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Gallone B, Kuyper TW, Nuytinck J. The genus Cortinarius should not (yet) be split. IMA Fungus 2024; 15:24. [PMID: 39138570 PMCID: PMC11321212 DOI: 10.1186/s43008-024-00159-4] [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: 03/15/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius was the single genus of the family Cortinariaceae, despite several attempts to provide a workable, lower-rank hierarchical structure based on subgenera and sections. The first phylogenomic study for this group elevated the old genus Cortinarius to family level and the family was split into ten genera, of which seven were described as new. Here, by careful re-examination of the recently published phylogenomic dataset, we detected extensive gene-tree/species-tree conflicts using both concatenation and multispecies coalescent approaches. Our analyses demonstrate that the Cortinarius phylogeny remains unresolved and the resulting phylogenomic hypotheses suffer from very short and unsupported branches in the backbone. We can confirm monophyly of only four out of ten suggested new genera, leaving uncertain the relationships between each other and the general branching order. Thorough exploration of the tree space demonstrated that the topology on which Cortinarius revised classification relies on does not represent the best phylogenetic hypothesis and should not be used as constrained topology to include additional species. For this reason, we argue that based on available evidence the genus Cortinarius should not (yet) be split. Moreover, considering that phylogenetic uncertainty translates to taxonomic uncertainty, we advise for careful evaluation of phylogenomic datasets before proposing radical taxonomic and nomenclatural changes.
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Affiliation(s)
- Brigida Gallone
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
| | - Thomas W Kuyper
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Soil Biology Group, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Jorinde Nuytinck
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
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2
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Brownstein CD, Zapfe KL, Lott S, Harrington R, Ghezelayagh A, Dornburg A, Near TJ. Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean. Curr Biol 2024; 34:2541-2550.e4. [PMID: 38788708 DOI: 10.1016/j.cub.2024.04.066] [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: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
Major ecological transitions are thought to fuel diversification, but whether they are contingent on the evolution of certain traits called key innovations1 is unclear. Key innovations are routinely invoked to explain how lineages rapidly exploit new ecological opportunities.1,2,3 However, investigations of key innovations often focus on single traits rather than considering trait combinations that collectively produce effects of interest.4 Here, we investigate the evolution of synergistic trait interactions in anglerfishes, which include one of the most species-rich vertebrate clades in the bathypelagic, or "midnight," zone of the deep sea: Ceratioidea.5 Ceratioids are the only vertebrates that possess sexual parasitism, wherein males temporarily attach or permanently fuse to females to mate.6,7 We show that the rapid transition of ancestrally benthic anglerfishes into pelagic habitats occurred during a period of major global warming 50-35 million years ago.8,9 This transition coincided with the origins of sexual parasitism, which is thought to increase the probability of successful reproduction once a mate is found in the midnight zone, Earth's largest habitat.5,6,7 Our reconstruction of the evolutionary history of anglerfishes and the loss of immune genes support that permanently fusing clades have convergently degenerated their adaptive immunity. We find that degenerate adaptive immune genes and sexual body size dimorphism, both variably present in anglerfishes outside the ceratioid radiation, likely promoted their transition into the bathypelagic zone. These results show how traits from separate physiological, morphological, and reproductive systems can interact synergistically to drive major transitions and subsequent diversification in novel environments.
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Affiliation(s)
- Chase D Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Katerina L Zapfe
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Spencer Lott
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
| | - Richard Harrington
- Department of Natural Resources, Marine Resources Division, 217 Ft. Johnson Road, Charleston, SC 29412-9110, USA
| | - Ava Ghezelayagh
- Department of Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA; Peabody Museum, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
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3
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Myers EA, Rautsaw RM, Borja M, Jones J, Grünwald CI, Holding ML, Grazziotin F, Parkinson CL. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus). Syst Biol 2024:syae018. [PMID: 38695290 DOI: 10.1093/sysbio/syae018] [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: 05/10/2023] [Indexed: 08/11/2024] Open
Abstract
Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.
