scholarly journals Low-Coverage Whole Genomes Reveal the Higher Phylogeny of Green Lacewings

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 857
Author(s):  
Yuyu Wang ◽  
Ruyue Zhang ◽  
Yunlong Ma ◽  
Jing Li ◽  
Fan Fan ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Sister Group ◽  
Data Matrix ◽  
Limited Sampling ◽  
Green Lacewings ◽  
Whole Genomes ◽  
History Of ◽  
Low Coverage ◽  
Cretaceous Period

Green lacewings are one of the largest families within Neuroptera and are widely distributed all over the world. Many species within this group are important natural predators that are widely used for the biological control of pests in agricultural ecosystems. Several proposed phylogenetic relationships among the three subfamilies of Chrysopidae have been extensively debated. To further understand the higher phylogeny as well as the evolutionary history of Chrysopidae, we newly sequenced and analyzed the low-coverage genomes of 5 species (Apochrysa matsumurae, Chrysopa pallens, Chrysoperla furcifera, Italochrysa pardalina, Nothochrysa sinica), representing 3 subfamilies of Chrysopidae. There are 2213 orthologs selected to reconstruct the phylogenetic tree. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches, based on different data matrices. All the results suggested that Chrysopinae were a monophyletic sister group to the branch Apochrysinae + Nothochrysinae. These results were completely supported, except by the concatenation analyses of the nt data matrix, which suggested that Apochrysinae were a sister group to Chrysopinae + Nothchrysinae. The different topology from the nt data matrix may have been caused by the limited sampling of Chrysopidae. The divergence time showed that Chrysopinae diverged from Apochrysinae + Nothochrysinae during the Early Cretaceous period (144–151 Ma), while Aporchrysinae diverged from Nothochrysinae around 117–133 Ma. These results will improve our understanding of the higher phylogeny of Chrysopidae and lay a foundation for the utilization of natural predators.

scholarly journals Reconstructing the evolutionary and ecological history of the sea skaters Halobates spp. (Heteroptera: Gerridae)

2015 ◽  
Author(s):  
Cristian Román Palacios ◽  
Daniela Moraga Lopez
Keyword(s):  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Open Water ◽  
Ecological Niches ◽  
Diversity Pattern ◽  
Ecological History ◽  
Independent Events ◽  
Starting Point ◽  
Pelagic Environment ◽  
History Of

The genus Halobates includes the only five insect species that have been successful in a pelagic marine environment. Different scenarios of independent colonization events of that environment have been proposed, considering the appearance of pelagic distribution in several non-sister clades in the phylogeny of the genus. In this paper, we aim to update the phylogenetic hypothesis under the criterion of Bayesian inference, calibrate a molecular clock using the only fossil described in the genus and also analyze the diversity pattern of the lineage since its divergence. High support values were found in the phylogenetic reconstruction, which tend to decrease with an increase of the distances from the root. Low supports for the most derived clades or relatively recent divergences cast doubt on the delimitation of some species. Although the divergence time for Halobates was estimated at 42.01 mya (± 8.13) the emergence of the lineage probably happened a few million years before, so the estimated time of divergence probably also marked the start of diversification of the marine lineages of this genus. Since divergence, the richness of genus showed continuous linear growth for approximately 24.4 my, when the lineages began to diversify more quickly with a significantly lower extinction rate.The colonization of the pelagic environment which occurred nearly 42 mya, could also have been the starting point of the colonization of the marine pelagic environment when changes in their morphology, physiology and behaviour enabled them to exploit novel ecological niches. Ancestors of pelagic marine insects probably inhabited areas close to the seacoast more than 41 mya ago. The ecological history of Halobates was probably not limited to a pair of open water colonization events as indicated by earlier proposals. We hypothesize instead that at least three independent events of open water colonization by Halobates species have occurred. In this sense, the ecological character of coastal or pelagic distribution is considered to be a homoplasic character without direct implications on the net diversification of Halobates.

scholarly journals An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

2019 ◽  
Vol 286 (1895) ◽  
pp. 20182076 ◽  
Author(s):  
Dominic A. Evangelista ◽  
Benjamin Wipfler ◽  
Olivier Béthoux ◽  
Alexander Donath ◽  
Mari Fujita ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Sister Group ◽  
Divergence Times ◽  
Sister Group Relationship ◽  
Time Analysis ◽  
The Social ◽  
History Of ◽  
Egg Care ◽  
Phylogenomic Study

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

scholarly journals Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data

2019 ◽  
Vol 20 (5) ◽  
pp. 1072 ◽  
Author(s):  
Yuyu Wang ◽  
Xiaofan Zhou ◽  
Liming Wang ◽  
Xingyue Liu ◽  
Ding Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Gene Selection ◽  
Homogeneous Model ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Data Matrix ◽  
Bootstrap Support ◽  
Heterogeneous Model ◽  
Phylogenomic Analyses ◽  
A Site

Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.

