Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The Vegetation of South Africa, Lesotho and Swaziland

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as FST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4905

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation.

Marine recreational fishing (MRF) is a popular activity that involves millions of people worldwide. While the impacts of recreational fishing on freshwater ecosystems received increasing attention ...

Potential Environmental Impacts of Recreational Fishing on Marine Fish Stocks and Ecosystems

Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes. Landscape genomics has tremendous potential for addressing fundamental and applied research questions in various research fields, including ecology, evolution, and conservation biology. However, the unique combination of different scientific disciplines and analytical approaches also constitute a challenge to most researchers wishing to apply landscape genomics. Here, we present an introductory overview of important concepts and methods used in current landscape genomics. For this, we first define the field and explain basic concepts and methods to capture different hypotheses of landscape influences on neutral genetic variation. Next, we highlight established and emerging genomic tools for quantifying adaptive genetic variation in landscape genomic studies. To illustrate the covered topics and to demonstrate the potential of landscape genomics, we provide empirical examples addressing a variety of research question, i.e., the investigation of evolutionary processes driving population differentiation, the landscape genomics of range expanding species, and landscape genomic patterns in organisms of special interest, including species inhabiting aquatic and terrestrial environments. We conclude by outlining remaining challenges and future research avenues in landscape genomics.

Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations

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

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.

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

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 sub-structuring patterns, and thus contrasting evolutionary trajectories for both species. Using ten 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.

This article is protected by copyright. All rights reserved.

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

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).

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

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

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

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

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