Editorial and retrospective 2008

Rieseberg, Loren H.; Vines, Tim; Kane, Nolan C.

doi:10.1111/j.1365-294x.2008.4032_1.x

Cited by 8 publications

(6 citation statements)

References 178 publications

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“…Mitochondrial genes have been widely used to characterize natural populations at the molecular level, mostly because of technical ease-of-use considerations such as clonality and high mutation rate (Galtier et al 2009). In particular, the DNA barcoding approach has stimulated the use of mitochondrial gene fragments, such as Cytochrome Oxidase 1 ( cox1 ).…”

Section: Introductionmentioning

confidence: 99%

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths

Marlétaz

Parco

Liu

et al. 2017

Genome Biology and Evolution

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The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.

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Section: Introductionmentioning

confidence: 99%

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths

Marlétaz

Parco

Liu

et al. 2017

Genome Biology and Evolution

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“…These characteristics, combined with the technical ease of collecting large amounts of sequence data that do not require phasing, make mtDNA the most popular marker for phylogeographic inquiry [2]–[5].…”

Section: Introductionmentioning

confidence: 99%

“…Little empirical evidence, however, supports the utility of multilocus sequence data for avian phylogeography [5]. For example, in a multi-locus study of the red-backed fairy wren ( Malurus melanocephalus ), 35 nuclear loci (almost 15,000 bp/individual) failed to recover phylogeographic structure which was readily recovered with only 467 bp of mtDNA [15].…”

Section: Introductionmentioning

confidence: 99%

Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila

Drovetski

Raković²,

Semenov

et al. 2014

PLoS ONE

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Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early - Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species.

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“…Until the end of the last glaciation period, lions were broadly distributed and roamed most parts of southern Europe, Asia, the Middle East, North America, northern part of South America, and sub-Saharan Africa (Coheleach 1982; Turner and Anton 1997; Bauer and Vander Merwe 2004; Werdelin and Lewis 2005). They were believed to have had the widest geographical distributions of any large terrestrial mammal in the late Pleistocene (Guthrie 1990; Kitchener 1991; Nowell and Jackson 1996; Sunquist and Sunquist 2002; Patterson 2004; Barnett et al 2009) before their disappearance as part of the end-Pleistocene megafaunal mass extinction (Martin and Steadman 1999). Today, wild lions are found only in some parts of sub-Saharan Africa and at one locality in India, where they are confined mainly to protected areas such as national parks and game reserves.…”

Section: Introductionmentioning

confidence: 99%

“…All Pleistocene and modern day lions have been assigned to the genus Panthera , but with little consensus about the extent of overlap in their distribution (Barnett et al 2009). Just like other big cats (e.g., leopard Panthera pardus , tiger P. tigris , jaguar P. onca, and snow leopard P. uncia ), the lion displays several distinct phenotypic variations in body size, skull characteristics, coat color and thickness, retention of juvenile spots, and the presence or absence of mane in males.…”

Section: Introductionmentioning

confidence: 99%

Dual phylogenetic origins ofNigerian lions (Panthera leo)

Tende

Bensch

Ottosson³

et al. 2014

Ecology and Evolution

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Lion fecal DNA extracts from four individuals each from Yankari Game Reserve and Kainji-Lake National Park (central northeast and west Nigeria, respectively) were Sanger-sequenced for the mitochondrial cytochrome b gene. The sequences were aligned against 61 lion reference sequences from other parts of Africa and India. The sequence data were analyzed further for the construction of phylogenetic trees using the maximum-likelihood approach to depict phylogenetic patterns of distribution among sequences. Our results show that Nigerian lions grouped together with lions from West and Central Africa. At the smaller geographical scale, lions from Kainji-Lake National Park in western Nigeria grouped with lions from Benin (located west of Nigeria), whereas lions from Yankari Game Reserve in central northeastern Nigeria grouped with the lion populations in Cameroon (located east of Nigeria). The finding that the two remaining lion populations in Nigeria have different phylogenetic origins is an important aspect to consider in future decisions regarding management and conservation of rapidly shrinking lion populations in West Africa.

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Editorial and retrospective 2008

Cited by 8 publications

References 178 publications

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths

Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila

Dual phylogenetic origins ofNigerian lions (Panthera leo)

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