scholarly journals Technical Comment on “The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals”

Science ◽  
2013 ◽  
Vol 341 (6146) ◽  
pp. 613.2-613 ◽  
Author(s):  
Mark S. Springer ◽  
Robert W. Meredith ◽  
Emma C. Teeling ◽  
William J. Murphy
Keyword(s):  
Nucleotide Substitution ◽  
Phylogenetic Analyses ◽  
Placental Mammal ◽  
Divergence Times ◽  
Research Article ◽  
Early Paleocene

O’Leary et al. (Research Article, 8 February 2013, p. 662) examined mammalian relationships and divergence times and concluded that a single placental ancestor crossed the Cretaceous-Paleogene (K-Pg) boundary. This conclusion relies on phylogenetic analyses that fail to discriminate between homology and homoplasy and further implies virus-like rates of nucleotide substitution in early Paleocene placentals.

scholarly journals A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment

2020 ◽  
Author(s):  
Wenbin Zhou ◽  
John Soghigian ◽  
Qiu-yun (Jenny) Xiang
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Disjunct Distribution ◽  
Divergence Times ◽  
Target Enrichment ◽  
Sequencing Technologies ◽  
Duplication Events ◽  
The Witch ◽  
Phylogenomic Analyses

ABSTRACTTarget enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies, and the choice between methods is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms, especially in plants, where extensive genome duplication events may complicate phylogenomic analyses. Unfortunately, currently widely used pipelines for target enrichment data analysis do not have a vigorous procedure for remove paralogs in Hyb-Seq data. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian-eastern North American disjunct distribution. We compared these two methods side by side and developed a new pipeline (PPD) with a more vigorous removal of putative paralogs from Hyb-Seq data. The new pipeline considers both sequence similarity and heterozygous sites at each locus in identification of paralogous. We used our pipeline to construct robust datasets for comparison between methods and downstream analyses on the two genera. Our results demonstrated that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed significant differences between data from HybPiper and data from our new PPD pipeline, likely due to the error signals from the paralogous genes undetected by HybPiper, but trimmed by PPD. We found that phylogenies and divergence times estimated from our RAD-seq and Hyb-Seq-PPD were largely congruent. We highlight the importance of removal paralogs in enrichment data, and discuss the merits of RAD-seq and Hyb-Seq. Finally, phylogenetic analyses of RAD-seq and Hyb-Seq resulted in well-resolved species relationships, and revealed ancient introgression in both genera. Biogeographic analyses including fossil data revealed a complicated history of each genus involving multiple intercontinental dispersals and local extinctions in areas outside of the taxa’s modern ranges in both the Paleogene and Neogene. Our study demonstrates the value of additional steps for filtering paralogous gene content from Angiosperm 353 data, such as our new PPD pipeline described in this study. [RAD-seq, Hyb-Seq, paralogs, Castanea, Hamamelis, eastern Asia-eastern North America disjunction, biogeography, ancient introgression]

scholarly journals Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation

2015 ◽  
Vol 112 (20) ◽  
pp. 6407-6412 ◽  
Author(s):  
Akito Y. Kawahara ◽  
Jesse R. Barber
Keyword(s):  
Evolutionary History ◽  
Tactile Stimulation ◽  
Phylogenetic Analyses ◽  
Physical Contact ◽  
Divergence Times ◽  
Entire Group ◽  
Multigene Phylogeny ◽  
Late Oligocene ◽  
Entire Family ◽  
Big Brown Bats

The bat–moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18–14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.

scholarly journals Rapid morphological evolution in placental mammals post-dates the origin of the crown group

2019 ◽  
Vol 286 (1898) ◽  
pp. 20182418 ◽  
Author(s):  
Thomas J. D. Halliday ◽  
Mario dos Reis ◽  
Asif U. Tamuri ◽  
Henry Ferguson-Gow ◽  
Ziheng Yang ◽  
...  
Keyword(s):  
Fossil Record ◽  
Morphological Evolution ◽  
Relative Rate ◽  
Molecular Data ◽  
Placental Mammal ◽  
Dental Morphology ◽  
Crown Group ◽  
Rates Of Evolution ◽  
Early Paleocene ◽  
Molecular Evolutionary Rates

