explicitly considered how functional trait diversity may mediate patterns of community saturation. Here, we combine data from biodiversity surveys with functional and phylogenetic data to explore if the colonisation events after the Great American Biotic Interchange (closure of the Panamanian Isthmus) resulted in increases in species richness of communities of the snake family Dipsadidae. We determined the number and the direction of dispersal events between Central and South America by estimating ancestral areas based on a Bayesian time-calibrated phylogenetic analysis. We then evaluated whether variation in community saturation was mediated by the functional similarity of six traits for the resident and colonizing snakes and/or local environmental conditions. We found that colonised communities did not support more species than those that were not colonised. Moreover, we did not find an association between the functional diversity across sites and whether they were colonised by members from the lineages dispersing across the Isthmus or not. Instead, variation in species richness was predicted best by covariates such as time since colonisation and local environment. Taken together, our results suggest that snake communities of the Dipsadidae across the neotropics are saturated. Moreover, our research highlights two important factors to consider in studies of community saturation: extinction debt and the functional differences and similarities in species' ecological roles.
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Affiliation(s)
- Juan P Ramírez
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Tod W Reeder
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Marko J Spasojevic
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
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46
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Peach DAH, Blake AJ. Mosquito (Diptera: Culicidae) Vision and Associated Electrophysiological Techniques. Cold Spring Harb Protoc 2023; 2023:107671. [PMID: 36972954 DOI: 10.1101/pdb.top107671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Mosquitoes are considered the world's deadliest animal because of the pathogens they spread. Additionally, they are an unbearable nuisance in many areas. Visual stimuli play an important role in the mosquito life cycle, helping them find vertebrate hosts, floral nectar, and oviposition sites. Here, we review mosquito vision, including its influences on mosquito behavior, the photoreceptors involved, and mosquito spectral sensitivity, as well as provide an overview of techniques used for the analysis of mosquito vision, including electroretinograms, single-cell recordings, and the use of opsin-deficient mutants. We anticipate that this information will be useful for researchers studying mosquito physiology, evolution, ecology, and management.
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Affiliation(s)
- Daniel A H Peach
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Savannah River Ecology Laboratory, Department of Infectious Diseases, The University of Georgia, Aiken, South Carolina 29802, USA
| | - Adam J Blake
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
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47
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Grismer LL, Pawangkhanant P, Idiiatullina SS, Trofimets AV, Nazarov RA, Suwannapoom C, Poyarkov NA. A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand. Zootaxa 2023; 5352:109-136. [PMID: 38221458 DOI: 10.11646/zootaxa.5352.1.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Indexed: 01/16/2024]
Abstract
An integrative taxonomic analysis recovers a distinctive new species of the gekkonid genus Cyrtodactylus Gray, 1827 from Satun Province in extreme southern Thailand as the sister species to the Cyrtodactylus intermedius group of southern Indochina, approximately 600 km to the northeast across the Gulf of Thailand. Based on 1449 base pairs of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNAs, the new species, C. disjunctus sp. nov., bears a pairwise sequence divergence from the mean divergences of the intermedius group species ranging from 17.923.6%. Three different principal component analyses (PCA) and a multiple factor analysis (MFA) recover C. disjunctus sp. nov. as a highly distinctive karst cave-adapted species based on morphology and color pattern. Its sister species relationship to the intermedius groupto which it is added herefurther underscores a growing body of analyses that have recovered a trans-Gulf of Thailand connection across the submerged Sunda Shelf between the southern Thai-Malay Peninsula and southern Indochina. Fragmented karstic archipelagos stretching across Indochina have served as foci for the independent evolution of nearly 25% of the species of Cyrtodactylus. The description of C. disjunctus sp. nov. continues to highlight the fact that karstic habitats support an ever-increasing number of threatened site-specific endemics that compose much of the reptile diversity of many Asian nations but, as of yet, most of these landscapes have no legal protection.
