scholarly journals Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas

2020 ◽  
Vol 37 (6) ◽  
pp. 1577-1592 ◽  
Author(s):  
XiaoYun Wang ◽  
Dan Liang ◽  
Wei Jin ◽  
MingKun Tang ◽  
Shalayiwu ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Evolutionary History ◽  
Middle Miocene ◽  
Divergence Time ◽  
Sister Group ◽  
Last Common Ancestor ◽  
Center Of Origin ◽  
History Of ◽  
Phylogenomic Analyses ◽  
Alpine Environments

Abstract Pikas are widely distributed in the Northern Hemisphere and are highly adapted to cold and alpine environments. They are one of the most complex and problematic groups in mammalian systematics, and the origin and evolutionary history of extant pikas remain controversial. In this study, we sequenced the whole coding sequences of 105 pika samples (29 named species and 1 putative new species) and obtained DNA data for more than 10,000 genes. Our phylogenomic analyses recognized four subgenera of extant pikas: Alienauroa, Conothoa, Ochotona, and Pika. The interrelationships between the four subgenera were strongly resolved as (Conothoa, (Alienauroa, (Ochotona, Pika))), with the mountain group Conothoa being the sister group of all other pikas. Our divergence time and phylogeographic analyses indicated that the last common ancestor of extant pikas first occurred on in the middle Miocene, ∼14 Ma. The emergence of opportunities related to the climate, food supply, and spreading paths in concert promoted the dispersal of pikas from the Qinghai-Tibetan Plateau (QTP) to other parts of Eurasia and North America. We found that the genes that were positively selected in the early evolution of pikas were most concentrated in functional categories related to cold tolerance. These results suggest that the QTP may have served as a training ground for cold tolerance in early pikas, which gives pikas a great advantage when the climate continued to cool after the middle Miocene. Our study highlights the importance of the QTP as a center of origin for many cold-adapted animals.

scholarly journals Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Time Estimation ◽  
Adjacent Region ◽  
Rapid Radiation ◽  
Divergence Time Estimation ◽  
Species Diversification ◽  
The Third ◽  
Evolutionary Line ◽  
History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

A new endemic family of New Zealand passerine birds: adding heat to a biodiversity hotspot

2007 ◽  
Vol 55 (2) ◽  
pp. 73 ◽  
Author(s):  
Amy Driskell ◽  
Les Christidis ◽  
B. J. Gill ◽  
Walter E. Boles ◽  
F. Keith Barker ◽  
...  
Keyword(s):  
New Zealand ◽  
Evolutionary History ◽  
Divergence Time ◽  
Biodiversity Hotspot ◽  
Passerine Birds ◽  
New Family ◽  
Close Relationship ◽  
History Of ◽  
Anthornis Melanura ◽  
Notiomystis Cincta

The results of phylogenetic analysis of two molecular datasets sampling all three endemic New Zealand ‘honeyeaters’ (Prosthemadera novaeseelandiae, Anthornis melanura and Notiomystis cincta) are reported. The undisputed relatedness of the first two species to other honeyeaters (Meliphagidae), and a close relationship between them, are demonstrated. However, our results confirm that Notiomystis is not a honeyeater, but is instead most closely related to the Callaeidae (New Zealand wattlebirds) represented by Philesturnus carunculatus in our study. An estimated divergence time for Notiomystis and Philesturnus of 33.8 mya (Oligocene) suggests a very long evolutionary history of this clade in New Zealand. As a taxonomic interpretation of these data we place Notiomystis in a new family of its own which takes the name Notiomystidae. We expect this new phylogenetic and taxonomic information to assist policy decisions for the conservation of this rare bird.

