Data from: Novel trophic niches drive variable progress toward ecological speciation within an adaptive radiation of pupfishes

Adaptive radiation is recognized by a rapid burst of phenotypic, ecological, and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation among nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey specialist (durophage), yet the radiation is less than 10,000 years old. Both specialists and an abundant generalist species all coexist in the benthic zone of lakes on San Salvador Island, Bahamas. Based on 13,912 single-nucleotide polymorphisms (SNPs), we found consistent differences in genetic differentiation between each specialist species and the generalist across seven lakes. The scale-eater showed the greatest genetic differentiation and clustered by species across lakes, whereas durophage populations often clustered with sympatric generalist populations, consistent with parallel speciation across lakes. However, we found strong evidence of admixture between durophage populations in different lakes, supporting a single origin of this species and genome-wide introgression with sympatric generalist populations. We conclude that the scale-eater is further along the speciation-with-gene-flow continuum than the durophage and suggest that different adaptive landscapes underlying these two niche environments drive variable progress toward speciation within the same habitat. Our previous measurements of fitness surfaces in these lakes support this conclusion: the scale-eating fitness peak may be more distant than the durophage peak on the complex adaptive landscape driving adaptive radiation.

适应性辐射（adaptive radiation）的典型特征为表型、生态与物种多样化的快速爆发。然而学界尚未明确，同一适应性辐射事件内的不同物种，其生殖隔离的演化速率是否存在差异。本研究利用测序分型技术（genotyping by sequencing），对鲤齿鳉属（Cyprinodon）鳉鱼（pupfishes）的适应性辐射事件中新生物种的遗传分化模式开展了比较分析。与经典适应性辐射事件类似，该演化支展现出极快的形态多样化速率；其中两个物种为新型营养特化类群：一类为食鳞者（scale-eater），另一类为硬壳猎物专性者（durophage，硬食专性种），且该辐射事件的发生时长不足1万年。这两种特化物种与一种数量丰度较高的广食性物种，共同栖息于巴哈马圣萨尔瓦多岛湖泊的底栖带中。基于13912个单核苷酸多态性（single-nucleotide polymorphisms, SNPs）标记，我们在7个湖泊中均观测到，每一种特化物种与广食性物种之间的遗传分化均存在稳定差异。食鳞者展现出最高的遗传分化程度，且在跨湖泊样本中按物种聚类；而硬食专性种种群则常与同湖栖息的广食性种群聚类，这与跨湖泊平行成种的模式相符。但我们观测到不同湖泊内的硬食专性种种群间存在强烈的基因混合信号，这支持该物种的单一起源，以及其与同湖栖息广食性种群间的全基因组渐渗（introgression）现象。据此我们得出结论：食鳞者在“存在基因流的物种形成（speciation-with-gene-flow）”连续体上的演化阶段要早于硬食专性种；并提出，这两种生态位环境背后的不同适应性景观（adaptive landscape），驱动了同一栖息地内物种形成进程的差异。我们此前在这些湖泊中测得的适合度曲面（fitness surface）数据支持这一结论：在驱动该适应性辐射事件的复杂适应性景观中，食鳞者的适合度峰（fitness peak）相较于硬食专性种的适合度峰，距离初始种群的位置更远。