Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology

2021 ◽  
Vol 155 ◽  
pp. 107011
Author(s):  
Bruna Plese ◽  
Nathan James Kenny ◽  
Maria Eleonora Rossi ◽  
Paco Cárdenas ◽  
Astrid Schuster ◽  
...  
Keyword(s):  
Divergence Time ◽  
Genome Biology ◽  
Mitochondrial Evolution

Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽  
2009 ◽  
Vol 2107 (1) ◽  
pp. 41-52 ◽  
Author(s):  
CAROLINA M VOLOCH ◽  
PABLO R FREIRE ◽  
CLAUDIA A M RUSSO
Keyword(s):  
Fossil Record ◽  
Divergence Time ◽  
Penaeid Shrimp ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Global Clock ◽  
Late Tertiary ◽  
The Family ◽  
Molecular Studies ◽  
Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

scholarly journals Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 455
Author(s):  
Na Ra Jeong ◽  
Min Jee Kim ◽  
Sung-Soo Kim ◽  
Sei-Woong Choi ◽  
Iksoo Kim
Keyword(s):  
Phylogenetic Analysis ◽  
First Generation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Mitochondrial Coi ◽  
Feeding Type ◽  
Pine Trees ◽  
Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

scholarly journals Indirect identification of horizontal gene transfer

2021 ◽  
Vol 83 (1) ◽  
Author(s):  
David Schaller ◽  
Manuel Lafond ◽  
Peter F. Stadler ◽  
Nicolas Wieseke ◽  
Marc Hellmuth
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Polynomial Time ◽  
Divergence Time ◽  
Recognition Algorithm ◽  
Vertex Coloring ◽  
Implicit Methods ◽  
Colored Graphs ◽  
Wide Range ◽  
Complete Multipartite

AbstractSeveral implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question “how much information about all HGT events is contained in LDT graphs” with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

scholarly journals Unexpected larger distribution of paleogene stem-rollers (AVES, CORACII): new evidence from the Eocene of Patagonia, Argentina

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Federico J. Degrange ◽  
Diego Pol ◽  
Pablo Puerta ◽  
Peter Wilf
Keyword(s):  
Hind Limb ◽  
Divergence Time ◽  
First Record ◽  
Morphological Data ◽  
New Taxon ◽  
Early Eocene ◽  
Important Data ◽  
New Material ◽  
Holarctic Region ◽  
New Evidence

AbstractHere we present the first record of a stem-Coracii outside the Holarctic region, found in the early Eocene of Patagonia at the Laguna del Hunco locality. Ueekenkcoracias tambussiae gen. et sp. nov. consists of an incomplete right hind limb that presents the following combination of characters, characteristic of Coracii: relatively short and stout tibiotarsus, poorly developed crista cnemialis cranialis, short and wide tarsometatarsus, with the tuberositas m. tibialis cranialis located medially on the shaft, and curved and stout ungual phalanges. Although the presence of a rounded and conspicuous foramen vasculare distale and the trochlea metatarsi II strongly deflected medially resemble Primobucconidae, a fossil group only found in the Eocene of Europe and North America, our phylogenetic analysis indicates the new taxon is the basalmost known Coracii. The unexpected presence of a stem-Coracii in the Eocene of South America indicates that this clade had a more widespread distribution than previously hypothesized, already extending into the Southern Hemisphere by the early Eocene. Ueekenkcoracias tambussiae represents new evidence of the increasing diversity of stem lineages of birds in the Eocene. The new material provides novel morphological data for understanding the evolutionary origin and radiation of rollers and important data for estimates of the divergence time of the group.

scholarly journals Global phylogeography of a pantropical mangrove genus Rhizophora

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Koji Takayama ◽  
Yoichi Tateishi ◽  
Tadashi Kajita
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Dna ◽  
Divergence Time ◽  
Long Distance ◽  
F1 Hybrid ◽  
The Pacific ◽  
Comprehensive Picture ◽  
Dated Phylogeny ◽  
Stochastic Mapping ◽  
Historical Scenario

AbstractRhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.

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.

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