Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Abstract

Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that (i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins; (ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.Cyprininae, polyploid, schizothoracins, the Tibetan Plateau, diversifications Citation:Wang, X., Gan, X., Li J., Chen, Y., and He, S. (2016). Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau.

Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai–Tibetan Plateau

“…As the first attempt to characterize the phylogenetic relationships and divergence times of Schizothoracines on the basis of transcriptomic data, our results indicated that the common ancestor of the four Schizothoracines lived at the early part of the Oligocene (32.7 MYA), when the QTP was in the first phase of uplift (Favre et al 2015; Li and Fang 1999). The common ancestor of the two primitive Schizothoracines, S. prenanti and S. gongshanensis (which belong to the genus Schizothorax ), was estimated to be ∼5.2 MYA, which has been previously estimated to be in the Late Miocene (∼10 MYA) (He et al 2004; Wang et al 2016). Our results suggested that the common ancestor of P. kaznakovi and G. dobula diverged ∼8.1 MYA, when the QTP was in the second phase of uplift.…”

“…For example, the common ancestor of the schizothroacine subfamily was estimated to live at the end of the Late Cretaceous (68.2 MYA) by Y. Li et al (2013), or at the Oligocene-Miocene boundary (∼23 MYA) or older by Ruber et al (2007) and Wang et al (2016). As the first attempt to characterize the phylogenetic relationships and divergence times of Schizothoracines on the basis of transcriptomic data, our results indicated that the common ancestor of the four Schizothoracines lived at the early part of the Oligocene (32.7 MYA), when the QTP was in the first phase of uplift (Favre et al 2015; Li and Fang 1999).…”

“…These results suggested divergent evolutionary processes in highland and subhighland Schizothoracines. Previous phylogenetic studies indicated that the morphologically primitive Schizothoracine groups might have had independent origins and migrated independently of the morphologically specialized and highly specialized groups (Yonezawa et al 2014; Wang et al 2016). The divergent adaptive evolution revealed by this study supported these findings.…”

Genetic structure and phylogeographic relationships of the Bellamya complex: A nascent aquacultural snail in the Pearl River basin, China

“…The extensive uplift of the Himalayas and subsequent uplift of the Southeastern Tibet and Yunnan Plateau (Figure S2) during the early Miocene to Pliocene (Cao et al, ; Favre et al, ; Harrison, Copeland, Kidd, & Yin, ; Ruddiman, ; Shi et al, ) would have completely divided the Bellamya lineage in the Pearl River basin from that in India and Thailand. Many studies have associated the divergence of organisms, such as in lizards, birds, frogs and fish, with the Miocene uplift of the QTP and simultaneous climate changes (Che et al, ; Guo & Wang, ; Johansson et al, ; Wang, Gan, Li, Chen, & He, ). Furthermore, the divergence between the India lineage and Thailand lineage approximately 13.03 mya (15.02 ~ 11.55 mya), coinciding with the Himalayan and Indo‐Burma Mountains (Figure S2), rapidly uplifted during the early to middle Miocene (Alam, Alam, Curray, Chowdhury, & Gani, ; Khin, Sakai, & Zaw, ; Wang et al, ).…”

Chromosomes of Asian cyprinid fishes: cytogenetic analysis of two representatives of small paleotetraploid tribe Probarbini

“…bichirs, sturgeons, paddlefishes, gars and bowfin) [2, 3]. Furthermore, additional whole-genome duplications (WGDs) took place independently in several other teleostean lineages, such as, e.g., Catostomidae [4], Cobitidae [5], Callichthyidae [6, 7], Salmoniformes [8] and especially Cyprinidae [9–11]. …”