Harbor porpoise losing its edge: Genetic time series suggests a rapid population decline in Iberian waters over the last 30 years.

Impact of climate change is expected to be especially noticeable at the edges of a species' distribution, where they meet suboptimal habitat conditions. In Mauritania and Iberia, two genetically differentiated populations of harbor porpoises (Phocoena phocoena) form an ecotype adapted to local upwelling conditions and distinct from other ecotypes further north on the NE Atlantic continental shelf and in the Black Sea. By analyzing the evolution of mitochondrial genetic variation in the Iberian population between two temporal cohorts (1990-2002 vs. 2012-2015), we report a substantial decrease in genetic diversity. Phylogenetic analyses including neighboring populations identified two porpoises in southern Iberia carrying a divergent haplotype closely related to those from the Mauritanian population, yet forming a distinct lineage. This suggests that Iberian porpoises may not be as isolated as previously thought, indicating possible dispersion from Mauritania or an unknown population in between, but none from the northern ecotype. Demo-genetic scenario testing by approximate Bayesian computation showed that the rapid decline in the Iberian mitochondrial diversity was not simply due to the genetic drift of a small population, but models support instead a substantial decline in effective population size, possibly resulting from environmental stochasticity, prey depletion, or acute fishery bycatches. These results illustrate the value of genetics time series to inform demographic trends and emphasize the urgent need for conservation measures to ensure the viability of this small harbor porpoise population in Iberian waters.

No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications.

Understanding species responses to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three subspecies. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes, and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modeling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern subspecies, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phocoena). Yet, we identified important departures from random mating and restricted dispersal forming a highly significant isolation by distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared with nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.

Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.

Genetic homogeneity in the face of morphological heterogeneity in the harbor porpoise from the Black Sea and adjacent waters (Phocoena phocoena relicta).

Absence of genetic differentiation is usually taken as an evidence of panmixia, but can also reflect other situations, including even nearly complete demographic independence among large-sized populations. Deciphering which situation applies has major practical implications (e.g., in conservation biology). The endangered harbor porpoises in the Black Sea illustrates this point well. While morphological heterogeneity suggested that population differentiation may exist between individuals from the Black and Azov seas, no genetic study provided conclusive evidence or covered the entire subspecies range. Here, we assessed the genetic structure at ten microsatellite loci and a 3904 base-pairs mitochondrial fragment in 144 porpoises across the subspecies range (i.e., Aegean, Marmara, Black, and Azov seas). Analyses of the genetic structure, including FST, Bayesian clustering, and multivariate analyses revealed a nearly complete genetic homogeneity. Power analyses rejected the possibility of underpowered analyses (power to detect FST ≥ 0.008 at microsatellite loci). Simulations under various demographic models, evaluating the evolution of FST, showed that a time-lag effect between demographic and genetic subdivision is also unlikely. With a realistic effective population size of 1000 individuals, the expected "gray zone" would be at most 20 generations under moderate levels of gene flow (≤10 migrants per generation). After excluding alternative hypotheses, panmixia remains the most likely hypothesis explaining the genetic homogeneity in the Black Sea porpoises. Morphological heterogeneity may thus reflect other processes than population subdivision (e.g., plasticity, selection). This study illustrates how combining empirical and theoretical approaches can contribute to understanding patterns of weak population structure in highly mobile marine species.

Molecular Characterization Reveals Diverse and Unknown Malaria Vectors in the Western Kenyan Highlands.

The success of mosquito-based malaria control is dependent upon susceptible bionomic traits in local malaria vectors. It is crucial to have accurate and reliable methods to determine mosquito species composition in areas subject to malaria. An unexpectedly diverse set of Anopheles species was collected in the western Kenyan highlands, including unidentified and potentially new species carrying the malaria parasite Plasmodium falciparum. This study identified 2,340 anopheline specimens using both ribosomal DNA internal transcribed spacer region 2 and mitochondrial DNA cytochrome oxidase subunit 1 loci. Seventeen distinct sequence groups were identified. Of these, only eight could be molecularly identified through comparison to published and voucher sequences. Of the unidentified species, four were found to carry P. falciparum by circumsporozoite enzyme-linked immunosorbent assay and polymerase chain reaction, the most abundant of which had infection rates comparable to a primary vector in the area, Anopheles funestus. High-quality adult specimens of these unidentified species could not be matched to museum voucher specimens or conclusively identified using multiple keys, suggesting that they may have not been previously described. These unidentified vectors were captured outdoors. Diverse and unknown species have been incriminated in malaria transmission in the western Kenya highlands using molecular identification of unusual morphological variants of field specimens. This study demonstrates the value of using molecular methods to compliment vector identifications and highlights the need for accurate characterization of mosquito species and their associated behaviors for effective malaria control.

Unexpected diversity of Anopheles species in Eastern Zambia: implications for evaluating vector behavior and interventions using molecular tools.

The understanding of malaria vector species in association with their bionomic traits is vital for targeting malaria interventions and measuring effectiveness. Many entomological studies rely on morphological identification of mosquitoes, limiting recognition to visually distinct species/species groups. Anopheles species assignments based on ribosomal DNA ITS2 and mitochondrial DNA COI were compared to morphological identifications from Luangwa and Nyimba districts in Zambia. The comparison of morphological and molecular identifications determined that interpretations of species compositions, insecticide resistance assays, host preference studies, trap efficacy, and Plasmodium infections were incorrect when using morphological identification alone. Morphological identifications recognized eight Anopheles species while 18 distinct sequence groups or species were identified from molecular analyses. Of these 18, seven could not be identified through comparison to published sequences. Twelve of 18 molecularly identified species (including unidentifiable species and species not thought to be vectors) were found by PCR to carry Plasmodium sporozoites - compared to four of eight morphological species. Up to 15% of morphologically identified Anopheles funestus mosquitoes in insecticide resistance tests were found to be other species molecularly. The comprehension of primary and secondary malaria vectors and bionomic characteristics that impact malaria transmission and intervention effectiveness are fundamental in achieving malaria elimination.