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Woronowicz KC, Esin EV, Markevich GN, Martinez CS, McMenamin SK, Daane JM, Harris MP, Shkil FN. Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.24.529919. [PMID: 38712299 PMCID: PMC11071292 DOI: 10.1101/2023.02.24.529919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Recent adaptive radiations provide evolutionary case studies, which provide the context to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phylogenetics as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, species flocks normally comprise only two to three lineages. Dolly Varden charr inhabiting Lake Kronotske represent the most extensive radiation described for the charr genus, containing at least seven lineages, each with defining morphological and ecological traits. Here, we perform the first genome-wide analysis of this species flock to parse the foundations of adaptive change. Our data support distinct, reproductively isolated lineages with little evidence of hybridization. We also find that specific selection on thyroid signaling and craniofacial genes forms a genomic basis for the radiation. Thyroid hormone is further implicated in subsequent lineage partitioning events. These results delineate a clear genetic basis for the diversification of specialized lineages, and highlight the role of developmental mechanisms in shaping the forms generated during adaptive radiation.
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Affiliation(s)
- Katherine C Woronowicz
- Department of Orthopaedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Evgeny V Esin
- AN Severtsov Institute of Ecology and Evolution, RAS; Leninskiy-33, 119071 Moscow, Russian Federation
| | - Grigorii N Markevich
- Kronotsky Nature Biosphere Reserve; Ryabikova-48, 68400 Yelizovo, Russian Federation
| | | | | | - Jacob M Daane
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204
| | - Matthew P Harris
- Department of Orthopaedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Fedor N Shkil
- AN Severtsov Institute of Ecology and Evolution, RAS; Leninskiy-33, 119071 Moscow, Russian Federation
- NK Koltzov Institute of Developmental Biology, RAS; Vavilova-26, 119334 Moscow, Russian Federation
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2
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Gautney JR. A new approach to exploratory data analysis in hominin phylogenetic reconstruction. J Hum Evol 2023; 182:103412. [PMID: 37499423 DOI: 10.1016/j.jhevol.2023.103412] [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: 09/23/2022] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/29/2023]
Abstract
The phylogenetic relationships between fossil hominin taxa have been a contentious topic for decades. Recent discoveries of new taxa, rather than resolving the issue, have only further confused it. Compounding this problem are the limitations of some of the tools frequently used by paleoanthropologists to analyze these relationships. Most commonly, phylogenetic questions are investigated using analytical methods such as maximum parsimony and Bayesian analysis. While these are useful analytical tools, these tree-building methods can have limitations when investigating taxa that may have complex evolutionary histories. Exploratory data analysis can provide information about patterns in a dataset that are obscured by tree-based methods. These patterns include phylogenetic signal conflict, which is not depicted in tree-based methods. Signal conflict can have a number of sources, including methodological issues with character choice, taxonomic issues, homoplasy, and gene flow between taxa. In this study, an exploratory data analysis of fossil hominin morphological data is conducted using the tree-based analytical method neighbor-joining and the network-based analytical method neighbor-net with the goal of visualizing phylogenetic signal conflict within a hominin morphological data set. The data set is divided into cranial regions, and each cranial region is analyzed individually to investigate which regions of the skull contain the highest levels of signal conflict. Results of this analysis show that conflicting phylogenetic signals are present in the hominin fossil record during the relatively speciose period between 3 and 1 Ma, and they also indicate that levels of signal conflict vary by cranial region. Possible sources of these conflicting signals are then explored. Exploratory data analyses such as this can be a useful tool in generating phylogenetic hypotheses and in refining character choice. This study also highlights the value network-based approaches can bring to the hominin phylogenetic analysis toolkit.
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Affiliation(s)
- Joanna R Gautney
- Department of Sociology and Anthropology, Weber State University, 1299 Edvalson St., Ogden, UT, USA.
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3
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Lantiegne TH, Purchase CF. Can cryptic female choice prevent invasive hybridization in external fertilizing fish? Evol Appl 2023; 16:1412-1421. [PMID: 37622094 PMCID: PMC10445091 DOI: 10.1111/eva.13573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/08/2023] [Indexed: 08/26/2023] Open
Abstract
Polyandrous mating systems result in females mating with multiple males, generating opportunities for strong pre-mating and post-mating sexual selection. Polyandry also creates the potential for unintended matings and subsequent sperm competition with hybridizing species. Cryptic female choice allows females to bias paternity towards preferred males under sperm competition and may include conspecific sperm preference when under hybridization risk. The potential for hybridization becomes particularly important in context of invasive species that can novelly hybridize with natives, and by definition, have evolved allopatrically. We provide the first examination of conspecific sperm preference in a system of three species with the potential to hybridize: North American native Atlantic salmon (Salmo salar) and brook char (Salvelinus fontinalis), and invasive brown trout (Salmo trutta) from Europe. Using naturalized populations on the island of Newfoundland, we measured changes in sperm swimming performance, a known predictor of paternity, to determine the degree of modification in sperm swimming to female cues related to conspecific sperm preference. Compared to water alone, female ovarian fluid in general had a pronounced effect and changed sperm motility (by a mean of 53%) and swimming velocity (mean 30%), but not linearity (mean 6%). However, patterns in the degree of modification suggest there is no conspecific sperm preference in the North American populations. Furthermore, female cues from both native species tended to boost the sperm of invasive males more than their own. We conclude that cryptic female choice via ovarian fluid mediated sperm swimming modification is too weak in this system to prevent invasive hybridization and is likely insufficient to promote or maintain reproductive isolation between the native North American species.
