Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species <i>Archocentrus centrarchus</i>

Fruciano, Carmelo; Franchini, Paolo; Raffini, Francesca; Fan, Shaohua; Meyer, Axel

doi:10.1002/ece3.2184

Cited by 22 publications

(23 citation statements)

References 93 publications

(183 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Consistent with the results from Fruciano et al . (), even with our high‐resolution genomewide data set we did not detect any genetic clustering within Lake Xiloá, suggesting that there is no sympatric differentiation in A. centrarchus . Conversely, Kautt et al .…”

Section: Discussioncontrasting

confidence: 57%

“…In contrast, using microsatellite markers, Fruciano et al . () found a pattern that could have been interpreted as admixture in a few individuals – this interpretation was possibly due to a lack of power/resolution. Consistent with the results from Fruciano et al .…”

Section: Discussionmentioning

confidence: 99%

“…Therefore in the second data set, a single quaddRAD library was constructed by pooling 67 individuals of such a monomorphic closely related Neotropical cichlid fish (Archocentrus centrarchus) from two freshwater basins: the large tectonic Lake Managua and the small and young crater Lake Xilo a ( Fig. 2) (Fruciano et al 2016b). Four endemic species of Midas cichlids have been described from Lake Xilo a and can be distinguished based on morphological (Klingenberg et al 2003) and genetic clustering and these are all in turn morphologically and genetically differentiated from the Midas cichlid source population in Lake Managua (Elmer et al 2010;Recknagel et al 2013).…”

Section: Restrictionmentioning

confidence: 99%

“…) (Fruciano et al . ). Four endemic species of Midas cichlids have been described from Lake Xiloá and can be distinguished based on morphological (Klingenberg et al .…”

Section: Introductionmentioning

confidence: 97%

“…We used our genomewide biological data set, first, to test whether the apparent absence of genetic clusters within the lakes for A. centrarchus is simply due to a lack of power, as Fruciano et al . () used only twelve microsatellite markers. Recently, in Lake Apoyo, another Nicaraguan crater lake hosting Midas fishes, RADSeq data comparable to those used in this study identified five genetic clusters (Kautt et al .…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

et al. 2017

Self Cite

View full text Add to dashboard Cite

The identification of thousands of variants across the genomes and their accurate genotyping are crucial for estimating the genetic parameters needed to address a host of molecular ecological and evolutionary questions. With rapid advances of massively parallel high-throughput sequencing technologies, several methods have recently been developed to access genomewide data on population variation. One of the most successful and widely used techniques relies on the combination of restriction enzymes and sequencing-by-synthesis: restriction-site-associated DNA sequencing (RADSeq). We developed a new, more time- and cost-efficient double-digest RAD paired-end protocol (quaddRAD) that simplifies and speeds up the identification of PCR duplicates and permits large-scale multiplexing. Assessing its performance on a technical data set, we also applied the quaddRAD method on population samples of a Neotropical cichlid fish lineage (Archocentrus centrarchus) to assess its genetic structure and demographic history. While we identified allopatric interlake genetic divergence, most likely driven by drift, no signature of sympatric divergence was detected. This differs from what has been observed in the clade of Midas cichlids (Amphilophus citrinellus spp.), another cichlid lineage that inhabits the same lakes and shares a similar demographic history, but has evolved into small-scale adaptive radiations via sympatric speciation. We demonstrate that quaddRAD is a robust and efficient method for genotyping a massive number and widely overlapping set of loci with high accuracy. Furthermore, the results on A. centrarchus open new research avenues providing an ideal system to investigate genome-level mechanisms that could alter the speciation potential of different but closely related cichlid lineages.

show abstract

Section: Discussioncontrasting

confidence: 57%

Section: Discussionmentioning

confidence: 99%

Section: Restrictionmentioning

confidence: 99%

“…) (Fruciano et al . ). Four endemic species of Midas cichlids have been described from Lake Xiloá and can be distinguished based on morphological (Klingenberg et al .…”

