Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis

Whooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, pertussis has re-emerged in many countries and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study of 385 Australian B. pertussis isolates collected from 2008 to 2017. The Australian B. pertussis population was found to be composed of mostly ptxP3 strains carrying different fim3 alleles, with ptxP3-fim3A genotype expanded far more than ptxP3-fim3B. Within the former, there were six co-circulating epidemic lineages (EL1 to EL6). The multiple ELs emerged, expanded, and then declined at different time points over the two epidemics, likely driven by immune selection from pertussis vaccination and natural infection in addition to local and global transmission events. Both hard and soft selective sweeps through vaccine selection pressures determined the current B. pertussis population dynamics. Relative risk analysis found that once a new B. pertussis lineage emerged, it was more likely to spread locally within the first 1.5 years. However, after 1.5 years, any new lineage was likely to expand to a wider region and became no longer spatially structured across the country. Phylogenetic analysis revealed the expansion of ptxP3 strains was also associated with replacement of the type III secretion system allele bscI1 with bscI3. This study advanced our understanding of the epidemic population structure and spatial and temporal dynamics of B. pertussis in a highly immunised population.

Population Genetic Structure and Phylogeography of Co-Distributed Pachymeniopsis Species (Rhodophyta) along the Coast of Korea and Japan

Inferring phylogeographic patterns of macroalgal species is essential for understanding the population structure and for the conservation of macroalgal species. In this study, the phylogeographic patterns of two co-distributed macroalgal species along the coast of Korea and Japan, Pachymeniopsis lanceolata and Pachymeniopsis elliptica, were analyzed. Pachymeniopsis lanceolata (215 specimens from 36 sites) and P. elliptica (138 specimens from 24 sites), using the plastid rbcL gene, are characterized by fifteen and six haplotypes, respectively. Mitochondrial COI-5P gene sequences revealed a low variation for both species. An analysis of molecular variance (AMOVA), pairwise FSTcomparisons, and haplotype networks based on the rbcL data suggest a weak genetic differentiation of both species. The shared haplotypes (P. lanceolata: LR01; P. elliptica: ER01) found in the entire sampling range indicate that these two Pachymeniopsis species can disperse over long distances along the coast of Korea and Japan. Despite the similar phylogeographic pattern, our results suggest that P. lanceolata has a higher genetic diversity, with a wider distribution along the Korean Peninsula than P. elliptica. Moreover, it is adapted to low sea surface temperatures and survived in more of the available habitats during periods of climatic change, whereas P. elliptica is less adaptable and more susceptible to environmental disturbance. This phylogeographic study provides a rationale for the conservation of the wild Pachymeniopsis population.

Genetic differentiation in the genus Characodon: implications for conservation and taxonomy

The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.

Cirripectes matatakaro, a new species of combtooth blenny from the Central Pacific, illuminates the origins of the Hawaiian fish fauna

Included among the currently recognized 23 species of combtooth blennies of the genus Cirripectes (Blenniiformes: Blenniidae) of the Indo-Pacific are the Hawaiian endemic C. vanderbilti, and the widespread C. variolosus. During the course of a phylogeographic study of these species, a third species was detected, herein described as C. matatakaro. The new species is distinguished primarily by the configuration of the pore structures posterior to the lateral centers of the transverse row of nuchal cirri in addition to 12 meristic characters and nine morphometric characters documented across 72 specimens and ∼4.2% divergence in mtDNA cytochrome oxidase subunit I. The new species is currently known only from the Marquesas, Gambier, Pitcairns, Tuamotus, and Australs in the South Pacific, and the Northern Line Islands and possibly Johnston Atoll south of Hawaiʻi. Previous researchers speculated that the geographically widespread C. variolosus was included in an unresolved trichotomy with the Hawaiian endemic and other species based on a morphological phylogeny. Our molecular-phylogenetic analysis resolves many of the previously unresolved relationships within the genus and reveals C. matatakaro as the sister lineage to the Hawaiian C. vanderbilti. The restricted geographic distribution of Cirripectes matatakaro combines with its status as sister to C. vanderbilti to indicate a southern pathway of colonization into Hawaiʻi.

A comprehensive phylogeographic study of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Pulmonata: Arionidae) in Europe

Arion vulgaris Moquin-Tandon, 1855 is regarded as one of the 100 most invasive species in Europe. The native distribution range of this species is uncertain, but for many years, the Iberian Peninsula has been considered as the area of origin. However, recent studies indicate that A. vulgaris probably originated from France. We have investigated the genetic structure of 33 European populations (Poland, Norway, Germany, France, Denmark, Switzerland) of this slug, based on two molecular markers, mitochondrial cytochrome c oxidase subunit I (COI, mtDNA) and nuclear zinc finger (ZF, nDNA). Our investigation included published data from two previous studies, giving a total of 95 populations of A. vulgaris from 26 countries. This comprehensive dataset shows comparable haplotype diversity in Central, North and Western Europe, and significantly lower haplotype diversity in the East. All haplotypes observed in the East can be found in the other regions, and haplotype diversity is highest in the Central and Western region. Moreover, there is strong isolation by distance in Central and Western Europe, and only very little in the East. Furthermore, the number of unique haplotypes was highest in France. This pattern strongly suggests that A. vulgaris has originated from a region spanning from France to Western Germany; hence, the slug is probably alien/invasive in other parts of Europe, where it occurs. Our results indicate the necessity to cover as much of the distribution range of a species as possible before making conclusive assumptions about its origin and alien status.

Pilot biodiversity assessment of the Hkakabo Razi passerine avifauna in northern Myanmar – implications for conservation from molecular genetics

SummaryThe Hkakabo Razi region located in northern Myanmar is an Important Bird Area and part of the Eastern Himalayan Biodiversity Hotspot. Within the framework of the World Heritage Convention to enlist the site under criterion (ix) and (x), we conducted a biodiversity assessment for passerine birds using DNA barcoding and other molecular markers. Of the 441 bird species recorded, we chose 16 target species for a comparative phylogeographic study. Genetic analysis was performed for a larger number of species and helped identifying misidentified species. We found phylogeographic structure in all but one of the 16 study species. In 13 species, populations from northern Myanmar were genetically distinctive and local mitochondrial lineages differed from those found in adjacent regions by 3.9–9.9% uncorrected genetic distances (cytochrome-b). Since the genetic distinctiveness of study populations will be corroborated by further differences in morphology and song as in other South-East Asian passerines, many of them will be candidates for taxonomic splits, or in case an older taxon name is not available, for the scientific description of new taxa. Considering the short time frame of our study we predict that a great part of undetected faunal diversity in the Hkakabo Razi region will be discovered.