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Affiliation(s)
- Tyler H. Lantiegne
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland & LabradorCanada
| | - Craig F. Purchase
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland & LabradorCanada
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Raheem DC, Gower DJ, Breugelmans K, Ranawana KB, Backeljau T. The systematics and evolution of the Sri Lankan rainforest land snail Corilla: New insights from RADseq-based phylogenetics. Mol Phylogenet Evol 2023; 182:107731. [PMID: 36781030 DOI: 10.1016/j.ympev.2023.107731] [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: 08/15/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
The stylommatophoran land-snail genus Corilla is endemic to Sri Lanka and India's Western Ghats. On the basis of habitat distribution and shell morphology, the 10 extant Sri Lankan species fall into two distinct groups, lowland and montane. Here, we use phylogenetic analyses of restriction-site-associated DNA sequencing (RADseq) data and ancestral-state reconstructions of habitat association and shell morphology to clarify the systematics and evolution of Sri Lankan Corilla. Our dataset consists of 9 species of Corilla. Phylogenetic analyses were based on 88 assemblies (9,604-4,132,850 bp) generated by the RADseq assembler ipyrad, using four parameter combinations and different levels of missing data. Trees were inferred using a maximum likelihood (ML) approach. Ancestral states were reconstructed using maximum parsimony (MP) and ML approaches, with 1 binary state character analysed for habitat association (lowland vs montane) and 6 binary state characters analysed for shell morphology (shape, colour, lip width, length of upper palatal folds, orientation of upper palatal folds and collabral sculpture). Over a wide range of missing data (40-87 % missing individuals per locus) and assembly sizes (62,279-4,132,850 bp), nearly all trees conformed to one of two topologies (A and B), most relationships were strongly supported and total branch support approached the maximal value. Apart from the position of Corilla odontophora 'south', topologies A and B showed similar, well-resolved relationships at and above the species level. Our study agrees with the shell-based taxonomy of C. adamsi, C. beddomeae, C. carabinata, C. colletti and C. humberti (all maximally supported as monophyletic species). It shows that C. erronea and C. fryae constitute a single relatively widespread species (for which the valid name is C. erronea) and that the names C. gudei and C. odontophora each apply to at least two distinct, yet conchologically-cryptic species. The MP and ML ancestral-state reconstructions yielded broadly similar results and provide firm evidence that diversification in Sri Lankan Corilla has involved evolutionary convergence in the shell morphology of lowland lineages, with a pale shell and wide lip having evolved on at least two separate occasions (in C. carabinata and C. colletti) from montane ancestors having a dark, narrow-lipped shell.
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Affiliation(s)
- Dinarzarde C Raheem
- Department of Biological Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK.
| | - David J Gower
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Karin Breugelmans
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
| | - Kithsiri B Ranawana
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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Vargas RA, Soto-Aguilera S, Parra M, Herrera S, Santibañez A, Kossack C, Saavedra CP, Mora O, Pineda M, Gonzalez O, Gonzalez A, Maisey K, Torres-Maravilla E, Bermúdez-Humarán LG, Suárez-Villota EY, Tello M. Analysis of microbiota-host communication mediated by butyrate in Atlantic Salmon. Comput Struct Biotechnol J 2023; 21:2558-2578. [PMID: 37122632 PMCID: PMC10130356 DOI: 10.1016/j.csbj.2023.03.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Butyrate is a microbiota-produced metabolite, sensed by host short-chain fatty acid receptors FFAR2 (Gpr43), FFAR3 (Gpr41), HCAR2 (Gpr109A), and Histone deacetylase (HDAC) that promotes microbiota-host crosstalk. Butyrate influences energy uptake, developmental and immune response in mammals. This microbial metabolite is produced by around 79 anaerobic genera present in the mammalian gut, yet little is known about the role of butyrate in the host-microbiota interaction in salmonid fish. To further our knowledge of this interaction, we analyzed the intestinal microbiota and genome of Atlantic salmon (Salmo salar), searching for butyrate-producing genera and host butyrate receptors. We identified Firmicutes, Proteobacteria, and Actinobacteria as the main butyrate-producing bacteria in the salmon gut microbiota. In the Atlantic salmon genome, we identified an expansion of genes orthologous to FFAR2 and HCAR2 receptors, and class I and IIa HDACs that are sensitive to butyrate. In addition, we determined the expression levels of orthologous of HCAR2 in the gut, spleen, and head-kidney, and FFAR2 in RTgutGC cells. The effect of butyrate on the Atlantic salmon immune response was evaluated by analyzing the pro and anti-inflammatory cytokines response in vitro in SHK-1 cells by RT-qPCR. Butyrate decreased the expression of the pro-inflammatory cytokine IL-1β and increased anti-inflammatory IL-10 and TGF-β cytokines. Butyrate also reduced the expression of interferon-alpha, Mx, and PKR, and decreased the viral load at a higher concentration (4 mM) in cells treated with this molecule before the infection with Infectious Pancreatic Necrosis Virus (IPNV) by mechanisms independent of FFAR2, FFAR3 and HCAR2 expression that probably inhibit HDAC. Moreover, butyrate modified phosphorylation of cytoplasmic proteins in RTgutGC cells. Our data allow us to infer that Atlantic salmon have the ability to sense butyrate produced by their gut microbiota via different specific targets, through which butyrate modulates the immune response of pro and anti-inflammatory cytokines and the antiviral response.