Resolving the timing and pattern of early placental mammal evolution has been confounded by conflict among divergence date estimates from interpretation of the fossil record and from molecular-clock dating studies. Despite both fossil occurrences and molecular sequences favouring a Cretaceous origin for Placentalia, no unambiguous Cretaceous placental mammal has been discovered. Investigating the differing patterns of evolution in morphological and molecular data reveals a possible explanation for this conflict. Here, we quantified the relationship between morphological and molecular rates of evolution. We show that, independent of divergence dates, morphological rates of evolution were slow relative to molecular evolution during the initial divergence of Placentalia, but substantially increased during the origination of the extant orders. The rapid radiation of placentals into a highly morphologically disparate Cenozoic fauna is thus not associated with the origin of Placentalia, but post-dates superordinal origins. These findings predict that early members of major placental groups may not be easily distinguishable from one another or from stem eutherians on the basis of skeleto-dental morphology. This result supports a Late Cretaceous origin of crown placentals with an ordinal-level adaptive radiation in the early Paleocene, with the high relative rate permitting rapid anatomical change without requiring unreasonably fast molecular evolutionary rates. The lack of definitive Cretaceous placental mammals may be a result of morphological similarity among stem and early crown eutherians, providing an avenue for reconciling the fossil record with molecular divergence estimates for Placentalia.

scholarly journals Notes, outline and divergence times of Basidiomycota

2019 ◽  
Vol 99 (1) ◽  
pp. 105-367 ◽  
Author(s):  
Mao-Qiang He ◽  
Rui-Lin Zhao ◽  
Kevin D. Hyde ◽  
Dominik Begerow ◽  
Martin Kemler ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Divergence Times ◽  
Sequence Information ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
The Family ◽  
Life Mode ◽  
Species Type ◽  
Phylogeny And Evolution

AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

scholarly journals The Brain and Inner Ear of the Early Paleocene “Condylarth” Carsioptychus coarctatus : Implications for Early Placental Mammal Neurosensory Biology and Behavior

2018 ◽  
Vol 302 (2) ◽  
pp. 306-324 ◽  
Author(s):  
Joe Cameron ◽  
Sarah L. Shelley ◽  
Thomas E. Williamson ◽  
Stephen L. Brusatte
Keyword(s):  
Inner Ear ◽  
Placental Mammal ◽  
Early Paleocene ◽  
And Behavior ◽  
The Brain

Cf. Wortmania from the early Paleocene of Montana and an evaluation of the fossil record of the initial diversification of the Taeniodonta (Mammalia)

2013 ◽  
Vol 50 (3) ◽  
pp. 341-354 ◽  
Author(s):  
William A. Clemens
Keyword(s):  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Future Research ◽  
San Juan ◽  
Local Fauna ◽  
San Juan Basin ◽  
The North ◽  
Early Paleocene ◽  
Land Mammal ◽  
Channel Deposits

The Garbani Channel deposits, part of the Tullock Formation exposed in northeastern Montana, have yielded a large sample of vertebrates that probably lived during the Puercan 3 North American Land Mammal Age (NALMA). Four fossils in this sample — three isolated teeth and a medial phalanx — document the presence of a stylinodontid taeniodont, cf. Wortmania. Discovery of cf. Wortmania in the Tullock Formation extends the documented range of taeniodonts during Puercan 3 approximately 500 miles (800 km) northward from the San Juan Basin, New Mexico. Evaluation of the oldest records of taeniodonts, from the Lancian, Puercan, and Torrejonian NALMAs, highlights biases warranting future research. Recent phylogenetic analyses that resulted in numerous ghost lineages indicate that the available fossil record is far from complete. They open the possibility that the origin and initial radiation of taeniodonts occurred in areas yet to be sampled and their first occurrences might reflect immigration of invasive species. The available fossil record of taeniodonts is biased with significantly more abundant and complete specimens discovered in the San Juan Basin than at localities to the north. This bias is also apparent in the available samples of two other lineages of large Puercan mammals, the multituberculate Taeniolabis and the “triisodontid” Eoconodon. Where they occur, taeniodonts are relatively rare members of any local fauna. Is their rarity a product of an ecological bias or a reflection of decreasing population size related to increasing body size?

Separation of monophyletic groups into distinct genera should consider phenotypic discontinuities: the case of Lasiurini (Chiroptera: Vespertilionidae)

Zootaxa ◽  
2018 ◽  
Vol 4379 (3) ◽  
pp. 439 ◽  
Author(s):  
ROBERTO LEONAN M. NOVAES ◽  
GUILHERME S. T. GARBINO ◽  
VINÍCIUS C. CLÁUDIO ◽  
RICARDO MORATELLI
Keyword(s):  
Scientific Community ◽  
Phylogenetic Analyses ◽  
Tree Topology ◽  
Divergence Times ◽  
Genus Level

