Reconstructing the population history of the sandy beach amphipod Haustorioides japonicus using the calibration of demographic transition (CDT) approach

Abstract

Calibration of the molecular rate is one of the major challenges in marine population genetics. Although the use of an appropriate evolutionary rate is crucial in exploring population histories, calibration of the rate is always difficult because fossil records and geological events are rarely applicable for rate calibration. The acceleration of the evolutionary rate for recent coalescent events (or more simply, the time dependency of the molecular clock) is also a problem that can lead to overestimation of population parameters. Calibration of demographic transition (CDT) is a rate calibration technique that assumes a post-glacial demographic expansion, representing one of the most promising approaches for dealing with these potential problems in the rate calibration. Here, we demonstrate the importance of using an appropriate evolutionary rate, and the power of CDT, by using populations of the sandy beach amphipod Haustorioides japonicus along the Japanese coast of the northwestern Pacific Ocean. Analysis of mitochondrial sequences found that the most peripheral population in the Pacific coast of northeastern Honshu Island (Tohoku region) is genetically distinct from the other northwestern Pacific populations. By using the two-epoch demographic model and rate of temperature change, the evolutionary rate was modeled as a log-normal distribution with a median rate of 2.2%/My. The split-time of the Tohoku population was subsequently estimated to be during the previous interglacial period by using the rate distribution, which enables us to infer potential causes of the divergence between local populations along the continuous Pacific coast of Japan.

Response to suction dynamics on intertidal distribution of <i>Haustorioides</i> amphipod species on East Asian sandy beaches during diurnal tidal changes

“…Currently 10 species are recognized in the genus Haustorioides from East Asia (Jo 1988, Ogawa et al 2021. Ecological studies on these amphipods have been mostly concerned with H. japonicus whose geographic range extends from northern Kyushu to southern Hokkaido in Japan (Kamihira 1992, Sakuma et al, 2019. This species is a detritus and filter feeder (Kamihira 1992, Kogure & Takada 2012, Takamatsu & Yanai 2019, and inhabits in the swash zone of sandy beaches, burrowing into the surface layer of the sand substratum.…”

A New Species of the Sand-burrowing Dogielinotidae, <i>Haustorioides furotai</i>, from Tokyo Bay, Japan (Crustacea: Amphipoda)

“…On the other hand, H. munsterhjelmi was reported from eastern Hokkaido (Kamihira 1992). Recently, Takada et al (2018) recognized five genetic clades among the populations of H. japonicus along the Japanese coast of Japan Sea, East China Sea and the northwestern Pacific, and Sakuma et al (2019) reported an additional population from Miyagi Prefecture. However, the taxonomic status of those clades still remains undetermined.…”