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Secci-Petretto G, Englmaier GK, Weiss SJ, Antonov A, Persat H, Denys GPJ, Schenekar T, Romanov VI, Taylor EB, Froufe E. Evaluating a species phylogeny using ddRAD SNPs: Cyto-nuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae). Mol Phylogenet Evol 2023; 178:107654. [PMID: 36336233 DOI: 10.1016/j.ympev.2022.107654] [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: 06/10/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Hybridization and introgression are very common among freshwater fishes due to the dynamic nature of hydrological landscapes. Cyclic patterns of allopatry and secondary contact provide numerous opportunities for interspecific gene flow, which can lead to discordant paths of evolution for mitochondrial and nuclear genomes. Here, we used double digest restriction-site associated DNA sequencing (ddRADseq) to obtain a genome-wide single nucleotide polymorphism (SNP) dataset comprehensive for allThymallus (Salmonidae)species to infer phylogenetic relationships and evaluate potential recent and historical gene flow among species. The newly obtained nuclear phylogeny was largely concordant with a previously published mitogenome-based topology but revealed a few cyto-nuclear discordances. These incongruencies primarily involved the placement of internal nodes rather than the resolution of species, except for one European species where anthropogenic stock transfers are thought to be responsible for the observed pattern. The analysis of four contact zones where multiple species are found revealed a few cases of mitochondrial capture and limited signals of nuclear introgression. Interestingly, the mechanisms restricting interspecific gene flow might be distinct; while in zones of secondary contact, small-scale physical habitat separation appeared as a limiting factor, biologically based reinforcement mechanisms are presumed to be operative in areas where species presumably evolved in sympatry. Signals of historical introgression were largely congruent with the routes of species dispersal previously inferred from mitogenome data. Overall, the ddRADseq dataset provided a robust phylogenetic reconstruction of the genus Thymallus including new insights into historical hybridization and introgression, opening up new questions concerning their evolutionary history.
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Affiliation(s)
- Giulia Secci-Petretto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - Gernot K Englmaier
- University of Graz, Institute of Biology, Universitätsplatz 2, 8010 Graz, Austria
| | - Steven J Weiss
- University of Graz, Institute of Biology, Universitätsplatz 2, 8010 Graz, Austria.
| | - Alexander Antonov
- Institute of Water and Ecological Problems, Far East Branch, Russian Academy of Sciences, ul. Kim Yu Chena 65, Khabarovsk, 680063 Russia
| | - Henri Persat
- Société Française d'Ichthyologie, Muséum National d'Histoire Naturelle Paris, France, 57 rue Cuvier CP26, 75005 Paris, France
| | - Gael P J Denys
- Unité Patrimoine Naturel - Centre d'expertise et de données (2006 OFB - CNRS - MNHN), Muséum national d'Histoire naturelle, 36 rue Geoffroy Saint-Hilaire CP 41, 75005 Paris, France; Biologie des organismes et écosystèmes aquatiques (BOREA 8067), MNHN, CNRS, IRD, SU, UCN, UA, 57 rue Cuvier CP26, 75005 Paris, France
| | - Tamara Schenekar
- University of Graz, Institute of Biology, Universitätsplatz 2, 8010 Graz, Austria
| | | | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z, Canada
| | - Elsa Froufe
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.
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7
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [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: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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Martin Cerezo ML, Raval R, de Haro Reyes B, Kucka M, Chan FY, Bryk J. Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol. Mol Ecol Resour 2022; 22:2860-2870. [PMID: 35668693 PMCID: PMC9796921 DOI: 10.1111/1755-0998.13661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/07/2023]
Abstract
Highly multiplexed approaches have become common in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals using combinatorially barcoded adapters. These strategies, however, can potentially misassigned reads to incorrect samples. Here, we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to 100 multiplexed samples per sequencing lane (639 samples in total). We created two types of sequencing libraries: four libraries of type A, where PCRs were run on individual samples before multiplexing, and three libraries of type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) than type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in type A and B libraries, respectively. We also show that increasing the number of mismatches allowed for barcode rescue to above 2 dramatically increases the number of recovered chimeric reads. We provide recommendations for developing highly multiplexed RAD-seq protocols and analysing the resulting data to minimize the generation of chimeric sequences, allowing their quantification and a finer control on the number of PCR cycles necessary to generate enough input DNA for library preparation.
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Affiliation(s)
- Maria Luisa Martin Cerezo
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK,IFM BiologyLinköping UniversityLinköpingSweden
| | - Rohan Raval
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| | - Bernardo de Haro Reyes
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK,IFM BiologyLinköping UniversityLinköpingSweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | | | - Jarosław Bryk
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
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Wright JJ, Bruce SA, Sinopoli DA, Palumbo JR, Stewart DJ. Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage. Sci Rep 2022; 12:16514. [PMID: 36192509 PMCID: PMC9529906 DOI: 10.1038/s41598-022-20875-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
The Bowfin (Amia calva), as currently recognized, represents the sole living member of the family Amiidae, which dates back to approximately 150 Ma. Prior to 1896, 13 species of extant Bowfins had been described, but these were all placed into a single species with no rationale or analysis given. This situation has persisted until the present day, with little attention given to re-evaluation of those previously described nominal forms. Here, we present a phylogenomic analysis based on over 21,000 single nucleotide polymorphisms (SNPs) from 94 individuals that unambiguously demonstrates the presence of at least two independent evolutionary lineages within extant Amia populations that merit species-level standing, as well as the possibility of two more. These findings not only expand the recognizable species diversity in an iconic, ancient lineage, but also demonstrate the utility of such methods in addressing previously intractable questions of molecular systematics and phylogeography in slowly evolving groups of ancient fishes.
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Affiliation(s)
- Jeremy J Wright
- Research & Collections, New York State Museum, 3140 Cultural Education Center, Albany, NY, USA.
| | - Spencer A Bruce
- Department of Information Technology Services, University at Albany-State University of New York, Albany, NY, USA
| | - Daniel A Sinopoli
- Department of Biological Sciences, Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Jay R Palumbo
- Department of Environmental Science & Ecology, State University of New York at Brockport, Brockport, NY, USA
| | - Donald J Stewart
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA.
