Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)

Abstract Complete mitochondrial (mtDNA) genomes have proved to be useful in reconstructing primate phylogenies with higher resolution and confidence compared to reconstructions based on partial mtDNA sequences. Here, we analyse complete mtDNA genomes of African green monkeys (genus Chlorocebus), a widely distributed primate genus in Africa representing an interesting phylogeographical model for the evolution of savannah species. Previous studies on partial mtDNA sequences revealed nine major clades, suggesting several cases of para- and polyphyly among Chlorocebus species. However, in these studies, phylogenetic relationships among several clades were not resolved, and divergence times were not estimated. We analysed complete mtDNA genomes for ten Chlorocebus samples representing major mtDNA clades to find stronger statistical support in the phylogenetic reconstruction than in the previous studies and to estimate divergence times. Our results confirmed para- and polyphyletic relationships of most Chlorocebus species, while the support for the phylogenetic relationships between the mtDNA clades increased compared to the previous studies. Our results indicate an initial west–east division in the northern part of the Chlorocebus range with subsequent divergence into north-eastern and southern clades. This phylogeographic scenario contrasts with that for another widespread African savannah primate genus, the baboons (Papio), for which a dispersal from southern Africa into East and West Africa was suggested.

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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Scientific Reports ◽

10.1038/s41598-021-83664-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maria Alejandra Serna-Sánchez ◽

Oscar A. Pérez-Escobar ◽

Diego Bogarín ◽

María Fernanda Torres-Jimenez ◽

Astrid Catalina Alvarez-Yela ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Divergence Times ◽

Molecular Clocks ◽

Phylogenetic Placement ◽

Plastid Genomes ◽

Phylogenetic Reconstructions ◽

A Genome ◽

Tree Models ◽

Phylogenomic Analyses ◽

First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

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High Resolution Analysis and Phylogenetic Network Construction Using Complete mtDNA Sequences in Sardinian Genetic Isolates

Molecular Biology and Evolution ◽

10.1093/molbev/msl084 ◽

2006 ◽

Vol 23 (11) ◽

pp. 2101-2111 ◽

Cited By ~ 38

Author(s):

Cristina Fraumene ◽

Elise M. S. Belle ◽

Loredana Castrì ◽

Simona Sanna ◽

Gianmaria Mancosu ◽

...

Keyword(s):

High Resolution ◽

Phylogenetic Network ◽

Mtdna Sequences ◽

Network Construction ◽

High Resolution Analysis ◽

Resolution Analysis ◽

Genetic Isolates ◽

Complete Mtdna

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Handbook of African Languages: Part III. The Non-Bantu Languages of North-Eastern Africa. By A. N. Tucker and M. A. Bryan. With a Supplement on the Non-Bantu Languages of Southern Africa by E. O. J. Westphal. London: O.U.P. for International African Institute. 1956. Pp. xvi, 228, 2 maps. 42s.

Africa ◽

10.2307/1156644 ◽

1957 ◽

Vol 27 (3) ◽

pp. 297-300 ◽

Cited By ~ 1

Author(s):

G. W. B. Huntingford

Keyword(s):

Southern Africa ◽

Eastern Africa ◽

African Languages ◽

Bantu Languages ◽

North Eastern

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Phylogenetic Relationships and Divergence Times among Mustelids (Mammalia: Carnivora) Based on Nucleotide Sequences of the Nuclear Interphotoreceptor Retinoid Binding Protein and Mitochondrial CytochromebGenes

ZOOLOGICAL SCIENCE ◽

10.2108/zsj.20.243 ◽

2003 ◽

Vol 20 (2) ◽

pp. 243-264 ◽

Cited By ~ 87

Author(s):

Jun J. Sato ◽

Tetsuji Hosoda ◽

Mieczyłlaw Wolsan ◽

Kimiyuki Tsuchiya ◽

Masahiko Yamamoto ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Binding Protein ◽

Nucleotide Sequences ◽

Divergence Times ◽

Interphotoreceptor Retinoid Binding Protein

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Mitochondrial Genome Diversity in the Central Siberian Plateau with Particular Reference to Prehistory of Northernmost Eurasia

10.1101/656181 ◽

2019 ◽

Author(s):

S. V. Dryomov ◽

A. M. Nazhmidenova ◽

E. B. Starikovskaya ◽

S. A. Shalaurova ◽

N. Rohland ◽

...

