Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

Pohl, Nélida; Sison-Mangus, Marilou P.; Yee, E.; Liswi, Saif W; Briscoe, Adriana D.

doi:10.1186/1471-2148-9-99

Cited by 37 publications

(35 citation statements)

References 79 publications

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“…The phylogeny estimated under a relaxed clock model in BEAST shows diversification dynamics that differ from previous estimates, with the deeper splits between the genera of Heliconiini estimated as substantially older than previously inferred with mitochondrial data, but younger than estimated with a small sample of nuclear genes (Table 1) Pohl et al 2009). The most species-rich genera Heliconius and Eueides separated 18.5 (95% highest posterior density: 16.5-20.4) Ma and both started to diversify, respectively, 11.8 (10.5-13.4) Ma and 10.2 (8.9-11.7) Ma.…”

Section: Tempo Of Diversificationcontrasting

confidence: 69%

“…Although most age estimates for Heliconius agree with other studies, the deeper nodes are older than previously suggested (Table 1). There is little agreement on the dates above the species level, and the studies to date either suffer from insufficient taxon sampling (Pohl et al 2009;Wahlberg et al 2009;Cuthill and Charleston 2012; Table 3), or use markers unlikely to be informative above a relatively low level of divergence ). For instance, the mean age of the split between Heliconius and Agraulis is estimated as 32 Ma in the study of Pohl et al (2009), which includes only three species of Heliconiini; 26.5 Ma in Wahlberg et al (2009), including one species per genus; or 23.8 Ma in the present study ( Fig.…”

Section: Divergence Time Estimatesmentioning

confidence: 99%

“…Thus, Heliconiini are an excellent system for the study of convergence from both genomic and organismal perspectives (e.g., Duenez-Guzman et al 2009;Hines et al 2011;Bybee et al 2012;Heliconius Genome Consortium 2012;Martin et al 2012;Pardo-Diaz et al 2012;Jones et al 2013;Nadeau et al 2013;Supple et al 2013;Arias et al 2014). In addition to studies of wing pattern evolution, there has been a recent proliferation of comparative molecular and genomic studies of other traits including vision (Pohl et al 2009), chemosensation (Briscoe et al 2013) and cyanogenesis (Chauhan et al 2013). A robust and stable molecular phylogeny is therefore especially desirable for this clade.…”

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confidence: 99%

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Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

Kozak

Wahlberg

Neild

et al. 2014

Preprint

129

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Abstract.-Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a data set of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal, and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach failed to reflect the underlying variation in the history of individual loci. However, the supermatrix represents a useful approximation where multiple rare species represented by short sequences can be incorporated easily. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Neotropics over the past 23 myr, or changes caused by diversity-dependent effects on the rate of diversification. We find that the rate of diversification has increased on the branch leading to the presently most species-rich genus Heliconius, but the change occurred gradually and cannot be unequivocally attributed to a specific environmental driver. Our study provides comprehensive comparison of philosophically distinct species tree reconstruction methods and provides insights into the diversification of an important insect radiation in the most biodiverse region of the planet.

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Section: Tempo Of Diversificationcontrasting

confidence: 69%

Section: Divergence Time Estimatesmentioning

confidence: 99%

mentioning

confidence: 99%

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Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

Kozak

Wahlberg

Neild

et al. 2014

Preprint

129

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“…Phylogenetic relationships between species are derived from a recent molecular phylogeny (47) after retaining nodes with bootstrap support ≥0.98. Estimated age of Heliconius radiation is derived from a recent molecular clock study (48). Only a subset of Heliconius wing pattern diversity is represented here.…”

Section: Discussionmentioning

confidence: 99%

Diversification of complex butterfly wing patterns by repeated regulatory evolution of aWntligand

Martin

Papa

Nadeau

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

242

282

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Although animals display a rich variety of shapes and patterns, the genetic changes that explain how complex forms arise are still unclear. Here we take advantage of the extensive diversity of Heliconius butterflies to identify a gene that causes adaptive variation of black wing patterns within and between species. Linkage mapping in two species groups, gene-expression analysis in seven species, and pharmacological treatments all indicate that cis-regulatory evolution of the WntA ligand underpins discrete changes in color pattern features across the Heliconius genus. These results illustrate how the direct modulation of morphogen sources can generate a wide array of unique morphologies, thus providing a link between natural genetic variation, pattern formation, and adaptation.Mü llerian mimicry | Wnt pathway | Mendelian genetics | evolutionary-developmental biology

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“…This process has occurred frequently, and sometimes rapidly, in evolutionary time (Pohl et al, 2009;Gojobori and Innan, 2009;Trezise and Collin, 2005). The recent expansion in genomic data of invertebrates has shown that even animals lacking morphologically complex eyes are often rich in opsin genes.…”

Section: A M Sweeney and Othersmentioning

confidence: 99%

Twilight spectral dynamics and the coral reef invertebrate spawning response

Sweeney

Boch

Johnsen

et al. 2011

Journal of Experimental Biology

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SUMMARYThere are dramatic and physiologically relevant changes in both skylight color and intensity during evening twilight as the pathlength of direct sunlight through the atmosphere increases, ozone increasingly absorbs long wavelengths and skylight becomes increasingly blue shifted. The moon is above the horizon at sunset during the waxing phase of the lunar cycle, on the horizon at sunset on the night of the full moon and below the horizon during the waning phase. Moonlight is red shifted compared with daylight, so the presence, phase and position of the moon in the sky could modulate the blue shifts during twilight. Therefore, the influence of the moon on twilight color is likely to differ somewhat each night of the lunar cycle, and to vary especially rapidly around the full moon, as the moon transitions from above to below the horizon during twilight. Many important light-mediated biological processes occur during twilight, and this lunar effect may play a role. One particularly intriguing biological event tightly correlated with these twilight processes is the occurrence of mass spawning events on coral reefs. Therefore, we measured downwelling underwater hyperspectral irradiance on a coral reef during twilight for several nights before and after the full moon. We demonstrate that shifts in twilight color and intensity on nights both within and between evenings, immediately before and after the full moon, are correlated with the observed times of synchronized mass spawning, and that these optical phenomena are a biologically plausible cue for the synchronization of these mass spawning events.

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Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

Cited by 37 publications

References 79 publications

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

Diversification of complex butterfly wing patterns by repeated regulatory evolution of aWntligand

Twilight spectral dynamics and the coral reef invertebrate spawning response

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