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Zhou W, Jenny Xiang QY. Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches. Mol Phylogenet Evol 2022; 176:107592. [DOI: 10.1016/j.ympev.2022.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 10/31/2022]
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Polgar G, Iaia M, Righi T, Volta P. The Italian Alpine and Subalpine trouts: Taxonomy, Evolution, and Conservation. BIOLOGY 2022; 11:biology11040576. [PMID: 35453775 PMCID: PMC9026872 DOI: 10.3390/biology11040576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary In a great part of the world, trout fishing has long inspired human spiritual ideals of immersion into nature and recreation, far removed from the fast-encroaching urbanization. Concurrently, these values and emotions fueled a white-hot business, establishing a florid market of outdoor recreation. Since the 20th century, the trout-culture industry strived to provide anglers with fishing entertainment by stocking massive amounts of non-native trouts in dozens of countries, irrespective of the lakes’ and rivers’ carrying capacity. This had dire consequences on the structural and functional diversity of these ecosystems. “Trout wars” sparked throughout the world between the promoters of stocking activities and the promoters of “wild trout management” and ethics. The “Italian trout war” has been fought on the harsh battleground of trout taxonomy, ecology, distribution, and native vs. non-native interfertile species. Northern Italy, home to the Italian Alpine and subalpine trouts and economic center of the national trout-culture and stocking industry, was particularly affected by this clash. We review here the state of art of this ongoing debate, outlining our scientific view of the taxonomy, evolution, distribution, and sustainable management of the native Italian trouts of northern Italy. Abstract During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers’ demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth, and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of the art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the South-western Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy.
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Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Europe, the S. trutta complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the S. trutta complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term Salmo macrostigma should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena.
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Gundappa MK, To TH, Grønvold L, Martin SAM, Lien S, Geist J, Hazlerigg D, Sandve SR, Macqueen DJ. Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution. Mol Biol Evol 2022; 39:msab310. [PMID: 34718723 PMCID: PMC8760942 DOI: 10.1093/molbev/msab310] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The long-term evolutionary impacts of whole-genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologs) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnolog sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent "explosion" of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnolog divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial "wave" of rediploidization in the late Cretaceous (85-106 Ma). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnolog divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
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Affiliation(s)
- Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Thu-Hien To
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Lars Grønvold
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Juergen Geist
- Aquatic Systems Biology Unit, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - David Hazlerigg
- Department of Arctic and Marine Biology, Faculty of BioSciences Fisheries & Economy, University of Tromsø, Norway
| | - Simen R Sandve
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
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14
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Ortiz D, Pekár S, Dianat M. Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics. Cladistics 2021; 38:320-334. [PMID: 34699083 DOI: 10.1111/cla.12493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2021] [Indexed: 11/28/2022] Open
Abstract
RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czechia
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czechia
| | - Malahat Dianat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czechia
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15
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Levin B, Simonov E, Franchini P, Mugue N, Golubtsov A, Meyer A. Rapid adaptive radiation in a hillstream cyprinid fish in the East African White Nile River basin. Mol Ecol 2021; 30:5530-5550. [PMID: 34409661 DOI: 10.1111/mec.16130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Adaptive radiation of freshwater fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that riverine and stream environments also provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeast Asia to West Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have probably been found among these ecomorphs in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra ("thick-lipped" and "predatory") that had not been discovered before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intrabasin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide single nucleotide polymorphism data, mitochondrial DNA was unable to identify any genetic structure suggesting recent and rapid speciation events. Some data suggest a hybrid origin of the novel "thick-lipped" ecomorph. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly radiated in a riverine environment promoted by the evolution of novel feeding strategies.
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Affiliation(s)
- Boris Levin
- Papanin Institute of Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.,Zoological Institute of Russian Academy of Sciences, Cherepovets State University, St. Petersburg, Russia
| | - Evgeniy Simonov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, Russia
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nikolai Mugue
- Koltzov Institute for Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Golubtsov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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16
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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17
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Ikert H, Osokin S, Saito JR, Craig PM. Responses of microRNA and predicted mRNA and enzymatic targets in liver of two salmonids (Oncorhynchus mykiss and Salvelinus fontinalis) following air exposure. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110646. [PMID: 34271192 DOI: 10.1016/j.cbpb.2021.110646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
The acute stress response is well-characterized, with rainbow trout as a teleost model for physiological and molecular responses. Air exposure, which stimulates an acute stress response, modulates liver microRNAs in rainbow trout; however, these highly conserved non-coding RNAs that bind to mRNA and repress translation, have never been measured in brook trout and it is unknown how miRNA expression responds following air exposure in this less studied salmonid. Our objective was to characterize the effects of air exposure on rainbow and brook trout liver miRNA expression, as well as the mRNA expression and enzyme activity that the miRNAs are predicted to target. Brook and rainbow trout were sampled pre- and 1-, 3-, and 24-h post- a three-minute air exposure. Plasma cortisol, glucose, and lactate were measured. Relative expression of miR-21a-5p, miR-143-3p, let-7a-5p and relative expression and enzyme activities of five predicted targets (pyruvate kinase, glucokinase, citrate synthase, cytochrome c oxidase, and catalase) were measured in liver. Rainbow and brook trout both had increases in plasma cortisol and lactate, while only rainbow trout had significant post-stress increases in plasma glucose. Furthermore, both trout species had increased miR-143-3p and miR-21a-5p relative expression 24-h post-stress. Four of the five enzymes measured had altered activity following stress. Brook trout miRNAs had inverse relative expression with relative catalase mRNA expression and cytochrome c oxidase enzyme activity, but no relationship was found in rainbow trout. Therefore, we have further characterized the transcriptional and enzymatic response to air exposure in two salmonids.
