scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2020 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Time Estimation ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background : Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group. Conclusions : We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly ( D. teugelsi, D. fasciolatus ) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa’s continental ichthyofaunal communities.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2020 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Time Estimation ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background: Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution.Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group.Conclusions: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa’s continental ichthyofaunal communities.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2020 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Time Estimation ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background : Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group. Conclusions : We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly ( D. teugelsi, D. fasciolatus ) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa’s continental ichthyofaunal communities.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2019 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Time Estimation ◽  
Geographic Range ◽  
Molecular Dating ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background: Distichodus, the type genus of the endemic African characiform family Distichodontidae, is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group.Conclusions: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment ever conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies might be a consequence of deep coalescence and recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting acomplex scenario for the assemblage of Africa’s continental ichthyofaunal communities. Keywords: Distichodontidae, Distichodus, Congo Basin, molecular phylogeny, African fishes, geographic range evolution, molecular dating.

The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)

Zootaxa ◽  
2017 ◽  
Vol 4250 (6) ◽  
pp. 577 ◽  
Author(s):  
MICHAEL J. GHEDOTTI ◽  
MATTHEW P. DAVIS
Keyword(s):  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Species Group ◽  
Total Evidence ◽  
Morphological Data ◽  
Fossil Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
Extant Species

The fossils species †Fundulus detillae, †F. lariversi, and †F. nevadensis from localities in the western United States are represented by well-preserved material with date estimations. We combined morphological data for these fossil taxa with morphological and DNA-sequence data to conduct a phylogenetic analysis and a tip-based divergence-time estimation for the family Fundulidae. The resultant phylogeny is largely concordant with the prior total-evidence phylogeny. The fossil species do not form a monophyletic group, and do not represent a discrete western radiation of Fundulus as previously proposed. The genus Fundulus diverged into subgeneric clades likely in the Eocene or Oligocene (mean age 34.6 mya, 53–23 mya), and all subgeneric and most species-group clades had evolved by the middle Miocene. †Fundulus lariversi is a member of subgenus Fundulus in which all extant species are found only in eastern North America, demonstrating that fundulids had a complicated biogeographic history. We confirmed †Fundulus detillae as a member of the subgenus Plancterus. †F. nevadensis is not classified in a subgenus but likely is related to the subgenera Plancterus and Wileyichthys. 

scholarly journals Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

2022 ◽  
Vol 12 ◽  
Author(s):  
Chia-Lun Hsieh ◽  
Chih-Chieh Yu ◽  
Yu-Lan Huang ◽  
Kuo-Fang Chung
Keyword(s):  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Time Estimation ◽  
Nuclear Ribosomal Dna ◽  
Length Variation ◽  
Lineage Sorting ◽  
Divergence Time Estimation ◽  
Generic Delimitation ◽  
History Of

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae’s taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

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.

Molecular phylogeny, species delimitation and biogeographic history of the Stegana (Steganina) shirozui species group (Diptera: Drosophilidae) from East Asia

2020 ◽  
Author(s):  
Ya-Lian Wang ◽  
Jin-Ming Lu ◽  
Yuan Zhang ◽  
Hong-Wei Chen
Keyword(s):  
Molecular Phylogeny ◽  
East Asia ◽  
Species Delimitation ◽  
Time Estimation ◽  
Species Group ◽  
28S Rrna ◽  
West China ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
South West

Abstract The Stegana (Steganina) shirozui species group is mainly distributed in East Asia. In the present study, the molecular phylogeny of the S. shirozui group was investigated based on mitochondrial (COI and ND2) and nuclear (28S rRNA) markers. The resulting trees support the S. shirozui group as monophyletic and indicate that in this group, species associated with closer affinities show higher structural homogeneity in male genitalia. Molecular species delimitation assess most species limits and recognize four new species in the S. shirozui group from south-west China: S. alianya sp. nov., S. diodonta sp. nov., S. zebromyia sp. nov. and S. zopheria sp. nov. One new synonym was also recognized. Additionally, three typical male genital characters of the S. shirozui group were placed on the molecular phylogenetic framework. The outcome of both divergence-time estimation and ancestral area reconstruction suggests that the S. shirozui group likely originated in south-west China in the Middle Miocene.

Genetic Differentiation and Divergence Time of Chinese Parnassius (Lepidoptera: Papilionidae) Species Based on Nuclear Internal Transcribed Spacer (ITS) Sequence Data

2020 ◽  
Vol 55 (4) ◽  
pp. 520-546
Author(s):  
Chengcai Si ◽  
Keke Chen ◽  
Ruisong Tao ◽  
Chengyong Su ◽  
Junye Ma ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Differentiation ◽  
Species Identification ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Western China ◽  
Tibet Plateau ◽  
Divergence Time Estimation

