Data from: Phylogenomic structure and speciation in an emerging model: The Sphagnum magellanicum complex (Bryophyta)

The moss genus Sphagnum has unparalleled ecological importance because
some 30% of the total terrestrial carbon pool is bound up in
Sphagnum-dominated peatlands. A major peat-former, S. magellanicum, is one
of two species for which a reference-quality genome exists to facilitate
research in ecological genomics, but recently published work indicated
that S. magellanicum s. str. is restricted to South America and two other
species, S. divinum and S. medium occur in North America and Europe. We
report herein that there are four clades/species within the S.
magellanicum complex in eastern North America, two in South America, and
another in eastern Asia. The reference genome belongs to S. divinum.
Phylogenetic analyses at the whole genome and chromosome levels, using
genome resequencing and RADseq, resolve sister group relationships within
the complex. Species are monophyletic in most analyses and exhibit tens of
thousands (RADseq) to millions (resequencing) of fixed nucleotide
differences, but two, referred to informally as S. diabolicum and S. magni
because they have not been formally described, are differentiated by only
hundreds (RADseq) to thousands (resequencing) of differences. Data from 14
of the 19 resequenced chromosomes (7 chromosomes for RADseq) resolve the
reciprocal monophyly of S. magni and S. diabolicum. These two appear to be
in the process of speciation and because they differ in geographic ranges
and the climate zones they occupy – S. diabolicum in boreal peatlands and
S. magni in warm temperate to subtropical communities of the southern U.S.
– they provide an exciting opportunity for comparative genomic analyses of
climate niche evolution. Introgression among species in the complex is
demonstrated using D-statistics and f4-ratios. One ecologically important
functional trait that underlies peat (carbon) accumulation, tissue
decomposability, does not differ between segregate North American species
in the S. magellanicum complex although previous research showed that many
related Sphagnum species have evolved differences in
decomposability/carbon sequestration. Phylogenetic resolution and more
accurate species delimitation in the S. magellanicum complex substantially
increase the value of this group for studying the early evolutionary
stages of climate adaptation, and ecological evolution more broadly.

泥炭藓属（Sphagnum）具有无可比拟的生态重要性，因为陆地总碳库中约30%的碳储存于泥炭藓主导的泥炭地中。作为主要的泥炭形成植物，大泥炭藓（S. magellanicum）是拥有参考级基因组（reference-quality genome）以推动生态基因组学（ecological genomics）研究的两个物种之一，但近期发表的研究表明，严格意义上的大泥炭藓（S. magellanicum s. str.）仅限于南美洲，而另外两个物种——神圣泥炭藓（S. divinum）和中型泥炭藓（S. medium）则分布于北美和欧洲。本文报告，在北美东部的大泥炭藓复合体（S. magellanicum complex）中存在四个分支/物种，南美洲有两个，东亚另有一个。参考基因组属于神圣泥炭藓。利用基因组重测序（genome resequencing）和RADseq技术，通过全基因组及染色体水平的系统发育分析（phylogenetic analyses），我们解析了该复合体内部的姐妹群关系。多数分析显示物种为单系类群，且存在数万（RADseq数据）至数百万（重测序数据）的固定核苷酸差异；但两个暂被非正式命名为恶魔泥炭藓（S. diabolicum）和巨型泥炭藓（S. magni）的类群（因尚未正式描述）仅存在数百（RADseq数据）至数千（重测序数据）的差异。19条重测序染色体中的14条（RADseq数据中的7条）解析了巨型泥炭藓与恶魔泥炭藓的互单系性。这两个类群似乎正处于物种形成（speciation）过程中，且其地理分布及所处气候区不同——恶魔泥炭藓分布于北方泥炭地，巨型泥炭藓则分布于美国南部的暖温带至亚热带群落——为气候生态位演化的比较基因组分析提供了绝佳契机。通过D统计量（D-statistics）和f4比率（f4-ratios），我们证实了该复合体物种间存在基因渐渗（introgression）。尽管先前研究表明许多近缘泥炭藓物种在可分解性/碳封存能力上已演化出差异，但北美大泥炭藓复合体中分离物种的组织可分解性（泥炭碳积累的关键功能性状）并无显著差异。大泥炭藓复合体的系统发育解析及更精准的物种界定（species delimitation），显著提升了该类群在研究气候适应早期演化阶段及更广泛生态演化中的价值。