Phylogenetic and biogeographic relationships of the mouse opossum Thylamys (Didelphimorphia,Didelphidae) in southern South America

Nucleotide sequence data from the mitochondrial cytochrome b gene were used to evaluate the phylogenetic relationships among mouse opossum species of the genus Thylamys. Based on approximately 1000 bp in five of the six species of the genus and including different localities for some of the species, we concluded that T. macrura from the subtropical forests of eastern Paraguay is the most primitive taxon. Subsequent radiation of the genus is explained mainly via founder effect speciation. This evolutionary scenario would account for the speciation of T. pusilla, T. venusta, T. pallidior, and T. elegans in the Chaco, southern Bolivia and northern Argentina, the Andean Altiplano, the Coastal Desert of Chile, and coastal Perú, respectively. Calibration of a molecular clock set the Pleistocene as the period for the differentiation of Thylamys species. The molecular results confirm the strong genetic connection between populations that inhabit the "pre-cordillera" of northern Chile (T. pallidior) and the canyons that run through the Atacama Desert to the lowlands in northern Chile. Our results confirm the occurrence of two Thylamys species in Chile, T. pallidior and T. elegans, within and south to the Atacama Desert, respectively.     

Extended phylogeny of the Craspedida (Choanomonada)

Currently choanoflagellates are classified into two distinct orders: loricate Acanthoecida and non-loricate Craspedida. The morphologically based taxonomy of the order Craspedida is in need of a revision due to its controversial, paraphyletic and inconsistent systematics and nomenclature. In this study, we add molecular data (SSU and parts of the LSU rDNA) of six new Craspedida species isolated from saline, brackish and freshwater habitats to the existing knowledge. Four of these six organisms could be described as new species: Paramonosiga thecata, “Salpingoeca” euryoecia, “Salpingoeca” ventriosa, “Sphaeroeca” leprechaunica, whereas two are assigned to previous morphologically described species: “Salpingoeca” fusiformis Saville Kent, 1880 and “Salpingoeca” longipes Saville Kent, 1880. Paramonosiga is established as a new genus of the Craspedida based on its phylogenetic position. Extending the dataset by six additional sequences shows that the craspedid taxonomy is still unsolved as the type specimen Salpingoeca gracilis has not yet been sequenced and hence a clear assignment to the genus Salpingoeca is not possible. Trying to assign morphological and ecological data to phylogenetic clades is not successful. We give an improved/emended morphological diagnosis for the two redescribed species and add molecular data for all six species, shedding light on their phylogenetic position.     

Higher level taxonomy and molecular phylogenetics of the Choanoflagellatea

The choanoflagellates (Choanoflagellatea) comprise a major group of nanoflagellates, which are ubiquitous in the aquatic environment. Recent molecular phylogenies have shown them to be the sister group to the Metazoa. However, the phylogeny of the choanoflagellates is still far from understood. We present here a 29 taxon, multigene phylogeny that robustly places the root of the choanoflagellates. One of the original nonloricate families, Codonosigidae is shown to be a polyphyletic assemblage nested within the Salpingoecidae. We elaborate on a revised taxonomy that divides Choanoflagellatea into two orders: Craspedida and Acanthoecida. Craspedida is composed of species that possess an organic cell coating and contains the single family Salpingoecidae. Members of the predominantly marine Acanthoecida produce a siliceous lorica in addition to an organic coat and are contained in two families--the Acanthoecidae and Stephanoecidae fam. n. Previous studies of choanoflagellates have been hindered by cases of taxon misidentification as well as the limited resolution of 18S small subunit (SSU) rDNA phylogenies. Unfortunately, cases of misidentification have been heavily repeated in the literature. In an attempt to avoid further confusion, we highlight known instances of misnamed taxa. We also examine the suitability of SSU rDNA sequences alone for choanoflagellate phylogenetics and recommend the use of protein-coding genes, such as hsp90 and tubA, whenever possible.     

Biogeography,autecology, and phylogeny of Percolomonads based on newly described species

Percolomonads (Heterolobosea) are aquatic heterotrophic flagellates frequently found in saline waters up to hypersaline environments. We isolated and cultivated seven strains of percolomonad flagellates from marine waters and sediments as well as from a hypersaline inland lake in the Atacama Desert. Morphological characterizations, comprising light and scanning electron microscopy, revealed only slight differences between the strains mainly limited to the cell shape, length of flagella, and length of the ventral feeding groove. Phylogenetic analyses of the 18S and 28S rDNA genes showed the formation of three fully supported clades within the Percolomonadida: the Percolomonadidae, the Barbeliidae fam. nov. and the Lulaidae fam. nov. We describe two new families (Barbeliidae fam. nov., Lulaidae fam. nov.), a new genus (Nonamonas gen. nov.), and five new species (Percolomonas adaptabilis sp. nov., Lula levis sp. nov., Barbelia pacifica sp. nov., Nonamonas montiensis gen. et sp. nov., Nonamonas santamariensis gen. et sp. nov.). Salinity experiments showed that P. adaptabilis sp. nov. from the Atlantic was better adapted to high salinities than all other investigated strains. Moreover, comparisons of our cultivation-based approach with environmental sequencing studies showed that P. adaptabilis sp. nov. seems to be globally distributed in marine surface waters while other species seem to be more locally restricted.     

Disrupted phylogeographical microsatellite and chloroplast DNA patterns indicate a vicariance rather than long‐distance dispersal origin for the disjunct distribution of the Chilean endemic Dioscorea biloba (Dioscoreaceae) around the Atacama Desert

Aim The Chilean endemic Dioscorea biloba (Dioscoreaceae) is a dioecious geophyte that shows a remarkable 600 km north–south disjunction in the peripheral arid area of the Atacama Desert. Its restricted present‐day distribution and probable Neogene origin indicate that its populations have a history linked to that of the Atacama Desert, making this an ideal model species with which to investigate the biogeography of the region. Location Chile, Atacama Desert and peripheral arid area. Methods Two hundred and seventy‐five individuals from nine populations were genotyped for seven nuclear microsatellite loci, and plastid trnL–F and trnT–L sequences were obtained for a representative subset of these. Analyses included the estimation of genetic diversity and population structure through clustering, Bayesian and analysis of molecular variance analyses, and statistical parsimony networks of chloroplast haplotypes. Isolation by distance was tested against alternative dispersal hypotheses. Results Microsatellite markers revealed moderate to high levels of genetic diversity within populations, with those from the southern Limarí Valley showing the highest values and northern populations showing less exclusive alleles. Bayesian analysis of microsatellite data identified three genetic groups that corresponded to geographical ranges. Chloroplast phylogeography revealed no haplotypes shared between northern and southern ranges, and little haplotype sharing between the two neighbouring southern valleys. Dispersal models suggested the presence of extinct hypothetical populations between the southern and northern ranges. Main conclusions Our results are consistent with prolonged isolation of the northern and southern groups, mediated by the life‐history traits of the species. Significant isolation was revealed at both large and moderate distances as gene flow was not evident even between neighbouring valleys. Bayesian analyses of microsatellite and chloroplast haplotype diversity identified the southern area of Limarí as the probable area of origin of the species. Our data do not support recent dispersal of D. biloba from the southern range into Antofagasta, but indicate the fragmentation of an earlier wider range, concomitant with the Pliocene–Pleistocene climatic oscillations, with subsequent extinctions of the Atacama Desert populations and the divergence of the peripheral ones as a consequence of genetic drift.     

First description of an euryoecious acanthoecid choanoflagellate species,Enibas tolerabilis gen. et sp. nov. from a salar in the Chilean Andes based on morphological and transcriptomic data