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Affiliation(s)
- Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, Gómez Palacio, Durango., Mex
| | - Jason Jones
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
| | - Christoph I Grünwald
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
- Biodiversa A.C., Avenida de la Ribera #203, C.P. 45900, Chapala, Jalisco, Mexico
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe Grazziotin
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
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Sidlauskas BL, Mathur S, Aydoğan H, Monzyk FR, Black AN. Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish. BMC Ecol Evol 2024; 24:2. [PMID: 38177987 PMCID: PMC10765885 DOI: 10.1186/s12862-023-02191-1] [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: 08/09/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA.
| | - Samarth Mathur
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W 12th Ave, Columbus, OH, 43210, USA
| | - Hakan Aydoğan
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA
| | - Fred R Monzyk
- Oregon Department of Fish and Wildlife, Corvallis Research Lab, 28655 OR-34, Corvallis, OR, 97333, USA
| | - Andrew N Black
- Center for Quantitative Life Sciences, Oregon State University, 2750 SW Campus Way, Corvallis, OR, 97331, USA
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Frankel LE, Ané C. Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages. Syst Biol 2023; 72:1357-1369. [PMID: 37698548 DOI: 10.1093/sysbio/syad056] [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: 01/24/2023] [Revised: 07/07/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023] Open
Abstract
The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods are based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly violated in many groups. In this work, we quantify the effects of rate variation on the D test (also known as ABBA-BABA test), the D3 test, and HyDe. All 3 tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and rate variation across gene-tree edges. We simulated species networks according to a birth-death-hybridization process, so as to capture a range of realistic species phylogenies. For all 3 methods tested, we found a marked increase in the false discovery of reticulation (type-1 error rate) when there is rate variation across species lineages. The D3 test was the most sensitive, with around 80% type-1 error, such that D3 appears to more sensitive to a departure from the clock than to the presence of reticulation. For all 3 tests, the power to detect hybridization events decreased as the number of hybridization events increased, indicating that multiple hybridization events can obscure one another if they occur within a small subset of taxa. Our study highlights the need to consider rate variation when using site-based summary statistics, and points to the advantages of methods that do not require assumptions on evolutionary rates across lineages or across genes.
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Affiliation(s)
- Lauren E Frankel
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
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Suchocki CR, Ka'apu-Lyons C, Copus JM, Walsh CAJ, Lee AM, Carter JM, Johnson EA, Etter PD, Forsman ZH, Bowen BW, Toonen RJ. Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae). Sci Rep 2023; 13:15810. [PMID: 37737242 PMCID: PMC10517014 DOI: 10.1038/s41598-023-41719-9] [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: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
The Gila robusta species complex in the lower reaches of the Colorado River includes three nominal and contested species (G. robusta, G. intermedia, and G. nigra) originally defined by morphological and meristic characters. In subsequent investigations, none of these characters proved diagnostic, and species assignments were based on capture location. Two recent studies applied conservation genomics to assess species boundaries and reached contrasting conclusions: an ezRAD phylogenetic study resolved 5 lineages with poor alignment to species categories and proposed a single species with multiple population partitions. In contrast, a dd-RAD coalescent study concluded that the three nominal species are well-supported evolutionarily lineages. Here we developed a draft genome (~ 1.229 Gbp) to apply genome-wide coverage (10,246 SNPs) with nearly range-wide sampling of specimens (G. robusta N = 266, G. intermedia N = 241, and G. nigra N = 117) to resolve this debate. All three nominal species were polyphyletic, whereas 5 of 8 watersheds were monophyletic. AMOVA partitioned 23.1% of genetic variance among nominal species, 30.9% among watersheds, and the Little Colorado River was highly distinct (FST ranged from 0.79 to 0.88 across analyses). Likewise, DAPC identified watersheds as more distinct than species, with the Little Colorado River having 297 fixed nucleotide differences compared to zero fixed differences among the three nominal species. In every analysis, geography explains more of the observed variance than putative taxonomy, and there are no diagnostic molecular or morphological characters to justify species designation. Our analysis reconciles previous work by showing that species identities based on type location are supported by significant divergence, but natural geographic partitions show consistently greater divergence. Thus, our data confirm Gila robusta as a single polytypic species with roughly a dozen highly isolated geographic populations, providing a strong scientific basis for watershed-based future conservation.
