Diversification of the shell shape and size in Baikal Candonidae ostracods inferred from molecular phylogeny

  • Claude, J., Paradis, E., Tong, H. & Auffray, J. C. A geometric morphometric assessment of the effects of environment and cladogenesis on the evolution of the turtle shell. Biol. J. Linn. Soc. 79, 485–501 (2003).

    Article 

    Google Scholar
     

  • Klingenberg, C. P., Duttke, S., Whelan, S. & Kim, M. Developmental plasticity, morphological variation and evolvability: A multilevel analysis of morphometric integration in the shape of compound leaves. J. Evol. Biol. 25, 115–129 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chazot, N. et al. Morpho morphometrics: Shared ancestry and selection drive the evolution of wing size and shape in Morpho butterflies. Evolution 70, 181–194 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Hedrick, B. P. et al. Morphological diversification under high integration in a hyper diverse mammal clade. J. Mamm. Evol. 27, 563–575 (2020).

    Article 

    Google Scholar
     

  • Adams, D. C., Korneisel, D., Young, M. & Nistri, A. Natural history constrains the macroevolution of foot morphology in European plethodontid salamanders. Am. Nat 190, 292–297 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Benson, R. H. Form, function, and architecture of ostracode shell. Annu. Rev. Earth Planet. Sci. 9, 59–80 (1981).

    Article 
    ADS 

    Google Scholar
     

  • Karanovic, I. & Sitnikova, T. Y. Phylogenetic position and age of Lake Baikal candonids (Crustacea, Ostracoda) inferred from multigene sequence analyzes and molecular dating. Ecol. Evol. 7, 7091–7103 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bukharov, A. A. Baikal in Numbers (Baikal Museum, Siberian Branch of the Russian Academy of Sciences, 2001).


    Google Scholar
     

  • Logachev, N. A. History and geodynamics of the Baikal rift. Geol. Geofiz. 44, 391–406 (2003).


    Google Scholar
     

  • Mats, V. D. & Perepelova, T. I. A new perspective on evolution of the Baikal Rift. Geosci. Front. 2, 349–365 (2011).

    Article 

    Google Scholar
     

  • Timoshkin, O. A. Lake Baikal: Diversity of fauna, problems of its immiscibility and origin, ecology and “exotic” communities. In Index of Animal Species Inhabiting Lake Baikal and Its Catchment Area (ed. Timoshkin, O. A.) 74–113 (Nauka, 2001).


    Google Scholar
     

  • Kondratov, I. G. et al. Amazing discoveries of benthic fauna from the Abyssal Zone of lake Baikal. Biology (Basel) 10, 972 (2021).

    CAS 
    PubMed 

    Google Scholar
     

  • Naumenko, S. A. et al. Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: Fast speciation accompanied by frequent episodes of positive selection. Mol. Ecol. 26, 536–553 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • St. John, C. A. et al. Diversification along a benthic to pelagic gradient contributes to fish diversity in the world’s largest lake (Lake Baikal, Russia). Mol. Ecol. 31, 238–251 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Schön, I., Pieri, V., Sherbakov, DYu. & Martens, K. Cryptic diversity and speciation in endemic Cytherissa (Ostracoda, Crustacea) from Lake Baikal. Hydrobiologia 800, 61–79 (2017).

    Article 

    Google Scholar
     

  • Schön, I. & Martens, K. Molecular analyses of ostracod flocks from Lake Baikal and Lake Tanganyika. Hydrobiology 682, 91–110 (2012).

    Article 

    Google Scholar
     

  • Mikulić, F. Nove Candona vrste iz Ohridskog Jezera. Bull. Mus. Hist. Nat. Belgrade 17, 87–108 (1961).


    Google Scholar
     

  • Krstić, N. Rod Candona (Ostracoda) iz Kongerijskih Slojeva Južnog Dela Panonskog Basena (Serbian Academy of Sciences and Arts Monograph, 1972).


    Google Scholar
     

  • Danielopol, D. L., Gross, M., Piller, W. E. & Baltanás, A. Ostracods of the Paratethys Sea and Lake Pannon—Perspectives for renewal of cooperative projects. Senckenb. Lethaea 88, 141–145 (2008).

    Article 

    Google Scholar
     

  • Karanovic, I. Recent Freshwater Ostracods of the World (Springer, 2012).

    Book 

    Google Scholar
     

  • Karanovic, I. Candoninae (Ostracoda) from the Pilbara Region in Western Australia. Crustac. Monogr. 7, 433 (2007).


    Google Scholar
     

  • Bronstein, Z. S. Ostracoda Presnyh Vod. Fauna SSSR. Rakoobraznye, Tom II, Vol. 1 (Akedemii Nauk SSR, 1947).

