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opencc-zeroNov 2019View details →

Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities

1. Anthropogenic environmental changes are known to affect the Earth's ecosystems. However, how these changes influence assembly trajectories of the impacted communities remains a largely open question. 2. In this study, we investigated the effect of elevated nitrogen (N) deposition and increased precipitation on plant taxonomic and phylogenetic β-diversity in a 9-year field experiment in the temperate semi-arid steppe of Inner Mongolia, China. 3. We found that both N and water addition significantly increased taxonomic β-diversity, whereas N, not water, addition significantly increased phylogenetic β-diversity. After the differences in local species diversity were controlled using null models, the standard effect size of taxonomic β-diversity still increased with both N and water addition, while water, not N, addition, significantly reduced the standard effect size of phylogenetic β-diversity. The increased phylogenetic convergence observed in the water addition treatment was associated with the colonization of different, but phylogenetically closely related, species into different replicate plots of the treatment. Species colonization in this treatment was found to be trait-based, with leaf nitrogen concentration being the key functional trait. 4. Synthesis. Our analyses demonstrate that anthropogenic environmental changes may affect the assembly trajectories of plant communities at both taxonomic and phylogenetic scales. Our results also suggest that while stochastic processes may cause communities to diverge in species composition, deterministic process could still drive communities to converge in phylogenetic community structure.

opencc-by-4.0Dec 2015View details →

Fig. 4. Maximum Likelihood phylogenetic tree generated using N in The African buffalo parasite Theileria. sp. (buffalo) can infect and immortalize cattle leukocytes and encodes divergent orthologues of Theileria parva antigen genes

Fig. 4. Maximum Likelihood phylogenetic tree generated using N-terminal sequences of T. sp. (buffalo) and T. parva PIM antigen genes. Maximum composite likelihood trees were constructed using 1000 bootstrap replicates as implemented in MEGA5; the optimal nucleotide substitution model was identified using data monkey. The tree constructed with RAxML (Stamatakis et al., 2014) using a GTR/G/I model with 100 bootstrap iterations.

FIGURE 5 in Population level genetic divergence and phylogenetic placement of Mexican shortfin mollies (Mollienesia: Poecilia: Poeciliidae)

FIGURE 5 | Cytochrome b (1,140 bp) mitochondrial gene Bayesian phylogeny, parsimony haplotype network, and sampling distribution of Atlantic taxa Poecilia limantouri (Turqouise-North of the Trans Mexican Volcanic Belt, forest green-South of the Trans Mexican Belt), P. sulphuraria/P. thermalis (yellow-South of the Isthmus of Tehuantepec), and P. mexicana (baby blue-North of the Trans Mexican Volcanic Belt, light green-South of the Trans Mexican Volcanic Belt, purple-North of the Isthmus of Tehuantepec, orange-South of the Isthmus of Tehuantepec) across geographic barriers along the Atlantic coast of Mexico. The phylogeny has Bayesian posterior values followed by bootstrap values with asterisks representing support of 95% or above. The Parsimony network values correspond to the haplotype values and are colored according by geographic locations separated by barriers; circle sizes correspond to the number of individuals with that haplotype (larger circles reflect more individuals), and black circles indicate unsampled haplotypes. The capital letters at the end of each sample represents the state of origin in Mexico, from North to South: NVL = Nuevo Leon, T = Tamaulipas, V = Veracruz, H = Hidalgo, Tb = Tabasco, C = Chiapas.

FIGURE 3 in Population level genetic divergence and phylogenetic placement of Mexican shortfin mollies (Mollienesia: Poecilia: Poeciliidae)

FIGURE 3 | Cytochrome b (1,140 bp) mitochondrial gene Bayesian phylogeny, parsimony haplotype network, and sampling distribution of Poecilia sphenops (aqua-Atlantic North of the Trans Mexican Volcanic Belt, pink- Balsas River Drainage, purple- Atlantic North of the Isthmus of Tehuantepec, red- Pacific North of the Isthmus of Tehuantepec, orange- Atlantic South of the Isthmus of Tehuantepec, and yellow- Pacific South of the Trans Mexican Volcanic Belt) across geographic barriers along the coasts of Mexico. The phylogeny has Bayesian posterior values followed by bootstrap values with asterisks representing support of 95% or above. The Parsimony network values correspond to the haplotype values and are colored according by geographic locations separated by barriers; circle sizes correspond to the number of individuals with that haplotype (larger circles reflect more individuals), and black circles indicate unsampled haplotypes. The capital letters at the end of each sample represents the state of origin in Mexico, from North to South: V = Veracruz, H = Hidalgo, M = Michoacan, G = Guerrero, O = Oaxaca, C = Chiapas.

