scholarly journals Molecular Phylogeny and Historical Biogeography of the Butterfly Tribe Aeromachini Tutt (Lepidoptera: Hesperiidae) from China

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 294 ◽  
Author(s):  
Yuanyuan Li ◽  
Jianqing Zhu ◽  
Chen Ge ◽  
Ying Wang ◽  
Zimiao Zhao ◽  
...  
Keyword(s):  
Divergence Time ◽  
Strong Support ◽  
Distribution Patterns ◽  
Historical Biogeography ◽  
Central China ◽  
Ancestral Area ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Extant Species ◽  
Dispersal Events

: The butterfly tribe Aeromachini Tutt, 1906 is a large group of skippers. In this study, a total of 10 genera and 45 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2093 bp). The combined dataset was analyzed with maximum likelihood inference using IQtree. We found strong support for monophyly of Aeromachini from China and support for the most recent accepted species in the tribe. Two paraphyletic genera within Aeromachini are presented and discussed. The divergence time estimates with BEAST and ancestral-area reconstructions with RASP provide a detailed description about the historical biogeography of the Aeromachini from China. The tribe very likely originated from the Hengduan Mountains in the late Ecocene and expanded to the Himalaya Mountains and Central China Regions. A dispersal-vicariance analysis suggests that dispersal events have played essential roles in the distribution of extant species, and geological and climatic changes have been important factors driving current distribution patterns.

scholarly journals Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2696 ◽  
Author(s):  
Victoria Sosa ◽  
Juan Francisco Ornelas ◽  
Santiago Ramírez-Barahona ◽  
Etelvina Gándara
Keyword(s):  
Cloud Forest ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Phenotypic Traits ◽  
Cloud Forests ◽  
Altitudinal Distribution ◽  
Ancestral Area ◽  
Divergence Time Estimates ◽  
Tree Ferns ◽  
Extant Species

BackgroundCloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remainedin situor expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence.MethodsHere we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences.ResultsBayesian trees retrievedCyathea, Alsophyla, GymnosphaeraandSphaeropterisin monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except forGymnosphaerathat was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations.ConclusionsOur data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors.

scholarly journals Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera

AoB Plants ◽  
2016 ◽  
Vol 8 ◽  
pp. plw041 ◽  
Author(s):  
Qin-Qin Li ◽  
Song-Dong Zhou ◽  
De-Qing Huang ◽  
Xing-Jin He ◽  
Xian-Qin Wei
Keyword(s):  
Molecular Phylogeny ◽  
Divergence Time ◽  
Historical Biogeography ◽  
Divergence Time Estimates ◽  
Time Estimates

scholarly journals Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae)

2020 ◽  
Author(s):  
Sebastián Escobar ◽  
Andrew J. Helmstetter ◽  
Rommel Montúfar ◽  
Thomas L. P. Couvreur ◽  
Henrik Balslev
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Historical Biogeography ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Early Diversification ◽  
Time Calibration ◽  
Vegetable Ivory ◽  
Andean Uplift ◽  
Magdalena River

AbstractThe vegetable ivory palms (Phytelepheae) form a small group of Neotropical palms whose phylogenetic relationships are not fully understood. Three genera and eight species are currently recognized; however, it has been suggested that Phytelephas macrocarpa could include the species Phytelephas seemannii and Phytelephas schottii because of supposed phylogenetic relatedness and similar morphology. We inferred their phylogenetic relationships and divergence time estimates using the 32 most clock-like loci of a custom palm bait-kit formed by 176 genes and four fossils for time calibration. We additionally explored the historical biogeography of the tribe under the recovered phylogenetic relationships. Our fossil-dated tree showed the eight species previously recognized, and that P. macrocarpa is not closely related to P. seemanii and P. schottii, which, as a consequence, should not be included in P. macrocarpa. The ancestor of the vegetable ivory palms was widely-distributed in the Chocó, the inter-Andean valley of the Magdalena River, and the Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma can be attributed to trans-Andean vicariance between the Chocó/Magdalena and the Amazonia. Our results support the role of Andean uplift in the early diversification of Phytelephas under new phylogenetic relationships inferred from genomic data.

