Reporting and Methodological Observations on Prognostic and Diagnostic Machine Learning Studies

Common reporting and methodological patterns were observed from the peer reviews of prognostic and diagnostic machine learning modeling studies submitted to JMIR AI. In this editorial, we summarized some key observations to inform future studies and their reporting.


Introduction
The genus Lysimachia L., a large genera of Primulaceae s. l. (APG III 2009), consists of over 180 species of annual or perennial herbs (Hu and Kelso 1996). Lysimachia has a nearly cosmopolitan distribution, mainly occurring in the temperate and subtropi-cal parts of the northern hemisphere, with a few species in Africa, Australia and South America Kelso 1996, Liu et al. 2014a). Southwestern China and its neighboring region of Indochina Peninsula have an extremely high species diversity with ca. 130 species and have been considered to be the diversity center of the genus (Yan et al. 2017).
During our expedition in 2017 and 2019 to the Youshui River valley in western Hunan, China, an unusual population of Lysimachia, with the plants having revolute succulent leaves, caught our attention. After consulting the relevant literature (Chen et al. 1989, Hu and Kelso 1996, Yan and Hao 2012, Liu et al. 2014a, Liu et al. 2014b, Zhou et al. 2015, Wang et al. 2018) and checking relevant specimens, we determined that the population represents a new species. Additionally, the new species is supported by a molecular phylogenetic analysis of some Lysimachia species based on ITS sequence data.

Taxon sampling and morphological analysis
The type specimens and fresh materials of the new species were collected from Huayuan County and Jishou City, Hunan Province, central China. Morphological observations and measurements were randomly made on flowering and fruiting plants. We examined related specimens kept in JIU and HUN and also specimen images in the online database of Chinese Virtual Herbarium (http://www.cvh.ac.cn) and JSTOR Global Plants (https://plants.jstor.org).
A total of 39 nuclear ribosomal ITS sequences for 34 species (Appendix S1) were downloaded from GenBank, following a study of Lysimachia (Zhang et al. 2011, Zhou et al. 2015. Two accessions of the putatively new species were sequenced for this study (GenBank Acc. No.: MN647744,MN647745). Ardisia verbascifolia Mez was selected as outgroup following Zhang et al. (2011). Voucher specimens of those specimens of the new species used for sequencing were deposited in JIU.

Molecular analyses
Total genomic DNA of the two accessions of the putatively new species was isolated from silica gel-dried leaves using a modified cetyltrimethylammonium bromide procedure (Doyle and Doyle 1987). The ITS region was amplified and sequenced by method of Zhang et al. (2011).
Phylogenetic trees were constructed using maximum likelihood (ML) and Bayesian inference (BI). The models determined for the datasets using the Akaike information criterion (Burnham and Anderson 2003) as implemented in MrModeltest 2.3 (Nylander 2004). ML trees were generated in RAxML 7.2.6 (Stamatakis 2006) with 1000 bootstrap replicates. BI trees were inferred in MrBayes version 3.1.2 (Huelsenbeck and Ronquist 2001). Four chains, each starting with a random tree, were run for 1,000,000 generations with trees sampled every 1000 generations. The convergence of the two runs was accessed with the average standard deviation of split frequencies less than 0.01. After the first ca. 25% discarded as burn-in, the remaining trees were imported into PAUP* v.4.0b10 (Swofford 2002) and a 50% majority rule consensus tree was produced to obtain posterior probabilities (PP) of the clades.
Morphologically, the new species is most similar to L. melampyroides R. Knuth in Engler with which it shares such features as the plants densely strigillose, leaves subglabrous adaxially, and flowers that are usually solitary in axils of upper leaves. However, the new species differs from L. melampyroides by the succulent leaves, the creeping or drooping stems 15-25 cm long, and the suborbicular to broadly elliptic corolla lobes. A morphological comparison between the new species and L. melampyroides is presented in Table 1.

Phylogenetic position
The aligned lengths of ITS are 655 bp with gaps treated as missing data. BI and ML analyses produced similar topology and only the BI tree was presented in Figure 1.  Diagnosis. The new species differs from L. melampyroides by the succulent leaves; the creeping or drooping stems (15-25 cm long); and the suborbicular to broadly elliptic corolla lobes.
Phenology. Flowering May-June, fruiting July-August. Distribution and habitat. This new species is currently known from Huayuan County and Jishou City in western Hunan Province, central China. It usually grows on limestone cliffs in valleys (Figure 2), and is associated with e.g. Eriophorum comosum (Wallich) Nees in Wight, Pteris vittata Linnaeus, Pteris deltodon Baker, and Dryopteris sp.
Etymology. The specific epithet "xiangxiensis", literally meaning western Hunan, refers to the Xiangxi Tujia and Miao Autonomous Prefecture in central China, to which Huayuan County and Jishou City belong. The Chinese name of the Lysimachia xiangxiensis is xiang xi guo lu huang in Pinyin.
Conservation status. Lysimachia xiangxiensis usually grows on limestone cliffs in valleys so we suggest its placement in the Data Deficient category of IUCN (2017) Additional collection. CHINA. Hunan Province, Jishou City, Aizhai Town, National Forest Park, cliff of a valley, 31 May 2019, Y. Wu 0531001(paratype, JIU!).