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1. Insights from a comprehensive study of Trypanosoma cruzi: A new mitochondrial clade restricted to North and Central America and genetic structure of TcI in the region

   https://doi.org/10.1371/journal.pntd.0010043  

   Lima-Cordón, Raquel Asunción; Cahan, Sara Helms; McCann, Cai; Dorn, Patricia L.; Justi, Silvia Andrade; Rodas, Antonieta; Monroy, María Carlota; Stevens, Lori (December 2021, PLOS Neglected Tropical Diseases)

   Dutra, Walderez O. (Ed.)

   More than 100 years since the first description of Chagas Disease and with over 29,000 new cases annually due to vector transmission (in 2010), American Trypanosomiasis remains a Neglected Tropical Disease (NTD). This study presents the most comprehensive Trypanosoma cruzi sampling in terms of geographic locations and triatomine species analyzed to date and includes both nuclear and mitochondrial genomes. This addresses the gap of information from North and Central America. We incorporate new and previously published DNA sequence data from two mitochondrial genes, Cytochrome oxidase II (COII) and NADH dehydrogenase subunit 1 (ND1). These T . cruzi samples were collected over a broad geographic range including 111 parasite DNA samples extracted from triatomines newly collected across North and Central America, all of which were infected with T . cruzi in their natural environment. In addition, we present parasite reduced representation (Restriction site Associated DNA markers, RAD-tag) genomic nuclear data combined with the mitochondrial gene sequences for a subset of the triatomines (27 specimens) collected from Guatemala and El Salvador. Our mitochondrial phylogenetic reconstruction revealed two of the major mitochondrial lineages circulating across North and Central America, as well as the first ever mitochondrial data for TcBat from a triatomine collected in Central America. Our data also show that within mtTcIII, North and Central America represent an independent, distinct clade from South America, named here as mtTcIII NA-CA , geographically restricted to North and Central America. Lastly, the most frequent lineage detected across North and Central America, mtTcI, was also an independent, distinct clade from South America, noted as mtTcI NA-CA . Furthermore, nuclear genome data based on Single Nucleotide Polymorphism (SNP) showed genetic structure of lineage TcI from specimens collected in Guatemala and El Salvador supporting the hypothesis that genetic diversity at a local scale has a geographical component. Our multiscale analysis contributes to the understanding of the independent and distinct evolution of T . cruzi lineages in North and Central America regions. 

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2. A phylogenomic perspective reveals mitochondrial-nuclear discordance and previously undescribed species nested within a widespread East African Reed frog species (Hyperolius substriatus Ahl, 1931)

   https://doi.org/10.1371/journal.pone.0318951  

   Lawson, Lucinda P; Bittencourt-Silva, Gabriela B; Conradie, Werner; Portik, Daniel M; Loader, Simon P (April 2025, PLOS ONE)

   Meegaskumbura, Madhava (Ed.)

   The sub-montane East African Reed Frog,Hyperolius substriatusAhl, 1931 (Spotted Reed Frog) has a fragmented highland distribution throughout East Africa. Previous studies show extensive mitochondrial divergence between four lineages of African Spotted Reed Frogs that roughly correspond to previously-recognized subspecies. These may have conservation implications if formally described. However, as mitochondrial-based population models only track maternal patterns, further genomic datasets are necessary to assess the distinctness of these lineages in relation to historically recognized morphological subspecies. In this study, we expanded sampling to newly discovered localities and assessed mitochondrial and genomic data to better understand phylogeography and landscape genomics of this species. We found that genomic clades (biparentally inherited) confirm some of the mitochondrial structure (female inherited), but also revealed multiple cases of mitonuclear discordance particularly within the Udzungwa Mountain block, which may have two separate founding events based on peripatric mitochondrial lineages and panmictic genomic signals. Taken together, the three clades within the geographical range ofH. substriatusthrough Tanzania, Malawi, and Mozambique correspond to three previously-identified subspecies and lineages, and have both spatially cohesive and population-specific patterns of geneflow and isolation with neighboring highland locations. 

