Inferring the Tree of Life of the order Cypriniformes, the earth＇s most diverse clade of freshwater fishes： Implications of varied taxon and character sampling

The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future cli-matic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent mo-lecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.

Reproductive characteristics of Psilorhynchus homaloptera Hora and Mukerji,1935 (Cyprinidae: Psilorhynchidae) in the lower Yarlung Zangbo River,Tibet

Psilorhynchus homaloptera mainly inhabits turbulent waters in the lower reach of the Yarlung Zangbo River,Tibet,China,and it is the only species of Psilorhynchus in China.However,many important aspects of its biology remain poorly documented,which hinders the conservation eff orts.Therefore,we studied its reproduction using 801 specimens from the Motuo sector of the lower Yarlung Zangbo River from December 2015 to November 2016.The sex ratio was 0.68꞉1(male꞉female)for the overall population.Females reached a larger total length and weight(134 mm and 18.6 g)than males did(113 mm and 12.2 g).Lengths at maturity were estimated 80.0 mm for males and 93.1 mm for females.Our analyses of gonad development and the size distribution of oocytes suggest that P.homaloptera is a single spawner with the peak spawning period between September and October.Furthermore,the estimated mean absolute fecundity was 557±204 eggs per fish,and mean relative fecundity was 50.9±10.9 eggs per g of female weight.The fecundity of P.homaloptera increased linearly with increasing total length,total weight,ovary weight,and age.This study on the reproductive biology of P.homaloptera demonstrates that the fish was in a vulnerable state due to the increasing anthropogenic activities in the lower Yarlung Zangbo River.

Changes in fish resources 5 years after implementation of the 10-year fishing ban in the Chishui River,the first river with a complete fishing ban in the Yangtze River Basin

Background To rehabilitate the depleted fish resources of the Yangtze River Basin,China,a 10-year fishing ban has been implemented.This national initiative has attracted worldwide attention.The present study aimed to explore the ecological process and recovery effectiveness of this complete fishing ban in the Chishui River,the first river where the fishing ban was enacted in the Yangtze River Basin.Changes in fish resources were analyzed based on investigations conducted 5 years before(2012–2016)and 5 years after(2017–2021)the implementation of the fish-ing ban in four reaches along the longitudinal gradient.Results A total of 140 fish species,including 127 native and 13 exotic species,were collected during the study period.The number of fish species as well as the diversity indices showed no significant temporal changes.However,11 native species that had disappeared for many years appeared again after the fishing ban.The occurrence rates of some key protected species,Procypris rabaudi,Acipenser dabryanus,Euchiloglanis davidi and Myxocyprinus asiaticus,increased after the fishing ban,while Coreius guichenoti,Percocypris pingi,Onychostoma angustistomata and Leptobotia rubrilabris showed no obvious recovery.The fish assemblage structure in nearly all reaches(except the headwater)showed significant temporal changes with an increase in the relative abundance of larger body-sized species.The population structure of most dominant species improved greatly with the mean standard length and the mean body weight as well as the proportion of larger-sized individuals clearly increasing.In addition,the density of fishes changed dramatically with the catch per unit effort(CPUE)increasing by 140–210%for different study reaches.Conclusions The present study confirmed that the complete fishing closure is an effective measure to facilitate fish resources recovery.These results provide valuable references for evaluating the effectiveness of the 10-year fishing ban policy in the entire Yangtze River.

Macro-evolutionary patterns of East Asian opsariichthyin-xenocyprinin-cultrin fishes related to the formation of river and river-lake environments under monsoon climate

Although the East Asian monsoon is believed to be an important driver for the origin and evolution of the biotas in this region,the association has rarely been rigorously tested.Here,using phylogenetic comparative methods and analyses of key innovations of adaptive traits,we investigated evolutionary patterns of the East Asian cyprinid opsariichthyin-xenocyprinin-cultrin clade;the dominant species in lakes and rivers,which are the typical productions of monsoon climate.Our molecular phylogenetic analyses revealed the relationships as(Opsariichthystribe t(((Oxygaster-tribe t Aphyocypris-tribe)t Metzia-tribe)t(Paralaubuca-tribe t(Squaliobarbus-tribe t(Hypophthalmichthys-tribe t(xenocyprinins t cultrins)))))).Based on Bayesian relaxed-clock methods,we found that origins of the Squaliobarbus-and Hypophthalmichthys-tribes bearing the key adaptation of riverine spawning with drifting eggs occurred 22.5 and 21.1 Mya,respectively.These times are consistent with the Early Miocene origin of major rivers(e.g.,Yangtze River)and the appearance of the East Asian monsoon climate.Diversification of the cultrins,characterized by spawning of adhesive eggs as well as swimming and feeding in lentic waters,were estimated to have evolved 16.6 to 0.2 Mya.This period covers three phases of enhancement of the East Asian monsoon from the Middle Miocene to the Pliocene(around 15–13,10–7,and 3.5 Mya).The habitats of these cultrins and their evolution also suggest the appearance and development of a lake-river environment during those periods.Therefore,our results suggest close relationships between the evolution of these fishes and geological events in East Asia.Further,they provide knowledge that may help facilitate future conservation strategies such as the maintenance of high river flows during dam construction and operation.

Novel insights into the reproductive strategies of wild Chinese sturgeon(Acipenser sinensis)populations based on the kinship analysis

Understanding the reproductive strategy of an organism is important in conservation ecology as it directly affects the population performance under changing environmental conditions.Chinese sturgeon(Acipenser sinensis)are the largest anadromous fish in the Yangtze River,China.Currently,the species has only one spawning ground and has failed to spawn in recent years,leading it to the brink of extinction.To develop effective conservation measures,a further understanding of its reproductive strategy is needed.In our study,we conducted kinship analyses by using mitochondrial and microsatellite DNA data from 216 wild juveniles collected over nine years(2006
2013,2015)to understand the mating system,breeding interval,effective number of breeding adults,and reproductive success.The results from these analyses suggested polygynandry,with some parents contributing up to eight half-sibling juvenile genotypes.Although the spawning ground was restricted to a limited area,genetic diversity was maintained at a relatively high level(observed heterozygosity from 0.698 to 0.787 and expected heterozygosity from 0.763 to 0.787)and inbreeding coefficients in each year-class ranged from
1% to 9%(low to modest detrimental effects on offspring).A parental inference analysis revealed that Chinese sturgeon have a breeding interval of 2-6 years,indicating that it has the potential to feed,accumulate nutrition in the ocean,and then migrate back to the Yangtze River for iteroparous reproduction.The annual effective number of breeders in the Yangtze River ranged from 14 to 161 during the study period,and it decreased by 62.1%from the 2011
2014 year-classes.This sharp population decline likely contributes to the reproduction failure.However,the ratios of effective to census population size(Ne/Nc)were all larger than 0.20 after the 2010 year-class,indicating relatively even reproductive success.Based on these results,a suggested approach to protect this species is to restock parent fish to increase the reproductive stock size and optimize the discharge of the Three Gorges Dam to reduce the unsuitable hydrological conditions and rehabilitate spawning ground habitats.