DOI: 10.5061/dryad.rxwdbrv61
title: Taxon pulse dynamics, episodic dispersal, and host colonization across Beringia drive diversification of a holarctic tapeworm assemblage

description: Aim: We test the predictions of the Stockholm Paradigm, a synthesis of
 eco-evolutionary theory explaining the nature of faunal assembly, host
 range and parasite diversification. Faunal diversification and assembly,
 manifested in patterns of host colonization, co-adaptation and parasite
 speciation, is predicted to emerge as a consequence of alternating
 episodes of ecological disruption and stability. Specifically, for a
 diverse cestode genus (Arostrilepis), we evaluate the number and direction
 of Pleistocene dispersal events across Beringia, the number and relative
 timing of host colonization events, and the relationship between host and
 parasite biogeographic histories and associations through time. Location:
 Beringia and adjacent temperate to arctic biomes in North America and
 Eurasia. Taxon: Arostrilepis (Cyclophyllidea: Hymenolepididae) and its
 rodent hosts. Methods: Multi-locus phylogenetic reconstruction and
 biogeographic ancestral range estimation. Results: Arostrilepis lineages
 crossed Beringia eastward into North America a minimum of four times and
 westward into Asia twice in association with temporally disjunct
 geographic expansions of three major tribes of cricetid rodents
 (Arvicolini, Myodini, Lemmini). Inferences of ancestral host associations
 support at least nine instances of host-colonization involving shifts from
 one rodent tribe or family to another. Several previously unrecognized
 lineages of Arostrilepis are revealed. Main conclusions: Consistent with
 expectations of the Stockholm Paradigm, episodes of intercontinental
 dispersal were both frequent in the history of Arostrilepis and preceded a
 majority of inferred host-colonization events. Events of historical
 geographic expansion created numerous opportunities for development of
 novel host-parasite associations through ecological fitting, as parasites
 tracked historically conserved resources available across diverse host
 taxa. Beringia played a major role in shaping rodent/parasite assemblages
 by mediating dispersal between the northern continents during glacial
 episodes of the Pleistocene, rather than by serving as a zone of refugial
 isolation.
description: Whole genomic DNA was extracted from 3-10 posterior proglottids
 from individual tapeworms using a Qiagen™ DNeasy Tissue Kit®.  These
 templates were used to PCR-amplify and sequence four genomic regions: 1) a
 portion of the mitochondrial cytochrome b<i> </i>(CYTB; ~570
 base pairs), 2) subunit I of the mitochondrial NADH dehydrogenase complex
 (ND1; ~780 base pairs), 3) nuclear 28S ribosomal RNA (28S; ~1340 base
 pairs), and 4) a portion of the 5.8s region and the second internal
 transcribed spacer of nuclear ribosomal DNA (ITS2; ~740 base
 pairs). We amplified the four markers using the
 following primers – CYTB: HYM01 paired with either HYM08, HYMLEM02
 (Makarikov et al., 2013), or HYM24 (5’GGATTATTACTACCTCTCTTATGCAAAT); ND1:
 Cyclo_nad1F and Cyclo_trnNR (Littlewood, Waeschenbach, & Nikolov,
 2008); 28S: LSU5 and 1200R (Littlewood, Curini-Galletti, &
 Herniou, 2000; Lockyer, Olson, & Littlewood, 2003); and ITS2: 3S
 and A28 (Okamoto, Agatsuma, Kurosawa, & Ito, 1997). Annealing
 temperatures were 50ºC for CYTB<i> </i>and ITS2, 45ºC for ND1,
 and 52ºC for 28S.  Most ITS2 products were cloned using 1/3 volume
 reactions of Invitrogen’s™ Topo TA Cloning® kit with pCR®2.1-TOPO® vector.
 We sequenced between 4 and 8 separate clones from each specimen and
 determined the consensus sequence of the most frequently cloned allele.
 For all markers, PCR products were sequenced in both directions and
 assembled using Geneious®
 v6. Two species<i>, A. rauschorum
 </i>Makarikov, Galbreath et Hoberg, 2013 and<i> Arostrilepis
 microtis</i> Gulyaev et Chechulin, 1997, were previously reported
 to<i> </i>contain NUMTs (Makarikov et al., 2013). To
 efficiently separate mitochondrial sequence from putative nuclear
 sequence, we designed primers to target only mitochondrial sequence during
 CYTB amplification.  These targeted primer pairs were HYM29
 (5’TGATTAATATTATACGACGT) and HYM30 (5’TGTGCAAATAAAATAAATGT) for probable
 <i>A. rauschorum</i>, and HYM32 (5’AATGTAAAAACATTAAGCCC) and
 HYM33 (5’TACGACGTAATTTAATTGAT) for probable <i>A. microtis</i>
 (50ºC annealing). Data from GenBank supplemented our
 molecular dataset.  For <i>Arostrilepis</i> species, 37
 CYTB<i> </i>sequences (Galbreath, Ragaliauskaitė,
 Kontrimavichus, Makarikov, & Hoberg, 2013; Makarikov et al., 2020;
 Makarikov et al., 2013)<i>,</i> two ND1 sequences (Binkiene,
 Kornienko, & Tkach, 2015),<i> </i>three 28S sequences
 (Haukisalmi et al., 2010), and 12 ITS2 sequences (Galbreath et al., 2013;
 Makarikov et al., 2020) were assembled from previously published datasets.