Wood anatomy of the Mascarene Dombeyoideae: Systematic and ecological implications

IAWA Journal ◽  
2011 ◽  
Vol 32 (4) ◽  
pp. 493-519 ◽  
Author(s):  
Anaïs Boura ◽  
Timothée Le Péchon ◽  
Romain Thomas
Keyword(s):  
Evolutionary History ◽  
Wood Anatomy ◽  
Sister Group ◽  
Biological Data ◽  
Sister Group Relationship ◽  
Anatomical Features ◽  
Ecological Implications ◽  
History Of ◽  
Mascarene Islands ◽  
Almost All

The Dombeyoideae (Malvaceae) are one of the most diversified groups of plants in the Mascarene Islands. Species of Dombeya Cav., Ruizia Cav. and Trochetia DC. are distributed in almost all parts of the archipelago and show a wide diversity in their growth forms. This study provides the first wood anatomical descriptions of 17 out of the 22 Mascarene species of Dombeyoideae. Their wood anatomy is similar to that of previously described species: wide vessels, presence of both apotracheal and paratracheal parenchyma, and storied structure. In addition, we also found a second wood anatomical pattern with narrower vessels, high vessel frequency and thick-walled fibres. The two aforementioned wood patterns are considered in a phylogenetic context and used to trace the evolutionary history of several wood anatomical features. For example, the pseudoscalariform pit arrangement supports a sister group relationship between Trochetia granulata Cordem. and T. blackburniana Bojer ex Baker and may be a new synapomorphy of the genus Trochetia. Finally, wood variability is evaluated in relation to geographic, climatic and biological data. Despite the juvenile nature of some of the specimens studied, we discuss how the habit, but also factors related to humidity, influence the variability observed in the Mascarene Dombeyoideae wood structure.

scholarly journals Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo Micolino ◽  
Maykon Passos Cristiano ◽  
Natália Martins Travenzoli ◽  
Denilce Meneses Lopes ◽  
Danon Clemes Cardoso
Keyword(s):  
Evolutionary History ◽  
Chromosomal Rearrangements ◽  
Atlantic Coast ◽  
Ecological Impact ◽  
Divergence Time ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Integrative Approach ◽  
Most Recent Common Ancestor ◽  
History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

Human Evolution

1984 ◽  
Vol 8 ◽  
pp. 182-198
Author(s):  
Catherine Badgley
Keyword(s):  
Human Evolution ◽  
Evolutionary History ◽  
Pan Paniscus ◽  
Homo Sapiens ◽  
Great Apes ◽  
Sister Group ◽  
The Family ◽  
History Of ◽  
Living Species ◽  
Single Living

The evolutionary history of humans is well understood in outline, compared to that of many other groups of mammals. But human evolution remains enigmatic in its details, and these are compelling both scientifically and personally because they relate to the biological uniqueness of humans. Humans are placed in the primate family Hominidae, which, in traditional classifications, contains a single living species, Homo sapiens. The closest living relatives of humans are great apes: the chimpanzees Pan paniscus and Pan troglodytes, the gorilla Gorilla gorilla, and the orangutan Pongo pygmaeus. These apes have traditionally been placed in the family Pongidae as the sister group of Hominidae. Living Hominidae and Pongidae, together with Hylobatidae (gibbons) comprise the modern representatives of the primate suborder Hominoidea.

scholarly journals Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 70 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Nigel French
Keyword(s):  
Evolutionary History ◽  
State Of The Art ◽  
Molecular Techniques ◽  
Evolutionary Significance ◽  
Phylogenetic Structure ◽  
Bayesian Approaches ◽  
Phylogenetic Studies ◽  
Anchored Phylogenomics ◽  
History Of ◽  
Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

scholarly journals The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

2012 ◽  
Vol 279 (1736) ◽  
pp. 2246-2254 ◽  
Author(s):  
Fabien Burki ◽  
Noriko Okamoto ◽  
Jean-François Pombert ◽  
Patrick J. Keeling
Keyword(s):  
Evolutionary History ◽  
Expressed Sequence Tag ◽  
Level Data ◽  
Guillardia Theta ◽  
History Of ◽  
The Common ◽  
Genome Level ◽  
Phylogenomic Analyses ◽  
New Hypothesis ◽  
Expressed Sequence

