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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/28434199/repeated-evolution-of-digital-adhesion-in-geckos-a-reply-to-harrington-and-reeder
#1
Tony Gamble, Eli Greenbaum, Todd R Jackman, Anthony P Russell, Aaron M Bauer
We published a phylogenetic comparative analysis that found geckos had gained and lost adhesive toepads multiple times over their long evolutionary history (Gamble et al. 2012). This was consistent with decades of morphological studies showing geckos had evolved adhesive toepads on multiple occasions and that the morphology of geckos with ancestrally padless digits can be distinguished from secondarily padless forms. Recently, Harrington and Reeder (2017) reanalyzed data from Gamble et al. (2012) and found little support for the multiple origins hypothesis...
April 23, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28428869/rapid-maximum-likelihood-ancestral-state-reconstruction-of-continuous-characters-a-rerooting-free-algorithm
#2
Eric W Goolsby
Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28406561/lower-ilium-evolution-in-apes-and-hominins
#3
Ashley S Hammond, Sergio Almécija
Elucidating the pelvic morphology of the Pan-Homo last common ancestor (LCA) is crucial for understanding ape and human evolution. The pelvis of Ardipithecus ramidus has been the basis of controversial interpretations of the LCA pelvis. In particular, it was proposed that the lower ilium became elongate independently in the orangutan and chimpanzee clades, making these taxa poor analogues for the pelvis of the LCA. This study examines the variation in relative lower ilium height between and within living and fossil hominoid species (and other anthropoids), and models its evolution using available fossil hominoids as calibration points...
May 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/28403902/phylodynamics-of-foot-and-mouth-disease-virus-o-panasia-in-vietnam-2010-2014
#4
Barbara Brito, Steven J Pauszek, Michael Eschbaumer, Carolina Stenfeldt, Helena C de Carvalho Ferreira, Le T Vu, Nguyen T Phuong, Bui H Hoang, Nguyen D Tho, Pham V Dong, Phan Q Minh, Ngo T Long, Donald P King, Nick J Knowles, Do H Dung, Luis L Rodriguez, Jonathan Arzt
Foot-and-mouth disease virus (FMDV) is endemic in Vietnam, a country that plays an important role in livestock trade within Southeast Asia. The large populations of FMDV-susceptible species in Vietnam are important components of food production and of the national livelihood. In this study, we investigated the phylogeny of FMDV O/PanAsia in Vietnam, reconstructing the virus' ancestral host species (pig, cattle or buffalo), clinical stage (subclinical carrier or clinically affected) and geographical location...
April 13, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28389535/experimental-evaluation-of-host-adaptation-of-lactobacillus-reuteri-to-different-vertebrate-species
#5
Rebbeca M Duar, Steven A Frese, Xiaoxi B Lin, Samodha C Fernando, Thomas E Burkey, Guergana Tasseva, Daniel A Peterson, Jochen Blom, Cory Q Wenzel, Christine M Szymanski, Jens Walter
The species Lactobacillus reuteri has diversified into host-specific lineages implying a long term association with different vertebrates. Strains from rodent lineages show specific adaptations to mice, but the processes underlying the evolution of L. reuteri in other hosts remain unknown. We administered three standardized inocula composed of strains from different host-confined lineages to mice, pigs, chickens and humans. The ecological performance of each strain in the gastrointestinal tract of each host was determined by typing random colonies recovered from fecal samples collected over five consecutive days post-administration...
April 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28387789/evolution-of-wood-anatomical-characters-in-nepenthes-and-close-relatives-of-caryophyllales
#6
Rachel Schwallier, Barbara Gravendeel, Hugo de Boer, Stephan Nylinder, Bertie Joan van Heuven, Anton Sieder, Sukaibin Sumail, Rogier van Vugt, Frederic Lens
Background and Aims: Nepenthes attracts wide attention with its spectacularly shaped carnivorous pitchers, cultural value and horticultural curiosity. Despite the plant's iconic fascination, surprisingly little anatomical detail is known about the genus beyond its modified leaf tip traps. Here, the wood anatomical diversity of Nepenthes is explored. This diversity is further assessed with a phylogenetic framework to investigate whether the wood characters within the genus are relevant from an evolutionary or ecological perspective, or rather depend on differences in developmental stages, growth habits, substrates or precipitation...
