Phylogeography, colouration, and cryptic speciation across the Indo-Pacific in the sea urchin genus Echinothrix

Simon E Coppard,Harilaos A Lessios,Holly Jessop

doi:10.1038/s41598-021-95872-0

Simon E Coppard, Harilaos A Lessios + Show 1 more

Open Access

https://doi.org/10.1038/s41598-021-95872-0

Copy DOI

Abstract

The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level differentiation among clades of E. calamaris. Colour variation was extensive in E. calamaris, but not clade or locality specific. There was little colour polymorphism in E. diadema.

Highlights

The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific
Colour variation may correlate with genetic divergence and possible speciation. Mortensen[13] suggested that regional colour differences existed in E. calamaris, with darker colour morphs prevailing in the western part of the Indian Ocean and lighter colour morphs being most common in the Malay Archipelago
Maximum Likelihood (ML) resolved the concatenated sequence of the hybrid specimen as sister to all E. calamaris (Fig. 1), whereas Bayesian Inference (BI) placed the sequence of the hybrid individual as sister to clade 3 of E. calamaris, reflecting its mtDNA haplotype

Summary

Introduction

The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level differentiation among clades of E. calamaris. Echinothrix diadema maintains on-going gene flow throughout the 5400 km of uninterrupted deep water between the central and the eastern Pacific[17] As crossing this Eastern Pacific Barrier (EPB) between Kiribati and Clipperton Island is virtually impossible for most shallow water marine invertebrates[18,19,20,21], the ability of E. diadema to do so suggests high dispersal potential. Colour variation may correlate with genetic divergence and possible speciation. Mortensen[13] suggested that regional colour differences existed in E. calamaris, with darker colour morphs prevailing in the western part of the Indian Ocean and lighter colour morphs being most common in the Malay Archipelago

Methods

Results

Conclusion