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Aim: This study compares the phylogeography, population structure and evolution of four butterflyfish species in the Chaetodon subgenus Corallochaetodon, with two widespread species (Indian Ocean - C. trifasciatus and Pacific Ocean - C. lunulatus), and two species that are largely restricted to the Red Sea (C. austriacus) and north-western (NW) Indian Ocean (G melapterus). Through extensive geographical coverage of these taxa, we seek to resolve patterns of genetic diversity within and between closely related butterflyfish species in order to illuminate biogeographical and evolutionary processes. Location: Red Sea, Indian Ocean and Pacific Ocean. Methods: A total of 632 individuals from 24 locations throughout the geographical ranges of all four members of the subgenus Corallochaetodon were sequenced using a 605 bp fragment (cytochrome b) of mtDNA. In addition, 10 microsatellite loci were used to assess population structure in the two widespread species. Results: Phylogenetic reconstruction indicates that the Pacific Ocean lunulatus diverged from the Indian Ocean C. trifasciatus approximately 3 Ma, while C. melapterus and C. austriacus comprise a cluster of shared haplotypes derived from G trifasciatus within the last 0.75 Myr. The Pacific C. lunulatus had significant population structure at peripheral locations on the eastern edge of its range (French Polynesia, Johnston Atoll, Hawai'i), and a strong break between two ecoregions of the Hawaiian Archipelago. The Indian Ocean C. trifasciatus showed significant structure only at the Chagos Archipelago in the central Indian Ocean, and the two range-restricted species showed no population structure but evidence of recent population expansion. Main conclusions: Patterns of endemism and genetic diversity in Corallochaetodon butterflyfishes have been shaped by (1) Plio-Pleistocene sea level changes that facilitated evolutionary divergences at biogeographical barriers between Indian and Pacific Oceans, and the Indian Ocean and Red Sea, and (2) semi-permeable oceanographic and ecological barriers working on a shorter time-scale. The evolution of range-restricted species (Red Sea and NW Indian Ocean) and isolated populations (Hawai'i) at peripheral biogeographical provinces indicates that these areas are evolutionary incubators for reef fishes.

The delineation of reef fish species by coloration is problematic, particularly for the pygmy angelfishes (genus Centropyge ), whose vivid colors are sometimes the only characters available for taxonomic classification. The Lemonpeel Angelfish ( Centropyge flavissima ) has Pacific and Indian Ocean forms separated by approximately 3,000 km and slight differences in coloration. These disjunct populations hybridize with Eibl’s Angelfish ( Centropyge eibli ) in the eastern Indian Ocean and the Pearl-Scaled Angelfish ( Centropyge vrolikii ) in the western Pacific. To resolve the evolutionary history of these species and color morphs, we employed mitochondrial DNA (mtDNA) cytochrome b and three nuclear introns (TMO, RAG2, and S7). Phylogenetic analyses reveal three deep mtDNA lineages ( d  = 7.0–8.3 %) that conform not to species designation or color morph but to geographic region: (1) most Pacific C. flavissima plus C. vrolikii , (2) C. flavissima from the Society Islands in French Polynesia, and (3) Indian Ocean C. flavissima plus C. eibli . In contrast, the nuclear introns each show a cluster of closely related alleles, with frequency differences between the three geographic groups. Hence, the mtDNA phylogeny reveals a period of isolation (ca . 3.5–4.2 million years) typical of congeneric species, whereas the within-lineage mtDNA Φ ST values and the nuclear DNA data reveal recent or ongoing gene flow between species. We conclude that an ancient divergence of C. flavissima , recorded in the non-recombining mtDNA, was subsequently swamped by introgression and hybridization in two of the three regions, with only the Society Islands retaining the original C. flavissima haplotypes among our sample locations. Alternatively, the yellow color pattern of C. flavissima may have appeared independently in the central Pacific Ocean and eastern Indian Ocean. Regardless of how the pattern arose, C. flavissima seems to be retaining species identity where it interbreeds with C. vrolikii and C. eibli , and sexual or natural selection may help to maintain color differences despite apparent gene flow.

Aim: We assess genetic differentiation among biogeographical provinces and colour morphs of the threadfin butterflyfish, Chaetodon auriga. This species is among the most broadly distributed butterflyfishes in the world, occurring on reefs from the Red Sea and western Indian Ocean to French Polynesia and Hawai'i. The Red Sea form lacks a conspicuous 'eye-spot' on the dorsal fin, which may indicate an evolutionary distinction. Location: Red Sea, Indian Ocean and Pacific Ocean. Methods: Specimens were obtained at 17 locations (n = 358) spanning the entire range of this species. The genetic data included 669 base pairs of mitochondrial DNA (mtDNA) cytochrome b and allele frequencies at six microsatellite loci. Analysis of molecular variance, STRUCTURE plots, haplotype networks and estimates of population expansion time were used to assess phylogeographical patterns. Results: Population structure was low overall, but significant and concordant between molecular markers (mtDNA: ϕST = 0.027, P < 0.001; microsatellites: FST = 0.023, P < 0.001). Significant population-level partitions were only detected at peripheral locations including the Red Sea and Hawai'i. Population expansion events in the Red Sea and Socotra are older (111,940-223,881 years) relative to all other sites (16,343-87,910 years). Main conclusions: We find little genetic evidence to support an evolutionary partition of a previously proposed Red Sea subspecies. The oldest estimate of population expansion in the Red Sea and adjacent Gulf of Aden indicates a putative refuge in this region during Pleistocene glacial cycles. The finding of population separations at the limits of the range, in the Red Sea and Hawai'i, is consistent with peripheral speciation.