  • Mazepova, G. F. Rakushkovye Rachki (Ostracoda) Baykala (Akademija Nauk SSSR, Sibirskoe Otdelenie, Limnologicheskii Institut, 1990).


    Google Scholar
     

  • Danielopol, D. L., Baltanás, A., Morocutti, U. & Österreicher, F. On the need to renew the taxonomic system of the Candoninae (non-marine Ostracoda, Crustacea). Reflections from an analysis of data using the Yule Process. Geo-Eco-Marina 17, 197–212 (2011).


    Google Scholar
     

  • Meisch, C. Freshwater Ostracoda of Western and Central Europe (Spektrum Akademischer Verlag GmbH, 2000).


    Google Scholar
     

  • Danielopol, D. L. et al. The implementation of taxonomic harmonisation for Candoninae (Ostracoda, Cypridoidea): A heuristic solution for Fabaeformiscandona tricicatricosa (Diebel and Pietrzeniuk). Geo-Eco-Marina 21, 111–158 (2015).


    Google Scholar
     

  • Sánchez-Gonzáles, J. R., Baltanás, A. & Danielopol, D. L. Patterns of morphospace occupation in recent Cypridoidea (Crustacea, Ostracoda). Rev. Española de Micropaleont. 36, 13–27 (2004).


    Google Scholar
     

  • Baltanás, A. & Danielopol, D. L. Geometric morphometrics and its use in ostracod research: A short guide. Joannea Geol. Paläontol. 11, 235–272 (2011).


    Google Scholar
     

  • Karanovic, I., Lavtižar, V. & Djurakic, M. A complete survey of normal pores on a smooth shell ostracod (Crustacea): Landmark-based versus outline geometric morphometrics. J. Morphol. 8, 1091–1104 (2017).

    Article 

    Google Scholar
     

  • Wrozyna, C., Neubauer, T. A., Meyer, J., Ramos, M. I. F. & Piller, W. E. Significance of climate and hydrochemistry on shape variation—A case study on Neotropical cytheroidean Ostracoda. Biogeosicences 15, 5489–5502 (2018).

    Article 
    ADS 

    Google Scholar
     

  • Karanovic, I., Huyen, P. T. M. & Brandão, S. N. Ostracod shell plasticity across longitudinal and bathymetric ranges. Deep Sea Res. Part I 143, 115–126 (2019).

    Article 

    Google Scholar
     

  • Ramos, L. Y. et al. Morphological diversity and discrimination tools of the non-marine ostracod Cypridopsis silvestrii across temporal and spatial scales from Patagonia. An. Acad. Bras. Cienc. 93, e20200635 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Koenders, A., Schön, I., Halse, S. & Martens, K. Valve shape is not linked to genetic species in the Eucypris virens (Ostracoda, Crustacea) species complex. Zool. J. Linn. Soc. 180, 36–46 (2017).


    Google Scholar
     

  • Karanovic, I., Huyen, P. T. M., Yoo, H., Nakao, Y. & Tsukagoshi, A. Shell and appendages variability in two allopatric ostracod species seen through the light of molecular data. Contrib. Zool. 89, 247–269 (2020).

    Article 

    Google Scholar
     

  • Laffont, R. et al. Biodiversity and evolution in the light of morphometrics: From patterns to processes. C. R. Palevol 10, 133–142 (2011).

    Article 

    Google Scholar
     

  • Hunt, G. Evolutionary divergence in directions of high phenotypic variance in the ostracode genus Poseidonamicus. Evolution 61, 1560–1576 (2007).

    Article 
    PubMed 

    Google Scholar
     

  • Hunt, G. Testing the link between phenotypic evolution and speciation: An integrated palaeontological and phylogenetic analysis. Methods Ecol. Evol. 4, 714–723 (2013).

    Article 

    Google Scholar
     

  • Maddison, W. P. Gene trees in species trees. Syst. Biol. 46, 523–536 (1997).

    Article 

    Google Scholar
     

  • Wortley, A. H. & Scotland, R. W. The effect of combining molecular and morphological data in published phylogenetic analyses. Syst. Biol. 55, 677–685 (2006).

    Article 
    PubMed 

    Google Scholar
     

  • Parins-Fukuchi, C., Stull, G. W. & Smith, A. A. Phylogenomic conflict coincides with rapid morphological innovation. PNAS 118, e2023058118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Muschick, M., Indermaur, A. & Salzburger, W. Convergent evolution within an adaptive radiation of cichlid fishes. Curr. Biol. 22, 2362–2368 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stange, M., Aguirre-Fernández, G., Salzburger, W. & Sánchez-Villagra, M. R. Study of morphological variation of northern Neotropical Ariidae reveals conservatism despite macrohabitat transitions. BMC Evol. Biol. 18, 38 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gray, J. A., Sherratt, A., Hutchinson, M. N. & Jones, M. E. H. Evolution of cranial shape in a continental-scale evolutionary radiation of Australian lizards. Evolution 73, 2216–2229 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Foth, C., Sookias, R. B. & Ezcurra, M. D. Rapid initial morphospace expansion and delayed morphological disparity peak in the first 100 million years of the archosauromorph evolutionary radiation. Front. Earth Sci. 9, 723973 (2021).

