DOI: 10.5281/zenodo.15159356
title: Table 6 in Complex geohistory of continental islands advanced allopatric evolution even for the highly dispersive generalist red fox % Vulpes vulpes): multiple phylogenetic groups in the Japanese Archipelago

description: Table 6. Result of AMOVA in the Hondo red fox population* computed based on the 1510 bp combined sequence of the mtDNA cytb gene and the D-loop region. Hierarchy for source of variation was set to among islands within a population* among subpopulations within islands* and among individuals within subpopulations. DF* SS* VC* and F are the degree of freedom* sum of squares* variance component* and F -statistics (F CT among islands* F SC among subpopulations* and F ST among individuals)* respectively.
HierarchyDFSSVCVariation (%)FPIsland250.10.5114.640.150.40Subpopulation277.61.1232.540.380.00Individual121220.81.8352.820.470.00
The phylogenetic tree suggests with high support rates that the Hondo clade diverged internally into the HNa and HNb subclades. The divergence time between those was the same as the tMRCA of the Hondo clade because each subclade was most basal within the clade. Thus* the Hondo red fox may have experienced a cladogenesis event between subclades shortly after their colonization of Paleo-Honshu Island. The tMRCAs of the HNa and HNb subclades were ~0.083 (0.147–0.034) and ~0.087 (0.155–0.034) Ma* respectively* and correspond to the early Last Glacial. Therefore* the modern Hondo red fox may have been chiefly descended from two ancestral populations established during that period.
Geographic mapping of each subclade revealed that the HNa and HNb subclades are mainly distributed in eastern and western Japan* respectively. This finding suggests that the ancestor of the Hondo red fox divided their distribution range over a long period into eastern and western Paleo-Honshu Island* and evolved into different subclades in each population. The high values of the pairwise F ST and corrected Pi between the eastern Honshu XY and Shikoku or Kyushu subpopulations* non-hierarchical genetic structure* and bimodal mismatch distribution strengthen the east–west vicariance hypothesis. In addition* the medianjoining network indicated that haplotypes belonging to each subclade have a different distributional pattern. This result supports that the formation process of the distribution differs between subclades. Prolonged distributional fragmentation within a narrow geographic area* such as Paleo-Honshu Island* is a rare case worldwide for the highly dispersive red fox (Kutschera et al. 2013 * Statham et al. 2014). Therefore* the complex geohistory and ecosystem characteristic of continental islands may have influenced the formation process of their distribution range.
Despite the independent analyses of the BSP and divergence time estimation* the root heights of the Hondo clade were almost
description: Published as part of Watanabe & Yamazaki, Yuji, 2024, Complex geohistory of continental islands advanced allopatric evolution even for the highly dispersive generalist red fox % Vulpes vulpes): multiple phylogenetic groups in the Japanese Archipelago, pp. 11 in Zoological Journal of the Linnean Society 202 (3) on page 11, DOI: 10.1093/zoolinnean/zlae007, http://zenodo.org/record/14423471