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Invertebrate Systematics Invertebrate Systematics Society
Systematics, phylogeny and biogeography
RESEARCH ARTICLE

A revised phylogeny of the New Caledonian endemic genus Troglosiro (Opiliones : Cyphophthalmi : Troglosironidae) with the description of four new species

Gonzalo Giribet https://orcid.org/0000-0002-5467-8429 A C , Caitlin M. Baker https://orcid.org/0000-0002-9782-4959 A and Prashant P. Sharma https://orcid.org/0000-0002-2328-9084 B
+ Author Affiliations
- Author Affiliations

A Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.

B Department of Integrative Biology, University of Madison—Wisconsin, 352 Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA.

C Corresponding author. Email: ggiribet@g.harvard.edu

Invertebrate Systematics 35(1) 59-89 https://doi.org/10.1071/IS20042
Submitted: 21 May 2020  Accepted: 2 August 2020   Published: 5 January 2021

Abstract

The Cyphophthalmi genus Troglosiro (the only genus of the family Troglosironidae) is endemic to New Caledonia, representing one of the oldest lineages of this emerged part of Zealandia. Its species are short-range endemics, many known from single localities. Here we examined the phylogenetic relationships of Troglosironidae using standard Sanger-sequenced markers (nuclear 18S rRNA, 28S rRNA, and mitochondrial 16S rRNA and cytochrome c oxidase subunit I) and a combination of phylogenetic methods, including parsimony under Direct Optimization and maximum likelihood with static homology. We also applied a diversity of species delimitation methods, including distance-based, topology-based and unsupervised machine learning to evaluate previous species designations. Finally, we used a combination of genetic and morphological information to describe four new species – T. dogny sp. nov., T. pin sp. nov., T. pseudojuberthiei sp. nov. and T. sharmai sp. nov. – and discuss them in the broader context of the phylogeny and biogeographic history of the family. A key to the species of Troglosiro is also provided.

urn:lsid:zoobank.org:pub:93541314-8309-468C-BB77-B34C3A81137E

Keywords: biogeography, New Caledonia, short-range endemics, species delimitation, Sternophthalmi, unsupervised machine learning.


References

Abadi, M., Barham, P., Chen, J., Chen, Z., Davis, A., Dean, J., Devin, M., Ghemawat, S., Irving, G., Isard, M., Kudlur, M., Levenberg, J., Monga, R., Moore, S., Murray, D. G., Steiner, B., Tucker, P., Vasudevan, V., Warden, P., Wicke, M., Yu, Y., Zheng, X., and Brain, G. (2016). TensorFlow: a system for large-scale machine learning. In ‘12th USENIX Symposium on Operating Systems Design and Implementation (OSDI ‘16)’, 2–4 November 2016, Savannah, GA, USA.) pp. 265–283. (USENIX Association.) Available at https://www.usenix.org/system/files/conference/osdi16/osdi16-abadi.pdf [Verified 22 August 2020].

Boyer, S. L., and Giribet, G. (2007). A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New Zealand. Cladistics 23, 337–361.
A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New Zealand.Crossref | GoogleScholarGoogle Scholar |

Clouse, R. M., and Giribet, G. (2007). Across Lydekker’s Line – first report of mite harvestmen (Opiliones: Cyphophthalmi: Stylocellidae) from New Guinea. Invertebrate Systematics 21, 207–227.
Across Lydekker’s Line – first report of mite harvestmen (Opiliones: Cyphophthalmi: Stylocellidae) from New Guinea.Crossref | GoogleScholarGoogle Scholar |

Clouse, R. M., General, D. M., Diesmos, A. C., and Giribet, G. (2011). An old lineage of Cyphophthalmi (Opiliones) discovered on Mindanao highlights the need for biogeographical research in the Philippines. The Journal of Arachnology 39, 147–153.
An old lineage of Cyphophthalmi (Opiliones) discovered on Mindanao highlights the need for biogeographical research in the Philippines.Crossref | GoogleScholarGoogle Scholar |