Keyword(s):

Geographic Area ◽

Mtdna Sequences ◽

The Past ◽

South Central ◽

Sayan Region ◽

History Of ◽

Mitochondrial Genome Diversity ◽

The Last Glacial Maximum ◽

Complete Mtdna ◽

The Last Glacial

AbstractThe Central Siberian Plateau was last geographic area in Eurasia to become habitable by modern humans after the Last Glacial Maximum (LGM). Through comprehensive mitochondrial DNA genomes retained in indigenous Siberian populations, the Ket, Tofalar, and Todzhi - we explored genetic links between the Yenisei-Sayan region and Northeast Eurasia over the last 10,000 years. Accordingly, we generated 218 new complete mtDNA sequences and placed them into compound phylogenies along with 7 newly obtained and 70 published ancient mt genomes. Our findings reflect the origins and expansion history of mtDNA lineages that evolved in South-Central Siberia, as well as multiple phases of connections between this region and distant parts of Eurasia. Our result illustrates the importance of jointly sampling modern and prehistoric specimens to fully measure the past genetic diversity and to reconstruct the process of peopling of the high latitudes of the Siberian subcontinent.

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Phylogenetic relationships and estimation of divergence times among Sisoridae catfishes

Science China Life Sciences ◽

10.1007/s11427-012-4305-z ◽

2012 ◽

Vol 55 (4) ◽

pp. 312-320 ◽

Cited By ~ 6

Author(s):

MeiLing Yu ◽

ShunPing He

Keyword(s):

Phylogenetic Relationships ◽

Divergence Times

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Phylogenetic relationships of the tooth-carpAphanius(Teleostei: Cyprinodontidae) in the river systems of southern and south-western Iran based on mtDNA sequences

Zoology in the Middle East ◽

10.1080/09397140.2014.892329 ◽

2014 ◽

Vol 60 (1) ◽

pp. 29-38 ◽

Cited By ~ 11

Author(s):

Hamid Reza Esmaeili ◽

Azad Teimori ◽

Golnaz Sayyadzadeh ◽

Mojtaba Masoudi ◽

Bettina Reichenbacher

Keyword(s):

Phylogenetic Relationships ◽

Mtdna Sequences ◽

River Systems ◽

Western Iran

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A Sibling Species Group of Hydractinia in the North-Eastern United States

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315400032215 ◽

1989 ◽

Vol 69 (4) ◽

pp. 857-874 ◽

Cited By ~ 50

Author(s):

Leo W. Buss ◽

Philip O. Yund

Keyword(s):

United States ◽

Sibling Species ◽

Host Species ◽

Larval Dispersal ◽

Phylogenetic Reconstruction ◽

Species Group ◽

Eastern United States ◽

The North ◽

North Eastern ◽

Symbiotic Organisms

Many symbiotic organisms are narrowly distributed on one or a few host species. These associations are intriguing, as they invite the development of hypotheses regarding the pattern and process of speciation and serve as laboratories for the testing of methods of phylogenetic reconstruction (Kraus, 1978; Futuyma & Slatkin, 1983; Stone & Hawks worth, 1986). The evolution of host-specificity in the sea may be expected to be severely constrained by the difficulty of achieving reproductive isolation in taxa whose gametes are freely released into the water column and/or whose larvae are potentially widely distributed (Scheltema, 1977). Yet this difficulty may well be overestimated, given the recent demonstrations of limited gamete (Pennington, 1985; Yund, in press) and larval dispersal (Knight-Jones & Moyse, 1961; Ryland, 1981; Olsen, 1985; Jackson & Coates, 1986; Grosberg, 1987). Indeed, if gamete and larval dispersal are as limited as has recently been contended (Jackson, 1986), local isolation of populations may be a routine occurence, offering repeated opportunities for speciation.

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