FIGURE 4 in Population level genetic divergence and phylogenetic placement of Mexican shortfin mollies (Mollienesia: Poecilia: Poeciliidae)

FIGURE 4 | Cytochrome b (1,140 bp) mitochondrial gene Bayesian phylogeny, parsimony haplotype network, and sampling distribution of the Pacific sister taxa Poecilia butleri (blue-North of the Trans Mexican Volcanic Belt) and P. nelsoni (lime green-South of the Trans Mexican Volcanic Belt, pink- Balsas River Drainage, red- North of the Isthmus of Tehuantepec, and yellow- South of the Trans Mexican Volcanic Belt) across geographic barriers along the coast of Mexico. The phylogeny has Bayesian posterior values followed by bootstrap values with asterisks representing support of 95% or above. The Parsimony network values correspond to the haplotype values and are colored according by geographic locations separated by barriers; circle sizes correspond to the number of individuals with that haplotype (larger circles reflect more individuals), and black cirles indicate unsampled haplotypes. The capital letters at the end of each sample represents the state of origin in Mexico, from North to South: S = Sinaloa, N = Nayarit, J = Jalisco, Cl = Colima, M = Michoacan, G = Guerrero, O = Oaxaca, C = Chiapas.

FIGURE 1 in Population level genetic divergence and phylogenetic placement of Mexican shortfin mollies (Mollienesia: Poecilia: Poeciliidae)

FIGURE 1 | Sampling localities of species in the subgenus Mollienesia in Mexico and the main physiographic barriers throughout the country. The main physiographic barriers in Mexico from north to south are Northwestern Plains and Sierras, Sierra Madre Occidental, Sierra Madre Oriental, Gulf Coast Plain, Trans Mexican Volcanic Belt, Balsas Depression, Sierra Madre del Sur, Isthmus of Tehuantepec, and Sierra Madre de Chiapas.

FIGURE 2 in Population level genetic divergence and phylogenetic placement of Mexican shortfin mollies (Mollienesia: Poecilia: Poeciliidae)

FIGURE 2 | Bayesian tree from the MrBayes partitioned analysis of Poecilia spp. for two mitochondrial genes (Cyt b and ND2, 2187 base pairs) and one nuclear (RAG1, 1561 base pairs) rooted with other poeciliid outgroups. Species names in black pertain to species outside of Mexico and species names in red are species found within Mexico. Species labels represent slope: (A) = Atlantic, (P) = Pacific, and (B) = Bi-coastal. Nodal support shown (left to right; respectively): Bayesian Posterior Probabilities followed by RAxML bootstrap support values. Asterisks denote nodal support of 95% or above for the two methods, and a single asterisk at a node indicates support values of 95% or above for both methods. Nodes with no values present either had low values or were of little interest for this study. The capital letters at the end of each sample represents the state of origin in Mexico, from North to South: T = Tamaulipas, NVL = Nuevo León, V = Veracruz, H = Hidalgo, M = Michoacan, G = Guerrero, O = Oaxaca, Tb = Tabasco, C = Chiapas.

opencc-zeroAug 2021View details →

Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.

FIGURE 5 in The Mitochondrial Genome of Allonautilus (Mollusca: Cephalopoda): Base Composition, Noncoding-Region Variation, and Phylogenetic Divergence

FIGURE 5. Phylogenetic relationships among some cephalopod species (and their orders) based on mitochondrial DNA sequences. Parsimony phylogram is based on COX and ATPase genes for cephalopod species whose mitogenomes have been sequenced; Katharina tunicata was used as an outgroup (not shown). Bootstrap values are shown along branches.

FIGURE 2 in The Mitochondrial Genome of Allonautilus (Mollusca: Cephalopoda): Base Composition, Noncoding-Region Variation, and Phylogenetic Divergence

FIGURE 2. Arrangement of the mitogenome of Allonautilus scrobiculatus; the lengths of the individual genes are drawn approximately to scale. Genes encoding on the same strand as CO1 are shown (in white) on the outer portion of the circular genome and are transcribed in the clockwise direction. Genes on the other strand are transcribed in the counterclockwise direction and are indicated on the inner portion of the genome and shaded in blue; the nine largest noncoding regions (20 bp or greater) are shown in gray.

FIGURE 4 in The Mitochondrial Genome of Allonautilus (Mollusca: Cephalopoda): Base Composition, Noncoding-Region Variation, and Phylogenetic Divergence

FIGURE 4. Base composition of the major genes (excluding tRNAs) in the mitogenome of Allonautilus. Plusstrand (+) defined as the coding strand for CO1.

