Data from: Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographic breaks congruent with fish community boundaries?

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to determine if phylogeographic breaks in this species were congruent with previously-defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we might find four clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographic regions. We generated DNA sequence data (mitochondrial cyt b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analyzed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow, and effective population size. Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographic community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not predicted by community province boundaries.

系统发育地理学（phylogeography）的核心初衷之一，便是借助遗传数据甄别可能导致种群间分化的历史事件。本研究针对采自哥斯达黎加的一种常见胎生鱼类——吉氏花鳉（Poecilia gillii）开展系统发育地理学分析。本研究旨在明确该物种的系统发育地理学分化是否与此前划定的四个鱼类群落区（fish community provinces）边界相契合。我们提出假说：若非生物因子（abiotic factors）同时影响吉氏花鳉的群落边界与遗传结构（genetic structuring），则该目标物种内应存在四个沿群落边界线地理隔离的演化支（clades）。同理，我们预期吉氏花鳉的绝大多数遗传变异将分布于这四个地理区域之间。我们为分布于哥斯达黎加的42个种群的260个个体生成了DNA序列数据，涵盖线粒体细胞色素b（mitochondrial cyt b）与核S7小核糖体亚基（nuclear S7 small ribosomal subunit）。本研究采用系统发育分析方法（简约法（parsimony）与似然法（likelihood））及溯祖分析方法（coalescent approaches）对上述数据进行分析，以估算单倍型（haplotypes）间的系统发育关系、基因流（gene flow）模式与有效种群大小（effective population size）。但与预期相悖的是，我们并未发现能够清晰对应四个地理群落区的单系群（monophyletic groups）。不过，其中一个演化支仅分布于单个群落区，这表明共同的地球历史事件（earth history events）或许同时塑造了吉氏花鳉的遗传结构与该区域的鱼类群落组成（fish community composition）。但本研究结果显示，哥斯达黎加其余区域的基因流模式较为复杂，其遗传结构并未受群落区边界的预期约束。