    Article 

    Google Scholar
     

  • Adams, D., Berns, C. M., Kozak, K. H. & Wiens, J. J. Are rates of species diversification correlated with rates of morphological evolution?. Proc. R. Soc. B 276, 2729–2738 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Macdonald, K. S. III., Yampolsky, L. & Duffy, J. E. Molecular and morphological evolution of the amphipod radiation of Lake Baikal. Mol. Phylogenet. Evol. 35, 323–343 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kovalenkova, M., Sitnikova, T. & Sherbakov, D. Genetic and morphological diversification in gastropods of the Baicaliidae family. Russ. J. Genet. Appl. Res. 11, 3–11 (2013).


    Google Scholar
     

  • Stelbrink, B. et al. Conquest of the deep, old and cold: An exceptional limpet radiation in Lake Baikal. Biol. Lett. 11, 1–4 (2015).

    Article 

    Google Scholar
     

  • Sitnikova, T., Teterina, V., Maximova, N. & Kirilchink, S. Discordance of genetic diversification between deep- and shallow-water species of Kobeltocochlea Lindholm, 1909 (Caenogastropoda: Truncatelloidea: Benedictiidae) endemic to Lake Baikal with the description of a new species, review of the genus, and notes on its origin. J. Zool. Syst. Evol. Res. 59, 1775–1797 (2021).

    Article 

    Google Scholar
     

  • Gurkov, A. et al. Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species. BMC Ecol. Evol. 19, 138 (2019).


    Google Scholar
     

  • Bininda-Emonds, O. R. P. 18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera. BMC Ecol. Evol. 21, 118 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Field, K. G. et al. Molecular phylogeny of the animal kingdom. Science 239, 748–753 (1988).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Kong, Q., Karanovic, I. & Yu, N. Phylogeny of the genus Chrissia (Ostracoda: Cyprididae) with description of a new species from China. J. Crustac. Biol. 34, 782–794 (2014).

    Article 

    Google Scholar
     

  • Pham, T. H. M., Tanaka, H. & Karanovic, I. Molecular and morphological diversity of Heterodesmus Brady and its phylogenetic position within Cypridinidae. Zool. Sci. 37, 240–254 (2020).

    Article 

    Google Scholar
     

  • Schubart, C. D., Neigel, J. E. & Felder, D. L. Use of the mitochondrial 16S rRNA gene for phylogenetic and population studies of Crustacea. Crustac. Issues 12, 817–830 (2000).


    Google Scholar
     

  • Mantelatto, F. L., Robles, R. & Felder, D. L. Molecular phylogeny of the western Atlantic species of the genus Portunus (Crustacea, Brachyura, Portunidae). Zool. J. Linn. Soc. 150, 211–220 (2007).

    Article 

    Google Scholar
     

  • Vences, M., Thomas, M., Van Der Meijden, A., Chiari, Y. & Vieites, D. R. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front. Zool. 2, 1–12 (2005).

    Article 

    Google Scholar
     

  • Zheng, L., He, J., Lin, Y., Cao, W. & Zhang, W. 16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China. Acta Oceanol. Sin. 33, 55–76 (2014).

    Article 

    Google Scholar
     

  • Wu, R. et al. DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the Indo-West Pacific oceans based on COI and 16S rRNA genes. J. Oceanol. Limnol. 36, 1753–1770 (2018).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Wilke, T., Schultheiß, R. & Albrecht, C. As time goes by: A simple fool’s guide to molecular clock approaches in invertebrates. Am. Malacol. Bull. 27, 25–45 (2009).

    Article 

    Google Scholar
     

  • Schön, I., Poux, C., Verheyen, E. & Martens, K. High cryptic diversity and persistent lineage segregation in endemic Romecytheridea (Crustacea, Ostracoda) from the ancient Lake Tanganyika (East Africa). Hydrobiologia 739, 119–131 (2014).

    Article 

    Google Scholar
     

  • Karanovic, I. Recent Candoninae (Crustacea, Ostracoda) of North America. Rec. West. Aust. Mus. Suppl. 71, 1–75 (2006).

    Article 

    Google Scholar
     

  • Cabral, M. C. & Colin, J. P. Taxonomie et paléoécologie de nouveaux ostracodes limniques Candonidae dans l’Oxfordien (Jurassique supérieur) du Portugal. Geodiversitas 24, 61–76 (2002).


    Google Scholar
     

  • Klingenberg, C. P. Morphological integration and developmental modularity. Annu. Rev. Ecol. Evol. Syst. 39, 115–132 (2008).