FIGURE 1 in The Mitochondrial Genome of Allonautilus (Mollusca: Cephalopoda): Base Composition, Noncoding-Region Variation, and Phylogenetic Divergence

FIGURE 1. Allonautilus differs from Nautilus in the size and shape of the umbilicus, type of periostracum, and texture of the hood (e.g., Saunders et al., 1987). A. Allonautilus scrobiculatus, Little Ndrova Island, Papua New Guinea, AMNH 101045. B. Nautilus macromphalus, New Caledonia, AMNH 94104.

FIGURE 3 in The Mitochondrial Genome of Allonautilus (Mollusca: Cephalopoda): Base Composition, Noncoding-Region Variation, and Phylogenetic Divergence

FIGURE 3. Architecture of the large noncoding region of extant nautilid mitogenomes. Features are shown for the strand on which CO1 is coded. Nautilus macromphalus (Boore, 2006) was characterized by a microsatellite, six copies of a 62 bp repeat (R1–R6), and a poly-T monomer; in Allonautilus, the microsatellite and first copy of the repeat were missing in one individual (indel pattern A), and an additional repeat was missing in two other individuals (indel pattern B); all individuals possessed the poly-T monomer (blue bar). The frequency of T and G nucleotides varied considerably through the noncoding region: their frequencies, in a 100 bp sliding window, are shown in the lower panel.

publicAug 2021View details →

Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

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publicDec 2019View details →

Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities

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opencc-zeroDec 2017View details →

Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)

With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element (UCE) data set (>3000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum-likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also result in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species-tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species-delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species-tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.

opencc-zeroApr 2022View details →

Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus

Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus Sebastes, which experienced an adaptive radiation between 3 to 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus Sebastosomus using over 11,600 SNPs. This reconstruction includes the two recently diverged species, Sebastes mystinus and S. diaconus, that were first described genetically in 2008 using mtDNA control region sequence data and six microsatellite loci. We confirmed the relationship of these cryptic species as sister-taxa and found evidence that S. melanops and S. flavidus were also sister-taxa. The latter contradicts prior studies but is supported by our reconstruction using nuclear DNA and measures of genetic differentiation tests and a discriminant analysis of principal components. The relationships between the species of Sebastosomus are further supported by morphological, biological, and ecological justifications.

zenodo36/100

Data from: Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis

<pre>Data from: Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis Author information Shizuka Koshimizu1, Naoki Minamino2, Tomoaki Nishiyama3, Emiko Yoro4, Mayuko Sato5, Mayumi Wakazaki5, Kiminori Toyooka5, Kazuo Ebine2,6, Keiko Sakakibara4, Takashi Ueda2,6, and Kentaro Yano1 1 School of Agriculture, Meiji University, Kawasaki 214-8571, Japan 2 Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki 444-8585, Japan 3 Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-0934, Japan 4 Department of Life Science, Rikkyo University, Tokyo 171‐8501, Japan 5 RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan 6 Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan This directory contains 0_README (this file) 1_Marchantia_FL_data 2_Physcomitrella_FL_data 3_Physcomitrella_TEM_images 4_PAML 1_Marchantia_FL_data Raw image data using quantification of spermatid phenotypes in Marchantia. quantification.xlsx: Summary of quantification data. 211111 and 211210: Observation date. ∟Mpbld10-1, Mpbld10-2, and Tak-1: Observed lines. ∟raw data: *.lsm files are raw image data. ∟binary image: *.tif files are binarization images of the Hoechst33342 data. ∟DIC: *.tif files are maximum intensity projection images of the C2 channels (detection of DIC images) of the raw data. ∟Hoechst33342: *.tif files are maximum intensity projection images of the C1 channels (detection of Hoechst33342 signals) of the raw data. 2_Physcomitrella_FL_data Merged data of DIC and Hoechst33342 signal images using quantification of spermatid phenotypes in Physcomitrella. line22-*.png: The images of Ppbld10-22 mutant. line30-*.png: The images of Ppbld10-30 mutant. wt.png: The images of wild type. Number in the images 1: With flagella 2: Without flagella 3_Physcomitrella_TEM_images TEM images of spermatids in the Ppbld10-30 mutant, except for images shown in Supporting Information Fig. S11. 4_PAML Files using analysis by PALM. input.fasta: Input multi fasta file. species_tree.nwk: The gene tree file for the global clock model (rooted using chlorophytes as an outgroup). species_tree_marked.nwk: A gene tree file with marks specifying land plant stem and crown branches as category #1 (for a local clock model). clock1: A directory containing output files of a PAML run with the global clock model (clock = 1) clock2: A directory containing output files of a PAML run with a local clock model (clock = 2). The branches assumed to have a different rate (r1) than the default rate r0 are specified with #1 in species_tree_marked.nwk.</pre>

opencc-by-4.0May 2022View details →

publicDec 2016View details →

Data from: Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis

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