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- Drivers of Cape Verde archipelagic endemism in keyhole limpetsPublication . Lopes Da Cunha, Regina; Assis, J.; Madeira, Celine; Seabra, Rui; Lima, Fernando P.; Lopes, Evandro P.; Williams, Suzanne T.; Castilho, RitaOceanic archipelagos are the ideal setting for investigating processes that shape species assemblages. Focusing on keyhole limpets, genera Fissurella and Diodora from Cape Verde Islands, we used an integrative approach combining molecular phylogenetics with ocean transport simulations to infer species distribution patterns and analyse connectivity. Dispersal simulations, using pelagic larval duration and ocean currents as proxies, showed a reduced level of connectivity despite short distances between some of the islands. It is suggested that dispersal and persistence driven by patterns of oceanic circulation favouring self-recruitment played a primary role in explaining contemporary species distributions. Mitochondrial and nuclear data revealed the existence of eight Cape Verde endemic lineages, seven within Fissurella, distributed across the archipelago, and one within Diodora restricted to Boavista. The estimated origins for endemic Fissurella and Diodora were 10.2 and 6.7 MY, respectively. Between 9.5 and 4.5 MY, an intense period of volcanism in Boavista might have affected Diodora, preventing its diversification. Having originated earlier, Fissurella might have had more opportunities to disperse to other islands and speciate before those events. Bayesian analyses showed increased diversification rates in Fissurella possibly promoted by low sea levels during Plio-Pleistocene, which further explain differences in species richness between both genera.
- Distinctive genetic signatures of two fairy shrimp species with overlapping ranges in Iberian temporary pondsPublication . Lopes Da Cunha, Regina; Sala, Jordi; Machado, Margarida; Boix, Dani; Madeira, Celine; Madeira, Pedro M.; Cristo, Margarida; Cancela Da Fonseca, Luís; Castilho, RitaTemporary 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.
- Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genusPublication . Cunha, Regina L.; Nicastro, Katy; Zardi, Gerardo I.; Madeira, Celine; McQuaid, Christopher D.; J. Cox, Cymon; Castilho, RitaBackground: 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.