In general, acanthoecid choanoflagellates have been described to occur exclusively in brackish water to marine habitats. Only recently, two studies have proven their existence in inland waters. One of them has shown, that an acanthoecid species from a small lake (near Apia on the island of Upolu, Samoa) is strictly freshwater adapted, not able to tolerate even brackish water. In this study, we present the first euryoecious acanthoecid species, able to live and reproduce in freshwater as well as under hypersaline conditions. The new species, Enibas tolerabilis gen. et sp. nov. was isolated in 2017 from the Salar de Ascotán in the Altiplano at 3750 m a. s. l., Northern Chile. The salinity at the time of sampling was 6 PSU. A series of autecological experiments have revealed a salinity tolerance from freshwater up to 70 PSU. In our phylogenetic analysis, E. tolerabilis gen. et sp. nov. clustered within the family of Acanthoecidae, forming a well-supported sister clade together with two other, environmental choanoflagellate sequences. We erected a new genus, Enibas gen. nov. and described the morphology, molecular biology and autecology for E. tolerabilis gen. et sp. nov. which has a stephanoecid-like lorica morphology. We emphasize that the definition of the genus Stephanoeca, being polyphyletic, is in urgent need of revision as we showed that this morphology is present in both acanthoecid families.     

Fungal diversity in the Atacama Desert

Fungi are generally easily dispersed, able to colonise a wide variety of substrata and can tolerate diverse environmental conditions. However, despite these abilities, the diversity of fungi in the Atacama Desert is practically unknown. Most of the resident fungi in desert regions are ubiquitous. Some of them, however, seem to display specific adaptations that enable them to survive under the variety of extreme conditions of these regions, such as high temperature, low availability of water, osmotic stress, desiccation, low availability of nutrients, and exposure to high levels of UV radiation. For these reasons, fungal communities living in the Atacama Desert represent an unknown part of global fungal diversity and, consequently, may be source of new species that could be potential sources for new biotechnological products. In this review, we focus on the current knowledge of the diversity, ecology, adaptive strategies, and biotechnological potential of the fungi reported in the different ecosystems of the Atacama Desert.     

Three-dimensional images of choanoflagellate loricae

Choanoflagellates are unicellular filter-feeding protozoa distributed universally in aquatic habitats. Cells are ovoid in shape with a single anterior flagellum encircled by a funnel-shaped collar of microvilli. Movement of the flagellum creates water currents from which food particles are entrapped on the outer surface of the collar and ingested by pseudopodia. One group of marine choanoflagellates has evolved an elaborate basket-like exoskeleton, the lorica, comprising two layers of siliceous costae made up of costal strips. A computer graphic model has been developed for generating three-dimensional images of choanoflagellate loricae based on a universal set of 'rules' derived from electron microscopical observations. This model has proved seminal in understanding how complex costal patterns can be assembled in a single continuous movement. The lorica, which provides a rigid framework around the cell, is multifunctional. It resists the locomotory forces generated by flagellar movement, directs and enhances water flow over the collar and, for planktonic species, contributes towards maintaining cells in suspension. Since the functional morphology of choanoflagellate cells is so effective and has been highly conserved within the group, the ecological and evolutionary radiation of choanoflagellates is almost entirely dependent on the ability of the external coverings, particularly the lorica, to diversify.     

Choanoflagellate lorica construction and assembly: the nudiform condition. II. Acanthoeca spectabilis Ellis

Acanthoeca spectabilis is one of the most common loricate choanoflagellates found in marine biofilms everywhere. However, it is special for two reasons; firstly, it is probably the most distinctive member of the small nudiform clade of loricate choanoflagellates. Secondly, the lorica chamber of Acanthoeca comprises a closely wound left-handed coil of costae that is unique amongst choanoflagellates. Mathematical analysis of the lorica chamber shows that the helical costae undergo two turns. This species, more than any, demonstrates that the helical coiling of costae can only be achieved by a rotational movement generated by the cell during lorica assembly. Comparison of the lorica morphology of Acanthoeca with that of the closely related genus Polyoeca indicates that the helical costae of Acanthoeca are probably homologous with the outer longitudinal costae of Polyoeca. This is unusual because helical costae are usually the innermost layer of costae. However, since there is no 'true' inner layer in the chamber of Acanthoeca the outer layer of costae are adjacent to the cell surface and therefore available for coiling. In contrast to tectiform choanoflagellates, which number more than one hundred species and inhabit a wide variety of microniches, the six known extant nudiform species must either represent a minor evolutionary development or be the remnants of a previously more extensive radiation.     