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Affiliation(s)
- Heather Ikert
- University of Waterloo, 200 University Ave W., Waterloo, Ontario, Canada.
| | - Slava Osokin
- University of Waterloo, 200 University Ave W., Waterloo, Ontario, Canada
| | - Joshua R Saito
- University of Waterloo, 200 University Ave W., Waterloo, Ontario, Canada
| | - Paul M Craig
- University of Waterloo, 200 University Ave W., Waterloo, Ontario, Canada
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18
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Kartavtsev YP. Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society. Animals (Basel) 2021; 11:1473. [PMID: 34065552 PMCID: PMC8160991 DOI: 10.3390/ani11051473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 01/27/2023] Open
Abstract
Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
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19
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Hashemzadeh Segherloo I, Freyhof J, Berrebi P, Ferchaud AL, Geiger M, Laroche J, Levin BA, Normandeau E, Bernatchez L. A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)? Mol Phylogenet Evol 2021; 162:107204. [PMID: 34015446 DOI: 10.1016/j.ympev.2021.107204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.
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Affiliation(s)
- Iraj Hashemzadeh Segherloo
- Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahr-e-Kord University, Shahr-e-Kord, Iran; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada.
| | - Jörg Freyhof
- Museum für Naturkunde Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany
| | - Patrick Berrebi
- Genome - Research & Diagnostic, 697 avenue de Lunel, 34400 Saint-Just, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Matthias Geiger
- Zoologisches Forschungsmuseum Museum Alexander Koenig, Leibniz Institute for Animal Biodiversity, 53133 Bonn, Germany
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Boris A Levin
- Papanin Institute of Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia & Cherepovets State University, Cherepovets, Vologda Region, Russia
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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20
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Oleinik AG, Skurikhina LA, Kukhlevsky AD, Semenchenko AA. The first complete mitochondrial genomes of two species of charr, Salvelinus boganidae and Salvelinus elgyticus, from Lake El’gygytgyn (Chukotka). Polar Biol 2021. [DOI: 10.1007/s00300-021-02861-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Weiss SJ, Gonçalves DV, Secci-Petretto G, Englmaier GK, Gomes-Dos-Santos A, Denys GPJ, Persat H, Antonov A, Hahn C, Taylor EB, Froufe E. Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00468-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractGraylings (Thymallus) are among the less well-studied groups of salmonid fishes, especially across their Asian distribution range. Here we perform a comprehensive global review of their phylogeography, systematic diversity and range distributions, including biogeographic reconstruction and assessment of both conservation and taxonomic status of each species. Based on a mitogenomic phylogenetic analysis, three approaches to the delineation of molecular operational units, and evaluation of 15 a-priori defined species, we provide biological support for the recognition of 13 grayling species, plus two additional species tentatively. Several instances of paraphyly and its potential effect on systematic inferences are discussed. Overall, the genus displays increasing species diversity and decreasing range size from higher to lower latitudes and ancestral trait reconstruction supports an East Asian origin for extant diversity, most likely centred in the Amur River drainage. Europe’s colonization by Thymallus took place as early as the late Miocene, at least two colonisations of North America are supported, and multiple dispersal events likely took place into Western Siberia. The conservation status for the 15 taxa was estimated to be: 6 least concern, 1 near-threatened, 2 vulnerable, 3 endangered and 3 data deficient.
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Uckele KA, Adams RP, Schwarzbach AE, Parchman TL. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 2020; 156:107022. [PMID: 33242585 DOI: 10.1016/j.ympev.2020.107022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022]
Abstract
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.
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Affiliation(s)
- Kathryn A Uckele
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
| | - Robert P Adams
- Baylor University, Utah Lab, 201 N 5500 W, Hurricane, UT 84790, USA.
| | - Andrea E Schwarzbach
- Department of Health and Biomedical Sciences, University of Texas - Rio Grande Valley, 1 W University Drive, Brownsville, TX 78520, USA.
| | - Thomas L Parchman
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
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Campbell MA, Buser TJ, Alfaro ME, López JA. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. PeerJ 2020; 8:e9389. [PMID: 32685284 PMCID: PMC7337038 DOI: 10.7717/peerj.9389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo.
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Affiliation(s)
- Matthew A. Campbell
- University of Alaska Museum, University of Alaska—Fairbanks, Fairbanks, AK, USA
| | - Thaddaeus J. Buser
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - J. Andrés López
- University of Alaska Museum, University of Alaska—Fairbanks, Fairbanks, AK, USA
- College of Fisheries and Ocean Sciences, University of Alaska—Fairbanks, Fairbanks, AK, USA
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24
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Bohling J. Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets. Ecol Evol 2020; 10:7585-7601. [PMID: 32760550 PMCID: PMC7391306 DOI: 10.1002/ece3.6483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/29/2022] Open
Abstract
The advent of high-throughput sequencing (HTS) has made genomic-level analyses feasible for nonmodel organisms. A critical step of many HTS pipelines involves aligning reads to a reference genome to identify variants. Despite recent initiatives, only a fraction of species has publically available reference genomes. Therefore, a common practice is to align reads to the genome of an organism related to the target species; however, this could affect read alignment and bias genotyping. In this study, I conducted an experiment using empirical RADseq datasets generated for two species of salmonids (Actinopterygii; Teleostei; Salmonidae) to address these questions. There are currently reference genomes for six salmonids of varying phylogenetic distance. I aligned the RADseq data to all six genomes and identified variants with several different genotypers, which were then fed into population genetic analyses. Increasing phylogenetic distance between target species and reference genome reduced the proportion of reads that successfully aligned and mapping quality. Reference genome also influenced the number of SNPs that were generated and depth at those SNPs, although the affect varied by genotyper. Inferences of population structure were mixed: increasing reference genome divergence reduced estimates of differentiation but similar patterns of population relationships were found across scenarios. These findings reveal how the choice of reference genome can influence the output of bioinformatic pipelines. It also emphasizes the need to identify best practices and guidelines for the burgeoning field of biodiversity genomics.
