scholarly journals Mountains as Islands: Species Delimitation and Evolutionary History of the Ant-Loving Beetle Genus Panabachia (Coleoptera, Staphylinidae) from the Northern Andes

Insects ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 64
Author(s):  
Sofía Muñoz-Tobar ◽  
Michael Caterino
Keyword(s):  
Species Delimitation ◽  
Divergence Time ◽  
Morphological Characters ◽  
Protein Coding ◽  
Widespread Species ◽  
Mitochondrial Coi ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Putative Species ◽  
History Of

The ant-loving beetle genus Panabachia Park 1942 is a poorly studied beetle lineage from the new world tropics. We recently collected Panabachia from several previously unrecorded locations in the páramo biome of the high Ecuadorian Andes, with males exhibiting great morphological variation in the distribution of the foveae and depressions in the pronotum, as well as aspects of the male genitalia. Here, we employ phylogenetic and species delimitation methods with mitochondrial (COI) and nuclear protein-coding (wingless) gene sequences to examine the concordance of morphological characters and geography with hypothesized species boundaries. Three methods of species delimitation (bPTP, GMYC and Stacey) were used to estimate the number of species, and divergence times between putative species using molecular clock calibration. Phylogenetic analysis revealed two parallel radiations, and species delimitation analyses suggest there are between 17 and 22 putative species. Based on clade support and concordance across species delimitation methods we hypothesize 17 distinct clusters, with allopatric speciation consistent with most geographic patterns. Additionally, a widespread species appears to be present in northern páramo sites, and some sister species sympatry may indicate other diversification processes have operated on certain lineages of Panabachia. Divergence time estimates suggest that Panabachia originated in the Miocene, but most species analyzed diverged during the Pliocene and Pleistocene (5.3–0.11 Mya), contemporaneous with the evolution of páramo plant species.

scholarly journals Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

2021 ◽  
pp. 1-28
Author(s):  
Yoshimasa Kumekawa ◽  
Haruka Fujimoto ◽  
Osamu Miura ◽  
Ryo Arakawa ◽  
Jun Yokoyama ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Ryukyu Archipelago ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

scholarly journals What drives results in Bayesian morphological clock analyses?

2017 ◽  
Author(s):  
Caroline Parins-Fukuchi ◽  
Joseph W. Brown
Keyword(s):  
Morphological Evolution ◽  
Divergence Time ◽  
Morphological Characters ◽  
Morphological Data ◽  
Divergence Times ◽  
High Profile ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Geological Information ◽  
Positive Effect

AbstractRecently, approaches that estimate species divergence times using fossil taxa and models of morphological evolution have exploded in popularity. These methods incorporate diverse biological and geological information to inform posterior reconstructions, and have been applied to several high-profile clades to positive effect. However, there are important examples where morphological data are misleading, resulting in unrealistic age estimates. While several studies have demonstrated that these approaches can be robust and internally consistent, the causes and limitations of these patterns remain unclear. In this study, we dissect signal in Bayesian dating analyses of three mammalian clades. For two of the three examples, we find that morphological characters provide little information regarding divergence times as compared to geological range information, with posterior estimates largely recapitulating those recovered under the prior. However, in the cetacean dataset, we find that morphological data do appreciably inform posterior divergence time estimates. We supplement these empirical analyses with a set of simulations designed to explore the efficiency and limitations of binary and 3-state character data in reconstructing node ages. Our results demonstrate areas of both strength and weakness for morphological clock analyses, and help to outline conditions under which they perform best and, conversely, when they should be eschewed in favour of purely geological approaches.

Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

2020 ◽  
Vol 84 (4) ◽  
pp. 317-330
Author(s):  
Francisco J. García-Cárdenas ◽  
Mónica Núñez-Flores ◽  
Pablo J. López-González
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

Phylogeny, historical biogeography and divergence time estimates of the genus Colophon Gray (Coleoptera : Lucanidae)

2014 ◽  
Vol 28 (3) ◽  
pp. 326 ◽  
Author(s):  
Angelika K. Switala ◽  
Catherine L. Sole ◽  
Clarke H. Scholtz
Keyword(s):  
Divergence Time ◽  
Cape Floristic Region ◽  
High Mountain ◽  
Western Cape ◽  
Mitochondrial Coi ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Phylogenetic Status ◽  
Early Paleocene ◽  
Molecular Dataset

The flightless Cape High-mountain stag beetle genus Colophon (Coleoptera: Lucanidae) is studied. All species are endemic to the Cape Floristic Region of the Western Cape, South Africa. The study aimed to determine the specific and phylogenetic status of the described species of Colophon and to determine the main factors driving their evolution by testing the hypothesis of a lowland origin. This was achieved by analysing the mitochondrial COI, 16S rRNA and nuclear CAD genes, using a maximum likelihood and Bayesian approach. Timing of key biogeographical events in the diversification of Colophon was estimated in BEAST. The combined molecular dataset supports the described species. High genetic divergence was found between the described taxa. The mean estimated divergence of the genus was mid-Cretaceous, with a split into two lineages during the early Paleocene to mid Eocene. Species divergence was shown to have occurred during mid to late Miocene. Most species of Colophon showed an allopatric distribution, although contact zones between geographically adjacent species are likely. Climate seems to be the main driving factor behind Colophon evolution and the hypothesis of a lowland origin appears to be supported.