A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates

Biosilicification is widespread across the eukaryotes and requires concentration of silicon in intracellular vesicles. Knowledge of the molecular mechanisms underlying this process remains limited, with unrelated silicon-transporting proteins found in the eukaryotic clades previously studied. Here, we report the identification of silicon transporter (SIT)-type genes from the siliceous loricate choanoflagellates Stephanoeca diplocostata and Diaphanoeca grandis. Until now, the SIT gene family has been identified only in diatoms and other siliceous stramenopiles, which are distantly related to choanoflagellates among the eukaryotes. This is the first evidence of similarity between SITs from different eukaryotic supergroups. Phylogenetic analysis indicates that choanoflagellate and stramenopile SITs form distinct monophyletic groups. The absence of putative SIT genes in any other eukaryotic groups, including non-siliceous choanoflagellates, leads us to propose that SIT genes underwent a lateral gene transfer event between stramenopiles and loricate choanoflagellates. We suggest that the incorporation of a foreign SIT gene into the stramenopile or choanoflagellate genome resulted in a major metabolic change: the acquisition of biomineralized silica structures. This hypothesis implies that biosilicification has evolved multiple times independently in the eukaryotes, and paves the way for a better understanding of the biochemical basis of silicon transport through identification of conserved sequence motifs.     

Historical and ecological divergence among populations of Monttea chilensis (Plantaginaceae), an endemic endangered shrub bordering the Atacama Desert,Chile

The coastal deserts of northern Chile show an important latitudinal gradient of aridity with more arid areas to the north of the Atacama Desert than to the south. Several plant species have disjunct distributions that correspond with the extremes of this latitudinal gradient. In this study, using genetic (chloroplast and nuclear DNA), morphological (vegetative and floral traits of various kinds) and climatic and topographic information, we explored ecological and historical events that have putatively shaped patterns of variation among Monttea chilensis populations—a species that shows this disjunct distribution. Through phylogeographic and phylogenetic analyses, two divergent lineages were identified located at the latitudinal extremes. The lineage located northern lineage (NG) of the Atacama Desert showed more genetic diversity and better-resolved phylogeographic structure than the southern lineage (SG). Considerable morphological variation across the geographical range corresponds with these genetic groups. We observed contrasting relationships between floral and vegetative traits: populations from the most arid region NG possessed larger flowers, but smaller vegetative values, and vice versa. Niche modelling and multivariate analyses, including environmental data, revealed different environmental requirements for each lineage. NG plants occur in regions with warmer and drier climatic conditions and at higher altitudes, while SG populations inhabit colder and more humid environments and lower altitudes. The evolutionary history of M. chilensis exhibits a phylogeographical footprint consistent with past fragmentation and allopatric differentiation, where the hyper-arid zone formed by the Atacama Desert clearly acted as an important gene flow barrier. This barrier has led to considerable differentiation in morphology and ecology, resulting in two ecotypes or geographical races, suggesting incipient speciation promoted by local adaptation and geographical isolation.     

Cryptic diversity within the choanoflagellate morphospecies complex Codosiga botrytis - Phylogeny and morphology of ancient and modern isolates

Choanoflagellates are closely related to metazoans and fungi according to recent phylogenetic studies; therefore the systematics of these organisms is of particular interest. The choanoflagellate morphospecies Codosiga botrytis is the first described choanoflagellate, and is one of the most frequently reported choanoflagellate species. In this study we present phylogenetic and morphological data on eight different strains of Codosiga botrytis. Among these there are five ancient strains; these cultures have been established from up to 43,000 years old cysts from Siberian permafrost. We found that based on the variable V4 region of the small subunit (SSU) of the rDNA, all the investigated freshwater isolates of Codosiga botrytis, together with Sphaeroeca volvox, form a cluster at the base of all other choanoflagellate species. Moreover, the morphospecies described classically as Codosiga botrytis contains at least four different genotypes separated by considerably high genetic distance. All these 'cryptic species' have identical general morphology and cell structure. Strains have a similar life cycle with several different life forms and large morphological plasticity. For the first time we were able to establish cultures from cryo-conserved cysts of choanoflagellates. The ancient strains did not differ significantly in partial SSU rDNA from the modern ones. Besides, no biogeographically pattern could be established. This fact and the low genetic distances of some strains from remote locations support the distribution of dormant stages via air.     