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Affiliation(s)
- L Lee Grismer
- Herpetology Laboratory; Department of Biology; La Sierra University; 4500 Riverwalk Parkway; Riverside; California 92505; USA; Department of Herpetology; San Diego Natural History Museum; PO Box 121390; San Diego; California; 92112; USA; Institute for Tropical Biology and Conservation; Universiti Malaysia Sabah; Kota Kinabalu; Malaysia.
| | - Parinya Pawangkhanant
- Division of Fishery; School of Agriculture and Natural Resources; University of Phayao; Phayao; Thailand.
| | - Sabira S Idiiatullina
- Department of Vertebrate Zoology; Lomonosov Moscow State University; Leninskiye Gory; GSP1; Moscow 119991; Russia.
| | - Alexei V Trofimets
- Department of Vertebrate Zoology; Lomonosov Moscow State University; Leninskiye Gory; GSP1; Moscow 119991; Russia.
| | - Roman A Nazarov
- Zoological Museum; Moscow State University; Moscow; 2 Bolshaya Nikitskaya St.; Moscow 125009; Russia.
| | - Chatmongkon Suwannapoom
- Division of Fishery; School of Agriculture and Natural Resources; University of Phayao; Phayao; Thailand.
| | - Nikolay A Poyarkov
- Zoological Museum; Moscow State University; Moscow; 2 Bolshaya Nikitskaya St.; Moscow 125009; Russia; Joint Vietnam - Russia Tropical Science and Technology Research Centre; 63 Nguyen Van Huyen Road; Nghia Do; Cau Giay; Hanoi; Vietnam.
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48
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Chacón JL, Chacón RD, Sánchez-Llatas CJ, Morín JG, Astolfi-Ferreira CS, Piantino Ferreira AJ. Antigenic and molecular characterization of isolates of the Brazilian genotype BR-I (GI-11) of infectious bronchitis virus supports its recognition as BR-I serotype. Avian Pathol 2023; 52:323-338. [PMID: 37477586 DOI: 10.1080/03079457.2023.2228725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
The antigenic and molecular characteristics of BR-I infectious bronchitis viruses (IBVs) isolated from Brazil are reported. IBVs isolated from commercial flocks with different clinical manifestations between 2003 and 2019 were submitted to antigenic and molecular characterization. The complete S1 glycoprotein gene of 11 field isolates was amplified and sequenced. The virus neutralization (VN) test showed 94.75% neutralization with a BR-I isolate and 30% or less against other worldwide reference strains. The nucleotide and amino acid sequence analyses revealed 84.3-100% and 83.5-100% identity among them, respectively. The identity values ranged from 57.1 to 82.6% for nucleotides and from 46.6-84.4% for amino acids compared with those of other genotypes. By phylogenetic tree analysis, the Brazilian isolates were branched into the BR-I genotype (lineage GI-11), which was differentiated from foreign reference strains. Selective pressure analyses of BR-I IBVs revealed evolution under purifying selection (negative pressure) for the complete S1 gene but four specific sites (87, 121, 279, and 542) under diversifying selection (positive pressure). Profiles of cleavage sites and potential N-glycosylation sites differed from those of other genotypes. The low molecular relationship among the Brazilian viruses and foreign serotypes was concordant with the VN test results. The low antigenic relatedness (ranging from 5.3-30% between Brazilian genotype BR-I and reference IBV serotypes of North America, Europe, and Asia) indicates that the BR-I genotype is a different serotype, referred to for the first time and hereafter as serotype BR-I. RESEARCH HIGHLIGHTSStrains of the BR-I genotype presented robust antigenic and molecular similarity.BR-I strains evolved under purifying selection mode (negative pressure).The BR-I genotype originated in Brazil and dispersed to other countries.BR-I genotype viruses can be referred to as the BR-I serotype.