April 6, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28382230/mountain-colonisation-miniaturisation-and-ecological-evolution-in-a-radiation-of-direct-developing-new-guinea-frogs-choerophryne-microhylidae
#7
Paul M Oliver, Amy Iannella, Stephen J Richards, Michael S Y Lee
AIMS: Mountain ranges in the tropics are characterised by high levels of localised endemism, often-aberrant evolutionary trajectories, and some of the world's most diverse regional biotas. Here we investigate the evolution of montane endemism, ecology and body size in a clade of direct-developing frogs (Choerophryne, Microhylidae) from New Guinea. METHODS: Phylogenetic relationships were estimated from a mitochondrial molecular dataset using Bayesian and maximum likelihood approaches...
2017: PeerJ
https://www.readbyqxmd.com/read/28356450/terrestrial-reproduction-as-an-adaptation-to-steep-terrain-in-african-toads
#8
H Christoph Liedtke, Hendrik Müller, Julian Hafner, Johannes Penner, David J Gower, Tomáš Mazuch, Mark-Oliver Rödel, Simon P Loader
How evolutionary novelties evolve is a major question in evolutionary biology. It is widely accepted that changes in environmental conditions shift the position of selective optima, and advancements in phylogenetic comparative approaches allow the rigorous testing of such correlated transitions. A longstanding question in vertebrate biology has been the evolution of terrestrial life histories in amphibians and here, by investigating African bufonids, we test whether terrestrial modes of reproduction have evolved as adaptations to particular abiotic habitat parameters...
March 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28345775/quantification-of-the-position-and-depth-of-the-flexor-hallucis-longus-groove-in-euarchontans-with-implications-for-the-evolution-of-primate-positional-behavior
#9
Gabriel S Yapuncich, Erik R Seiffert, Doug M Boyer
OBJECTIVE: On the talus, the position and depth of the groove for the flexor hallucis longus tendon have been used to infer phylogenetic affinities and positional behaviors of fossil primates. This study quantifies aspects of the flexor hallucis longus groove (FHLG) to test if: (1) a lateral FHLG is a derived strepsirrhine feature, (2) a lateral FHLG reflects inverted and abducted foot postures, and (3) a deeper FHLG indicates a larger muscle. METHODS: We used linear measurements of microCT-generated models from a sample of euarchontans (n = 378 specimens, 125 species) to quantify FHLG position and depth...
March 27, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28345239/the-anatomy-of-the-blood-vascular-system-of-the-giant-vestimentiferan-tubeworm-riftia-pachyptila-siboglinidae-annelida
#10
Nadezhda N Rimskaya-Korsakova, Sergey V Galkin, Vladimir V Malakhov
The giant dimensions of vestimentiferan Riftia pachyptila (Jones, ) are achieved thanks to the well-developed vascular system. In the vestimentum, there is a complicated net of lacunae, including the brain blood supply and the ventral lacuna underlying the ciliary field. The trunk region has an extensive network of blood vessels feeding the gonads («rete mirabile»). The thick muscular lining of the mesenterial vessels in the trunk and the dorsal vessel in the opisthosome serves as an additional pump, pushing blood into numerous vessels in the segments...
March 27, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28331531/an-integrative-systematic-framework-helps-to-reconstruct-skeletal-evolution-of-glass-sponges-porifera-hexactinellida
#11
Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N A Hooper, Henry M Reiswig
BACKGROUND: Glass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans)...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/28325970/making-the-most-of-your-host-the-metrosideros-feeding-psyllids-hemiptera-psylloidea-of-the-hawaiian-islands
#12
Diana M Percy
The Hawaiian psyllids (Psylloidea, Triozidae) feeding on Metrosideros (Myrtaceae) constitute a remarkable radiation of more than 35 species. This monophyletic group has diversified on a single, highly polymorphic host plant species, Metrosideros polymorpha. Eleven Metrosideros-feeding species included in the Insects of Hawaii by Zimmerman are redescribed, and an additional 25 new species are described. Contrary to previous classifications that placed the Metrosideros-feeders in two genera, Trioza Foerster, 1848 and Kuwayama Crawford, 1911, all 36 named species are placed in Pariaconus Enderlein, 1926; and the relationship of this genus to other Pacific taxa within the family Triozidae, and other Austro-Pacific taxa feeding on host plants in Myrtaceae is clarified...
2017: ZooKeys
https://www.readbyqxmd.com/read/28323330/insights-on-the-evolutionary-origin-of-detarioideae-a-clade-of-ecologically-dominant-tropical-african-trees
#13
Manuel de la Estrella, Félix Forest, Jan J Wieringa, Marie Fougère-Danezan, Anne Bruneau
African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae...