An important missing piece in the puzzle of how plastids spread across the eukaryotic tree of life is a robust evolutionary framework for the host lineages. Four assemblages are known to harbour plastids derived from red algae and, according to the controversial chromalveolate hypothesis, these all share a common ancestry. Phylogenomic analyses have consistently shown that stramenopiles and alveolates are closely related, but haptophytes and cryptophytes remain contentious; they have been proposed to branch together with several heterotrophic groups in the newly erected Hacrobia. Here, we tested this question by producing a large expressed sequence tag dataset for the katablepharid Roombia truncata , one of the last hacrobian lineages for which genome-level data are unavailable, and combined this dataset with the recently completed genome of the cryptophyte Guillardia theta to build an alignment composed of 258 genes. Our analyses strongly support haptophytes as sister to the SAR group, possibly together with telonemids and centrohelids. We also confirmed the common origin of katablepharids and cryptophytes, but these lineages were not related to other hacrobians; instead, they branch with plants. Our study resolves the evolutionary position of haptophytes, an ecologically critical component of the oceans, and proposes a new hypothesis for the origin of cryptophytes.

scholarly journals Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

2013 ◽  
Vol 11 (2) ◽  
pp. 319-326 ◽  
Author(s):  
Alexandre C. Ribeiro ◽  
Rodrigo M. Jacob ◽  
Ronnayana R. S. R. Silva ◽  
Flávio C. T. Lima ◽  
Daniela C. Ferreira ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Evolutionary History ◽  
Distribution Patterns ◽  
Sister Group ◽  
Freshwater Fishes ◽  
Drainage Basins ◽  
Vicariant Event ◽  
Shared History ◽  
History Of ◽  
Pantanal Wetland

The analysis of the distribution patterns presented by examples of freshwater fishes restricted to headwater habitat: the anostomid Leporinus octomaculatus, the characins Jubiaba acanthogaster, Oligosarcus perdido, Moenkhausia cosmops, Knodus chapadae, Planaltina sp., the loricariid Hypostomus cochliodon, and the auchenipterid Centromochlus sp. provided evidences of a relatively recent shared history between the highlands of the upper rio Paraguay and adjoining upland drainage basins. Restricted to headwater of the uplands in the upper rio Paraguay and adjoining basins, these species provide biological evidence of the former extension of the central Brazilian plateau before the origin of the Pantanal Wetland. Disjunction took place due to an ecological barrier to these rheophilic taxa represented tectonic subsidence related to the origin of the Pantanal Wetland. Molecular analysis of Jubiaba acanthogaster revealed that the sample from the upper rio Xingu basin are the sister-group of a clade that includes samples from the upper rio Arinos (upper rio Tapajós) plus the upper rio Paraguay basin, supporting the assumption that the origin of the upper rio Paraguay basin causing vicariance between this basin and the upper rio Tapajós is the least vicariant event in the evolutionary history of the group.

Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

2017 ◽  
Vol 31 (6) ◽  
pp. 765 ◽  
Author(s):  
Phillip Barden ◽  
Brendon Boudinot ◽  
Andrea Lucky
Keyword(s):  
Evolutionary History ◽  
Morphological Evolution ◽  
Sister Group ◽  
Morphological Characters ◽  
Fossil Material ◽  
First Case ◽  
History Of ◽  
The Impact ◽  
Surprising Discovery

The distinctive ant genus Leptomyrmex Mayr, 1862 had been thought to be endemic to Australasia for over 150 years, but enigmatic Neotropical fossils have challenged this view for decades. The present study responds to a recent and surprising discovery of extant Leptomyrmex species in Brazil with a thorough evaluation of the Dominican Republic fossil material, which dates to the Miocene. In the first case study of direct fossil inclusion within Formicidae Latreille, 1809, we incorporated both living and the extinct Leptomyrmex species. Through simultaneous analysis of molecular and morphological characters in both Bayesian and parsimony frameworks, we recovered the fossil taxon as sister-group to extant Leptomyrmex in Brazil while considering the influence of taxonomic and character sampling on inferred hypotheses relating to tree topology, biogeography and morphological evolution. We also identified potential loss of signal in the binning of morphological characters and tested the impact of parameterisation on divergence date estimation. Our results highlight the importance of securing sufficient taxon sampling for extant lineages when incorporating fossils and underscore the utility of diverse character sources in accurate placement of fossil terminals. Specifically, we find that fossil placement in this group is influenced by the inclusion of male-based characters and the newly discovered Neotropical ‘Lazarus taxon’.

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