Clouse, R. M., Sharma, P. P., Stuart, J. C., Davis, L. R., Giribet, G., Boyer, S. L., and Wheeler, W. C. (2016). Phylogeography of the harvestman genus Metasiro (Arthropoda, Arachnida, Opiliones) reveals a potential solution to the Pangean paradox. Organisms, Diversity & Evolution 16, 167–184.
Phylogeography of the harvestman genus Metasiro (Arthropoda, Arachnida, Opiliones) reveals a potential solution to the Pangean paradox.Crossref | GoogleScholarGoogle Scholar |

de Bivort, B. L., and Giribet, G. (2004). A new genus of cyphophthalmid from the Iberian Peninsula with a phylogenetic analysis of the Sironidae (Arachnida: Opiliones: Cyphophthalmi) and a SEM database of external morphology. Invertebrate Systematics 18, 7–52.
A new genus of cyphophthalmid from the Iberian Peninsula with a phylogenetic analysis of the Sironidae (Arachnida: Opiliones: Cyphophthalmi) and a SEM database of external morphology.Crossref | GoogleScholarGoogle Scholar |

Derkarabetian, S., Castillo, S., Koo, P. K., Ovchinnikov, S., and Hedin, M. (2019). A demonstration of unsupervised machine learning in species delimitation. Molecular Phylogenetics and Evolution 139, 106562.
A demonstration of unsupervised machine learning in species delimitation.Crossref | GoogleScholarGoogle Scholar | 31323334PubMed |

Fernández, R., and Giribet, G. (2014). Phylogeography and species delimitation in the New Zealand endemic, genetically hypervariable harvestman species, Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi). Invertebrate Systematics 28, 401–414.
Phylogeography and species delimitation in the New Zealand endemic, genetically hypervariable harvestman species, Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi).Crossref | GoogleScholarGoogle Scholar |

Fontaine, B., Perrard, A., and Bouchet, P. (2012). 21 years of shelf life between discovery and description of new species. Current Biology 22, R943–R944.
21 years of shelf life between discovery and description of new species.Crossref | GoogleScholarGoogle Scholar | 23174292PubMed |

Giribet, G. (2003). Karripurcellia, a new pettalid genus (Arachnida: Opiliones: Cyphophthalmi) from Western Australia, with a cladistic analysis of the family Pettalidae. Invertebrate Systematics 17, 387–406.
Karripurcellia, a new pettalid genus (Arachnida: Opiliones: Cyphophthalmi) from Western Australia, with a cladistic analysis of the family Pettalidae.Crossref | GoogleScholarGoogle Scholar |

Giribet, G. (2007). Efficient tree searches with available algorithms. Evolutionary Bioinformatics Online 3, 341–356.
Efficient tree searches with available algorithms.Crossref | GoogleScholarGoogle Scholar | 19461977PubMed |

Giribet, G. (2011). Shearogovea, a new genus of Cyphophthalmi (Arachnida, Opiliones) of uncertain position from Oaxacan caves, Mexico. Breviora 528, 1–7.
Shearogovea, a new genus of Cyphophthalmi (Arachnida, Opiliones) of uncertain position from Oaxacan caves, Mexico.Crossref | GoogleScholarGoogle Scholar |

Giribet, G., and Baker, C. M. (2019). Further discussion on the Eocene drowning of New Caledonia: discordances from the point of view of zoology. Journal of Biogeography 46, 1912–1918.
Further discussion on the Eocene drowning of New Caledonia: discordances from the point of view of zoology.Crossref | GoogleScholarGoogle Scholar |

Giribet, G., and Boyer, S. L. (2002). A cladistic analysis of the cyphophthalmid genera (Opiliones, Cyphophthalmi). The Journal of Arachnology 30, 110–128.
A cladistic analysis of the cyphophthalmid genera (Opiliones, Cyphophthalmi).Crossref | GoogleScholarGoogle Scholar |

Giribet, G., Sharma, P. P., and Bastawade, D. B. (2007). A new genus and species of Cyphophthalmi (Arachnida: Opiliones) from the north-eastern states of India. Zoological Journal of the Linnean Society 151, 663–670.
A new genus and species of Cyphophthalmi (Arachnida: Opiliones) from the north-eastern states of India.Crossref | GoogleScholarGoogle Scholar |