March 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28288945/species-level-phylogeny-fruit-evolution-and-diversification-history-of-geranium-geraniaceae
#14
Thomas Marcussen, Andrea S Meseguer
The cosmopolitan genus Geranium L. (Geraniaceae) consists of c. 350 species distributed in temperate habitats worldwide, with most of its diversity concentrated in the Mediterranean region. Unlike other genera in Geraniaceae, the species of Geranium present contrasting seed discharge syndromes, i.e. the 'Erodium-type' (ET), the 'carpel-projection type' (CP), the 'seed-ejection type' (SE), and the 'inoperative type' (IT), which have been used to delimit major groups within the genus. However, phylogenetic relationships within Geranium are unknown and so is the evolution of the different seed discharge mechanisms...
May 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28286101/the-biogeographic-and-evolutionary-history-of-an-endemic-clade-of-middle-american-sparrows-melozone-and-aimophila-aves-passerellidae
#15
Luis Sandoval, Kevin L Epperly, John Klicka, Daniel J Mennill
The large number of endemic species in Middle America is frequently attributed to the interplay of geographical barriers and historical climatic changes in the region. This process promotes genetic divergence between populations, and given enough time, may yield new species. Animals that inhabit mid-elevation or highland habitats may be disproportionately affected in this way. Genetic analyses of animals in this region allow us to better understand how historical patterns of isolation have influenced the generation of new species in this biodiversity hotspot...
March 7, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28245805/clock-dated-phylogeny-for-48-of-the-700-species-of-crotalaria-fabaceae-papilionoideae-resolves-sections-worldwide-and-implies-conserved-flower-and-leaf-traits-throughout-its-pantropical-range
#16
Alexander Rockinger, Andréia Silva Flores, Susanne S Renner
BACKGROUND: With some 700 species, the pantropical Crotalaria is among the angiosperm's largest genera. We sampled 48% of the species from all sections (and representatives of the 15 remaining Crotalarieae genera) for nuclear and plastid DNA markers to infer changes in climate niches, flower morphology, leaf type, and chromosome numbers. RESULTS: Crotalaria is monophyletic and most closely related to African Bolusia (five species) from which it diverged 23 to 30 Ma ago...
February 28, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28245223/phylogeny-and-chromosomal-diversification-in-the-dichroplus-elongatus-species-group-orthoptera-melanoplinae
#17
Elio R D Castillo, Alberto Taffarel, Maximiliano M Maronna, María Marta Cigliano, Octavio M Palacios-Gimenez, Diogo C Cabral-de-Mello, Dardo A Martí
In an attempt to track the chromosomal differentiation in the Dichroplus elongatus species group, we analyzed the karyotypes of four species with classical cytogenetic and mapping several multigene families through fluorescent in situ hybridization (FISH). We improved the taxon sampling of the D. elongatus species group adding new molecular data to infer the phylogeny of the genus and reconstruct the karyotype evolution. Our molecular analyses recovered a fully resolved tree with no evidence for the monophyly of Dichroplus...
2017: PloS One
https://www.readbyqxmd.com/read/28228475/parallel-evolution-of-mound-building-and-grass-feeding-in-australian-nasute-termites
#18
Daej A Arab, Anna Namyatova, Theodore A Evans, Stephen L Cameron, David K Yeates, Simon Y W Ho, Nathan Lo
Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6-8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets...
February 2017: Biology Letters
https://www.readbyqxmd.com/read/28228094/sfreemap-a-simulation-free-tool-for-stochastic-mapping
#19
Diego Pasqualin, Marcos Barbeitos, Fabiano Silva
BACKGROUND: Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribution of states in its internal nodes. Common implementations rely on Continuous-time Markov Chain simulations whose parameters are difficult to adjust and subjected to inherent inaccuracy. Thus, researchers must run a large number of simulations in order to obtain adequate estimates...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28219758/resolving-relationships-at-the-animal-fungal-divergence-a-molecular-phylogenetic-study-of-the-protist-trichomycetes-ichthyosporea-eccrinida
#20
Nicole K Reynolds, Matthew E Smith, Eric D Tretter, Justin Gause, Dustin Heeney, Matías J Cafaro, James F Smith, Stephen J Novak, William A Bourland, Merlin M White
Trichomycetes is a group of microorganisms that was considered a class of fungi comprising four orders of commensal, gut-dwelling endosymbionts obligately associated with arthropods. Since molecular phylogenies revealed two of those orders (Amoebidiales and Eccrinales="protist trichos") to be closely related to members of the protist class Ichthyosporea (=Mesomycetozoea), trichomycetes have been considered an ecological association of both early-diverging fungi and protists. Understanding of the taxonomy, evolution, and diversity of the protist trichos is lacking largely due to the difficulties inherent in species collection that have contributed to undersampling and understudy...
April 2017: Molecular Phylogenetics and Evolution
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