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Affiliation(s)
- Christopher R Suchocki
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cassie Ka'apu-Lyons
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cameron A J Walsh
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Anne M Lee
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Julie Meka Carter
- Arizona Game and Fish Department, 5000 W. Carefree Highway, Phoenix, AZ, 85086, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
- Reefscape Restoration Initiative, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA.
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7
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Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
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Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
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Groeneveld MJ, Klein JD, Bennett RH, Bester-van der Merwe AE. Characterization of the complete mitochondrial genomes of two Critically Endangered wedgefishes: Rhynchobatus djiddensis and Rhynchobatus australiae. Mitochondrial DNA B Resour 2023; 8:352-358. [PMID: 36926642 PMCID: PMC10013529 DOI: 10.1080/23802359.2023.2167479] [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] [Indexed: 03/18/2023] Open
Abstract
We present the complete mitochondrial genomes of the Critically Endangered whitespotted wedgefish, Rhynchobatus djiddensis (Forsskål, 1775), and bottlenose wedgefish, Rhynchobatus australiae (Whitley, 1939), with the R. djiddensis mitogenome documented for the first time. The genomes for R. djiddensis and R. australiae are 16,799 and 16,805 bp in length, respectively. Both comprise 13 protein-coding regions, 22 tRNA genes, two rRNA genes, and a non-coding control region. All protein-coding regions consistently start with the ATG start codon; however, the alternative start codon GTG is observed at the start of the COX1 gene. NADH2, COX2, and NADH4 have incomplete stop codons: T or TA, and tRNALeu and tRNASer , have atypical codons: UAA, UGA, GCU, and UAG. The phylogenetic analysis places R. djiddensis and R. australiae within the Rhynchobatus genus, separate from other families in the order Rhinopristiformes. We also highlight the most variable gene regions to expedite future primer design, of which NADH2 was the most variable (4.5%) when taking gene length into account. These molecular resources could promote the taxonomic resolution of the whitespotted wedgefish species complex and aid in the genetic characterization of populations of these and related species.
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Affiliation(s)
- M J Groeneveld
- Department of Genetics, Molecular Breeding and Biodiversity Group, Stellenbosch University, Stellenbosch, South Africa
| | - J D Klein
- Department of Genetics, Molecular Breeding and Biodiversity Group, Stellenbosch University, Stellenbosch, South Africa
| | - R H Bennett
- Wildlife Conservation Society, Western Indian Ocean Shark and Ray Conservation Program, Bronx, NY, USA
| | - A E Bester-van der Merwe
- Department of Genetics, Molecular Breeding and Biodiversity Group, Stellenbosch University, Stellenbosch, South Africa
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9
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Chafin TK, Regmi B, Douglas MR, Edds DR, Wangchuk K, Dorji S, Norbu P, Norbu S, Changlu C, Khanal GP, Tshering S, Douglas ME. Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210727. [PMID: 34729207 PMCID: PMC8548808 DOI: 10.1098/rsos.210727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological 'ecotypes' observed in polyploid snowtrout (Cyprinidae: Schizothorax). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq (N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples (N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational 'ecotypes' were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively 'masks' previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 80309, USA
| | - Binod Regmi
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - David R. Edds
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Karma Wangchuk
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sonam Dorji
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Pema Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sangay Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Changlu Changlu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Gopal Prasad Khanal
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Singye Tshering
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
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