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Spiroplasma(classMollicutes) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions.Spiroplasmaare generally fastidious to culturein vitro, especially those that are vertically transmitted by their hosts, which include flies in the genusDrosophila.Drosophilahas been invaded by at least three independent clades ofSpiroplasma: Poulsonii (the best studied, contains reproductive manipulators and defensive mutualists associated with two major clades ofDrosophilaand has amongst the highest substitution rates within bacteria), Citri (restricted to therepletagroup ofDrosophila) and Ixodetis. We report the first genome drafts ofDrosophila-associated Citri cladeSpiroplasma: strainsMoj fromDrosophila mojavensis, strainsAld-Tx fromDrosophila aldrichifrom Texas (newly discovered; also associated withDrosophila mulleri) and strainsHy2 fromDrosophila hydei(the onlyDrosophilaspecies known to naturally also harbour a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have the following: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titres and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome-inactivating protein, which is implicated in the Poulsonii-conferred defence against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives ofDrosophila-associatedSpiroplasma, and in a very divergent newly discovered lineage (i.e. ‘clade X’). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations (sAld-Tx in this study;sMoj in prior work), fitness assays ofsMoj (this study) andsAld-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in theirDrosophilahost populations remains elusive. 

ABSTRACT Sister taxa that have diverged and persisted in sympatry have likely been exposed to the same general environmental changes throughout their evolutionary history and may thus exhibit similar phylogeographies. Here, we compare the phylogeographic patterns of two sister species of isopods (genusTylos) that have broadly overlapping distributions but distinct habitat preferences in the supralittoral zone of Chile. The dynamic geoclimatic history of this region during the Quaternary has been implicated in shaping the evolutionary histories of other coastal taxa.Tylos spinulosusis found in sandy beaches at latitudes ~27°–30° S, whereasTylos chilensishas been found in rocky shores at ~27°–33° S and at ~39°–42° S. We sampled both species across their ranges (collectively from 20 localities) and obtained sequences from at least one mitochondrial gene for 95 T. chilensisand 41 T. spinulosus. We used phylogenetics and population genetics methods to analyze four single‐gene and one concatenated datasets: 12S rDNA (n = 130); 16S rDNA (n = 31); Cytochrome oxidase subunit I (n = 28); Cytochrome b (n = 24); concatenation of the four genes (n = 24). Both species show high levels of isolation of local populations, consistent with expectations from their limited autonomous dispersal potential. However, they exhibit strikingly different mitochondrial phylogeographic patterns.Tylos chilensisshows evidence of multiple relatively deep divergence events leading to geographically restricted lineages that appear to have persisted over multiple glaciations. Surprisingly, one lineage ofT. chilensiswas found in geographically distant localities, suggesting the possibility of human‐mediated dispersal.Tylos spinulosusappears to have undergone a relatively recent bottleneck followed by a population/range expansion. Differences in life histories and habitat preferences or stochasticity may have contributed to these striking phylogeographic differences. Finally, the high levels of differentiation and isolation among populations indicate that they are highly vulnerable to extirpation. We discuss threats to their persistence and recommendations for their conservation. 

Resumen México es una región megadiversa con una historia geológica compleja, pero se desconoce el nivel de influencia de las barreras geográficas sobre las distribuciones de los peces dulceacuícolas. Este estudio examina las relaciones filogenéticas, a escala geográfica pequeña, de las especies del grupo de aletas cortas del subgénero Mollienesia (género Poecilia), un grupo de peces vivíparos ampliamente distribuidos en México. Se analizaron muestras de seis especies en más de 50 localidades, utilizando métodos filogenéticos y de redes de haplotipos, para evaluar la diversidad genética y precisar las distribuciones de especies en este grupo. Los resultados indican que las especies mexicanas se han diversificado a partir de múltiples invasiones independientes desde Mesoamérica. Se detectó estructura filogenética débil en dos especies distribuidas al norte del Eje Neovolcánico y una especie que atraviesa el Eje Neovolcánico, posiblemente debido a la ausencia de barreras fisiográficas, colonización reciente y altas tasas de dispersión entre regiones. En contraste, se detectaron niveles altos de estructura filogenética en tres especies distribuidas del Eje Neovolcánico, lo que refleja una presencia más prolongada en el área y la existencia de múltiples barreras fisiográficas que aislaron a las poblaciones. Este estudio identificó mecanismos que promueven la divergencia y la especiación, expandió el rango conocido de varias especies y resolvió incertidumbres taxonómicas de algunas poblaciones.