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Malawimonadida is a deep-level (arguably "kingdom-scale") lineage of eukaryotes whose phylogenetic affinities are uncertain but of great evolutionary interest, as the group is suspected to branch close to the root of the tree of eukaryotes. Part of the difficulty in placing Malawimonadida phylogenetically is its tiny circumscription: at present, it comprises only two described and one cultured but undescribed species, all of them are freshwater suspension-feeding nanoflagellates. In this study, we cultivated and characterised Imasa heleensis gen. nov., sp. nov. (Imasidae fam. nov.), the first marine malawimonad to be described. Light and electron microscopy observations show that Imasa is largely similar to other malawimonads, but more frequently adheres to the substrate, often by means of a pliable posterior extension. Phylogenetic analyses based on two ribosomal RNA genes and four translated protein-coding genes using three different taxon sets place Imasa as sister to the three freshwater malawimonad strains with strong support. Imasa's mitochondrial genome is circular-mapping and shows a similar gene complement to other known malawimonads. We conclude that Imasa represents an important expansion of the range of taxa available for future evolutionary study.

We reconstruct the phylogeny of imperial pigeons (genus Ducula) using mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. The divergence time analysis suggests that the basal divergences within Ducula occurred more recently than in the fruit doves (genus Ptilinopus), a group that is also well diversified in Oceania. The imperial pigeons colonized the Melanesian region several times independently, and the diversification within this region led to several species in sympatry, in particular in the Bismarck archipelago. Central Polynesia was also colonized several times, first by a lineage during the Miocene that led to the large D. latrans, sister to the New Caledonian endemic D. goliath, then more recently by the widespread D. pacifica, during the Pleistocene. The phylogenetic pattern obtained with the extant Ducula species showed that the Eastern Polynesian endemics do not form a monophyletic group, with the Pacific Imperial Pigeon D. pacifica sister species with good support to the Polynesian Imperial Pigeon D. aurorae. However, the impact of recent anthropic extinctions has been important for the imperial pigeons, more than for the smaller fruit doves, suggesting that several Ducula lineages might be missing today.

The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso- to eutrophic waters. Two 18S rDNA hypervariable sites, V4 and V8-V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2,741 (V4) and 2,606 (V8-V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. 18.4% (V4) and 13.8% (V8-V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply-branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information. This article is protected by copyright. All rights reserved.

Factors that influence speciation rates among groups of organisms are integral to deciphering macroevolutionary processes; however, they remain poorly understood. Here, we use molecular phylogenetic data and divergence time estimates to reconstruct the pattern and tempo of speciation within a widespread and homogeneous bird family (white-eyes, Zosteropidae) that contains an archetypal “great speciator.” Our analyses show that the majority of this species-rich family constitutes a clade that arose within the last 2 million years, yielding a per-lineage diversification rate among the highest reported for vertebrates (1.95–2.63 species per million years). However, unlike most rapid radiations reported to date, this burst of diversification was not limited in geographic scope, but instead spanned the entire Old World tropics, parts of temperate Asia, and numerous Atlantic, Pacific, and Indian Ocean archipelagos. The tempo and geographic breadth of this rapid radiation defy any single diversification paradigm, but implicate a prominent role for lineage-specific life-history traits (such as rapid evolutionary shifts in dispersal ability) that enabled white-eyes to respond rapidly and persistently to the geographic drivers of diversification.

Monarch flycatchers are a major component of Australo-Pacific and Wallacean avifaunas. To date, the family has received incomplete attention by molecular systematists who focused on subclades with minimal character and/or taxon sampling. As a result, Monarchidae taxonomy is still out-of-date, and biogeographic reconstructions have been based on poorly-resolved phylogenies, limiting their interpretation. Here, we produced a comprehensive, molecular phylogeny of the Monarchidae inferred from mitochondrial and nuclear loci using both concatenated and multilocus coalescent frameworks. We sampled 92% of the 99 recognized monarchid biological species and included deeper sampling within several phylogenetic species complexes, including Monarcha castaneiventris, Symposiachrus barbatus, and Terpsiphone rufiventer. Melampitta is identified as sister to the monarch flycatchers, which themselves comprise four major lineages. The first lineage comprises Terpsiphone and allies, the second lineage is Grallina, the third is Arses and Myiagra, and the fourth lineage comprises a diverse assemblage of genera including the “core monarchs” and the most geographically isolated groups like Chasiempis (Hawaii) and Pomarea (eastern Polynesia). Gene tree discordance was evident in Myiagra, which has implications for basal lineages in the genus (e.g., M. azureocapilla, M. hebetior, and M. alecto). Numerous genera within the core monarchs are paraphyletic, including Mayrornis and Pomarea, whereas the validity of others such as Metabolus are questionable. We recognize polytypic taxa as multiple species, including Lamprolia victoriae and Myiagra azureocapilla. In general, the topology of species complexes included short internodes that were not well resolved, owing to their rapid diversification across island archipelagos. Terpsiphone rufiventer comprises multiple lineages, including a heretofore-unappreciated West African lineage, but relationships within these rapid radiations will require extensive genomic sampling for further resolution. This study establishes a new benchmark for Monarchidae systematics and it provides an excellent framework for future work on biogeography and character evolution in a diverse Australo-Papuan radiation.