Baird et al. (2015) split Lasiurus into three distinct genera (Aeorestes, Dasypterus and Lasiurus) based on tree topology and divergence times for the tribe Lasiurini. This arrangement has not been widely adopted by the scientific community and was criticized by Ziegler et al. (2016). More recently, Baird et al. (2017) reinforced the taxonomic arrangement of Lasiurini comprised by three genera. Baird et al. (2015, 2017) provided the most comprehensive phylogenetic analyses of Lasiurus and offer important insights on the phylogeny and alpha-taxonomy of the group. However, we disagree with the taxonomic arrangement proposed at the genus level and explain our point below. 

scholarly journals Biodiversity lost: The phylogenetic relationships of a complete mitochondrial DNA genome sequenced from the extinct wolf population of Sicily

2019 ◽  
Author(s):  
Stefano Reale ◽  
Ettore Randi ◽  
Floriana Bonanno ◽  
Valentina Cumbo ◽  
Ignazio Sammarco ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Canis Lupus ◽  
Southern Italy ◽  
Phylogenetic Analyses ◽  
Divergence Times ◽  
Wolf Population ◽  
Basal Clade ◽  
First Time ◽  
Generation Sequencing ◽  
Mtdna Haplogroup

AbstractUsing next-generation sequencing, we obtained for the first time a complete mitochondrial DNA genome from a museum specimen of the extinct wolf (Canis lupus) population of the island of Sicily (Italy). Phylogenetic analyses showed that this genome, which was aligned with a number of historical and extant complete wolf and dog mtDNAs sampled worldwide, was closely related to an Italian wolf mtDNA genome (TN93 and p-distances = 0.0012), five to seven times shorter than divergence among Sicilian and any other known wolf mtDNA genomes (distance range = 0.0050 – 0.0070). Sicilian and Italian haplotypes joined a basal clade belonging to the mtDNA haplogroup-2 of ancient western European wolf populations (Pilot et al. 2010). Bayesian calibration of divergence times indicated that this clade coalesced at MRCA = 13.400 years (with 95% HPD = 4000 – 21.230 years). These mtDNA findings suggest that wolves probably colonized Sicily from southern Italy towards the end of the last Pleistocene glacial maximum, when the Strait of Messina was almost totally dry. Additional mtDNA and genomic data will further clarify the origin and population dynamics before the extinction of wolves in Sicily.

scholarly journals The evolution of brain size among the Homininae and selection at ASPM and MCPH1 genes

2021 ◽  
Vol 2 (2) ◽  
pp. 293-310
Author(s):  
Sandra Leyva-Hernández ◽  
Ricardo Fong-Zazueta ◽  
Luis Medrano-González ◽  
Ana Julia Aguirre-Samudio
Keyword(s):  
Positive Selection ◽  
Nucleotide Substitution ◽  
Brain Size ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Brain Evolution ◽  
Haplotype Blocks ◽  
Accelerated Evolution ◽  
Relationship Of ◽  
The Brain

We examined the evolutionary relationship of the ASPM (abnormal spindle-like microcephaly associated) and MCPH1 (microcephalin-1) genes with brain volume among humans and other primates. We obtained sequences of these genes from 14 simiiform species including hominins. Two phylogenetic analyses of ASPM exon 3 and MCPH1 exons 8 and 11 were performed to maximize taxon sampling or sequence extension to compare the nucleotide substitution and encephalization rates, and examine signals of selection. Further assessment of selection among humans was done through the analysis of non-synonymous and synonymous substitutions (dN/dS), and linkage disequilibrium (LD) patterns. We found that the accelerated evolution of brain size in hominids, is related to synchronic acceleration in the substitution rates of ASPM and MCPH1, and to signals of positive selection, especially in hominins. The dN/dS and LD analyses in Homo detected sites under positive selection and some regions with haplotype blocks at several candidate sites surrounded by blocks in LD-equilibrium. Accelerations and signals of positive selection in ASPM and MCPH1 occurred in different lineages and periods being ASPM more closely related with the brain evolution of hominins. MCPH1 evolved under positive selection in different lineages of the Catarrhini, suggesting independent evolutionary roles of this gene among primates.

scholarly journals Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6864 ◽  
Author(s):  
Marshal Hedin ◽  
Shahan Derkarabetian ◽  
Adan Alfaro ◽  
Martín J. Ramírez ◽  
Jason E. Bond
Keyword(s):  
Species Diversity ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Divergence Times ◽  
Phylogenomic Analysis ◽  
Early Tertiary ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Probe Set

The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (MecicobothriumandHexurella)key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.

Sign in / Sign up

Export Citation Format

Share Document