Evidence for allopolyploid speciation in Nymphoides (Menyanthaceae)

The floating-leaved aquatic plant genus Nymphoides includes diploid and polyploid species that are distributed worldwide. Prior studies found widespread incongruence between nuclear and plastid phylogenies, and this has prevented the construction of a unified phylogenetic hypothesis for the genus. In order to examine whether phylogenetic incongruence resulted from ancestral polyploidization events, we obtained DNA sequence data from two nuclear loci, phytoene desaturase (PDS) and transmembrane nine (TMN1), as well as the plastid trnT-trnF region. Multiple divergent copies of the nuclear genes were recovered from several species, and species with the most divergent copies were inferred to have originated through allopolyploidization. Our data support a scenario in which three groups of species descended from allopolyploidization events: a clade of North American species (N. aquatica and N. cordata), a clade of neotropical species (N. fallax, N. grayana, and N. humboldtiana), and the Aust...,
plastid matK/trnK and trnT-trnF alignment
This file contains aligned DNA sequences for Menyanthaceae species. Sequences from the matK/trnK region are followed by sequences from the trnT-trnF region in a concatenated alignment.
Meny-matKtrnL-cpmatch_16-0712_DNA.nex

nuclear phytoene desaturase (PDS) alignment
Meny-PDS-trim_16-0601_DNA.nex

nuclear transmembrane nine (TMN1) alignment
Meny-TMN1-trim_17-0110_DNA.nex

plastid matK/trnK and trnT-trnF phylogeny
Phylogeny obtained from BEAST analysis of plastid data.
Meny-matKtrnL-cpmatch_16-0712_BEAST.tre

nuclear phytoene desaturase (PDS) phylogeny
Phylogeny obtained from BEAST analysis of PDS data.
Meny-PDS-trim_16-0601_BEAST.tre

nuclear transmembrane nine (TMN1) phylogeny
Phylogeny obtained from BEAST analysis of TMN1 data.
Meny-TMN1-trim_17-0110_BEAST.tre

Combined data species tree
Phylogeny obtained using StarBEAST2 analysis of combined plastid and nuclear data to determine the species tree.
Meny-alldata-species_BEAST.tre
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浮叶水生植物莕菜属（Nymphoides）包含二倍体与多倍体物种，其分布遍及全球。既往研究显示，核基因组与质体基因组的系统发育关系普遍存在不一致性，这阻碍了该属统一系统发育假说的构建。为探究系统发育不一致性是否由祖先多倍化事件所导致，本研究获取了两个核基因座——八氢番茄红素脱氢酶（phytoene desaturase, PDS）与跨膜蛋白9（transmembrane nine, TMN1）——以及质体trnT-trnF区域的DNA序列数据。从多个物种中成功回收得到多个高度分化的核基因拷贝，推测携带分化程度最高拷贝的物种经由异源多倍化起源。本研究数据支持三类物种均源自异源多倍化事件的演化场景：一是北美物种分支（包含N. aquatica与N. cordata），二是新热带物种分支（包含N. fallax、N. grayana及N. humboldtiana），以及澳[原文此处截断]。

### 质体matK/trnK与trnT-trnF序列比对文件
本文件包含睡菜科（Menyanthaceae）物种的比对后DNA序列。质体matK/trnK区域的序列紧随trnT-trnF区域序列，构成串联比对序列。
对应文件：Meny-matKtrnL-cpmatch_16-0712_DNA.nex

### 核基因八氢番茄红素脱氢酶（PDS）序列比对文件
对应文件：Meny-PDS-trim_16-0601_DNA.nex

### 核基因跨膜蛋白9（TMN1）序列比对文件
对应文件：Meny-TMN1-trim_17-0110_DNA.nex

### 质体matK/trnK与trnT-trnF系统发育树
基于质体数据经BEAST分析得到的系统发育树。
对应文件：Meny-matKtrnL-cpmatch_16-0712_BEAST.tre

### 核基因八氢番茄红素脱氢酶（PDS）系统发育树
基于PDS数据经BEAST分析得到的系统发育树。
对应文件：Meny-PDS-trim_16-0601_BEAST.tre

### 核基因跨膜蛋白9（TMN1）系统发育树
基于TMN1数据经BEAST分析得到的系统发育树。
对应文件：Meny-TMN1-trim_17-0110_BEAST.tre

### 联合数据物种树
基于质体与核基因联合数据经StarBEAST2分析得到的物种树。
对应文件：Meny-alldata-species_BEAST.tre