Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus)

Heckman, Kellie L.; Mariani, Carol; Rasoloarison, Rodin M.; Yoder, Anne D.

doi:10.1016/j.ympev.2007.03.005

Cited by 69 publications

(74 citation statements)

References 79 publications

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“…Wolbachia infections can lead to divergent mitochondrial lineages within insect species (Smith et al 2012;Whitworth et al 2007), but this bacterial endoparasite has not yet been found in Chironomidae. Although other endosymbionts might cause similar patterns, we are not aware of such documentation in Chironomidae and regard incomplete lineage sorting (Ballard & Whitlock 2004;Heckman et al 2007;Willyard et al 2009) a better explanation for the observed differences in DNA barcodes.…”

Section: Dna Barcodes and Morphospeciesmentioning

confidence: 86%

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Stur

Ekrem

2018

Insect Syst. Evol.

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For over a decade, DNA barcoding has proven an effective modern tool in taxonomy, evolutionary biology and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. Using DNA barcodes, we uncovered a number of potential species within the Tanytarsus curticornis and Tanytarsus heusdensis species complexes (Diptera: Chironomidae) and detected morphological differences a posteriori that support the description of new species. Unusually large intraspecific divergence in COI p-distance (up to 10%) was observed for two species complexes. In total, eight species new to science are described and figured: T. adustus sp. n., T. heberti sp. n., T. madeiraensis sp. n., T. pseudoheusdensis sp. n., T. songi sp. n., T. thomasi sp. n., T. tongmuensis sp. n. and T. wangi sp. n.. Tanytarsus reei and T. tamaoctavus are redescribed, and T. tusimatneous is listed as a new junior synonym of T. tamaduodecimus. The diagnostic characters of the remaining species of the complexes are discussed. Keys to males and pupae are given.

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Section: Dna Barcodes and Morphospeciesmentioning

confidence: 86%

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Stur

Ekrem

2018

Insect Syst. Evol.

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“…Subsequently, all genes were analyzed in a combined data set in order to profit from the phylogenetic resolution provided in different parts of the tree by the separate data sets (Pereira et al, 2002;Heckman et al, 2007). Sequences of species of the hyloid genus Bufo as available from Genbank were used as outgroup.…”

Section: Methodsmentioning

confidence: 99%

“…Furthermore, the performances of the nuclear Rhodopsin and Tyrosinase fragments for reconstructing relationships among closely related amphibian species have not been subject to investigation yet. Assuming a relatively large ancestral population size, and taking into account the relatively young age of the hyperoliid radiation in Madagascar and the Seychelles, incomplete lineage sorting may be responsible for the partially different topologies obtained with these markers (Maddison, 1997;Heckman et al, 2007).…”

Section: Molecular Phylogeny Of Heterixalus and Tachycnemismentioning

confidence: 99%

Molecular phylogeny of Malagasy reed frogs, Heterixalus, and the relative performance of bioacoustics and color-patterns for resolving their systematics

Wollenberg

Glaw

Meyer

et al. 2007

Molecular Phylogenetics and Evolution

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The members of the genus Heterixalus constitute one of the endemic frog radiations in Madagascar. Here we present a complete spe cies level phylogeny based on DNA sequences (4876 base pairs) of three nuclear and four mitochondrial markers to clarify the phylo genetic relationships among and within all known species of this genus, as well as the phylogenetic position of the monospecific Seychellean Tachycnemis seychellensis. Although the performance to resolve supported clades of Heterixalus species differed among the investigated gene fragments when analyzed separately, we could identify five well supported species groups within Heterixalus in the combined analysis of all gene fragments. Our data strongly support a Heterixalus Tachycnemis clade, and indicate the probable monophyly of Heterixalus placed sister to Tachycnemis. However, the diversification of these lineages may have happened in a short interval of time, leading to an unstable placement of Tachycnemis in the single gene fragment phylogenies. Referring to the hitherto exist ing classification of Heterixalus, which is predominantly based on chromatic and bioacoustic characters, we examined the relative per formance of these data sets relative to our molecular phylogeny. A Bayesian tree reconstructed with a bioacoustic data set yielded a higher resemblance to the molecular phylogeny than a tree constructed using a chromatic data set, which supports the importance of bioacoustic characters for systematic analyses of these anurans.

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“…The coalescent process, which can lead to discordance between gene trees and species trees, has been extensively studied from both a theoretical [10,[17][18][19] and empirical [20][21][22] standpoint. It is known that there are extreme situations (the "anomaly zone") where the most common gene tree is discordant with the species tree [23].…”

Section: Introductionmentioning

confidence: 99%

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Patel

Kimball²,

Braun³

2013

Phylogenetics Evolutionary

104

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Many rapid radiations, or bushes, throughout the Tree of Life remain unresolved. Here, we investigated how the shape of a bush interacts with two key processes -coalescence and mutation -that can lead to errors in phylogenetic inference under specific conditions. For this study, we focused on the tradeoff between sampling more individuals per species and sampling more loci as well as the utility of a species tree method based upon gene tree reconciliation and the concatenation of multiple loci for resolving bushes. We examined different bush shapes, varying both the speciation rate during the radiation and the depth of the radiation, to encompass a broad range of situations. Using simulations based upon parameters derived from empirical studies, we investigated the performance of phylogenetic analyses under different conditions to identify approaches with the greatest potential to resolve difficult phylogenies. Sampling a single individual for more loci outperformed sampling multiple individuals for one locus in all cases except the most recent radiations. We found that error due to homoplastic mutations increased with depth, while error due to the coalescent process remained unchanged. These simulations also revealed that, for certain ancient bushes, analyses of concatenated data matrices surprisingly resulted in more accurate phylogenies than gene tree reconciliation. The poor performance of gene tree reconciliation in this study appeared to reflect the poor estimation of gene trees, not the superiority of concatenation per se. Our results suggest concatenation remains a useful approximate method for species tree estimation, even for rapid evolutionary radiations. However, improved estimation of gene trees combined with use of gene tree reconciliation has the greatest potential for resolving the remaining bushes of the Tree of Life.

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Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus)

Cited by 69 publications

References 79 publications

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Molecular phylogeny of Malagasy reed frogs, Heterixalus, and the relative performance of bioacoustics and color-patterns for resolving their systematics

Error in Phylogenetic Estimation for Bushes in the Tree of Life

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