Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation.

Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.

How many daddies: microsatellite genotyping reveals polyandry in a live-bearing clinid fish Muraenoclinus dorsalis.

Fishes belonging to the family Clinidae in South Africa display super-embryonation, a rare reproductive mode were females gestate broods at different gestational stages, but little is known regarding the mating systems of this family. Here we tested the hypothesis that multiple males would contribute not only to the offspring of each female, but that several males would contribute to each brood, by sampling Muraenoclinus dorsalis from three sampling locations along the west and south-west coast of South Africa. Larval (n = 97) and maternal (n = 14) genotpyes, generated with newly developed microsatellites, were used to estimate the number of potential mates per female. Our results show that up to 78% of females displayed multiple mating with an average of 2·1-2·2 males. In addition, 39-42% of females displayed polyandry with an average of 1·5-1·6 sires per brood. This study provides the evidence for multiple mating and polyandry within a clinid fish characterized by super-embryonation that offers important baseline information regarding rare reproductive strategies, highlighting several gaps in our knowledge concerning clinid reproduction and mating systems.

Ecological speciation along an elevational gradient in a tropical passerine bird?

Local adaptation of populations along elevational gradients is well known, but conclusive evidence that such divergence has resulted in the origin of distinct species in parapatry remains lacking. We integrated morphological, vocal, genetic and behavioural data to test predictions pertaining to the hypothesis of parapatric ecological speciation associated with elevation in populations of a tropical montane songbird, the Grey-breasted Wood-wren (Henicorhina leucophrys: Troglodytidae), from the Sierra Nevada de Santa Marta, Colombia. We confirmed that two distinct populations exist along the elevational gradient. Phylogenetic analyses tentatively indicate that the two populations are not sister taxa, suggesting they did not differentiate from a single ancestor along the gradient, but rather resulted from separate colonization events. The populations showed marked divergence in morphometrics, vocalizations and genetic variation in mitochondrial and nuclear loci, and little to no evidence of hybridization. Individuals of both populations responded more strongly to their own local songs than to songs from another elevation. Although the two forms do not appear to have differentiated locally in parapatry, morphological and vocal divergence along the elevational gradient is consistent with adaptation, suggesting a possible link between adaptive evolution in morphology and songs and the origin of reproductive isolation via a behavioural barrier to gene flow. The adaptive value of phenotypic differences between populations requires additional study.

Phylogeographic patterns and cryptic speciation across oceanographic barriers in South African intertidal fishes.

Biogeographic boundaries are the meeting zone of broadly distributed faunas, or the actual cause of a faunal break. In the latter case, closely related sister species should be found across such a boundary. To achieve such a situation, preliminary stages are expected, where phylogeographic breaks followed by genetic cryptic speciation would be observed. Biogeographic boundaries, in the Cape Point/Cape Agulhas region of southern Africa, offer an ideal system to test such predictions. Here, we studied two intertidal clinid fish species that are endemic to southern Africa, Clinus superciliosus (n = 127) and Muraenoclinus dorsalis (n = 114). Using mitochondrial control region, 16S rRNA, 12S rRNA and NADH2 genes and the nuclear rhodopsin and the first intron of the S7 ribosomal protein gene, we show both phylogeographic breaks and likely cryptic speciation in each species. Pairwise Φ(st) results suggest population genetic structuring for both species, with higher levels for M. dorsalis (Φ(st) = 0.34-0.93) than for C. superciliosus (Φ(st) = 0.1-0.74). Further, we recover two and three distinct lineages within M. dorsalis and C. superciliosus, respectively. Phylogenetic topologies, concordance between nuclear and mitochondrial markers and levels of sequence divergence, which are consistent with closely related sister species pairs, suggest the presence of cryptic species. Our results therefore meet the expectation for reduced gene flow at a biogeographic barrier, which translates into significant genetic breaks and cryptic sister species.