scholarly journals Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

2020 ◽  
Author(s):  
Alexandre Hassanin ◽  
Géraldine Véron ◽  
Anne Ropiquet ◽  
Bettine Jansen van Vuuren ◽  
Alexis Lécu ◽  
...  
Keyword(s):  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Early Eocene Climatic Optimum ◽  
Time Estimates ◽  
History Of ◽  
Nucleotide Divergence ◽  
Final Alignment ◽  
Complete Mitochondrial Genomes

AbstractThe order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

scholarly journals Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8033
Author(s):  
Siuli Mitra ◽  
Vaishnavi Kunteepuram ◽  
Klaus-Peter Koepfli ◽  
Neha Mehra ◽  
Wajeeda Tabasum ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Divergence Time ◽  
Protein Coding ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Phylogenetic Implications ◽  
The Family

The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.

Evolutionary history of trypanosomes from South American caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes

Parasitology ◽  
2008 ◽  
Vol 136 (1) ◽  
pp. 55-65 ◽  
Author(s):  
L. B. VIOLA ◽  
R. S. ALMEIDA ◽  
R. C. FERREIRA ◽  
M. CAMPANER ◽  
C. S. A. TAKATA ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Ssu Rdna ◽  
Tsetse Flies ◽  
South American ◽  
Data Set ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
History Of ◽  
Brazilian Pantanal

SUMMARYIn this study, using a combined data set of SSU rDNA and gGAPDH gene sequences, we provide phylogenetic evidence that supports clustering of crocodilian trypanosomes from the Brazilian Caiman yacare (Alligatoridae) and Trypanosoma grayi, a species that circulates between African crocodiles (Crocodilydae) and tsetse flies. In a survey of trypanosomes in Caiman yacare from the Brazilian Pantanal, the prevalence of trypanosome infection was 35% as determined by microhaematocrit and haemoculture, and 9 cultures were obtained. The morphology of trypomastigotes from caiman blood and tissue imprints was compared with those described for other crocodilian trypanosomes. Differences in morphology and growth behaviour of caiman trypanosomes were corroborated by molecular polymorphism that revealed 2 genotypes. Eight isolates were ascribed to genotype Cay01 and 1 to genotype Cay02. Phylogenetic inferences based on concatenated SSU rDNA and gGAPDH sequences showed that caiman isolates are closely related to T. grayi, constituting a well-supported monophyletic assemblage (clade T. grayi). Divergence time estimates based on clade composition, and biogeographical and geological events were used to discuss the relationships between the evolutionary histories of crocodilian trypanosomes and their hosts.

scholarly journals Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments

2019 ◽  
Vol 95 (1) ◽  
pp. 49-64 ◽  
Author(s):  
Felipe Polivanov Ottoni ◽  
José L. O. Mattos ◽  
Axel M. Katz ◽  
Pedro H.N. Bragança
Keyword(s):  
Phylogenetic Analysis ◽  
Species Delimitation ◽  
Species Recognition ◽  
Mitochondrial Gene ◽  
Divergence Time ◽  
Morphological Characters ◽  
Species Group ◽  
Nucleotide Substitutions ◽  
Divergence Time Estimates ◽  
Late Neogene

Three distinct and independent molecular-based species delimitation analyses were performed among the species and populations included within theAustraloherosautranigroup, based on sequences of the mitochondrial gene Cytochrome b: a tree-based method proposed by Wiens and Penkrot (WP), a Character-based DNA Barcoding (CBB) and coalescent species delimitation method termed the Bayesian Implementation of the Poisson tree processes (bPTP). The congruence of WP and CBB delimited 11 independent lineages (species), while the bPTP delimited just nine lineages. We did not favour any of the methods, and we considered the possibility of two slightly variant scenarios. A time-calibrated phylogenetic analysis is proposed based on the predominant congruence of the results of these three species delimitation methods herein applied. The monophyly of theA.autranispecies group was highly supported with maximum node support value and diagnosed by 11 nucleotide substitutions. The sister clade of theA.autranispecies group is the clade comprisingA.sp. Timbé do Sul andA.minuano. The phylogenetic analysis supports three main clades within theA.autranispecies group, supported by maximum node support value, with the Southern Mata Atlântica clade as the most basal clade. Divergence time estimates indicate that the diversification of theAustraloherosoriginated during the early Neogene, but only in the late Neogene did the processes of diversification in the southeast and north regions occur. Diversification within theAustraloherosautranispecies group occurred synchronically for the three main clades during the beginning of the Quaternary. It is demonstrated that molecular characters are valuable tools for species recognition, particularly in speciose groups with inconspicuous or difficult to record morphological characters. The resulting phylogeny of theAustraloherosautranigroup is highly compatible with the geological and biogeographic scenarios proposed for the Neogene and Quarternary shaping of the extant river basins of eastern Brazil. Despite the origin of theA.autranigroup being dated to the late Miocene, species level diversification occurred in the Pleistocene and was probably driven by headwater capture events and sea-level fluctuations.

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