Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes.

Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stocks in the past. Previous studies identified conflicting mtDNA genetic substructuring patterns and thus contrasting evolutionary trajectories for both species. Using 10 microsatellite loci, the control region of mtDNA and employing a seascape genetics approach, we investigated genetic connectivity and the impact of prolonged exploitation in the two species, which are characterized by different patterns of fishing pressure. Three consecutive years were sampled covering the entire distribution (N = 2100 fishes). Despite large estimated population sizes, both species exhibited low levels of contemporary genetic diversity (0.581 < HE  < 0.692), implying that fishing has had a significant impact on their genetic composition and evolutionary trajectories. Further, for M. paradoxus, significant temporal, but not spatial, divergence points to the presence of genetic chaotic patchiness. In contrast, M. capensis exhibited a clear latitudinal cline in genetic differentiation between Namibia and South Africa (FST  = 0.063, P < 0.05), with low (0.2% per generation) estimates of contemporary gene flow. Seascape analyses reveal an association with bathymetry and upwelling events, suggesting that adaptation to local environmental conditions may drive genetic differentiation in M. capensis. Importantly, our results highlight the need for temporal sampling in disentangling the complex factors that impact population divergence in marine fishes.

Limited dispersal in an ectoparasitic mite, Laelaps giganteus, contributes to significant phylogeographic congruence with the rodent host, Rhabdomys.

To explore how biogeography, parasite life history and host vagility influences evolutionary codivergences, we followed a comparative phylogeography approach using a host-specific nonpermanent mite, Laelaps giganteus, that occurs on four rodent species within the genus Rhabdomys. A mtDNA COI haplotype network derived for 278 parasite specimens showed marked phylogeographic congruence with host distributions. Analysis of the less variable nuclear intron Tropomyosin was in part consistent with these results. Although distance-based cophylogenetic analyses in axparafit failed to support significant mtDNA codivergences (P ≥ 0.02), event-based analyses revealed significant cophylogeny between sampling localities of Rhabdomys and Laelaps using core-pa (P = 0.046) and jane (P = 0.026; P = 0.00). These findings, in conjunction with the weak congruence previously reported among the permanent ectoparasitic lice Polyplax and Rhabdomys, suggest that host-parasite intimacy is not the most important driver of significant codivergence in our study system. Instead, the more restricted dispersal ability of L. giganteus, when compared to Polyplax, resulted in stronger spatial structuring and this could have resulted in significant codivergence. Host switching occurred predominantly on the edges of host distributions and was probably facilitated by climate-induced range shifts. When host ranges shift, the phylogeographic structure of L. giganteus is not reflecting the host movements as most of the nest bound parasites do not disperse with the host (they miss the boat) and the genetic contribution of the few dispersing mite individuals is often overwhelmed by the large number of individuals already present in nests within the new environment (causing them to drown on arrival).

Biogeography and host-related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts.

Parasites and hosts interact across both micro- and macroevolutionary scales where congruence among their phylogeographic and phylogenetic structures may be observed. Within southern Africa, the four-striped mouse genus, Rhabdomys, is parasitized by the ectoparasitic sucking louse, Polyplax arvicanthis. Molecular data recently suggested the presence of two cryptic species within P. arvicanthis that are sympatrically distributed across the distributions of four putative Rhabdomys species. We tested the hypotheses of phylogeographic congruence and cophylogeny among the two parasite lineages and the four host taxa, utilizing mitochondrial and nuclear sequence data. Despite the documented host-specificity of P. arvicanthis, limited phylogeographic correspondence and nonsignificant cophylogeny was observed. Instead, the parasite-host evolutionary history is characterized by limited codivergence and several duplication, sorting and host-switching events. Despite the elevated mutational rates found for P. arvicanthis, the spatial genetic structure was not more pronounced in the parasite lineages compared with the hosts. These findings may be partly attributed to larger effective population sizes of the parasite lineages, the vagility and social behaviour of Rhabdomys, and the lack of host-specificity observed in areas of host sympatry. Further, the patterns of genetic divergence within parasite and host lineages may also be largely attributed to historical biogeographic changes (expansion-contraction cycles). It is thus evident that the association between P. arvicanthis and Rhabdomys has been shaped by the synergistic effects of parasite traits, host-related factors and biogeography over evolutionary time.

The sympatric occurrence of two genetically divergent lineages of sucking louse, Polyplax arvicanthis (Phthiraptera: Anoplura), on the four-striped mouse genus, Rhabdomys (Rodentia: Muridae).

Within southern Africa, the widely distributed four-striped mouse genus (Rhabdomys) is parasitized by, amongst others, the specific ectoparasitic sucking louse, Polyplax arvicanthis. Given the presence of significant geographically structured genetic divergence in Rhabdomys, and the propensity of parasites to harbour cryptic diversity, the molecular systematics of P. arvicanthis was investigated. Representatives of P. arvicanthis were sampled from Rhabdomys at 16 localities throughout southern Africa. Parsimony and Bayesian gene trees were constructed for the mitochondrial COI, 12S rRNA, 16S rRNA and nuclear CAD genes. Our findings support the existence of 2 genetic groups within P. arvicanthis separated by at least 25% COI sequence divergence, which is comparable to that observed among recognized Polyplax species. We therefore propose that these 2 genetic lineages probably represent distinct species and that the apparent absence of clear morphological differences may point to cryptic speciation. The 2 taxa have sympatric distributions throughout most of the sampled host range and also occasionally occur sympatrically on the same host individual. The co-occurrence of these genetically distinct lineages probably resulted from parasite duplication via host-associated allopatric divergence and subsequent reciprocal range expansions of the 2 parasite taxa throughout southern Africa.

Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy.

Within southern Africa, a link between past climatic changes and faunal diversification has been hypothesized for a diversity of taxa. To test the hypothesis that evolutionary divergences may be correlated to vegetation changes (induced by changes in climate), we selected the widely distributed four-striped mouse, Rhabdomys, as a model. Two species are currently recognized, the mesic-adapted R. dilectus and arid-adapted R. pumilio. However, the morphology-based taxonomy and the distribution boundaries of previously described subspecies remain poorly defined. The current study, which spans seven biomes, focuses on the spatial genetic structure of the arid-adapted R. pumilio (521 specimens from 31 localities), but also includes limited sampling of the mesic-adapted R. dilectus (33 specimens from 10 localities) to act as a reference for interspecific variation within the genus. The mitochondrial COI gene and four nuclear introns (Eef1a1, MGF, SPTBN1, Bfib7) were used for the construction of gene trees. Mitochondrial DNA analyses indicate that Rhabdomys consists of four reciprocally monophyletic, geographically structured clades, with three distinct lineages present within the arid-adapted R. pumilio. These monophyletic lineages differ by at least 7.9% (±0.3) and these results are partly confirmed by a multilocus network of the combined nuclear intron dataset. Ecological niche modeling in MaxEnt supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that the geographic clades diverged between 3.09 and 4.30Ma, supporting the hypothesis that the radiation within the genus coincides with paleoclimatic changes (and the establishment of the biomes) characterizing the Miocene-Pliocene boundary. Marked genetic divergence at the mitochondrial DNA level, coupled with strong nuclear and mtDNA signals of non-monophyly of R. pumilio, support the notion that a taxonomic revision of the genus is needed.