Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data

The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar. The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We are most grateful to the Ahmanson Foundation, the Theodore F. and Claire M. Hubbard Family Foundation, the Primate Action Fund / Conservation International, the Margot Marsh Biodiversity Foundation, and the National Geographic Society, for financial assistance

Megaphylogeny resolves global patterns of mushroom evolution

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.Fil: Varga, Torda. Hungarian Academy Of Sciences; HungríaFil: Krizsán, Krisztina. Hungarian Academy Of Sciences; HungríaFil: Földi, Csenge. Hungarian Academy Of Sciences; HungríaFil: Dima, Bálint. Eötvös Loránd University; HungríaFil: Sánchez-García, Marisol. Clark University; Estados UnidosFil: Lechner, Bernardo Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Micología y Botánica. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Micología y Botánica; ArgentinaFil: Sánchez-Ramírez, Santiago. University of Toronto; CanadáFil: Szöllosi, Gergely J.. Eötvös Loránd University; HungríaFil: Szarkándi, János G.. University Of Szeged; HungríaFil: Papp, Viktor. Szent István University; HungríaFil: Albert, László. Hungarian Mycological Society; HungríaFil: Andreopoulos, William. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Angelini, Claudio. Jardin Botanico Nacional Ma. Moscoso; República DominicanaFil: Antonín, Vladimír. Moravian Museum; República ChecaFil: Barry, Kerrie W.. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Bougher, Neale L.. Western Australian Herbarium; AustraliaFil: Buchanan, Peter. Manaaki Whenua-landcare Research; Nueva ZelandaFil: Buyck, Bart. Muséum National d'Histoire Naturelle; FranciaFil: Bense, Viktória. Hungarian Academy Of Sciences; HungríaFil: Catcheside, Pam. State Herbarium Of South Australia; AustraliaFil: Chovatia, Mansi. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Cooper, Jerry. Manaaki Whenua-landcare Research; Nueva ZelandaFil: Dämon, Wolfgang. Oberfeldstrasse 9; AustriaFil: Desjardin, Dennis. San Francisco State University; Estados UnidosFil: Finy, Péter. Zsombolyai U. 56.; HungríaFil: Geml, József. Naturalis Biodiversity Center; Países BajosFil: Haridas, Sajeet. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Hughes, Karen. University of Tennessee; Estados UnidosFil: Justo, Alfredo. Clark University; Estados UnidosFil: Karasinski, Dariusz. Polish Academy of Sciences; Poloni

Megaphylogeny resolves global patterns of mushroom evolution

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Phylogeographic analyses of an epiphytic foliose lichen show multiple dispersal events westward from the Hengduan Mountains of Yunnan into the Himalayas.

Lobaria pindarensis is an endemic species of the Himalayas and the Hengduan Mountains. Little information is available on the phylogeography genetics and colonization history of this species or how its distribution patterns changed in response to the orographic history of the Himalayas and Hengduan Mountains. Based on samples covering a major part of the species' distribution range, we used 443 newly generated sequences of nine loci for molecular coalescent analyses in order to reconstruct the evolutionary history of L. pindarensis, and to reconstruct the species' ancestral phylogeographic distributions using Bayesian binary MCMC analyses. The results suggest that current populations originated from the Yunnan region of the Hengduan Mountains in the middle Pliocene, and that the Himalayas of Bhutan were colonized by a lineage that diverged from Yunnan ca. 2.72 Ma. The analysis additionally indicates that the Nepal and Xizang areas of the Himalayas were colonized from Yunnan as well, and that there was later a second dispersal event from Yunnan to Bhutan. We conclude that the change in climate and habitat related to the continuous uplift of the Himalayas and the Hengduan Mountains in the late Pliocene and middle Pleistocene influenced the geographic distribution pattern of L. pindarensis

Population Genetic Structure and Species Delimitation of a Widespread, Neotropical Dwarf Gecko

