Numerous mitochondrial DNA haplotypes reveal multiple independent polyploidy origins of hexaploids in Carassius species complex

Abstract

Evolutionary trajectory and occurrence history of polyploidy have been extensively studied in plants, but they remain quite elusive in vertebrates. Here, we sampled and gathered 4,159 specimens of polyploid Carassius species complex including 1,336 tetraploids and 2,823 hexaploids from a large geographic scale (49 localities) across East Asia, and identified a huge number of 427 diverse haplotypes of mitochondrial control region, in which 74 haplotypes with total occurrence frequency up to 75.498% were shared by hexaploids and tetraploids. Significantly, these diverse haplotypes were clustered into four major lineages, and many haplotypes of hexaploids and tetraploids were intermixed in every lineage. Moreover, the evolutionary trajectory and occurrence history of four different lineages were revealed by a simplified time‐calibrated phylogenetic tree, and their geographic distribution frequencies and haplotype diversity were also analyzed. Furthermore, lineage C and D were revealed to undergo population expansion throughout mainland China. Therefore, our current data indicate that hexaploids should undergo multiple independent polyploidy origins from sympatric tetraploids in the polyploid Carassius species complex across East Asia.

Coexistence of Three Divergent mtDNA Lineages in Northeast Asia Provides New Insights into Phylogeography of Goldfish (Carssius auratus)

“…One of the seven samples had identical CR and cytb haplotypes to those of the unique sample in our experimental station. Our results supported that “odd” CR of Sakai et al and “hidden” cytb sequences of Kalous et al represent the same lineage [ 16 , 17 ], which were neglected by Takada et al [ 14 ] and further studies [ 15 , 18 , 29 ].…”

“…For example, Japanese ichthyologists tend to take gynogenetic reproduction and polyploidy as diagnostic characteristics of C. a. langsdorfii [ 2 ]. However, previous studies have revealed that gynogenetic polyploids in all three known lineages within Japanese clade, and a sizable chunk of haplotypes were shared between polyploids and diploids [ 14 , 15 , 29 ].…”

Differential expression of innate and adaptive immune genes in the survivors of three gibel carp gynogenetic clones after herpesvirus challenge

“…Gibel carp ( C. gibelio ), as a natural polyploid fish [1, 2], widely distributes across the Eurasian continent [3–9] and is able to reproduce by unisexual gynogenesis or sexual reproduction [10–16]. Recently, we discriminated numerous various gynogenetic clones of gibel carp from 35 locations through mainland China by transferrin allele and mtDNA haplotype polymorphism [5, 6]. Along with the large-scale application of several improved varieties, all-female allogynogenetic gibel carp activated by heterologous sperm has become one of the most important farmed fish in China [17].…”

Morphological characterization and phylogenetic relationships of Indochinese box turtles—The Cuora galbinifrons complex

“…The indefinite geographical range of the wild population, the misinterpretations of molecular‐based phylogenies by different mitochondrial genes or nuclear mitochondrial pseudogenes, and the incomplete lineage sorting and introgression are the main reasons for the ambiguity of taxonomy and systematics of Cuora species. In this study, we used nuclear ( Rag1 ) and mitochondrial markers (genome and COI ) in conjunction with morphologic characters to construct the phylogeny among the C. galbinifrons complex ( galbinifrons , bourreti , and picturata ), as these geometric morphometrics and molecular markers have been extensively utilized to investigate the origin and evolutionary history of vertebrates, including the whale shark ( Rhincodon typus ; Md Tauqeer, Petit, Read, & Dove, ), Chinese three‐striped box turtle ( Cuora trifasciata ; Li, Zhang, Zhao, Shi, & Zhu, ), Carassius species complex (Liu, Li, et al, ), Conorhynchos (Sullivan, Lundberg, & Hardman, ), Hemiculter leucisculus (Cheng et al, ), and Magadi tilapia (Kavembe, Kautt, Machado‐Schiaffino, & Meyer, ). We detected morphological differences among the C. galbinifrons complex, and moreover, based on the results of nuclear and mitochondrial markers, we investigated whether the galbinifrons , bourreti , and picturata groups can be regarded as separate species or subspecies.…”