Mitochondrial DNA paradox: sex-specific genetic structure in a marine mussel--despite maternal inheritance and passive dispersal

Rejection of the genetic implications of the "Abundant Centre Hypothesis" in marine mussels

The ‘Abundant-Centre Hypothesis’ is a well-established but controversial hypothesis stating that the abundance of a species is highest at the centre of its range and decreases towards the edges, where conditions are unfavourable. As genetic diversity depends on population size, edge populations are expected to show lower intra-population genetic diversity than core populations, while showing high inter-population genetic divergence. Here, the genetic implications of the Abundant-Centre Hypothesis were tested on two coastal mussels from South Africa that disperse by means of planktonic larvae, the native Perna perna and the invasive Mytilus galloprovincialis. Genetic structure was found within P. perna, which, together with evidence from Lagrangian particle simulations, points to significant reductions in gene flow between sites. Despite this, the expected diversity pattern between centre and edge populations was not found for either species. We conclude that the genetic predictions of the Abundant-Centre Hypothesis are unlikely to be met by high-dispersal species with large population sizes, and may only become evident in species with much lower levels of connectivity.

Broad-scale genetic patterns of New Zealand abalone, Haliotis iris, across a distribution spanning 13° latitude and major oceanic water masses

The New Zealand black-foot abalone, Haliotis iris, or pāua, is endemic to the rocky reefs surrounding New Zealand, whose main land mass spans 13° of latitude and separates the Tasman Sea from the Pacific Ocean. In this study, we examined the population genetic structure of this important commercial, cultural and recreational species by genotyping nine microsatellite loci in 485 pāua from 27 locations distributed across mainland New Zealand and the Chatham Islands. We found low, but significant, levels of genetic differentiation. Key genetic breaks were identified among the Chatham Islands and mainland samples; patterns that are strongly corroborated by prior work employing mtDNA sequences. AMOVAs indicated that samples from the south of the North Island were more similar to the South Island samples than to other North Island samples, however multivariate analysis and Bayesian clustering could not identify a significant pattern. Differentiation between the Chatham Islands and the mainland is most likely due to isolation by distance, while differentiation of North Island samples corresponds with major components of New Zealand's oceanography, Cook Strait and the East Cape. Despite intense fishing pressure, we detected no signature of genetic bottlenecks in any region suggesting that population sizes have remained relatively stable over recent time or that the census size of this species is much larger than its effective population size.

Presence of two mitochondrial genomes in the mytilid Perumytilus purpuratus: Phylogenetic evidence for doubly uniparental inheritance

This study presents evidence, using sequences of ribosomal 16S and COI mtDNA, for the presence of two mitochondrial genomes in Perumytilus purpuratus. This may be considered evidence of doubly uniparental mtDNA inheritance. The presence of the two types of mitochondrial genomes differentiates females from males. The F genome was found in the somatic and gonadal tissues of females and in the somatic tissues of males; the M genome was found in the gonads and mantle of males only. For the mitochondrial 16S region, ten haplotypes were found for the F genome (nucleotide diversity 0.004), and 7 haplotypes for the M genome (nucleotide diversity 0.001), with a distance Dxy of 0.125 and divergence Kxy of 60.33%. For the COI gene 17 haplotypes were found for the F genome (nucleotide diversity 0.009), and 10 haplotypes for the M genome (nucleotide diversity 0.010), with a genetic distance Dxy of 0.184 and divergence Kxy of 99.97%. Our results report the presence of two well-differentiated, sex-specific types of mitochondrial genome (one present in the male gonad, the other in the female gonad), implying the presence of DUI in P. purpuratus. These results indicate that care must be taken in phylogenetic comparisons using mtDNA sequences of P. purpuratus without considering the sex of the individuals.

Gene flow and population structure of a solitary top carnivore in a human-dominated landscape

While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free-roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human-carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human-caused extinctions.

The influence of Pleistocene climatic changes and ocean currents on the phylogeography of the southern African barnacle, Tetraclita serrata (Thoracica; Cirripedia)

The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow in some geographical areas was hypothesized based on oceanic circulation patterns and known biogeographic regions. Barnacle population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (COI) region for 410 individuals sampled from 20 localities spanning the South African coast. The mtDNA data were augmented by generating nuclear internal transcribed spacer 1 (ITS1) sequences from a subset of samples. Phylogenetic and population genetic analyses of mitochondrial DNA data reveal two distinct clades with mostly sympatric distributions, whereas nuclear analyses reveal only a single lineage. Shallow, but significant structure (0.0041-0.0065, P<0.01) was detected for the mtDNA data set, with the south-west African region identified as harbouring the highest levels of genetic diversity. Gene flow analyses on the mtDNA data show that individuals sampled in south-western localities experience gene flow primarily in the direction of the Benguela Current, while south and eastern localities experience bi-directional gene flow, suggesting an influence of both the inshore currents and the offshore Agulhas Current in the larval distribution of T. serrata. The mtDNA haplotype network, Bayesian Skyline Plots, mismatch distributions and time since expansion indicate that T. serrata population numbers were not severely affected by the Last Glacial Maximum (LGM), unlike other southern African marine species. The processes resulting in the two morphologically cryptic mtDNA lineages may be the result of a recent historical allopatric event followed by secondary contact or could reflect selective pressures due to differing environmental conditions.