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<p>Members of the <i>Daphnia longispina</i> O. F. Müller, 1776 group (Branchiopoda: Cladocera) are keystone grazers in freshwater bodies around the world. Multiple cryptic species have been revealed and partially described within the last 20&#xa0;years. However, high phenotypic plasticity, hybridization, and the limited number of available genetic markers have hampered attempts to fully explore species diversity and speciation factors in this group. Here, we present the first dated phylogeny of the complete <i>D. longispina</i> group using whole-genome data. Multiple mitochondrial relationships including divergent mitochondrial lineages are not supported by nuclear DNA. Additionally, several morphologically distinct species within two species complexes show a low genealogical divergence index, raising the question of lumping by the method. Species trees based on SNPs and gene trees differ strongly in bootstrap support for older nodes. Concordance factors do not strongly support either phylogeny, most likely due to prevalent incomplete lineage sorting. Our analyses indicate that geography has a stronger effect on the speciation of the <i>D. longispina</i> group than the trophic status of their habitat or introgression. We only find evidence of ancient introgression between species known to hybridize concurrently. This study provides novel insights into the species relationships in the <i>D. longispina</i> group.</p>

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Whole-genome sequencing reveals cryptic diversity and ancient hybridization in key aquatic herbivore Daphnia

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月24日

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  • Jannik Beninde,
  • Melisa Olave,
  • Markus Möst,
  • Joachim Mergeay,
  • Stuart R. Dennis,
  • Piet Spaak

摘要

Members of the Daphnia longispina O. F. Müller, 1776 group (Branchiopoda: Cladocera) are keystone grazers in freshwater bodies around the world. Multiple cryptic species have been revealed and partially described within the last 20 years. However, high phenotypic plasticity, hybridization, and the limited number of available genetic markers have hampered attempts to fully explore species diversity and speciation factors in this group. Here, we present the first dated phylogeny of the complete D. longispina group using whole-genome data. Multiple mitochondrial relationships including divergent mitochondrial lineages are not supported by nuclear DNA. Additionally, several morphologically distinct species within two species complexes show a low genealogical divergence index, raising the question of lumping by the method. Species trees based on SNPs and gene trees differ strongly in bootstrap support for older nodes. Concordance factors do not strongly support either phylogeny, most likely due to prevalent incomplete lineage sorting. Our analyses indicate that geography has a stronger effect on the speciation of the D. longispina group than the trophic status of their habitat or introgression. We only find evidence of ancient introgression between species known to hybridize concurrently. This study provides novel insights into the species relationships in the D. longispina group.