One-way ticket to the blue: A large-scale, dated phylogeny revealed asymmetric land-to-water transitions in acariform mites (Acari: Acariformes).

Acariform mites are an ancient and megadiverse lineage that may have experienced a complex pattern of invasions into terrestrial and aquatic habitats. These among-realm transitions may relate to periods of turmoil in Earth's history or be simply results of uneven biodiversity patterns across habitats. Here, we inferred a dated, representative acariform phylogeny (five genes, 9,200 bp aligned, 367 terminals belonging to 150 ingroup plus 15 outgroup families, 23 fossil calibration points) which was used to infer transitions between marine/freshwater/terrestrial habitats. We detected four unambiguous transitions from terrestrial to freshwater habitats (Hydrozetes, Naiadacarus, Fusohericia, Afronothrus, Homocaligus); one from freshwater to marine (Pontarachnidae), and four from marine to brackish or freshwater transitions (all among Halacaridae: Acarothrix; Halacarellus petiti; Copidognathus sp.; clade Limnohalacarus + Soldanellonyx + Porohalacarus + Porolohmannella). One transition to the sea was inferred ambiguously with respect to the ancestor being either terrestrial or freshwater (Hyadesiidae), and another must be most carefully examined by adding potential related taxa (Selenoribatidae + Fortuyniidae). Finally, we inferred a single, remarkable transition from aquatic to terrestrial habitats involving early evolution of the large and ecologically diverse lineage: the ancestor of the Halacaridae + Parasitengona clade was probably freshwater given our dataset, thus making terrestrial Parasitengona secondarily terrestrial. Overall, our results suggested a strong asymmetry in environmental transitions: the majority occurred from terrestrial to aquatic habitats. This asymmetry is probably linked to mites' biological properties and uneven biodiversity patterns across habitats rather than Earth's geological history. Since the land holds more acariform diversity than water habitats, a shift from the former is more likely than from the latter. We inferred the following relationships: alicid endeostigmatid + eriophyoid (Alycidae, (Nanorchestidae, (Nematalycidae, Eriophyoidea))) being sister group to the remaining Acariformes: (proteonematalycid Endeostigmata, alicorhagiid Endeostigmata, Trombidiformes, Oribatida (including Astigmata)). Trombidiform relationships had several novel rearrangements: (i) traditional Eupodina lacked support for the inclusion of Bdelloidea; (ii) Teneriffidae, traditionally placed among Anystina, was consistently recovered in a clade including Heterostigmata in Eleutherengona; (iii) several lineages, such as Adamystidae, Paratydeidae, Caeculidae and Erythracaridae, were recovered in a large clade along other Anystina and Eleutherengona, suggesting single origins of several fundamental character states, such as the reduction of the cheliceral fixed digit and development of the palpal thumb-claw complex.

Tracing the Origin of Planktonic Protists in an Ancient Lake.

Ancient lakes are among the most interesting models for evolution studies because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world-Lake Baikal (Russia). By using 18S rDNA metabarcoding, we recovered 1414 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1-50 m) and representing pico/nano-sized cells. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the taxonomically unclassified protists. However, our results suggest that a fraction of Baikal protists could belong to glacial relicts and have close relationships with marine/brackish species. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found 16% of the OTUs belonging to potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria, and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Also, the 18S rDNA of a number of species (7% of the total) differed >10% from other known sequences. These taxa as well as those belonging to the flocks may be endemic to Lake Baikal. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae).

Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study, we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using micro-computed tomographic (µCT) scanning and geometric morphometrics, we quantified body shape, size, and vertebral counts of 31 belonid species. We then examined the pattern and tempo of body shape and size evolution using phylogenetic comparative methods. Our results show that transitions from marine to freshwater habitats have altered the adaptive landscape for needlefishes and expanded morphospace relative to marine taxa. We provide further evidence that freshwater taxa attain reduced sizes either through dwarfism (as inferred from axial skeletal reduction) or through developmental truncation (as inferred from axial skeletal loss). We propose that transitions to freshwater habitats produce morphological novelty in response to novel prey resources and changes in locomotor demands. We find that repeated invasions of different habitats have prompted predictable changes in morphology.

Molecular phylogeny of marine mites (Acariformes: Halacaridae), the oldest radiation of extant secondarily marine animals.

The family Halacaridae comprises more than one thousand mostly marine or rarely freshwater species. Many are predacious, but among marine mites, some genera evolved the ability to feed on macroalgae. We inferred a time-calibrated phylogeny based on 18S rDNA, 28S rDNA, and Cytochrome oxidase I (5,143 nt aligned) and all non-monotypic halacarid subfamilies plus a representative outgroup set (72 taxa). The family Halacaridae was rendered as the sister-group of Parasitengona, diverging 321.5, 264.0-381.3 Ma and radiating 271.3, 221.7-324.2 Ma (median, HPD). Thus, marine mites represent the oldest known extant animal lineage that secondarily invaded the sea, with the marine turtles being the second oldest such lineage (crown group 212.3, 194.9-231.4 Ma). Two freshwater mite lineages, represented by Limnohalacarus (219.2, 165.9-274.6) and Porohalacarus (175.3, 118.5-233.1), were inferred mutually non-monophyletic, suggesting two independent invasions to freshwater. The conventional subfamily Rhombognathinae (macroalgae feeders) was not recovered as monophyletic, with Metarhombognathus-Rhombognathides, restricted to the Northern Hemisphere, originating 177.5, 134.8-223.3 Ma and diversifying 88.3, 32.7-152.3 Ma. This is congruent to a previous hypothesis of their northern origin prior to the opening of the Norwegian Sea (58 Ma). Our phylogeny indicates the need for reclassification of the traditional subfamilies and suggests that previous molecular results (e.g., Rhombognathus deeply nested in Copidognathinae) is an analytical artifact due to a chimeric sequence.

Marine and giant viruses as indicators of a marine microbial community in a riverine system.

Viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. This study investigates riverine viral communities around a small rural town that influences local water inputs. Myoviridae, Siphoviridae, Phycodnaviridae, Mimiviridae, Herpesviridae, and Podoviridae were the most abundant families. Viral species upstream and downstream of the town were similar, with Synechoccocus phage, salinus, Prochlorococcus phage, Mimivirus A, and Human herpes 6A virus most abundant, contributing to 4.9-38.2% of average abundance within the metagenomic profiles, with Synechococcus and Prochlorococcus present in metagenomes as the expected hosts for the phage. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities provides some support for the Baas-Becking hypothesis "everything is everywhere, but, the environment selects." We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.

Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context.

Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.