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Affiliation(s)
- Justin Bohling
- Abernathy Fish Technology Center US Fish and Wildlife Service Longview WA USA
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25
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Jacobs A, Carruthers M, Yurchenko A, Gordeeva NV, Alekseyev SS, Hooker O, Leong JS, Minkley DR, Rondeau EB, Koop BF, Adams CE, Elmer KR. Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish. PLoS Genet 2020; 16:e1008658. [PMID: 32302300 PMCID: PMC7164584 DOI: 10.1371/journal.pgen.1008658] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/06/2020] [Indexed: 01/05/2023] Open
Abstract
Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Madeleine Carruthers
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Andrey Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Natalia V. Gordeeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey S. Alekseyev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Oliver Hooker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Jong S. Leong
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - David R. Minkley
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Eric B. Rondeau
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Ben F. Koop
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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Xue JY, Wang Y, Chen M, Dong S, Shao ZQ, Liu Y. Maternal Inheritance of U's Triangle and Evolutionary Process of Brassica Mitochondrial Genomes. FRONTIERS IN PLANT SCIENCE 2020; 11:805. [PMID: 32595682 PMCID: PMC7303332 DOI: 10.3389/fpls.2020.00805] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/19/2020] [Indexed: 05/21/2023]
Abstract
The sequences and genomic structures of plant mitochondrial (mt) genomes provide unique material for phylogenetic studies. The nature of uniparental inheritance renders an advantage when utilizing mt genomes for determining the parental sources of hybridized taxa. In this study, a concatenated matrix of mt genes was used to infer the phylogenetic relationships of six cultivated Brassica taxa and explore the maternal origins of three allotetraploids. The well-resolved sister relationships between two pairs of diploid and allotetraploid taxa suggest that Brassica carinata (car) possessed a maternal origin from Brassica nigra, while Brassica juncea (jun) was maternally derived from Brassica rapa (cam). Another allotetraploid taxon, Brassica napus (cv. Wester) may have been maternally derived from the common ancestor of B. rapa and Brassica oleracea (ole), and/or have undergone (an) extra hybridization event(s) along its evolutionary history. The characteristics of Brassica mt genomic structures also supported the phylogenetic results. Sinapis arvensis was nested inside the Brassica species, sister to the B. nigra-B. carinata lineage, and possessed an mt genome structure that mostly resembled B. nigra. Collectively, the evidence supported a systematic revision that placed S. arvensis within Brassica. Finally, ancestral mt genomes at each evolutionary node of Brassica were reconstructed, and the detailed and dynamic evolution of Brassica mt genomes was successfully reproduced. The mt genome of B. nigra structurally resembled that of the Brassica ancestor the most, with only one reversion of a block, and the Brassica oleracea underwent the most drastic changes. These findings suggested that repeat-mediated recombinations were largely responsible for the observed structural variations in the evolutionary history of Brassica mt genomes.
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Affiliation(s)
- Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yue Wang
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Min Chen
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Shanshan Dong
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Zhu-Qing Shao,
| | - Yang Liu
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Yang Liu,
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27
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Gruzdeva MA, Semenova AV, Kuzishchin KV, Ponomareva EV, Volkov AA, Pavlov DS. Genetic Variability of Dolly Varden (Salvelinus malma), White-Spotted Char (S. leucomaenis), and Interspecific Hybrids from the Utkholok River (Northwestern Kamchatka). RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419090060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Schneider K, Adams CE, Elmer KR. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC Genomics 2019; 20:1010. [PMID: 31870285 PMCID: PMC6929470 DOI: 10.1186/s12864-019-6361-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup. Results All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling. Conclusions Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
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Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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29
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Lehnert SJ, Christensen KA, Vandersteen WE, Sakhrani D, Pitcher TE, Heath JW, Koop BF, Heath DD, Devlin RH. Carotenoid pigmentation in salmon: variation in expression at BCO2-l locus controls a key fitness trait affecting red coloration. Proc Biol Sci 2019; 286:20191588. [PMID: 31615356 DOI: 10.1098/rspb.2019.1588] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carotenoids are primarily responsible for the characteristic red flesh coloration of salmon. Flesh coloration is an economically and evolutionarily significant trait that varies inter- and intra-specifically, yet the underlying genetic mechanism is unknown. Chinook salmon (Oncorhynchus tshawytscha) represents an ideal system to study carotenoid variation as, unlike other salmonids, they exhibit extreme differences in carotenoid utilization due to genetic polymorphisms. Here, we crossed populations of Chinook salmon with fixed differences in flesh coloration (red versus white) for a genome-wide association study to identify loci associated with pigmentation. Here, the beta-carotene oxygenase 2-like (BCO2-l) gene was significantly associated with flesh colour, with the most significant single nucleotide polymorphism explaining 66% of the variation in colour. BCO2 gene disruption is linked to carotenoid accumulation in other taxa, therefore we hypothesize that an ancestral mutation partially disrupting BCO2-l activity (i.e. hypomorphic mutation) allowed the deposition and accumulation of carotenoids within Salmonidae. Indeed, we found elevated transcript levels of BCO2-l in white Chinook salmon relative to red. The long-standing mystery of why salmon are red, while no other fishes are, is thus probably explained by a hypomorphic mutation in the proto-salmonid at the time of divergence of red-fleshed salmonid genera (approx. 30 Ma).