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 Using mitochondrial genomes to infer phylogenetic relationships among the oldest extant winged insects (Palaeoptera)

2017 ◽  
Author(s):  
Sereina Rutschmann ◽  
Ping Chen ◽  
Changfa Zhou ◽  
Michael T. Monaghan
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Data Matrix ◽  
Mitochondrial Genomes ◽  
Sampling Effort ◽  
Reconstruction Method ◽  
Marker Selection ◽  
Phylogenetic Resolution

AbstractPhylogenetic relationships among the basal orders of winged insects remain unclear, in particular the relationship of the Ephemeroptera (mayflies) and the Odonata (dragonflies and damselflies) with the Neoptera. Insect evolution is thought to have followed rapid divergence in the distant past and phylogenetic reconstruction may therefore be susceptible to problems of taxon sampling, choice of outgroup, marker selection, and tree reconstruction method. Here we newly sequenced three mitochondrial genomes representing the two most diverse families of the Ephemeroptera, one of which is a basal lineage of the order. We then used an additional 90 insect mitochondrial genomes to reconstruct their phylogeny using Bayesian and maximum likelihood approaches. Bayesian analysis supported a basal Odonata hypothesis, with Ephemeroptera as sister group to the remaining insects. This was only supported when using an optimized data matrix from which rogue taxa and terminals affected by long-branch attraction were removed. None of our analyses supported a basal Ephemeroptera hypothesis or Ephemeroptera + Odonata as monophyletic clade sister to other insects (i.e., the Palaeoptera hypothesis). Our newly sequenced mitochondrial genomes of Baetis rutilocylindratus, Cloeon dipterum, and Habrophlebiodes zijinensis had a complete set of protein coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Increased mayfly sampling, removal of problematic taxa, and a Bayesian phylogenetic framework were needed to infer phylogenetic relationships within the three ancient insect lineages of Odonata, Ephemeroptera, and Neoptera. Pruning of rogue taxa improved the number of supported nodes in all phylogenetic trees. Our results add to previous evidence for the Odonata hypothesis and indicate that the phylogenetic resolution of the basal insects can be resolved with more data and sampling effort.

scholarly journals Reconstructing the evolutionary and ecological history of the sea skaters Halobates spp. (Heteroptera: Gerridae)

2015 ◽  
Author(s):  
Cristian Román Palacios ◽  
Daniela Moraga Lopez
Keyword(s):  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Open Water ◽  
Ecological Niches ◽  
Diversity Pattern ◽  
Ecological History ◽  
Independent Events ◽  
Starting Point ◽  
Pelagic Environment ◽  
History Of

The genus Halobates includes the only five insect species that have been successful in a pelagic marine environment. Different scenarios of independent colonization events of that environment have been proposed, considering the appearance of pelagic distribution in several non-sister clades in the phylogeny of the genus. In this paper, we aim to update the phylogenetic hypothesis under the criterion of Bayesian inference, calibrate a molecular clock using the only fossil described in the genus and also analyze the diversity pattern of the lineage since its divergence. High support values were found in the phylogenetic reconstruction, which tend to decrease with an increase of the distances from the root. Low supports for the most derived clades or relatively recent divergences cast doubt on the delimitation of some species. Although the divergence time for Halobates was estimated at 42.01 mya (± 8.13) the emergence of the lineage probably happened a few million years before, so the estimated time of divergence probably also marked the start of diversification of the marine lineages of this genus. Since divergence, the richness of genus showed continuous linear growth for approximately 24.4 my, when the lineages began to diversify more quickly with a significantly lower extinction rate.The colonization of the pelagic environment which occurred nearly 42 mya, could also have been the starting point of the colonization of the marine pelagic environment when changes in their morphology, physiology and behaviour enabled them to exploit novel ecological niches. Ancestors of pelagic marine insects probably inhabited areas close to the seacoast more than 41 mya ago. The ecological history of Halobates was probably not limited to a pair of open water colonization events as indicated by earlier proposals. We hypothesize instead that at least three independent events of open water colonization by Halobates species have occurred. In this sense, the ecological character of coastal or pelagic distribution is considered to be a homoplasic character without direct implications on the net diversification of Halobates.

scholarly journals The phylogeny and taxonomic status of the Chlorocystini (sensu stricto) (Homoptera, Tibicinidae)

1995 ◽  
Vol 65 (4) ◽  
pp. 201-231 ◽  
Author(s):  
A.J. de Boer
Keyword(s):  
Computer Program ◽  
Computer Analysis ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Status ◽  
Sister Group ◽  
Sensu Stricto ◽  
Complete Data ◽  
Data Matrix ◽  
A Posteriori

The “Baeturia and related genera complex”, as defined earlier (De Boer, 1990) by shared aedeagal characters, is identified as the tribe Chlorocystini (sensu stricto). The Prasiini (sensu stricto) are identified as the sister group of the Chlorocystini (sensu stricto), while the genus Muda is recognized as the nearest outgroup. The phylogeny and biogeography of the sister group and outgroup is briefly discussed. Baeturia kuroiwae Matsumura is transferred to the genus Muda. A phylogenetic reconstruction of all 147 species of the Chlorocystini (sensu stricto) is presented, based on 154 characters and 409 character states. The computer program PAUP 3.1.1 (Swofford, 1993) was used for analysing the data; the genera Prasia and Muda were used as outgroups in this analysis. The results obtained from the computer analysis were slightly modified a posteriori, favouring some presumably phylogenetically important characters over strongly fluctuating ones. These final modifications were carried out with the aid of the computer program MacClade 3.0 (Maddison & Maddison, 1992). A complete data matrix and a list of characters and character states are given in an appendix; for descriptions and illustrations of these characters one is referred to previous publications.

scholarly journals Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160857 ◽  
Author(s):  
Sarah Lemer ◽  
Vanessa L. González ◽  
Rüdiger Bieler ◽  
Gonzalo Giribet
Keyword(s):  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
Sister Group ◽  
Data Matrix ◽  
Shell Microstructure ◽  
Bayesian Mixture Model ◽  
Bayesian Mixture ◽  
Exact Position ◽  
Adaptive Radiations ◽  
Basal Position

Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix ( Matrix 3 : 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.

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.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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