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

Sharing is caring? Measurement error and the issues arising from combining 3D morphometric datasets

Fruciano

Celik

Butler

et al. 2017

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

Geometric morphometrics is routinely used in ecology and evolution and morphometric datasets are increasingly shared among researchers, allowing for more comprehensive studies and higher statistical power (as a consequence of increased sample size). However, sharing of morphometric data opens up the question of how much nonbiologically relevant variation (i.e., measurement error) is introduced in the resulting datasets and how this variation affects analyses. We perform a set of analyses based on an empirical 3D geometric morphometric dataset. In particular, we quantify the amount of error associated with combining data from multiple devices and digitized by multiple operators and test for the presence of bias. We also extend these analyses to a dataset obtained with a recently developed automated method, which does not require human‐digitized landmarks. Further, we analyze how measurement error affects estimates of phylogenetic signal and how its effect compares with the effect of phylogenetic uncertainty. We show that measurement error can be substantial when combining surface models produced by different devices and even more among landmarks digitized by different operators. We also document the presence of small, but significant, amounts of nonrandom error (i.e., bias). Measurement error is heavily reduced by excluding landmarks that are difficult to digitize. The automated method we tested had low levels of error, if used in combination with a procedure for dimensionality reduction. Estimates of phylogenetic signal can be more affected by measurement error than by phylogenetic uncertainty. Our results generally highlight the importance of landmark choice and the usefulness of estimating measurement error. Further, measurement error may limit comparisons of estimates of phylogenetic signal across studies if these have been performed using different devices or by different operators. Finally, we also show how widely held assumptions do not always hold true, particularly that measurement error affects inference more at a shallower phylogenetic scale and that automated methods perform worse than human digitization.

show abstract

Lessons from a natural experiment: Allopatric morphological divergence and sympatric diversification in the Midas cichlid species complex are largely influenced by ecology in a deterministic way

2018

Self Cite

View full text Add to dashboard Cite

Explaining why some lineages diversify while others do not and how are key objectives in evolutionary biology. Young radiations of closely related species derived from the same source population provide an excellent opportunity to disentangle the relative contributions of possible drivers of diversification. In these settings, lineage‐specific effects are shared and can be ruled out. Moreover, the relevant demographic and ecological parameters can be estimated accurately. Midas cichlid fish in Nicaragua have repeatedly colonized several crater lakes, diverged from the same source populations, and, interestingly, diversified in some of them but not others. Here, using the most comprehensive molecular and geometric morphometric data set on Midas cichlids to date (∼20,000 SNPs, 12 landmarks, ∼700 individuals), we aim to understand why and how crater lake populations diverge and why some of them are more prone to diversify in sympatry than others. Taking ancestor‐descendant relationships into account, we find that Midas cichlids diverged in parallel from their source population mostly—but not exclusively—by evolving more slender body shapes in all six investigated crater lakes. Admixture among crater lakes has possibly facilitated this process in one case, but overall, admixture and secondary waves of colonization cannot predict morphological divergence and intralacustrine diversification. Instead, morphological divergence is larger the more dissimilar a crater lake is compared to the source lake and happens rapidly after colonization followed by a slow‐down with time. Our data also provide some evidence that founder effects may positively contribute to divergence. The depth of a crater lake is positively associated with variation in body shapes (and number of species), presumably by providing more ecological opportunities. In conclusion, we find that parallel morphological divergence in allopatry and the propensity for diversification in sympatry across the entire Midas cichlid fish radiation is partly predictable and mostly driven by ecology.

show abstract

Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus

Cited by 22 publications

References 93 publications

quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

Sharing is caring? Measurement error and the issues arising from combining 3D morphometric datasets

Lessons from a natural experiment: Allopatric morphological divergence and sympatric diversification in the Midas cichlid species complex are largely influenced by ecology in a deterministic way

Contact Info

Product

Resources

About