Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

Species delimitation is ever more critical for assessing biodiversity in
threatened regions of the world, especially when undescribed lineages may
be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of
a rapid radiation of morphologically cryptic species that are distributed
throughout Madagascar in its rapidly vanishing forested habitats. Here, we
focus on two pairs of sister lineages that occur in a region in
northeastern Madagascar that shows high levels of microendemism. We
revisit previous hypotheses of species diversity by filling geographic
sampling gaps and by generating new genomic data for three named species,
as well as an undescribed lineage previously identified to be of interest
due to its highly divergent mtDNA. We analyzed RADseq data with multiple
species delimitation methods based on the multispecies coalescent (MSC)
model while accounting for introgression. Non-sister lineages occur
sympatrically in two instances, despite an estimated divergence time of
less than 1 Ma, thus suggesting rapid evolution of reproductive isolation
in the mouse lemur clade. We note, however, that the divergence time
estimates reported here are based on the MSC and calibrated with
pedigree-based primate mutation rates. These dates are considerably more
recent than previous analyses that used traditional relaxed clock methods
and distant fossil calibrations. One pair of sister lineages passed all
species delimitation tests while the other pair failed most, largely due
to differences in Ne between the two pairs of lineages. Nevertheless,
delimitation results were also supported by differences in levels of gene
flow and patterns of isolation-by-distance between the two pairs. We
conclude that MSC-based species delimitation methods are valuable tools
for evaluating cryptic species, even though these methods can be strongly
affected by variable Ne. We suggest that this result has general
implications for species delimitation studies of other recently diverged
lineages.

物种界定（species delimitation）对评估全球受威胁区域的生物多样性日益关键，尤其是当未被描述的支系可能面临栖息地丧失风险之时。倭狐猴属（Microcebus）类群便是典型代表：该类群经历快速辐射演化，形成诸多形态隐存物种，广泛分布于马达加斯加境内快速缩减的森林栖息地中。本研究聚焦马达加斯加东北部一处呈现高度微特有现象的区域内的两对姐妹支系。我们通过填补地理采样空白、为3个命名物种以及1个此前因线粒体DNA（mtDNA）高度分化而备受关注的未描述支系生成全新基因组数据，重新审视了既往关于物种多样性的假说。研究团队基于多物种溯祖（multispecies coalescent, MSC）模型，结合多种物种界定方法分析了限制性位点关联DNA测序（RADseq）数据，并纳入基因渐渗（introgression）因素。尽管估算的分化时间不足1百万年，但仍有两例非姐妹支系呈现同域分布，这暗示倭狐猴演化支系中生殖隔离的快速演化。不过需要指出的是，本研究的分化时间估算基于MSC模型，并以基于谱系的灵长类突变率进行校准，该年代远早于既往使用传统宽松钟方法与远端化石校准的分析结果。其中一对姐妹支系通过了全部物种界定测试，而另一对则多数测试未通过，这主要源于两对支系间有效种群大小（Ne）的差异。尽管如此，两对支系间的基因流水平差异与距离隔离模式也为物种界定结果提供了支撑。我们最终得出结论：基于MSC的物种界定方法是评估隐存物种的有效工具，尽管该类方法极易受有效种群大小变异的影响。我们认为该研究结果对其他近期分化支系的物种界定研究具有普遍借鉴意义。