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Searle PC, Shiozawa DK, Evans RP, Hill JT, Suli A, Stark MR, Belk MC. Heterochronic shift in gene expression leads to ontogenetic morphological divergence between two closely related polyploid species. iScience 2024; 27:109566. [PMID: 38632992 PMCID: PMC11022054 DOI: 10.1016/j.isci.2024.109566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 11/04/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Heterochrony-alteration to the rate or timing of development-is an important mechanism of trait differentiation associated with speciation. Heterochrony may explain the morphological divergence between two polyploid species, June sucker (Chasmistes liorus) and Utah sucker (Catostomus ardens). The larvae of both species have terminal mouths; however, as adults, June sucker and Utah sucker develop subterminal and ventral mouths, respectively. We document a difference in the timing of shape development and a corresponding change in the timing of gene expression, suggesting the distinctive mouth morphology in June suckers may result from paedomorphosis. Specifically, adult June suckers exhibit an intermediate mouth morphology between the larval (terminal) and ancestral (ventral) states. Endemic and sympatric Chasmistes/Catostomus pairs in two other lakes also are morphologically divergent, but genetically similar. These species pairs could have resulted from the differential expression of genes and corresponding divergence in trait development. Paedomorphosis may lead to adaptive diversification in Catostomids.
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Affiliation(s)
- Peter C. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - R. Paul Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathon T. Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Arminda Suli
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Michael R. Stark
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Mark C. Belk
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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Barcenas-Peña A, Divakar PK, Crespo A, Nuñez-Zapata J, Lumbsch HT, Grewe F. Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota). J Fungi (Basel) 2023; 9:1180. [PMID: 38132781 PMCID: PMC10744373 DOI: 10.3390/jof9121180] [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: 10/30/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Cryptic species are common in lichen-forming fungi and have been reported from different genera in the most speciose family, Parmeliaceae. Herein, we address species delimitation in a group of mainly asexually reproducing Parmelina species. The morphologically distinct P. pastillifera was previously found nested within a morphologically circumscribed P. tiliacea based on several loci. However, these studies demonstrated a relatively high genetic diversity within P. tiliacea sensu lato. Here, we revisit the species delimitation in the group by analyzing single-nucleotide polymorphisms (SNPs) through genome-wide assessment using Restriction-Site-Associated sequencing and population genomic methods. Our data support previous studies and provide further insight into the phylogenetic relationships of the four clades found within the complex. Based on the evidence suggesting a lack of gene flow among the clades, we recognize the four clades as distinct species, P. pastillifera and P. tiliacea sensu stricto, and two new species, P. clandestina sp. nov. and P. mediterranea sp. nov.
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Affiliation(s)
- Alejandrina Barcenas-Peña
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Ana Crespo
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Jano Nuñez-Zapata
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - H. Thorsten Lumbsch
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Felix Grewe
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
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Dimitriou AC, Soares Campos-Filho I, Georgiou A, Taiti S, Sfenthourakis S. Intra-island patterns of cryptic diversity within an oceanic island: Insights from the differentiation of Schizidium Verhoeff, 1901 (Oniscidea, Armadillidiidae) within Cyprus, with descriptions of two new species. Mol Phylogenet Evol 2023; 187:107884. [PMID: 37467903 DOI: 10.1016/j.ympev.2023.107884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Cyprus is a Mediterranean island of volcanic origin isolated for at least 5.3 Myr from surrounding continental areas. The present study focuses on the diversification of the isopod genus Schizidium within the island, including also specimens from surrounding continental areas. The genus Schizidium sensu lato is probably non monophyletic, comprising 26 species distributed from Greece to Iran. Up to date the only representative of the genus reported from Cyprus was Schizidium fissum. Aiming to investigate the patterns of genetic diversity within the focal island, to evaluate the morphology-based taxonomy of the species in the genus, and at the same time to explore phylogenetic relationships with mainland populations, we applied genome-wide ddRADseq as well as Sanger sequencing targeting three mitochondrial (16S, COI and 12S) and the nuclear NaK loci. Results of phylogenetic analyses support the existence of two distinct epigean Schizidium clades with well-defined geographic boundaries that conform to the known paleogeography of Cyprus, plus one endogean clade with restricted distribution within the island. Genetic data and morphology corroborate the assignment of this latter endogean clade to a new species, Schizidium myrrae n. sp. The two epigean clades are also considered as distinct species, one corresponding to the known S. fissum at the eastern part of the island (Pentadaktylos massif) and the other to the newly described S. christosi n. sp. distributed along the western part of the island (Troodos massif). Even though detailed examination of many specimens could not retrieve any morphological differences among representatives of these two clades, clado-chronological analysis indicates a long isolation between them, estimated at ∼ 9 Mya, as well as the sharing of a common ancestor with S. tiberianum from Israel at ∼ 15 Mya. Hence, we can consider these epigean Schizidium species as one more case of cryptic diversity on Cyprus, exhibiting similar patterns with the recently described case in the genus Armadillo.
