Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis, which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size).

Continental copepods have been derived from several independent invasive events from the sea, but the subsequent evolutionary processes that account for the current diversity in lacustrine environments are virtually unknown. Salinity is highly variable among lakes and constitutes a source of divergent selection driving potential reproductive isolation. We studied four populations of the calanoid copepod Leptodiaptomus cf. sicilis inhabiting four neighboring lakes with a common history (since the Late Pleistocene) located in the Oriental Basin, Mexico; one lake is shallow and varies in salinity periodically (1.4–10 g L-1), while three are deep and permanent, with constant salinity (0.5, 1.1 and 6.5 g L-1, respectively). We hypothesized that (1) these populations belong to a different species than L. sicilis sensu stricto and (2) are experiencing ecologically based divergence due to salinity differences. We assessed morphological and molecular (mtDNA) COI variation, as well as fitness differences and tests of reproductive isolation. Although relationships of the Mexican populations with L. sicilis s.s. could not be elucidated, we identified a clear pattern of divergent selection driven by salinity conditions. The four populations can still be considered a single biological species (sexual recognition and hybridization are still possible in laboratory conditions), but they have diverged into at least three different phenotypes: two locally adapted, specialized in the lakes of constant salinity (saline vs. freshwater), and an intermediate generalist phenotype inhabiting the temporary lake with fluctuating salinity. The specialized phenotypes are poorly suited as migrants, so prezygotic isolation due to immigrant inviability is highly probable. This implication was supported by molecular evidence that showed restricted gene flow, persistence of founder events, and a pattern of allopatric fragmentation. This study showed how ecologically based divergent selection may explain diversification patterns in lacustrine copepods.

1. Salinity is a strong selective force for many aquatic organisms, affecting both ecological and evolutionary processes. Most of our knowledge on the effects of salinity on rotifers in the Brachionus plicatilis species complex is based mainly on populations from waterbodies that experience broad environmental changes both seasonally and annually. We tested the hypothesis that, despite the supposedly high potential for gene flow among rotifers inhabiting neighbouring environments, constant salinity has promoted local adaptation, genetic population divergence and even cryptic speciation in B. plicatilis complex populations from three deep maar lakes of distinct salinities [1.1, 6.5 and 9.0 g L )1 total dissolved solids (TDS)] in Central Mexico. 2. To look for local adaptation, we performed common garden experiments to test the effect of different salinities on population density and intrinsic growth rate (r). Then, we evaluated the genetic divergence by sequencing the cytochrome c oxidase subunit I (COI) gene and performed reproductive trials to assess the potential gene flow among the three populations and with other closely related B. plicatilis complex species. 3. We confirmed that the rotifer populations have phenotypic plasticity in tolerance of salinity, but only rotifers from the least saline lake are adapted to low salinity. Among the populations, sequence divergence at COI was very low (just a single haplotype was found), suggesting a persistent founder effect from a relatively recent single colonisation event and a subsequent dispersal from one lake to the others, and a very restricted immigration rate. In the phylogenetic analysis, rotifers from this area of Mexico clustered in the same clade with the middle-sized species Brachionus ibericus and B. sp. 'Almenara'. Mexican rotifers showed successful recognition, copulation and formation of hybrids among them, but interpopulation breeding with the Spanish B. ibericus and B. sp. 'Almenara' was unsuccessful. 4. We conclude that the B. plicatilis complex populations from these three lakes belong to a new biological species not yet described (presently named B. sp. 'Mexico'). To our knowledge, this is the first report of local adaptation of a natural B. plicatilis complex population living in freshwater conditions (1.1 g L )1 TDS).

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