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3. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi

   https://doi.org/10.1038/s42003-023-05299-8  

   Longley, Reid; Robinson, Aaron; Liber, Julian A.; Bryson, Abigail E.; Morales, Demosthenes P.; LaButti, Kurt; Riley, Robert; Mondo, Stephen J.; Kuo, Alan; Yoshinaga, Yuko; et al (September 2023, Communications Biology)

   Abstract Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera:Linnemannia(MRE-L) andBenniella(MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicateLinnemanniaandBenniellaMRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts. 

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4. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science

   https://doi.org/10.3767/persoonia.2023.51.01  

   Magain, N.; Miadlikowska, J.; Goffinet, B.; Goward, T.; Pardo-De la Hoz, C.J.; Jüriado, I.; Simon, A.; Mercado-Díaz, J.A.; Barlow, T.; Moncada, B.; et al (August 2023, Persoonia - Molecular Phylogeny and Evolution of Fungi)

   Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera . Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis , P. asiatica , P. borealis , P. borinquensis , P. chabanenkoae , P. clathrata , P. elixii , P. esslingeri , P. flabellae , P. gallowayi , P. hawaiiensis , P. holtanhartwigii , P. itatiaiae , P. hokkaidoensis , P. kukwae , P. massonii , P. mikado , P. nigriventris , P. orientalis , P. rangiferina , P. sipmanii , P. stanleyensis , P. vitikainenii and P. willdenowii ; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa ; and the following new combination is introduced: P. hymenina var. dissecta . Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza , P. neopolydactyla , P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. 

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5. ICDP workshop on the Lake Victoria Drilling Project (LVDP): scientific drilling of the world's largest tropical lake

   https://doi.org/10.5194/sd-33-21-2024  

   Berke, Melissa A; Peppe, Daniel J; the_LVDP_team (January 2024, Scientific Drilling)

   Abstract. Lake Victoria, which is bordered by Uganda, Tanzania, Kenya, and has a catchment that extends to Rwanda and Burundi, is home to the largest human population surrounding any lake in the world and provides critical resources across eastern Africa. Lake Victoria is also the world's largest tropical lake by surface area, but it is relatively shallow and without a major inlet, making it very sensitive to changes in climate, and especially hydroclimate. Furthermore, its size creates abundant habitats for aquatic fauna, including the iconic hyper-diverse cichlids, and serves as a major geographic barrier to terrestrial fauna across equatorial Africa. Given Lake Victoria's importance to the eastern African region, its sensitivity to climate, and its influences on terrestrial and aquatic faunal evolution and dispersal, it is vital to understand the connection between the lake and regional climate and how the lake size, shape, and depth have changed through its depositional history. This information can only be ascertained by collecting a complete archive of Lake Victoria's sedimentary record. To evaluate the Lake Victoria basin as a potential drilling target, ∼ 50 scientists from 10 countries met in Dar es Salaam, Tanzania, in July 2022 for the International Continental Scientific Drilling Program (ICDP)-sponsored Lake Victoria Drilling Project (LVDP) workshop. Discussions of the main scientific objectives for a future drilling project included (1) recovering the Pleistocene and Holocene sedimentary records of Lake Victoria that document the dynamic nature of the lake, including multiple lacustrine and paleosol sequences; (2) establishing the chronology of recovered sediments, including using extensive tephra fingerprinting and other techniques from deposits in the region; (3) reconstructing past climate, environment, lacustrine conditions, and aquatic fauna, using an integrated multi-proxy approach, combined with climate and hydrologic modeling; and (4) connecting new records with existing sedimentary snapshots and fossils exposed in deposits around the lake, tying archaeological, paleontological, sedimentological, tectonic, and volcanic findings to new drilling results. The LVDP provides an innovative way to address critical geological, paleontological, climatological, and evolutionary biological questions about Quaternary to modern landscapes and ecosystems in eastern Africa. Importantly, this project affords an excellent opportunity to help develop conservation and management strategies for regional responses to current and future changes in climate, land use, fisheries, and resiliency of at-risk communities in equatorial Africa. 

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