Abstract Parnassius (Lepidoptera: Papilionidae) is a genus of attractive butterflies mainly distributed in the mountainous areas of Central Asia, the Himalayas, and western China. In this study, we used the internal transcribed spacer (ITS1 and ITS2) sequence data as DNA barcodes to characterize the genetic differentiation and conduct the phylogenetic analysis and divergence time estimation of the 17 Parnassius species collected in China. Species identification and genetic differentiation analysis suggest that the ITS barcode is an effective marker for Parnassius species identification; additionally, a relatively high level of genetic diversity and low level of gene flow were detected in the five Parnassius species with diverse geographic populations. Phylogenetic analysis indicates that the 17 species studied were clustered in six clades (subgenera), with subgenus Parnassius at the basal position in the phylogenetic trees. Bayesian divergence time estimation shows that the genus originated about 18 million years ago during the early Miocene, correlated with orogenic events in the distribution region, probably southwestern China about 20–10 million years ago. Our estimated phylochronology also suggests that the Parnassius interspecific and intraspecific divergences were probably related with the rapid rising of the Qinghai-Tibet Plateau, the Tibet Movement, the Kunlun-Yellow River Tectonic Movement, and global cooling associated with intensified glaciation in the region during the Quaternary Period.

Eritreo-Arabian Affinities of the Socotran Flora as Revealed from the Molecular Phylogeny of Aerva (Amaranthaceae)

2006 ◽  
Vol 31 (3) ◽  
pp. 560-570 ◽  
Author(s):  
Mike Thiv ◽  
Mats Thulin ◽  
Norbert Kilian ◽  
H. Peter Linder
Keyword(s):  
Indian Ocean ◽  
Sequence Data ◽  
Plastid Dna ◽  
Molecular Dating ◽  
Tropical Asia ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
Biogeographic History ◽  
History Of ◽  
Taxonomic Groups

We investigated the colonization of the Indian Ocean archipelago of Socotra through phylogenetic analysis of Aerva (Amaranthaceae) based on nuclear and plastid DNA sequence data. The biogeographic history of the genus was tracked using ancestral area reconstructions and molecular dating. Three independent colonization lineages from the Eritreo-Arabian subregion of the Sudano-Zambesian Region were revealed: one endemic clade comprising Aerva revoluta / A. microphylla and once within A. lanata and A. javanica. Our results provide further support for the dominance of Eritreo-Arabian affinities in the flora of Socotra, in contrast to more rare affinities to Madagascar, the Mascarenes, southern Africa, and tropical Asia. Our data point towards colonization via dispersal, rather than a vicariance origin of the island elements. The overall biogeographic patterns of Aerva show only limited concordance with other taxonomic groups distributed on Indian Ocean islands.

scholarly journals The Biogeography of Dromiciops in Southern South America: middle Miocene transgressions, speciation and associations with Nothofagus

2020 ◽  
Author(s):  
Julian F. Quintero-Galvis ◽  
Pablo Saenz-Agudelo ◽  
Juan L. Celis-Diez ◽  
Guillermo C. Amico ◽  
Soledad Vazquez ◽  
...  
Keyword(s):  
South America ◽  
Middle Miocene ◽  
Nuclear Dna ◽  
Divergence Time ◽  
Time Estimation ◽  
Southern South America ◽  
Divergence Time Estimation ◽  
Fossil Calibration ◽  
Biogeographic History ◽  
Climatic Optimum

AbstractAimSeveral geological events affecting Southern South America during the middle Miocene climatic optimum acted as important drivers of diversification to the biota. This is the case of Microbiotheria, for which Dromiciops is considered the sole surviving lineage, the sister group of Eomarsupialia (Australian marsupials). Three main Dromiciops genetic lineages are known, whose divergence was initially attributed to recent Pleistocene glaciations. Using fossil-calibrated dating on nuclear and mitochondrial genes, here we reevaluate this hypothesis and report an older (Miocenic) biogeographic history for the genus.LocationSouthern South America.MethodsPhylogenetic reconstruction using sequences from two mitochondrial DNA and four nuclear DNA genes in 159 specimens, from 31 sites across Chile and Argentina. Divergence time estimation using fossil calibration.ResultsOur phylogenetic analysis resolved four well supported clades with discrete geographic distributions. The oldest and most differentiated clade corresponds to that of the northern distribution (35.2°S to 39.3°S), which would be a different species (D. bozinovici, sensu D’elia et al. 2016). According to our estimations, this species shared a common ancestor with D. gliroides (southern clades) about 13 million years ago (95% CI: 6.4-25.3). The southern clades (39.6°S to 42.0°S), showed a divergence time ranging from 9.57 to 6.5 Mya. Strong genetic structure was detected from north to south but not across the Andes, or between Chiloé island/ mainland. Demographic equilibrium is inferred to the northern clade, and recent demographic expansions was detected in the central and southern clades.Main conclusionsThe whole diversification of Dromiciops occurred within the Miocene, being the Middle Miocene transgression (MMT), the massive marine flooding that covered several lowlands of the western face of los Andes between 38-48° S, the most likely diversifying force. This was the result of an increase in global sea levels due to the Miocene climatic optimum, which shaped the biogeographic origin of several species, including Nothofagus forests, the habitat main of Dromiciops.

Sign in / Sign up

Export Citation Format

Share Document