We reconstruct the phylogeny of fruit doves (genus Ptilinopus) and allies with a dense sampling that includes almost all species, based on mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. We also investigate the evolution of one of the main plumage character of fruit doves (the color of the crown), and we propose several revisions of the group's systematics. All Ptilinopus taxa formed a monophyletic group that includes two morphologically distinct genera, Alectroenas and Drepanoptila, confirming a previous result found with less species and genes. The divergence time analysis suggests that the basal divergences within Ptilinopus dated to the Early Oligocene, and the biogeographic analysis indicates that fruit doves originated most probably from the proto New Guinea region. The earliest dispersals from the New Guinea region to Oceania occurred with the colonization of New Caledonia and Fiji. A large group of Polynesian species (Central and Eastern), as well as the three taxa found in Micronesia and four species from the Guinean-Moluccan region, form the "purpuratus" clade, the largest diversification of fruit doves within Oceania, which also has a New Guinean origin. However, the eastbound colonization of fruit doves was not associated with a significant increase of their diversification rate. Overall, the Melanesian region did not act as a cradle for fruit doves, in contrast to the New Guinea region which is found as the ancestral area for several nodes within the phylogeny.

Biologists have long used islands as natural laboratories for understanding the diversification of life. A conclusion from these studies — notably those of Ernst Mayr — is that life on far-flung archipelagos accumulates from a simple one-way flow of colonists from continents to islands. Filardi and Moyle set out to test this assumption by estimating the relationships of a pan-Pacific bird group, the monarch flycatchers that feature in Mayr's work, through space and time. Their molecular phylogenetic data show that the traditional idea of the islands as stepping stones, with species colonizing Australasia by island-hopping their way across the oceans, does not fit the facts. Instead, the diversity of life across the major Pacific archipelagos is the product of a single radiation involving colonization from islands to continents as well as vice versa. Oceanic islands have long served as natural laboratories for understanding the diversification of life1,2,3,4. In particular, the many thousands of islands spanning the tropical Pacific support an unparalleled array of terrestrial communities whose patterns of diversity contributed fundamental insights to the development of classical speciation and biogeographic theory4,5,6,7,8. Much of this work is founded on an assumption derived from traditional taxonomic approaches, namely that faunas on these widely separated archipelagos stem from a simple one-way, downstream flow of colonists from continents to islands2,4. Here we show, with the use of molecular phylogenetic data from one of the original bird families used to justify this assumption, that a diverse array of endemic island genera and species are the product of a single radiation that diversified across all major Pacific archipelagos in a non-stepping-stone fashion, and recently recolonized continental areas. The geographic scope and lineage-specific approach of this study reveal evolutionary patterns long obscured by traditional taxonomic surveys and indicate that widely dispersed archipelagos can be sources of biological diversity.

Systematic relationships among monarch flycatchers (genus Monarcha) are poorly understood despite dramatic patterns of morphological differentiation that have long attracted the attention of evolutionary biologists. With sequence data from the mitochondrial ND2 gene and Control Region, we produced a phylogenetic hypothesis for evolutionary relationships within Monarcha and among the biogeographically complex Solomon Island endemics. Outgroup analyses contradicted monophyly of the genus by imbedding a representative of the genus Clytorhynchus within one of two major clades recovered within Monarcha. These two monarch clades generally correspond with ecological and morphological distinctions, suggesting the genus may warrant revision pending the inclusion of taxa currently allied with Clytorhynchus (e.g., Neolalage spp.). Maximum likelihood reconstructions support monophyletic groupings of the two endemic Solomon Island monarch radiations, however, two currently recognized superspecies (Monarcha manadensis and M. melanopsis) were polyphyletic and paraphyletic, respectively. Interestingly, molecular and morphological differentiation were strikingly decoupled among several Solomon Island endemics and between migratory and non-migratory forms of Monarcha trivirgatus in eastern Australia, suggesting morphological evolution has masked the true history of speciation in these groups. This initial phylogeny provides a novel platform for ongoing exploration of the history underlying dramatic patterns of geographic variation among tropical Pacific flycatchers.