Evolutionary Drivers of Diversification and Distribution of a Southern Temperate Stream Fish Assemblage: Testing the Role of Historical Isolation and Spatial Range Expansion

<div><p>This study used phylogenetic analyses of mitochondrial cytochrome <i>b</i> sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (<i>Galaxias</i>, <i>Pseudobarbus</i> and <i>Sandelia</i>) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequences of <i>Galaxias</i>, 177 sequences of <i>Pseudobarbus</i> and 98 sequences of <i>Sandelia</i> from 146 localities across nine river systems in the south-western Cape Floristic Region (South Africa) were used. The data were analysed using phylogenetic and haplotype network methods and divergence times for the clades retrieved were estimated using *BEAST. Nine extremely divergent (3.5–25.3%) lineages were found within <i>Galaxias</i>. Similarly, deep phylogeographic divergence was evident within <i>Pseudobarbus</i>, with four markedly distinct (3.8–10.0%) phylogroups identified. <i>Sandelia</i> had two deeply divergent (5.5–5.9%) lineages, but seven minor lineages with strong geographical congruence were also identified. The Miocene-Pliocene major sea-level transgression and the resultant isolation of populations in upland refugia appear to have driven widespread allopatric divergence within the three genera. Subsequent coalescence of rivers during the Pleistocene major sea-level regression as well as intermittent drainage connections during wet periods are proposed to have facilitated range expansion of lineages that currently occur across isolated river systems. The high degree of genetic differentiation recovered from the present and previous studies suggest that freshwater fish diversity within the south-western CFR may be vastly underestimated, and taxonomic revisions are required.</p></div

Means and ranges (in parentheses) of model-corrected genetic divergences (%) between <i>Galaxias</i> lineages from the south-western CFR.

<p>Within lineage divergences are shown in bold. Fu’s <i>F</i>s value for each lineage is given in the last column (** <0.005; *<0.05).</p

Mean and range of model-corrected genetic divergence (%) between <i>Pseudobarbus</i> lineages from the south-western CFR.

<p>The ranges of the values are given in parentheses. Within lineage divergences are given in bold. Fu’s <i>F</i>s value for each lineage is given in the last column (** <0.005; *<0.05).</p

Hypotheses of factors that could have shaped genetic and distribution patterns of fishes in the south-western CFR.

<p>Panel (a) assumes that populations could have been historically connected probably during a period of a major sea-level regression. Panel (b) describes the hypothesis that truncation of rivers during the Miocene-Pliocene major sea-level transgression fragmented populations and isolated them into upland areas that were not inundated (Refugia hypothesis), leading to allopatric divergence and the formation of unique lineages (indicated by the different colours). Panel (c) shows the river systems that would have coalesced forming the palaeoriver systems of the Last Glacial Maximum (LGM) (Palaeoriver hypothesis), allowing the exchange of unique lineages between systems sharing a common confluence. Panel (d) illustrates the hypothesis that alternative dispersal routes such as freshwater connections through low drainage divides could have facilitated range expansion of unique lineages (Interdrainage Dispersal hypothesis), leading to unique lineages being distributed across river systems that did not coalesce during the LGM.</p

The Cape Floristic Region (CFR) of South Africa showing the Cape Fold Mountains.

<p>Location of the south-western CFR and the river systems (1–11) considered in the present study are indicated.</p

<i>Sandelia</i> lineage diversity.

<p>(a) Eight lineages with strong geographic affinities recovered with Maximum Likelihood phylogenetic analysis of mitochondrial cyt <i>b</i> haplotypes (1–30) identified in <i>Sandelia</i> from the south-western CFR. Bayesian posterior probabilities are given on the branches. The colours denote lineages and their distribution ranges are presented in Figure S3 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070953#pone.0070953.s002" target="_blank">Appendix S2</a>. (b) TCS network of cyt <i>b</i> haplotypes (1–30) from individuals of <i>Sandelia</i> from the south-western CFR. The sizes of circles are proportional to haplotype frequency, and the colours indicate the river system (s) where the haplotype occurred. Black dots represent missing haplotypes in the network. Each branch represents one mutation step.</p

<i>Galaxias</i> lineage diversity.

<p>(a) Maximum Likelihood phylogenetic estimate of relationships among mitochondrial cytochrome <i>b</i> haplotypes of <i>Galaxias</i> from the south-western CFR. Bayesian posterior probabilities are given on the branches. The numbers (1–74) represent unique haplotypes and the colours indicate lineages, corresponding to distribution maps in Figure S1 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070953#pone.0070953.s002" target="_blank">Appendix S2</a>. River systems in which the lineages occur are listed below the lineage names and their ranges are presented in Figure S1 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070953#pone.0070953.s002" target="_blank">Appendix S2</a>. (b) TCS network of cyt <i>b</i> haplotypes (1–74) from individuals of <i>Galaxias</i> from the south-western CFR. The sizes of circles are proportional to haplotype frequency, and the colours indicate the river system(s) where the haplotype occurred. Black dots represent missing haplotypes in the network. Each branch represents one mutation step.</p

Sea-level changes.

<p>Potential fragmentation of river systems during the Miocene-Pliocene sea-level transgression and the proposed palaeoriver systems (1–8) of the Last Glacial Maximum (LGM) in the south-western Cape Floristic Region (CFR). The potential range of the maximum transgression level is indicated by the area in yellow. The white area would therefore have been vulnerable to marine incursion, whereas the area in orange was possibly never affected by the Miocene-Pliocene transgression. The approximate LGM sea-level is represented by the −130 m contour line. The palaeorivers are 1) Palmiet, 2) Bot-Onrus, 3) Klein, 4) Uilkraals, 5) Haelkraal, 6) Ratel, 7) Breede-Heuningnes-Duiwenhoks and 8) Gouritz-Goukou.</p