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Maximum clade credibility (MCC) tree of Argyrodes lanyuensis from Philippines and Orchid Island Taiwan using BEAST 1.10

Citation

Responte, Mae et al. (2022), Maximum clade credibility (MCC) tree of Argyrodes lanyuensis from Philippines and Orchid Island Taiwan using BEAST 1.10, Dryad, Dataset, https://doi.org/10.5061/dryad.1ns1rn8tk

Abstract

Oceanic islands are unique geographic systems that promote local adaptations and allopatric speciation in many of their highly endemic taxa. This is a common case in the Philippine Archipelago, where numerous unrelated taxa on islands have been inferred to have diversified in isolation. However, few cases have been reported in invertebrates especially among parasitic organisms. Here, we tested for biogeographical structure in novel populations of the “generalist" kleptoparasitic spider, Argyrodes lanyuensis Yoshida, Tso & Severinghaus, 1998 in the Philippines. Results showed that, in addition to Orchid Island, this species has a wide geographic distribution in the Philippine Archipelago. The estimated divergence time of this lineage using the mitochondrial cytochrome oxidase 1 (mt-CO1) suggests that this species diverged ca 3.12 MYA, during the Pliocene. Two reciprocal monophyletic clades were elucidated in A. lanyuensis, but with limited differentiation across Pleistocene Aggregate Island Complex (PAIC) boundaries and modern-day islands. However, in our analyses of morphological variation, we identified two phenotypically differentiated units in males (Orchid Island, Taiwan+Luzon, Philippine PAIC populations versus Palawan+West Visayan+Mindanao PAIC populations). We infer that this species diverged in the southern portion of the Philippine Archipelago and only recently colonized Orchid Island. Our study provides new information on the extensive distribution of A. lanyuensis outside Orchid Island, Taiwan, but we documented a very limited geographically associated genetic variation. Our study points to behavioral phenomena such as foraging behavior as essential contributor to the evolutionary process of species diversification, in contrast to the traditionally invoked geographic drivers of divergence.

Methods

We amplified the mitochondrial cytochrome oxidase 1 and sequenced it. Contigs were generated from merged forward, and reverse, sequences and their consensus sequences were aligned using Geneious Pro 6.03. We reconstructed a time-calibrated phylogenetic tree using BEAST v1.10.4. We incorporated seven species (nine sequences in total) from GenBank as an outgroup. The GTR+I+G best-fit nucleotide substitution model, Yule process speciation tree model prior and the uncorrelated lognormal relaxed clock model were applied for node age time calibration. We used the ucld.mean=0.0112 site -1 My -1 based on the spider mitochondrial substitution rate estimates (Bidegaray-Batista and Arnedo 2011; Kuntner et al. 2013) with an arbitrary standard deviation (ucld.stdv=0.01). The MCMC parameters were fixed to 1 x 10 9 generations with tree sampling every 1 x 104 generations. Tracer v.1.7.1 was used to determine burn-in  (discarded the first 10% of the trees). MCC tree was then generated using the program TreeAnnotator v.1.8.4. 

Funding

Ministry of Science and Technology, Taiwan, Award: 107-2311-B-037-004-MY3

National Science Foundation, Award: 0743491

National Science Foundation, Award: 1654388