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Affiliation(s)
- S J Lehnert
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada.,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - K A Christensen
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada.,University of Victoria, Victoria, British Columbia, Canada
| | - W E Vandersteen
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| | - D Sakhrani
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| | - T E Pitcher
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - J W Heath
- Yellow Island Aquaculture Ltd., Quadra Island, British Columbia, Canada
| | - B F Koop
- University of Victoria, Victoria, British Columbia, Canada
| | - D D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - R H Devlin
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
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30
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31
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Buser TJ, Finnegan DL, Summers AP, Kolmann MA. Have Niche, Will Travel. New Means of Linking Diet and Ecomorphology Reveals Niche Conservatism in Freshwater Cottoid Fishes. Integr Org Biol 2019; 1:obz023. [PMID: 33791537 PMCID: PMC7671106 DOI: 10.1093/iob/obz023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evolutionary transitions between habitats have been catalysts for some of the most stunning examples of adaptive diversification, with novel niches and new resources providing ecological opportunity for such radiations. In aquatic animals, transitions from saltwater to freshwater habitats are rare, but occur often enough that in the Neotropics for example, marine-derived fishes contribute noticeably to regional ichthyofaunal diversity. Here, we investigate how morphology has evolved in a group of temperate fishes that contain a marine to freshwater transition: the sculpins (Percomorpha; Cottoidea). We devised a novel method for classifying dietary niche and relating functional aspects of prey to their predators. Coupled with functional measurements of the jaw apparatus in cottoids, we explored whether freshwater sculpins have fundamentally changed their niche after invading freshwater (niche lability) or if they retain a niche similar to their marine cousins (niche conservatism). Freshwater sculpins exhibit both phylogeographical and ecological signals of phylogenetic niche conservatism, meaning that regardless of habitat, sculpins fill similar niche roles in either saltwater or freshwater. Rather than competition guiding niche conservatism in freshwater cottoids, we argue that strong intrinsic constraints on morphological and ecological evolution are at play, contra to other studies of diversification in marine-derived freshwater fishes. However, several intertidal and subtidal sculpins as well as several pelagic freshwater species from Lake Baikal show remarkable departures from the typical sculpin bauplan. Our method of prey categorization provides an explicit, quantitative means of classifying dietary niche for macroevolutionary studies, rather than relying on somewhat arbitrary means used in previous literature.
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Affiliation(s)
- T J Buser
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97321, USA
| | - D L Finnegan
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - A P Summers
- Department of Biology and SAFS, University of Washington s Friday Harbor Laboratories, Friday Harbor, WA 98250, USA
| | - M A Kolmann
- Department of Biology and SAFS, University of Washington s Friday Harbor Laboratories, Friday Harbor, WA 98250, USA
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA
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32
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Lima CS, Magalhães RF, Marmontel M, Meirelles AC, Carvalho VL, Lavergne A, Thoisy BDE, Santos FR. A hybrid swarm of manatees along the Guianas coastline, a peculiar environment under the influence of the Amazon River plume. AN ACAD BRAS CIENC 2019; 91:e20190325. [PMID: 31460594 DOI: 10.1590/0001-3765201920190325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/29/2019] [Indexed: 12/23/2022] Open
Abstract
The West Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees have a sympatric occurrence at the mouth of the Amazon River. A result of this interspecific encounter is the occurrence of hybrids, which are frequently found along the coasts of Amapá state in Brazil, French Guiana and Guyana. Here we present new genetic evidence indicating the occurrence of a hybrid swarm along the Guianas Shield coastline, which is an interspecific hybrid zone that also separates T. manatus populations located east (Brazil) and west (Caribbean, Gulf of Mexico, Florida and Antilles). In addition, we suggest that this hybrid population occupies a peculiar mangrove-rich environment under strong influence of the Amazon River plume, which requires an independent management and should be considered a special conservation area.
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Affiliation(s)
- Camilla S Lima
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-010 Belo Horizonte, MG, Brazil
| | - Rafael F Magalhães
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Miriam Marmontel
- Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, 2584, Fonte Boa, 69553-225 Tefé, AM, Brazil
| | - Ana Carolina Meirelles
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos/Aquasis, Av. José Alencar, 150, Sesc Iparana, 61627-010 Caucaia, CE, Brazil
| | - Vitor Luz Carvalho
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos/Aquasis, Av. José Alencar, 150, Sesc Iparana, 61627-010 Caucaia, CE, Brazil
| | - Anne Lavergne
- Institut Pasteur de Guyane, 23 Avenue Pasteur, BP 6010, Cayenne Cedex 97306, French Guiana, France
| | - Benoit DE Thoisy
- Institut Pasteur de Guyane, 23 Avenue Pasteur, BP 6010, Cayenne Cedex 97306, French Guiana, France.,Kwata NGO, 16 Avenue Pasteur, BP 60672 97335, Cayenne, French Guiana, France
| | - Fabrício R Santos
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-010 Belo Horizonte, MG, Brazil
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33
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Whelan NV, Galaska MP, Sipley BN, Weber JM, Johnson PD, Halanych KM, Helms BS. Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla. Mol Ecol 2019; 28:1593-1610. [PMID: 30697854 DOI: 10.1111/mec.15032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/10/2019] [Accepted: 01/23/2019] [Indexed: 12/14/2022]
Abstract
Within riverine systems, headwater populations are hypothesized to harbour higher amounts of genetic distinctiveness than populations in the main stem of a river and display increased genetic diversity in large, downstream habitats. However, these hypotheses were mostly developed with insects and fish, and they have not been tested on many invertebrate lineages. Pleuroceridae gastropods are of particular ecological importance to rivers of eastern North America, sometimes comprising over 90% of macroinvertebrate biomass. Yet, virtually nothing is known of pleurocerid landscape genetics, including whether genetic diversity follows predictions made by hypotheses developed on more mobile species. Moreover, the commonly repeated hypothesis that intraspecific morphological variation in gastropods results from ecophenotypic plasticity has not been well tested on pleurocerids. Using 2bRAD-seq to discover single nucleotide polymorphisms, we show that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream-biased, conflicting with previous hypotheses. Both tributary and main stem populations harbour unique genomic profiles, and genetic diversity was highest in downstream populations. Furthermore, L. ampla shell morphology was more correlated with genetic differences among individuals and populations than habitat characteristics. We anticipate similar genetic and demographic patterns to be seen in other pleurocerids, and hypotheses about gene flow and population demographics that were based on more mobile taxa often, but not always, apply to freshwater gastropods. From a conservation standpoint, genetic structure of L. ampla populations suggests distinctive genetic diversity is lost with localized extirpation, a phenomenon common across the range of Pleuroceridae.