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Affiliation(s)
- Jorge L Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Ruy D Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Christian J Sánchez-Llatas
- Faculty of Biology, Department of Genetics, Physiology, and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Jaime G Morín
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Claudete S Astolfi-Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Antonio J Piantino Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
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Otomaru H, Nguyen HAT, Vo HM, Toizumi M, Le MN, Mizuta K, Moriuchi H, Bui MX, Dang DA, Yoshida LM. A decade of human metapneumovirus in hospitalized children with acute respiratory infection: molecular epidemiology in central Vietnam, 2007-2017. Sci Rep 2023; 13:15757. [PMID: 37735242 PMCID: PMC10514255 DOI: 10.1038/s41598-023-42692-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Human metapneumovirus (hMPV) can cause severe acute respiratory infection (ARI). We aimed to clarify the clinical and molecular epidemiological features of hMPV. We conducted an ARI surveillance targeting hospitalized children aged 1 month to 14 years in Nha Trang, Vietnam. Nasopharyngeal swabs were tested for respiratory viruses with PCR. We described the clinical characteristics of hMPV patients in comparison with those with respiratory syncytial virus (RSV) and those with neither RSV nor hMPV, and among different hMPV genotypes. Among 8822 patients, 278 (3.2%) were hMPV positive, with a median age of 21.0 months (interquartile range: 12.7-32.5). Among single virus-positive patients, hMPV cases were older than patients with RSV (p < 0.001) and without RSV (p = 0.003). The proportions of clinical pneumonia and wheezing in hMPV patients resembled those in RSV patients but were higher than in non-RSV non-hMPV patients. Seventy percent (n = 195) were genotyped (A2b: n = 40, 20.5%; A2c: n = 99, 50.8%; B1: n = 37, 19%; and B2: n = 19, 9.7%). The wheezing frequency was higher in A2b patients (76.7%) than in those with other genotypes (p = 0.033). In conclusion, we found a moderate variation in clinical features among hMPV patients with various genotypes. No seasonality was observed, and the multiple genotype co-circulation was evident.
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Affiliation(s)
- Hirono Otomaru
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hien Anh Thi Nguyen
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hien Minh Vo
- Department of Pediatrics, Khanh Hoa General Hospital, Nha Trang, Vietnam
| | - Michiko Toizumi
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Minh Nhat Le
- Antimicrobial Resistance Research Centre, National Institute of Infectious Disease (NIID), Sinjuku, Japan
- Tay Nguyen Institute of Science Research, Vietnam Academy of Science and Technology (VAST), Da Lat, Vietnam
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Hiroyuki Moriuchi
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Minh Xuan Bui
- Khanh Hoa Health Service Department, Nha Trang, Vietnam
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Lay-Myint Yoshida
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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50
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Pyrcz TW, Fhraeus C, Boyer P, Mahecha-J O, Lorenc-Brudecka J, Zajc KS, Willmott KR, Padrn S. The sunny butterflies: new species of high montane pierids of the Catasticta poujadei group from the Peruvian Andes (Pieridae, Pierinae, Aporiina). Zootaxa 2023; 5336:530-542. [PMID: 38221078 DOI: 10.11646/zootaxa.5336.4.4] [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: 08/23/2023] [Indexed: 01/16/2024]
Abstract
The Catasticta poujadei group, within the subgenus Hesperochoia Reissinger, is revised. Two new species, C. copernicus Pyrcz & Fhraeus sp. nov., and C. buszkoi Boyer & Pyrcz sp. nov. occurring near the timberline in Junn and Apurmac are described. Catasticta eximia Rber is reinstated as a species separate from C. poujadei, and a new subspecies, C. eximia tapuna ssp. nov., is described. The affinities of the species of the C. poujadei group are evaluated based on COI barcodes. Their distribution and habitats are described.
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Affiliation(s)
- Tomasz W Pyrcz
- Department of Invertebrate Evolution; Institute of Zoology and Biomedical Research; Jagiellonian University; Gronostajowa 9; 30-387 Krakw; Poland.
| | - Christer Fhraeus
- Biodiversity; Department of Biology; Lund University; Lund; Sweden.
| | - Pierre Boyer
- 7 Lotissement lHorizon; Le Puy-Sainte-Rparade; France.
| | - Oscar Mahecha-J
- Instituto de Ciencias Naturales ICN; Universidad Nacional de Colombia. Carrera 30 No.45-03; Bogot D.C.; Colombia. Biogeografa y Ecologa Evolutiva Neotropical BEEN; Universidad Distrital F.J.C.; Bogot; Colombia. Carrera 3 No. 26A 40.
| | | | - Kamila S Zajc
- Nature Education Centre; Jagiellonian University; Gronostajowa 5; 30-387 Krakw; Poland.
| | - Keith R Willmott
- McGuire Center for Lepidoptera and Biodiversity; Florida Museum of Natural History; University of Florida; Gainesville; Florida; USA.
| | - Sebastin Padrn
- Laboratorio de Entomologia; Universidad del Azuay. Avenida 24 de Mayo 7-77 y Hernan Malo. Cuenca; Ecuador.
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