Amazonia harbors the greatest biological diversity on Earth. One trend that spans Amazonian taxa is that most taxonomic groups either exhibit broad geographic ranges or small restricted ranges. This is likely because many traits that determine a species range size, such as dispersal ability or body size, are autocorrelated. As such, it is rare to find groups that exhibit both large and small ranges. Once identified, however, these groups provide a powerful system for isolating specific traits that influence species distributions. One group of terrestrial vertebrates, gecko lizards, tends to exhibit small geographic ranges. Despite one exception, this applies to the Neotropical dwarf geckos of the genus Gonatodes. This exception, Gonatodes humeralis, has a geographic distribution almost 1,000,000 km2 larger than the combined ranges of its 30 congeners. As the smallest member of its genus and a gecko lizard more generally, G. humeralis is an unlikely candidate to be a wide-ranged Amazonian taxon. To test whether or not G. humeralis is one or more species, we generated molecular genetic data using restriction-site associated sequencing (RADseq) and traditional Sanger methods for samples from across its range and conducted a phylogeographic study. We conclude that G. humeralis is, in fact, a single species across its contiguous range in South America. Thus, Gonatodes is a unique clade among Neotropical taxa, containing both wide-ranged and range-restricted taxa, which provides empiricists with a powerful model system to correlate complex species traits and distributions. Additionally, we provide evidence to support species-level divergence of the allopatric population from Trinidad and we resurrect the name Gonatodes ferrugineus from synonymy for this population

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

Elucidating the demographic and phylogeographic histories of species provides insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of histories and demographic parameters with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Even with genomic estimates of historical demographic parameters, we found the prominent diversification hypotheses to be untestable. We conclude that investigations into the multifarious processes shaping species histories, aided by genomic datasets, will provide greater resolution of diversification in the Neotropics, but that future efforts should focus on understanding the processes shaping the histories of lineages rather than trying to reconcile these histories with landscape and climatic events in Earth history.Comment: 61 pages, 4 figures (+3 supplemental), 3 tables (+6 supplemental

Andean orogeny and the diversification of lowland neotropical rain forest trees:A case study in Sapotaceae

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordUnderstanding how species diversify and evolve in species-rich areas like the lowland rain forest in the Neotropics is critical for conservation in times of unprecedented threats. To determine how the Andean uplift, the formation of the Panama land bridge, and Pleistocene climatic fluctuations affected dispersal and diversification in the Sapotaceae subfamily Chrysophylloideae, we collected 146 Chrysophylloideae accessions in previously under-explored areas, generating one of the most geographically complete data sets for neotropical Sapotaceae. Sapotaceae is a good model to test diversification hypotheses in lowland neotropical rain forests as it predominantly occurs <1000 m altitude, and it is an abundant and species-rich group in this biome. We generated a time calibrated phylogeny of 123 Sapotaceae species based upon the nuclear ribosomal internal transcribed spacer region that suggests migration between lineages to the east and the west Andean Cordilleras occurred before and after periods of major uplift, indicating that the Andes did not represent a significant barrier to dispersal for Sapotaceae, although it may have promoted vicariance in some cases. Dispersal between South and Central America occurred mainly prior to the formation of the Panama land bridge, suggesting that this event did not affect migration patterns in Chrysophylloideae. We inferred diversification rates and detected three shifts in the phylogeny, but they are not congruent with tectonic movements during the middle Miocene and climatic changes during the Pleistocene. Finally, some species with restricted distributions appear to be phylogenetically nested within species with broader ranges, suggesting ancestor descendent relationships and insights into patterns of speciation in rain forest trees.Natural Environment Research Council (NERC)National Science Foundation (NSF)Geological Society of Americ

High-resolution coproecology: Using coprolites to reconstruct the habits and habitats of New Zealand’s extinct upland Moa (Megalapteryx didinus)

Knowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand's largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 ¹⁴C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation