Lack of fine-scale genetic structure and distant mating in natural populations of Fucus vesiculosus

Fine-scale spatial genetic structure (SGS) within populations reflects the dispersal behaviour of genes and individuals. Here we studied very small-scale SGS and mating patterns in the brown seaweed Fucus vesiculosus, a dioecious marine broadcast spawner with immediate settlement upon gamete release, which is predicted to strongly restrict gene flow. We estimated SGS, inbreeding and kinship for adults and recruits from habitats with contrasting exposures and patchiness (open coast and estuarine ecosystems) using microsatellite loci. Heterozygote deficiency was found for most adult populations but it was even higher for recruits, indicating inbreeding depression. At the fine spatial resolution of this study there was no spatial genetic structuring for 3 of the 5 populations studied across different habitats. Habitat could not explain the unrestricted gene flow in some populations. In the kinship analyses, we identified more putative mothers than fathers, suggesting that male gamete dispersal mediates gene flow at broader distances. However, the vast majority of the parents of the recruits could not be found among the adults sampled nearby, indicating unrestricted gene flow at these small scales. We propose 3 nonexclusive hypotheses for our findings: (1) unrestricted gene flow, (2) inbreeding depression eliminating most inbred individuals resulting from nearby related parents, (3) temporal Wahlund effects, mediated by a hypothetic genetic pool of a bank of microscopic forms persisting from previous generations

Ancient Divergence in the Trans-Oceanic Deep-Sea Shark Centroscymnus crepidater

Unravelling the genetic structure and phylogeographic patterns of deep-sea sharks is particularly challenging given the inherent difficulty in obtaining samples. The deep-sea shark Centroscymnus crepidater is a medium-sized benthopelagic species that exhibits a circumglobal distribution occurring both in the Atlantic and Indo-Pacific Oceans. Contrary to the wealth of phylogeographic studies focused on coastal sharks, the genetic structure of bathyal species remains largely unexplored. We used a fragment of the mitochondrial DNA control region, and microsatellite data, to examine genetic structure in C. crepidater collected from the Atlantic Ocean, Tasman Sea, and southern Pacific Ocean (Chatham Rise). Two deeply divergent (3.1%) mtDNA clades were recovered, with one clade including both Atlantic and Pacific specimens, and the other composed of Atlantic samples with a single specimen from the Pacific (Chatham Rise). Bayesian analyses estimated this splitting in the Miocene at about 15 million years ago. The ancestral C. crepidater lineage was probably widely distributed in the Atlantic and Indo-Pacific Oceans. The oceanic cooling observed during the Miocene due to an Antarctic glaciation and the Tethys closure caused changes in environmental conditions that presumably restricted gene flow between basins. Fluctuations in food resources in the Southern Ocean might have promoted the dispersal of C. crepidater throughout the northern Atlantic where habitat conditions were more suitable during the Miocene. The significant genetic structure revealed by microsatellite data suggests the existence of present-day barriers to gene flow between the Atlantic and Pacific populations most likely due to the influence of the Agulhas Current retroflection on prey movements

Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus

Background: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods: To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the "primer-walking" method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results: The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.info:eu-repo/semantics/publishedVersio

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Distinctive genetic signatures of two fairy shrimp species with overlapping ranges in Iberian temporary ponds

Temporary lentic water bodies host biotic assemblages adapted to the transient nature of these freshwater habitats. Fairy shrimps (Crustacea, Branchiopoda, Anostraca) are one of the most important biological components of these unique environments and have a fossil record dating back to the Middle Jurassic (>150 million years). Some anostracan species show a geographically restricted distribution, whereas others are widely dispersed. We aimed to investigate the relationship between different geographic extents and patterns of genetic structure in species of Anostraca. Following this objective, we selected two species with contrasting ranges but overlapping geographic distributions and similar life-history traits in the study area. We analysed additional information that, from an ecological (e.g. egg-bank, niche breadth, and pond connectivity) and evolutionary (e.g. crown-group age of each species) perspective, may explain the obtained phylogeographic patterns. Between 2005 and 2018, we sampled two species of fairy shrimps (309 specimens of Branchipus cortesi and 264 specimens of Tanymastix stagnalis) from 53 temporary ponds of Portugal. We added five other locations from Spain and France to include other European locations for T. stagnalis. Additionally, we also sampled Branchipus schaefferi from two temporary water bodies (Spain and Morocco) to include in the dating analysis. Reconstructed phylogenies based on mitochondrial sequence data indicate the existence of deeply divergent clades with an unequivocal phylogeographic structure in T. stagnalis and shallower divergences in B. cortesi with a less clear geographic correspondence. We found evidence of frequent local and rare long-distance dispersal events in both species and limited intermediate dispersal, which was more common in B. cortesi. A Bayesian dating analysis using the Branchiopoda fossil record estimated the age of the most recent common ancestors of T. stagnalis and B. cortesi at 32.4 and 12.8 million years, respectively. Haplotype accumulation curves indicated that only a portion of the genetic composition of the species was sampled on each hydroperiod and showed the existence of large, genetically diverse egg banks that remain in the soil. These egg banks represent a genetic reservoir that guarantees the survival of the species because active populations from different hydroperiods may be genetically different and adapt to a changing environment. We hypothesise that the contrasting phylogeographic patterns displayed by the two fairy shrimp species may result from: (1) the earlier age of the most recent common ancestor of T. stagnalis, as older species have more time to accumulate mutations and, thus, are expected to exhibit higher genetic differentiation among populations; (2) slight differences in adult behaviour, life-history traits and cyst morphologies of T. stagnalis and B. cortesi favouring different animal dispersal vectors with distinct dispersal abilities. Therefore, phylogeographic patterns may be explained by both evolutionary and ecological processes, which operate in different time scales.UIDB/04326/2020; UID/MAR/04292/2019; EMBRC.PT ALG-01-0145-FEDER-022121; BIODATA.PT ALG-01-0145-FEDER-022231; DL 57/2016/CP1361/CT0013info:eu-repo/semantics/publishedVersio

Characterization, functioning and classification of two volcanic soil profiles under different land uses in Central Mexico

International audienceVolcanic soils constitute an important resource for agriculture and forestry in Central Mexico, as well as in various world regions. They exhibit unique properties and high productive potential related to the amorphous materials they contain. The relationship between amorphous materials, soil characteristic and functioning, has not been well studied. The objectives of the present work were to assess the influence of land use (agricultural and forest), topography and other soil forming factors on physical, chemical and mineralogical characteristics and pedological processes responsible for soil genesis and soil classification of two volcanic soil profiles derived from andesitic parent material located 150 m away from each other within the same toposequences. The toposequence is located in the Trans-Mexican Volcanic Belt (TMVB), a highly populated region of Central Mexico that provides part of the water for Mexico City megapolis. A series of field and laboratory techniques including physical, chemical, micromorphological, X-ray diffraction (XRD), transmission electron microscopy (TEM), infra-red analysis, Mössbauer spectroscopy were used. The main factor affecting the present morphology of the soil profiles was the topography. The mineralogical features of the upper layers of the maize profile (Pachic Andosol), indicate redistribution of soil material from the upper part of the toposequence. The land use change favored this redistribution. Deeper horizons of this profile were developed from volcanic ashes deposited in situ. hematite and ferrihydrite, considered markers of evolution in redistributed soil material were observed in this profile associated with allophane. The presence of hematite has been reported for the first time in Mexican Andosols. The present characteristics of the forest profile (Dystric Cambisol) are mainly due to the pedological process of the volcanic ash layers remaining in situ after the redistribution and volcanic breccia. It was concluded that the forest profile evolved from an Andosol to an Inceptisol, which was evidenced by desaturation, loss of silica and organic carbon. In this profile the Fe minerals were associated with the presence of gibbsite and halloysite. The position in the toposequence and the physical and chemical characteristics of these profiles define their present functioning, such as losses by erosion and C dynamics

Genetic diversity for all <i>Centroscymnus crepidater</i> sampled locations.

<p>For mitochondrial CR sequence data: number of individuals (N), number of haplotypes (NH), haplotype diversity (<i>h</i>), nucleotide diversity (π), and standard deviation (s. d.). For microsatellite data: number of individuals (N), mean number of alleles across loci (A), allelic richness (A_R), observed (H_O) and expected (H_E) heterozygosities and heterozygote deficiency (G_IS). Significance levels are indicated (*p<0.05, ***p<0.001); values in bold indicate significance after q-value correction).</p

Sampling locations of <i>Centroscymnus crepidater</i>.

<p>Haplotype frequencies and clade proportions (Clade I, in black and Clade II, in orange) based on the CR mtDNA data set are also depicted. The size of each slice is proportional to the number of individuals sharing the same haplotype. The letters A and B refer to the Atlantic and Pacific sampling locations, respectively. Sampling location codes: ROS (Rosemary Bank); ANT (Anton Dohrn Seamount); ROC (Rockall Trough); MAR (Mid-Atlantic Ridge); AZO (Azores); MAD (Madeira); GMB (Great Meteor Bank); TAS (Tasman Sea), and CHA (Chatham Rise).</p

Pairwise mismatch distributions using the CR mtDNA data set.

<p>(A) mismatch distribution including all sequences; (B) mismatch distribution including sequences from Clade I only. Vertical bars represent observed frequencies. Upper and lower dashed lines represent the upper and lower 95% limits based on 10000 replicates in Arlequin. Solid line represents the model (expected) frequency.</p

Discriminant analysis of principle components (DAPC) of multi-locus genotype data for all populations.

<p>Individual genotypes appear as circles, and black stroke circles represent the center of dispersion of each group. Populations are depicted in colors. X and Y axes are the first two principle components.</p