 These sequences are derived from specimens whose species identities have
 been morphologically validated, providing a reference for confirming
 identifications based on genetic identity.  No fresh tissue or sequence
 data are currently available from four species, <i>Arostrilepis
 horrida</i> (Linstow, 1901)<i>, Arostrilepis
 kontrimavichusi</i> Makarikov et Hoberg, 2016<i>, Arostrilepis
 mariettavogeae</i> Makarikov, Gardner et Hoberg, 2012<i>,
 </i>and <i>Arostrilepis schilleri</i> Makarikov, Gardner
 et Hoberg, 2012. We also acquired sequences representing
 <i>Hymenolepis diminuta</i> (Rudolphi, 1819),
 <i>Hymenolepis folkertsi</i>, <i>Lineolepis
 scutigera</i> (Dujardin, 1845), <i>Neoskrjabinolepis
 schaldybini</i> Spassky, 1947, <i>Soricinia infirma</i>
 (Zarnowski, 1955), and <i>Staphylocystis furcata</i> (Stieda,
 1862) from GenBank for use as outgroups. Assembled DNA
 datasets were aligned using MUSCLE (Edgar,
 2004) as implemented in MEGA v7 (Kumar,
 Stecher, & Tamura, 2016), and edited by eye. Sites with gaps in
 the ingroup taxa were excluded from the analysis, as were regions of
 ambiguous alignment. Ambiguous alignment was most severe in the ITS2
 dataset, especially between outgroup species and
 <i>Arostrilepis</i>. To mitigate this without losing
 informative variation within the ingroup sequences, ITS2 sequences for
 <i>Hymenolepis diminuta</i>, <i>Staphylocystis
 furcata</i>, and <i>Lineolepis scutigera</i> were
 truncated to include only the relatively conserved 5.8S portion of the
 sequence. References: Binkiene, R.,
 Kornienko, S. A., & Tkach, V. V. (2015). <i>Soricinia genovi
 </i>n. sp. from <i>Neomys fodiens </i>in Bulgaria, with
 redescription of <i>Soricinia globosa </i>(Baer, 1931)
 (Cyclophyllidea: Hymenolepididae). <i>Parasitology Research,
 114</i>, 209-218. doi:10.1007/s00436-014-4180-6 Galbreath, K. E.,
 Ragaliauskaitė, K., Kontrimavichus, V. L., Makarikov, A. A., &
 Hoberg, E. P. (2013). A widespread distribution for <i>Arostrilepis
 tenuicirrosa </i>(Eucestoda: Hymenolepididae) in <i>Myodes
 </i>voles (Cricetidae: Arvicolinae) from the Palearctic based on
 molecular and morphological evidence: historical and biogeographic
 implications. <i>Acta Parasitologica, 58</i>,
 441-452. Haukisalmi, V.,
 Hardman, L. M., Foronda, P., Feliu, C., Laakkonen, J., Niemimaa, J., . . .
 Henttonen, H. (2010). Systematic relationships of hymenolepidid cestodes
 of rodents and shrews inferred from sequences of 28S ribosomal RNA.
 <i>Zoologica Scripta, 39</i>, 631-641.
 doi:10.1111/j.1463-6409.2010.00444.x Kumar, S.,
 Stecher, G., & Tamura, K. (2016). MEGA7: Molecular Evolutionary
 Genetics Analysis version 7.0. <i>Molecular Biology and Evolution,
 33</i>, 1870-1874. doi:10.1093/molbev/msw054 Littlewood, D.
 T., Waeschenbach, A., & Nikolov, P. (2008). In search of
 mitochondrial markers for resolving the phylogeny of cyclophyllidean
 tapeworms (Platyhelminthes, Cestoda) — a test study with Davaineidae.
 <i>Acta Parasitologica, 53</i>, 133-144.
 doi:10.2478/s11686-008-0029-4 Littlewood, D. T.
 J., Curini-Galletti, M., & Herniou, E. A. (2000). The
 interrelationships of Proseriata (Platyhelminthes: Seriata) tested with
 molecules and morphology. <i>Molecular Phylogenetics and Evolution,
 16</i>, 449-466.
 doi:https://doi.org/10.1006/mpev.2000.0802 Lockyer, A. E.,
 Olson, P. D., & Littlewood, D. T. J. (2003). Utility of complete
 large and small subunit rRNA genes in resolving the phylogeny of the
 Neodermata (Platyhelminthes): implications and a review of the cercomer
 theory. <i>Biological Journal of the Linnean Society, 78</i>,
 155-171. doi:10.1046/j.1095-8312.2003.00141.x Makarikov, A. A.,
 Galbreath, K. E., Eckerlin, R. P., & Hoberg, E. P. (2020).
 Discovery of <i>Arostrilepis </i>tapeworms (Cyclophyllidea:
 Hymenolepididae) and new insights for parasite species diversity from
 Eastern North America. <i>Parasitology Research, 119</i>,
 567-585. doi:10.1007/s00436-019-06584-4 Makarikov, A. A.,
 Galbreath, K. E., & Hoberg, E. P. (2013). Parasite diversity at
 the Holarctic nexus: species of <i>Arostrilepis
 </i>(Eucestoda: Hymenolepididae) in voles and lemmings (Cricetidae:
 Arvicolinae) from greater Beringia. <i>Zootaxa, 3608</i>,
 401-439. doi:10.11646/zootaxa.3608.6.1 Okamoto, M.,
 Agatsuma, T., Kurosawa, T., & Ito, A. (1997). Phylogenetic
 relationships of three hymenolepidid species inferred from nuclear
 ribosomal and mitochondrial DNA sequences. <i>Parasitology,
 115</i>, 661-666.
description: These are Nexus formatted files that can be read using many
 standard phylogenetic packages such as PAUP, MrBayes, and Beast. Gaps are
 included in the alignments.  Sites that were excluded from analyses are
 indicated in the paup block using the "exclude" command.  Codes
 embedded in sequence identifiers cross-reference with Appendix S1 from the
 publication.