Giribet, G., Sharma, P. P., Benavides, L. R., Boyer, S. L., Clouse, R. M., de Bivort, B. L., Dimitrov, D., Kawauchi, G. Y., Murienne, J. Y., and Schwendinger, P. J. (2012). Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biological Journal of the Linnean Society. Linnean Society of London 105, 92–130.
Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement.Crossref | GoogleScholarGoogle Scholar |

Giribet, G., McIntyre, E., Christian, E., Espinasa, L., Ferreira, R. L., Francke, Ó. F., Harvey, M. S., Isaia, M., Kováč, Ĺ., McCutchen, L., Souza, M. F. V. R., and Zagmajster, M. (2014). The first phylogenetic analysis of Palpigradi (Arachnida) – the most enigmatic arthropod order. Invertebrate Systematics 28, 350–360.
The first phylogenetic analysis of Palpigradi (Arachnida) – the most enigmatic arthropod order.Crossref | GoogleScholarGoogle Scholar |

Giribet, G., Buckman-Young, R. S., Sampaio Costa, C., Baker, C. M., Benavides, L. R., Branstetter, M. G., Daniels, S. R., and Pinto-da-Rocha, R. (2018). The ‘Peripatos’ in Eurogondwana? – Lack of evidence that south-east Asian onychophorans walked through Europe. Invertebrate Systematics 32, 842–865.
The ‘Peripatos’ in Eurogondwana? – Lack of evidence that south-east Asian onychophorans walked through Europe.Crossref | GoogleScholarGoogle Scholar |

Goloboff, P. A. (1999). Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15, 415–428.
Analyzing large data sets in reasonable times: solutions for composite optima.Crossref | GoogleScholarGoogle Scholar |

Goloboff, P. A. (2002). Techniques for analyzing large data sets. In ‘Techniques in Molecular Systematics and Evolution’. (Eds R. DeSalle, G. Giribet, and W. Wheeler.) pp. 70–79. (Brikhäuser Verlag: Basel.)

Harvey, M. S. (2002). Short-range endemism among the Australian fauna: some examples from non-marine environments. Invertebrate Systematics 16, 555–570.
Short-range endemism among the Australian fauna: some examples from non-marine environments.Crossref | GoogleScholarGoogle Scholar |

Harvey, M. S., Rix, M. G., Framenau, V. W., Hamilton, Z. R., Johnson, M. S., Teale, R. J., Humphreys, G., and Humphreys, W. F. (2011). Protecting the innocent: studying short-range endemic taxa enhances conservation outcomes. Invertebrate Systematics 25, 1–10.
Protecting the innocent: studying short-range endemic taxa enhances conservation outcomes.Crossref | GoogleScholarGoogle Scholar |

Harvey, M. S., Rix, M. G., Harms, D., Giribet, G., Vink, C. J., and Walter, D. E. (2017). The biogeography of Australasian arachnids. In ‘Handbook of Australasian Biogeography’. (Ed. M. C. Ebach.) pp. 241–267. (CRC/Taylor and Francis Group.)

Juberthie, C. (1970). Les genres d’opilions Sironinae (Cyphophthalmes). Bulletin du Muséum National d’Histoire Naturelle, 2e série 41, 1371–1390.

Juberthie, C. (1979). Un Cyphophthalme nouveau d’une grotte de Nouvelle-Calédonie: Troglosiro aelleni n. gen., n. sp. (Opilion Sironinae). Revue Suisse de Zoologie 86, 221–231.
Un Cyphophthalme nouveau d’une grotte de Nouvelle-Calédonie: Troglosiro aelleni n. gen., n. sp. (Opilion Sironinae).Crossref | GoogleScholarGoogle Scholar |

Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., and Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14, 587–589.
ModelFinder: fast model selection for accurate phylogenetic estimates.Crossref | GoogleScholarGoogle Scholar | 28481363PubMed |

Kapli, P., Lutteropp, S., Zhang, J., Kobert, K., Pavlidis, P., Stamatakis, A., and Flouri, T. (2017). Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33, 1630–1638.
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.Crossref | GoogleScholarGoogle Scholar | 28108445PubMed |

