3DPhenoFish:Application for two-and three-dimensional fish morphological phenotype extraction from point cloud analysis

Fish morphological phenotypes are important resources in artificial breeding,functional gene mapping,and population-based studies in aquaculture and ecology.Traditional morphological measurement of phenotypes is rather expensive in terms of time and labor.More importantly,manual measurement is highly dependent on operational experience,which can lead to subjective phenotyping results.Here,we developed 3DPhenoFish software to extract fish morphological phenotypes from three-dimensional(3D)point cloud data.Algorithms for background elimination,coordinate normalization,image segmentation,key point recognition,and phenotype extraction were developed and integrated into an intuitive user interface.Furthermore,18 key points and traditional 2D morphological traits,along with 3D phenotypes,including area and volume,can be automatically obtained in a visualized manner.Intuitive fine-tuning of key points and customized definitions of phenotypes are also allowed in the software.Using 3DPhenoFish,we performed high-throughput phenotyping for four endemic Schizothoracinae species,including Schizopygopsis younghusbandi,Oxygymnocypris stewartii,Ptychobarbus dipogon,and Schizothorax oconnori.Results indicated that the morphological phenotypes from 3DPhenoFish exhibited high linear correlation(>0.94)with manual measurements and offered informative traits to discriminate samples of different species and even for different populations of the same species.In summary,we developed an efficient,accurate,and customizable tool,3DPhenoFish,to extract morphological phenotypes from point cloud data,which should help overcome traditional challenges in manual measurements.3DPhenoFish can be used for research on morphological phenotypes in fish,including functional gene mapping,artificial selection,and conservation studies.3DPhenoFish is an open-source software and can be downloaded for free at https://github.com/lyh24k/3DPhenoFish/tree/master.

Bridging gaps between environmental flows theory and practices in China

In recent decades,a series of policies and practices for environmental flows(e-flows)have been implemented in China,with the sustainable development goal of balancing the utilization and protection of water resources among social,economic,and ecological needs.The aims of this study were to determine the main challenges and issues in e-flows implementation at different scales by analyzing policies and practices for eflows in China,and to propose some recommendations for bridging the gaps between the science and implementation of e-flows.The gaps between the science and implementation of e-flows were found after review of literature,policies,and practices,and it was found that ecological flow was a more widely used term by the government,rather than e-flows,in implementation.The plans and effects of e-flows implementation are discussed in this paper and challenges of e-flows implementation are recognized:(1)limited water resources and uneven spatial and temporal distribution,(2)a weak scientific basis for e-flows implementation,(3)poor operability of e-flows science,and(4)ineffective supervision and guarantee measures.The recommendations are(1)to strengthen the scientific foundation of e-flows,(2)to improve effectiveness in application of e-flows science,and(3)to propose operable and effective supervision and guarantee measures.This paper elaborates the current understanding of e-flows science and provides practical recommendations for implementing e-flows and for improving the effectiveness in e-flows implementation.To bridge the gaps between science and implementation of e-flows and improve the operability of policies in future practices,more scientific research on practices is recommended through adaptive management.