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Affiliation(s)
- Andreas C Dimitriou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus.
| | | | - Anastasia Georgiou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
| | - Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy; Museo di Storia Naturale dell'Università di Firenze, Sezione di Zoologia "La Specola", Via Romana 17, 50125 Florence, Italy
| | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
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Campos-Filho IS, Dimitriou AC, Taiti S, Sfenthourakis S. The genus Armadillo Latreille, 1802 (Oniscidea, Armadillidae) from Cyprus, with descriptions of two new species. Zootaxa 2023; 5270:67-91. [PMID: 37518177 DOI: 10.11646/zootaxa.5270.1.3] [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: 04/18/2023] [Indexed: 08/01/2023]
Abstract
The present work aims to morphologically characterize the species of Armadillo from Cyprus. Moreover, two new species of the genus are described, A. konstantinoui sp. nov. from several places along the island, and A. karametae sp. nov. from Pafos region. The circum-Mediterranean species A. officinalis is also redescribed.
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Affiliation(s)
| | - Andreas C Dimitriou
- Department of Biological Sciences; University of Cyprus; Lefkosia (Nicosia); Cyprus..
| | - Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri; Consiglio Nazionale delle Ricerche; Sesto Fiorentino (Florence); Italy.; Museo di Storia Naturale; Sezione di Zoologia "La Specola"; Florence; Italy.,Department of Biological Sciences; University of Cyprus; Lefkosia (Nicosia); Cyprus..
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Otero A, Barcenas-Peña A, Lumbsch HT, Grewe F. Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' Genus Usnea (Parmeliaceae, Ascomycota). J Fungi (Basel) 2023; 9:99. [PMID: 36675920 PMCID: PMC9865703 DOI: 10.3390/jof9010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/03/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
Nearly 90% of fungal diversity, one of the most speciose branches in the tree of life, remains undescribed. Lichenized fungi as symbiotic associations are still a challenge for species delimitation, and current species diversity is vastly underestimated. The ongoing democratization of Next-Generation Sequencing is turning the tables. Particularly, reference-based RADseq allows for metagenomic filtering of the symbiont sequence and yields robust phylogenomic trees of closely related species. We implemented reference-based RADseq to disentangle the evolution of neuropogonoid lichens, which inhabit harsh environments and belong to Usnea (Parmeliaceae, Ascomycota), one of the most taxonomically intriguing genera within lichenized fungi. Full taxon coverage of neuropogonoid lichens was sampled for the first time, coupled with phenotype characterizations. More than 20,000 loci of 126 specimens were analyzed through concatenated and coalescent-based methods, including time calibrations. Our analysis addressed the major taxonomic discussions over recent decades. Subsequently, two species are newly described, namely U. aymondiana and U. fibriloides, and three species names are resurrected. The late Miocene and Pliocene-Pleistocene boundary is inferred as the timeframe for neuropogonoid lichen diversification. Ultimately, this study helped fill the gap of fungal diversity by setting a solid backbone phylogeny which raises new questions about which factors may trigger complex evolutionary scenarios.
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Affiliation(s)
- Ana Otero
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Science & Education, The Field Museum, Chicago, IL 60605, USA
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