Katoh, K., Rozewicki, J., and Yamada, K. D. (2019). MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20, 1160–1166.
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.Crossref | GoogleScholarGoogle Scholar | 28968734PubMed |

Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111–120.
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.Crossref | GoogleScholarGoogle Scholar | 7463489PubMed |

Kuraku, S., Zmasek, C. M., Nishimura, O., and Katoh, K. (2013). aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Research 41, W22–W28.
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.Crossref | GoogleScholarGoogle Scholar | 23677614PubMed |

Murphree, C. S. (1988). Morphology of the dorsal integument of ten opilionid species (Arachnida, Opiliones). The Journal of Arachnology 16, 237–252.

Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A., and Kent, J. (2000). Biodiversity hotspots for conservation priorities. Nature 403, 853–858.
Biodiversity hotspots for conservation priorities.Crossref | GoogleScholarGoogle Scholar | 10706275PubMed |

Nattier, R., Pellens, R., Robillard, T., Jourdan, H., Legendre, F., Caesar, M., Nel, A., and Grandcolas, P. (2017). Updating the phylogenetic dating of New Caledonian biodiversity with a meta-analysis of the available evidence. Scientific Reports 7, 3705.
Updating the phylogenetic dating of New Caledonian biodiversity with a meta-analysis of the available evidence.Crossref | GoogleScholarGoogle Scholar | 28623347PubMed |

Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., and Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32, 268–274.
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.Crossref | GoogleScholarGoogle Scholar | 25371430PubMed |

Nixon, K. C. (1999). The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407–414.
The Parsimony Ratchet, a new method for rapid parsimony analysis.Crossref | GoogleScholarGoogle Scholar |

Oberski, J. T., Sharma, P. P., Jay, K. R., Coblens, M. J., Lemon, K. A., Johnson, J. E., and Boyer, S. L. (2018). A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics. Molecular Phylogenetics and Evolution 127, 813–822.
A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics.Crossref | GoogleScholarGoogle Scholar | 29935300PubMed |

Puillandre, N., Lambert, A., Brouillet, S., and Achaz, G. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21, 1864–1877.
ABGD, Automatic Barcode Gap Discovery for primary species delimitation.Crossref | GoogleScholarGoogle Scholar | 21883587PubMed |

Schmidt, S. M., Buenavente, P. A. C., Blatchley, D. D., Diesmos, A. C., Diesmos, M. L., General, D. E. M., Mohagan, A. B., Mohagan, D. J., Clouse, R. M., and Sharma, P. P. (2019). A new species of Tithaeidae (Arachnida: Opiliones: Laniatores) from Mindanao reveals contemporaneous colonisation of the Philippines by Sunda Shelf opiliofauna. Invertebrate Systematics 33, 237–251.
A new species of Tithaeidae (Arachnida: Opiliones: Laniatores) from Mindanao reveals contemporaneous colonisation of the Philippines by Sunda Shelf opiliofauna.Crossref | GoogleScholarGoogle Scholar |

Schwentner, M., and Giribet, G. (2018). Phylogeography, species delimitation and population structure of a Western Australian short-range endemic mite harvestman (Arachnida: Opiliones: Pettalidae: Karripurcellia). Evolutionary Systematics 2, 81–87.
Phylogeography, species delimitation and population structure of a Western Australian short-range endemic mite harvestman (Arachnida: Opiliones: Pettalidae: Karripurcellia).Crossref | GoogleScholarGoogle Scholar |

Sharma, P. P. (2006). On the biogeography of New Caledonia: a revision of the Cyphophthalmi of New Caledonia with a phylogenetic analysis of the Troglosironidae (Arachnida, Opiliones, Cyphophthalmi). Undergraduate Senior Thesis, Harvard University.

