Genome-wide ultraconserved elements resolve phylogenetic relationships and biogeographic history among Neotropical leaf-nosed bats in the genus Anoura (Phyllostomidae)

2021 ◽  
pp. 107356
Author(s):  
Camilo A. Calderón-Acevedo ◽  
Justin C. Bagley ◽  
Nathan Muchhala
Keyword(s):  
Phylogenetic Relationships ◽  
Ultraconserved Elements ◽  
Biogeographic History ◽  
Genome Wide

scholarly journals Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation

2018 ◽  
Vol 5 (6) ◽  
pp. 172125 ◽  
Author(s):  
Sean J. Buckley ◽  
Fabricius M. C. B. Domingos ◽  
Catherine R. M. Attard ◽  
Chris J. Brauer ◽  
Jonathan Sandoval-Castillo ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Biogeographic History ◽  
Genome Wide ◽  
Mitochondrial Data ◽  
Australian Continent ◽  
History Of ◽  
Arid Habitat ◽  
East West

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

scholarly journals Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

2015 ◽  
Vol 92 ◽  
pp. 140-146 ◽  
Author(s):  
Princess S. Gilbert ◽  
Jonathan Chang ◽  
Calvin Pan ◽  
Eric M. Sobel ◽  
Janet S. Sinsheimer ◽  
...  
Keyword(s):  
Gene Markers ◽  
Ultraconserved Elements ◽  
Genome Wide ◽  
Phylogenetic Informativeness

scholarly journals Early diversification and permeable species boundaries in the Mediterranean firs

2019 ◽  
Vol 125 (3) ◽  
pp. 495-507 ◽  
Author(s):  
Francisco Balao ◽  
María Teresa Lorenzo ◽  
José Manuel Sánchez-Robles ◽  
Ovidiu Paun ◽  
Juan Luis García-Castaño ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Taxonomic Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Early Diversification ◽  
Genome Wide ◽  
History Of ◽  
The Mediterranean ◽  
Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

2019 ◽  
Author(s):  
Daniel Vitales ◽  
Sònia Garcia ◽  
Steven Dodsworth
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Similarity ◽  
Information Source ◽  
Repeat Sequence ◽  
Combined Application ◽  
Novel Approach ◽  
Genome Wide ◽  
History Of ◽  
Sequence Similarities ◽  
Phylogenetic Method

AbstractA recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.

Phylogenetic relationships in the lizard genus Diplodactylus Gray and resurrection of Lucasium Wermuth (Gekkota, Diplodactylidae)

2007 ◽  
Vol 55 (3) ◽  
pp. 197 ◽  
Author(s):  
Paul M. Oliver ◽  
Mark N. Hutchinson ◽  
Steven J. B. Cooper
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Arid Zone ◽  
Sister Group ◽  
Molecular Data ◽  
The Other ◽  
Sister Group Relationship ◽  
Considerable Uncertainty ◽  
Biogeographic History ◽  
Species Groups

Diplodactylid geckos offer a model system for investigating the biogeographic history of Australia and adaptive radiations in the arid zone, but there is considerable uncertainty in the systematics of several key genera. We used sequence data from mitochondrial DNA to carry out a comprehensive analysis of phylogenetic relationships of geckos in the genus Diplodactylus. Parsimony and Bayesian analyses were highly concordant and allocated all species to one of two monophyletic clades, one comprising the species placed in the vittatus and conspicillatus species groups, the other comprising species placed in the stenodactylus and steindachneri species groups, plus D. byrnei, formerly in the vittatus group. The distinctness of these two clades is supported by external morphology of the digits, body and limb proportions, and osteology of the bones in the orbital region, and we use these characters to formally define the two clades as genera. We revive and expand the genus Lucasium for D. byrnei, D. steindachneri and the stenodactylus group, with the other species staying in a redefined Diplodactylus. The monotypic Rhynchoedura is distinct from Lucasium, although the Bayesian mtDNA analysis (but not parsimony) gives some support for a sister-group relationship between Lucasium and Rhynchoedura. Molecular data suggest that each of these clades represents a distinct radiation into semiarid and arid terrestrial habitats during the mid-Tertiary, well before the hypothesised Pliocene onset of major aridification.

scholarly journals Phylogenomics Based on Transcriptome Data Provides Evidence for the Internal Phylogenetic Relationships and Potential Terrestrial Evolutionary Genes of Lungfish

2021 ◽  
Vol 8 ◽  
Author(s):  
Linlin Zhao ◽  
Shouqiang Wang ◽  
Fangrui Lou ◽  
Tianxiang Gao ◽  
Zhiqiang Han
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Information ◽  
Divergence Time ◽  
Sister Group ◽  
Terrestrial Environment ◽  
Phylogenetic Structure ◽  
Terrestrial Vertebrates ◽  
Genome Wide ◽  
Crucial Information ◽  
Related Stress