    Article 

    Google Scholar
     

  • Shao, S. et al. Evolution of body morphology and beak shape revealed by morphometric analysis of 14 Paridae species. Front. Zool. 13, 30 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sherratt, E., Serb, J. M. & Adams, D. C. Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops. BMC Evol. Biol. 17, 248 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Botton-Divet, L., Houssaye, S., Herrel, A., Fabre, A. & Cornette, R. Swimmers, differs, climbers and more, a study of integration across mustelids locomotor apparatus (Carnivora: Mustelidae). Evol. Biol. 45, 182–195 (2018).

    Article 

    Google Scholar
     

  • Goswami, A., Smaers, J. B., Soligo, C. & Polly, P. D. The macroevolutionary consequences of phenotypic integration: From development to deep time. Philos. Trans. R. Soc. B 369, 20130254 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Machado, F. A., Hubbe, A., Melo, D., Porto, A. & Marroig, G. Measuring the magnitude of morphological integration: The effect of differences in morphometric representations and the inclusion of size. Evolution 73, 2518–2518 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zúñiga-Reinoso, A. & Benítez, H. A. The overrated use of the morphological cryptic species concept: An example with Nyctelia darkbeetles (Coleoptera: Tenebrionidae) using geometric morphometrics. Zool. Anz. 255, 47–53 (2015).

    Article 

    Google Scholar
     

  • Karanovic, T. & Bláha, M. Taming extreme morphological variability through coupling of molecular phylogeny and quantitative phenotype analysis as a new avenue for taxonomy. Sci. Rep. 9, 2429 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Adams, M., Raadik, T. A., Burridge, C. P. & Georges, A. Global biodiversity assessment and hyper-cryptic species complexes: More than one species of elephant in the room?. Syst. Biol. 63, 518–533 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Karanovic, T., Djurakic, M. & Eberhard, S. Cryptic species or inadequate taxonomy? Implementation of 2D geometric morphometrics based on integumental organs as landmarks for delimitation and description of copepod taxa. Syst. Biol. 65, 304–328 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Zemskaya, T. I. et al. Faunal communities at sites of gas- and oil-bearing fluids in Lake Baikal. Geo-Mar. Lett. 32, 437–451 (2012).

    Article 
    ADS 

    Google Scholar
     

  • Sitnikova, T. Yu. et al. Sluggish methane discharge and biological traits of benthic invertebrates in Lake Baikal. Hydrobiologia 849, 1947–1968 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Hiruta, S. F., Kobayashi, N., Katoh, T. & Kajihara, H. Molecular phylogeny of cypridoid freshwater Ostracods (Crustacea: Ostracoda), inferred from 18S and 28S rDNA sequences. Zool. Sci. 33, 179–185 (2016).

    Article 

    Google Scholar
     

  • Williams, B. D., Schrank, B., Huynh, C., Shownkeen, R. & Waterston, R. H. A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites. Genetics 131, 609–624 (1992).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 20, 1160–1166 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Löytynoja, A. & Goldman, N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320, 1632–1635 (2008).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Trifinopoulos, J., Nguyen, L. T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acid Res. 44, W232–W235 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Akaike, H. A new look at the statistical model identification. IEEE Trans. Autom. Control 19, 716–723 (1974).

    Article 
    ADS 
    MathSciNet 
    MATH 

    Google Scholar
     

  • Bouckaert, R. et al. BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rohlf, J. F. The tps series of software. Hystrix 26, 1–4 (2015).


    Google Scholar
     

  • Rohlf, F. J. TpsUtil, tps file utility program, version 1.52. life.bio.sunysb.edu/morph (2004).

  • Klingenberg, C. P. MorphoJ: An integrated software package for geometric morphometrics. Mol. Ecol. Res. 11, 353–357 (2011).

    Article 

    Google Scholar
     

  • Dryden, I. L. & Mardia, K. V. Statistical Shape Analysis (Wiley, 1998).

    MATH 

    Google Scholar
     

  • Klingenberg, C. P. & McIntyre, G. S. Geometric morphometrics of developmental instability: Analyzing patterns of fluctuating asymmetry with Procrustes methods. Evolution 52, 1363–1375 (1998).

    Article 
    PubMed 

    Google Scholar
     

  • Klingenberg, C. P., Barluenga, M. & Meyer, A. Shape analysis of symmetric structures: Quantifying variation among individuals and asymmetry. Evolution 56, 1909–1920 (2002).

    PubMed 

    Google Scholar
     

  • Klingenberg, C. P. Size, shape, and form: Concepts of allometry in geometric morphometrics. Dev. Genes Evol. 226, 113–137 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Klingenberg, C. P. & Gidaszewski, N. A. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Syst. Biol. 59, 245–261 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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