Heterotrophic amoebae,flagellates and heliozoa from Arctic marine waters (North West Territories,Canada and West Greenland)

Summary Thirty eight taxa of heterotrophic protists (amoebae, flagellates and heliozoa) were encountered in cultures established from marine samples from Disko Bay (West Greenland) and Foxe Basin (N.W.T. Canada). Most species are flagellates representing the choanoflagellates, the euglenids, the kinetoplastids, the bicosoecids, the chrysomonads, the pedinellids and a variety of taxa of uncertain affinities (Protista incertae sedis). A new species of thecate choanoflagellate, Salpingoeca intermedia sp. nov., is described, and 4 new types of triangular scales, representing the genus Thaumatomastix Lauterborn, 1899, are presented.     

Adaptive eukaryote-to-eukaryote lateral gene transfer: stress-related genes of algal origin in the closest unicellular relatives of animals

In addition to mutation, gene duplication and recombination, the transfer of genetic material between unrelated species is now regarded as a potentially significant player in the shaping of extant genomes and the evolution and diversification of life. Although this is probably true for prokaryotes, the extent of such genetic exchanges in eukaryotes (especially eukaryote-to-eukaryote transfers) is more controversial and the selective advantage and evolutionary impact of such events are less documented. A laterally transferred gene could either be added to the gene complement of the recipient or replace the recipient's homologue; whereas gene replacements can be either adaptive or stochastic, gene additions are most likely adaptive. Here, we report the finding of four stress-related genes (two ascorbate peroxidase and two metacaspase genes) of algal origin in the closest unicellular relatives of animals, the choanoflagellates. At least three of these sequences represent additions to the choanoflagellate gene complement, which is consistent with these transfers being adaptive. We suggest that these laterally acquired sequences could have provided the primitive choanoflagellates with additional or more efficient means to cope with stress, especially in relation to adapting to freshwater environments and/or sessile or colonial lifestyles.     

A new genus, Helgoeca gen. nov., for a nudiform choanoflagellate

A new genus, Helgoeca gen. nov., has been designated to accommodate a nudiform loricate choanoflagellate (American Type Culture Collection strain ATCC 50073) that was incorrectly attributed to the tectiform genus Acanthoecopsis (=Acanthocorbis). The first indication that this species might be nudiform came from a four-gene phylogeny of the choanoflagellates which recovered ATCC 50073 within a strongly supported monophyletic clade comprising two other nudiform taxa. Fortunately an isolate of the species in question was available from the ATCC and when observed in rapidly growing culture it was immediately apparent that this species divided with the production of 'naked' motile cells; a typically nudiform character. The beaker-shaped lorica of this species consists of an outer layer of approximately 11 longitudinal costae, which terminate anteriorly as spines, and an equal or larger number of helical costae, with a left-handed conformation, each of which terminates anteriorly adjacent to the base of a spine. The pattern of costae in this species is indistinguishable from that of Acanthocorbis nana Thomsen and for this reason A. nana has been transferred to the new genus Helgoeca gen. nov., as the type species.     

Hsp70 sequences indicate that choanoflagellates are closely related to animals.

Over 130 years ago, James-Clark noted a remarkable structural similarity between the feeding cells of sponges (choanocytes) and a group of free-living protists, the choanoflagellates. Both cell types possess a single flagellum surrounded by a collar of fine tentacles. The similarity led to the hypothesis that sponges, and, by implication, other animals, evolved from choanoflagellate-like ancestors. Phylogenetic analysis of ribosomal DNA neither supports nor refutes this hypothesis. Here, we report the sequence of an hsp70 gene and pseudogene from the freshwater choanoflagellate Monosiga ovata. These represent the first nuclear-encoded protein-coding sequences reported for any choanoflagellate. We find that Monosiga and most bilaterian hsp70 genes have high GC contents that may distort phylogenetic tree construction; therefore, protein sequences were used for phylogenetic reconstruction. Our analyses indicate that Monosiga is more closely related to animals than to fungi. We infer that animals and at least some choanoflagellates are part of a clade that excludes the fungi. This is consistent with the origin of animals from a choanoflagellate-like ancestor.