The evolutionary relationships of lungfish can provide crucial information on the transition from Sarcopterygii to tetrapods. Phylogenomics is necessary to explore accurate internal phylogenetic relationships among all lungfish species. In the context of the lack of genome-wide genetic information for Protopterus amphibious, we are the first to systematically report the transcriptome of P. amphibius and these sequences can be used to enrich the genome-wide genetic information of lungfish. Meanwhile, we also found significant differences in the expression levels of 3,189 genes between the lung and heart of P. amphibious. Based on phylogenomics, 1,094 shared orthologous genes were identified and then applied to reconstruct the internal phylogenetic structure of lungfish species. The reconstructed phylogenetic relationships provide evidence that lungfish is the sister group of terrestrial vertebrates and that Neoceratodus forsteri is the most primitive lungfish. Moreover, the divergence time between the most primitive lungfish and other lungfish species is between 186.11 and 195.36 MYA. Finally, 43 protein metabolism-related, stress response-related, and skeletogenesis-related genes were found to have undergone positive selection and fast evolution in N. forsteri. We suspected that these genes possibly helped ancient fish adapt to the new terrestrial environment and ultimately contributed to its spreading to land.

Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae)

2020 ◽  
Author(s):  
Jeffrey L Weinell ◽  
Anthony J Barley ◽  
Cameron D Siler ◽  
Nikolai L Orlov ◽  
Natalia B Ananjeva ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Oceanic Islands ◽  
Species Level ◽  
Boiga Irregularis ◽  
Brown Tree Snake ◽  
Biogeographic History ◽  
The Pacific ◽  
History Of ◽  
Dispersal Events

Abstract The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in South-East Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian extinctions on small islands of the Pacific), species-level phylogenetic relationships and the biogeographic history of this ecologically and morphologically distinct clade are poorly understood. In this study, we sequenced mitochondrial and nuclear DNA for 24 Boiga species and used these data to estimate a robust phylogenetic inference, in order to (1) test the hypothesis that Boiga is monophyletic, (2) evaluate the validity of current species-level taxonomy and (3) examine whether geographic range evolution in Boiga is consistent with expectations concerning dispersal and colonization of vertebrates between continents and islands. Our results support the prevailing view that most dispersal events are downstream – from continents to oceanic islands – but we also identify a role for upstream dispersal from oceanic islands to continents. Additionally, the novel phylogeny of Boiga presented here is informative for updating species-level taxonomy within the genus.

scholarly journals Phylogenetic relationships and biogeographic history of the unique Saxifraga sect. Irregulares (Saxifragaceae) from eastern Asia

2019 ◽  
Vol 58 (6) ◽  
pp. 958-971 ◽  
Author(s):  
Meng‐Hua Zhang ◽  
Chao‐Yong Wang ◽  
Cheng Zhang ◽  
Dai‐Gui Zhang ◽  
Ke‐Gang Li ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Eastern Asia ◽  
Biogeographic History ◽  
History Of

scholarly journals Genome-wide identification and analysis of the basic leucine zipper (bZIP) transcription factor gene family in Ustilaginoidea virens

Genome ◽  
2017 ◽  
Vol 60 (12) ◽  
pp. 1051-1059 ◽  
Author(s):  
Weixiao Yin ◽  
Peng Cui ◽  
Wei Wei ◽  
Yang Lin ◽  
Chaoxi Luo
Keyword(s):  
Transcription Factor ◽  
Phylogenetic Relationships ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Pathogenic Fungi ◽  
Bzip Transcription Factor ◽  
Basic Leucine Zipper ◽  
Ustilaginoidea Virens ◽  
Infection Period ◽  
Genome Wide

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the largest and most diverse TF families widely distributed across the eukaryotes. The bZIP TF family plays an important role in growth, development, and response to abiotic or biotic stresses, which have been well characterized in plants, but not in plant pathogenic fungi. In this study, we performed genome-wide and systematic bioinformatics analysis of bZIP genes in the fungus Ustilaginoidea virens, the causal agent of rice false smut disease. We identified 28 bZIP family members in the U. virens genome by searching for the bZIP domain in predicted genes. The gene structures, motifs, and phylogenetic relationships were analyzed for bZIP genes in U. virens (UvbZIP). Together with bZIP proteins from two other fungi, the bZIP genes can be divided into eight groups according to their phylogenetic relationships. Based on RNA-Seq data, the expression profiles of UvbZIP genes at different infection stages were evaluated. Results showed that 17 UvbZIP genes were up-regulated during the infection period. Furthermore, 11 infection-related UvbZIP genes were investigated under H2O2 stress and the expression level of eight genes were changed, which confirmed their role in stress tolerance and pathogenicity. In summary, our genome-wide systematic characterization and expression analysis of UvbZIP genes provided insight into the molecular function of these genes in U. virens and provides a reference for other pathogens.

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