Molecular phylogeny and historical biogeography of the cosmopolitan parasitic wasp subfamily Doryctinae (Hymenoptera:Braconidae)

2008 ◽  
Vol 22 (3) ◽  
pp. 345 ◽  
Author(s):  
Alejandro Zaldivar-Riverón ◽  
Sergey A. Belokobylskij ◽  
Virginia León-Regagnon ◽  
Rosa Briceño-G. ◽  
Donald L. J. Quicke
Keyword(s):  
Sequence Data ◽  
Parasitic Wasp ◽  
Divergence Time ◽  
Molecular Dating ◽  
Cytochrome C Oxidase I ◽  
Mt Dna ◽  
Bayesian Analyses ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Dispersal Events

The phylogenetic relationships among representatives of 64 genera of the cosmopolitan parasitic wasps of the subfamily Doryctinae were investigated based on nuclear 28S ribosomal (r) DNA (~650 bp of the D2–3 region) and cytochrome c oxidase I (COI) mitochondrial (mt) DNA (603 bp) sequence data. The molecular dating of selected clades and the biogeography of the subfamily were also inferred. The partitioned Bayesian analyses did not recover a monophyletic Doryctinae, though the relationships involved were only weakly supported. Strong evidence was found for rejecting the monophylies of both Doryctes Haliday, 1836 and Spathius Nees, 1818. Our results also support the recognition of the Rhaconotini as a valid tribe. A dispersal–vicariance analysis showed a strong geographical signal for the taxa included, with molecular dating estimates for the origin of Doryctinae and its subsequent radiation both occurring during the late Paleocene–early Eocene. The divergence time estimates suggest that diversification in the subfamily could have in part occurred as a result of continental break-up events that took place in the southern hemisphere, though more recent dispersal events account for the current distribution of several widespread taxa.

scholarly journals Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

2021 ◽  
Author(s):  
David Černý ◽  
Rossy Natale
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Total Evidence ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Early Diversification ◽  
Extant Species ◽  
Tree Inference ◽  
The Impact

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been instrumental to resolving the suprafamilial backbone of the charadriiform tree, several higher-level relationships, including the monophyly of plovers (Charadriidae) and the phylogenetic positions of several monotypic families, have remained unclear. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 336 ingroup taxa (89\% of all extant species), 24 loci (15 mitochondrial and 9 nuclear), and 69 morphological characters. Using this phylogeny, we clarify the charadriiform evolutionary timeline by conducting a node-dating analysis based on a subset of 8 loci tested to be clock-like and 16 carefully selected, updated, and vetted fossil calibrations. Our concatenated, species-tree, and total-evidence analyses consistently support plover monophyly and are generally congruent with the topologies of previous studies, suggesting that the higher-level relationships among shorebirds are largely settled. However, several localized conflicts highlight areas of persistent uncertainty within the gulls (Laridae), true auks (Alcinae), and sandpipers (Scolopacidae). At shallower levels, our phylogenies reveal instances of genus-level nonmonophyly that suggest changes to currently accepted taxonomies. Our node-dating analyses consistently support a mid-Paleocene origin for the Charadriiformes and an early diversification for most major subclades. However, age estimates for more recent divergences vary between different relaxed clock models, and we demonstrate that this variation can affect phylogeny-based macroevolutionary studies. Our findings demonstrate the impact of fossil calibration choice on the resulting divergence time estimates, and the sensitivity of diversification rate analyses to the modeling assumptions made in time tree inference.

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 Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods

2012 ◽  
Vol 279 (1742) ◽  
pp. 3501-3509 ◽  
Author(s):  
Prashant P. Sharma ◽  
Gonzalo Giribet
Keyword(s):  
Late Cretaceous ◽  
Divergence Time ◽  
Disjunct Distribution ◽  
Continental Margins ◽  
Divergence Time Estimates ◽  
Evolutionary Origins ◽  
Source Regions ◽  
Time Estimates ◽  
Fiji Islands ◽  
The Pacific

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous ( ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

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