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Affiliation(s)
- Nathan V Whelan
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, United States Fish and Wildlife Service, Auburn, Alabama.,School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, Alabama
| | - Matthew P Galaska
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | - Breanna N Sipley
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Jennifer M Weber
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Paul D Johnson
- Alabama Department of Conservation and Natural Resources, Alabama Aquatic Biodiversity Center, Marion, Alabama
| | | | - Brian S Helms
- Department of Biological and Environmental Sciences, Troy University, Troy, Alabama
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34
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Houston RD, Macqueen DJ. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Anim Genet 2019; 50:3-14. [PMID: 30426521 PMCID: PMC6492011 DOI: 10.1111/age.12748] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high-quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole-genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome-wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.
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Affiliation(s)
- R. D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianEH25 9RGUK
| | - D. J. Macqueen
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUK
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35
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Rancilhac L, Goudarzi F, Gehara M, Hemami MR, Elmer KR, Vences M, Steinfarz S. Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis. Mol Phylogenet Evol 2019; 133:189-197. [PMID: 30659915 DOI: 10.1016/j.ympev.2019.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/01/2019] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. kaiseri, and N. derjugini) against coalescent-based species-delimitation approaches of our genome-wide genetic data set. While the position of N. strauchii as sister species to all other Neurergus species was consistent in all of our analyses, the phylogenetic relationships between the three remaining species changed depending on the applied method. The concatenation approach, as well as quartet-based species-tree inference, supported a topology with N. kaiseri as the closest relative to N. derjugini, while full-coalescent species-tree inference approaches supported N. crocatus as sister species of N. derjugini. Investigating the individual signal of gene trees highlighted an extensive variation among gene histories, most likely resulting from incomplete lineage sorting. Coalescent-based species-delimitation models suggest that the current taxonomy might underestimate the species richness within Neurergus and supports seven species. Based on the current sampling, our analysis suggests that N. strauchii, N. derjugini and N. kaiseri might each be subdivided into further species. However, as amphibian species are known to be composed of deep conspecific lineages that do not always warrant species status, these results need to be cautiously interpreted in an integrative taxonomic framework. We hypothesize that the rather shallow divergences detected within N. kaiseri and N. derjugini likely reflect an ongoing speciation process and thus require further investigation. On the contrary, the much deeper genetic divergence found between the two morphologically and geographically differentiated subspecies of N. strauchii leads us to propose that N. s. barani should be considered a distinct species, Neurergus barani Öz, 1994.
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Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany.
| | - Forough Goudarzi
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany; Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Marcelo Gehara
- American Museum of Natural History, Department of Herpetology, Central Park West at 79th St, New York, NY 10024, USA
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
| | - Sebastian Steinfarz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
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36
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Kahnt B, Theodorou P, Soro A, Hollens-Kuhr H, Kuhlmann M, Pauw A, Paxton RJ. Small and genetically highly structured populations in a long-legged bee, Rediviva longimanus, as inferred by pooled RAD-seq. BMC Evol Biol 2018; 18:196. [PMID: 30567486 PMCID: PMC6300007 DOI: 10.1186/s12862-018-1313-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/28/2018] [Indexed: 11/10/2022] Open
Abstract
Adaptation to local host plants may impact a pollinator's population genetic structure by reducing gene flow and driving population genetic differentiation, representing an early stage of ecological speciation. South African Rediviva longimanus bees exhibit elongated forelegs, a bizarre adaptation for collecting oil from floral spurs of their Diascia hosts. Furthermore, R. longimanus foreleg length (FLL) differs significantly among populations, which has been hypothesised to result from selection imposed by inter-population variation in Diascia floral spur length. Here, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to investigate the population genetic structure of R. longimanus and to test if phenotypic differences in FLL translate into increased genetic differentiation (i) between R. longimanus populations and (ii) between phenotypes across populations. We also inferred the effects of demographic processes on population genetic structure and tested for genetic markers underpinning local adaptation. RESULTS: Populations showed marked genetic differentiation (average FST = 0.165), though differentiation was not statistically associated with differences between populations in FLL. All populations exhibited very low genetic diversity and were inferred to have gone through recent bottleneck events, suggesting extremely low effective population sizes. Genetic differentiation between samples pooled by leg length (short versus long) rather than by population of origin was even higher (FST = 0.260) than between populations, suggesting reduced interbreeding between long and short-legged individuals. Signatures of selection were detected in 1119 (3.8%) of a total of 29,721 SNP markers, CONCLUSIONS: Populations of R. longimanus appear to be small, bottlenecked and isolated. Though we could not detect the effect of local adaptation (FLL in response to floral spurs of host plants) on population genetic differentiation, short and long legged bees appeared to be partially differentiated, suggesting incipient ecological speciation. To test this hypothesis, greater resolution through the use of individual-based whole-genome analyses is now needed to quantify the degree of reproductive isolation between long and short legged bees between and even within populations.
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Affiliation(s)
- Belinda Kahnt
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - Panagiotis Theodorou
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Antonella Soro
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Hilke Hollens-Kuhr
- Institute of Landscape Ecology, Westfälische Wilhelms-Universität Münster, Heisenbergstraße 2, 48149, Münster, Germany
| | - Michael Kuhlmann
- Zoological Museum, Kiel University, Hegewischstr. 3, 24105, Kiel, Germany
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Anton Pauw
- Department of Botany and Zoology, Stellenbosch University, Matieland, 7602, South Africa
| | - Robert J Paxton
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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