Sharma, P., and Giribet, G. (2005). A new Troglosiro species (Opiliones, Cyphophthalmi, Troglosironidae) from New Caledonia. Zootaxa 1053, 47–60.
A new Troglosiro species (Opiliones, Cyphophthalmi, Troglosironidae) from New Caledonia.Crossref | GoogleScholarGoogle Scholar |

Sharma, P., and Giribet, G. (2009a). A relict in New Caledonia: phylogenetic relationships of the family Troglosironidae (Opiliones: Cyphophthalmi). Cladistics 25, 279–294.
A relict in New Caledonia: phylogenetic relationships of the family Troglosironidae (Opiliones: Cyphophthalmi).Crossref | GoogleScholarGoogle Scholar |

Sharma, P. P., and Giribet, G. (2009b). The family Troglosironidae (Opiliones: Cyphophthalmi) of New Caledonia. In ‘Zoologia Neocaledonica. 7. Biodiversity Studies in New Caledonia’. (Ed. P. Grandcolas.) pp. 83–123 (Mémoires du Muséum national d’Histoire naturelle: Paris, France.)

Sharma, P. P., Vahtera, V., Kawauchi, G. Y., and Giribet, G. (2011). Running WILD: The case for exploring mixed parameter sets in sensitivity analysis. Cladistics 27, 538–549.
Running WILD: The case for exploring mixed parameter sets in sensitivity analysis.Crossref | GoogleScholarGoogle Scholar |

Shear, W. A. (1993). The genus Troglosiro and the new family Troglosironidae (Opiliones, Cyphophthalmi). The Journal of Arachnology 21, 81–90.

Sutherland, R., Dickens, G. R., Blum, P., Agnini, C., Alegret, L., Asatryan, G., Bhattacharya, J., Bordenave, A., Chang, L., Collot, J., Cramwinckel, M. J., Dallanave, E., Drake, M. K., Etienne, S. J. G., Giorgioni, M., Gurnis, M., Harper, D. T., Huang, H.-H. M., Keller, A. L., Lam, A. R., Li, H., Matsui, H., Morgans, H. E. G., Newsam, C., Park, Y.-H., Pascher, K. M., Pekar, S. F., Penman, D. E., Saito, S., Stratford, W. R., Westerhold, T., and Zhou, X. (2020). Continental-scale geographic change across Zealandia during Paleogene subduction initiation. Geology 48, 419–424.
Continental-scale geographic change across Zealandia during Paleogene subduction initiation.Crossref | GoogleScholarGoogle Scholar |

Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A., and Minh, B. Q. (2016). W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44, W232–W235.
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.Crossref | GoogleScholarGoogle Scholar | 27084950PubMed |

Wheeler, W. C. (1995). Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology 44, 321–331.
Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data.Crossref | GoogleScholarGoogle Scholar |

Wheeler, W. (1996). Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12, 1–9.
Optimization alignment: the end of multiple sequence alignment in phylogenetics?Crossref | GoogleScholarGoogle Scholar |

Wheeler, W. C. (2003). Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search. Cladistics 19, 261–268.
Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search.Crossref | GoogleScholarGoogle Scholar | 12901383PubMed |

Wheeler, W. C., Aagesen, L., Arango, C. P., Faivovich, J., Grant, T., D’Haese, C., Janies, D., Smith, W. L., Varón, A., and Giribet, G. (2005). ‘Dynamic Homology and Phylogenetic Systematics: a Unified Approach using POY.’ (American Museum of Natural History: New York.)

Wheeler, W. C., Lucaroni, N., Hong, L., Crowley, L. M., and Varón, A. (2015). POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria. Cladistics 31, 189–196.
POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria.Crossref | GoogleScholarGoogle Scholar |

Willemart, R. H., and Giribet, G. (2010). A scanning electron microscopic survey of the cuticle in Cyphophthalmi (Arachnida, Opiliones) with the description of novel sensory and glandular structures. Zoomorphology 129, 175–183.
A scanning electron microscopic survey of the cuticle in Cyphophthalmi (Arachnida, Opiliones) with the description of novel sensory and glandular structures.Crossref | GoogleScholarGoogle Scholar |

Zhang, J., Kapli, P., Pavlidis, P., and Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29, 2869–2876.
A general species delimitation method with applications to phylogenetic placements.Crossref | GoogleScholarGoogle Scholar | 23990417PubMed |