scholarly journals Phylogenetic incongruence and the origins of cardenolide-resistant forms of Na+, K+- ATPase in North American Danaus butterflies

2016 ◽  
Author(s):  
Matthew L. Aardema ◽  
Peter Andolfatto
Keyword(s):  
North American ◽  
Host Plants ◽  
Incomplete Lineage Sorting ◽  
Danaus Plexippus ◽  
Orthologous Gene ◽  
Transcriptome Data ◽  
Lineage Sorting ◽  
Rapid Radiation ◽  
Sodium Potassium ◽  
Phylogenetic Incongruence

AbstractRapid species radiations can obscure phylogenetic relationships between even distantly related species and lead to incorrect evolutionary inferences. For this reason, we examined evolutionary relationships among the three North American milkweed butterflies, Danaus plexippus, D. gilippus and D. eresimus using >400 orthologous gene sequences assembled from transcriptome data. Contrary to previous phylogenetic assessments, our results indicate that D. plexippus and D. eresimus are the sister taxa among these species. This result explains many previously noted phylogenetic incongruences such as an amino acid substitution in the sodium-potassium pump (Na+,K+-ATPase) of D. eresimus and D. plexippus, which increases resistance to the toxins found in these butterflies’ host plants. In accordance with a rapid radiation of Danaus butterflies, we also find evidence that both incomplete lineage sorting and post-speciation genetic exchange have contributed significantly to the evolutionary histories of these species. Furthermore, our findings suggest that D. plexippus is highly derived both morphologically and behaviorally.

scholarly journals The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)

2020 ◽  
Author(s):  
Bradley T. Martin ◽  
Tyler K. Chafin ◽  
Marlis R. Douglas ◽  
John S. Placyk ◽  
Roger D. Birkhead ◽  
...  
Keyword(s):  
Machine Learning ◽  
North American ◽  
Species Delimitation ◽  
Species Concept ◽  
Incomplete Lineage Sorting ◽  
Signal To Noise Ratio ◽  
Lineage Sorting ◽  
Biogeographic History ◽  
Box Turtles ◽  
A Minor

AbstractModel-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (Terrapene spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.

scholarly journals Population Structure and Mitochondrial Polyphyly in North American Gadwalls (Anas Strepera)

The Auk ◽  
2007 ◽  
Vol 124 (2) ◽  
pp. 444-462 ◽  
Author(s):  
Jeffrey L. Peters ◽  
Kevin E. Omland
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
North America ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Population Expansion ◽  
Lineage Sorting ◽  
Clade B ◽  
Base Pair Fragment ◽  
Anas Strepera

Abstract We examined population genetic structure in Gadwalls (Anas strepera) to test the prediction that female philopatry and fidelity to migratory flyways have contributed to the partitioning of mitochondrial variation across North America. Sequencing a 658–659 base-pair fragment of the mitochondrial DNA (mtDNA) control region from 348 Gadwalls, we found two distinct clades that were broadly intermixed across both breeding and nonbreeding populations. Clade A was abundant in North America as well as among published sequences from Eurasia. Clade B was sequenced from 5.5% of North American Gadwalls and was more similar to Asian Falcated Duck (A. falcata) haplotypes than to clade A haplotypes. Maximum likelihood indicated that Gadwall clade B haplotypes were a monophyletic group nested within Falcated Duck haplotypes, which suggests mtDNA introgression of clade B into Gadwalls. However, that topology was weakly supported, and we could not reject topologies that were consistent with incomplete lineage-sorting as the cause of mitochondrial polyphyly. Migratory flyways did not contribute significantly to population structure and, in general, we found a lack of genetic structure among most populations. However, Gadwalls sampled in Alaska and Washington were well differentiated from other populations. Coalescent analyses supported a historical population expansion for clade A, and this expansion could have contributed to the high genetic similarity among some populations but the strong differentiation of others. Female-mediated gene flow, along with both historical and contemporary population and range expansions, has likely contributed to the overall weak mtDNA structure in North American Gadwalls. Estructura Poblacional y Polifilia Mitocondrial en Anas strepera

scholarly journals Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation

Insects ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 209
Author(s):  
Erin Thompson ◽  
Jason Baumsteiger ◽  
Ryan I. Hill
Keyword(s):  
Adaptive Radiation ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Legal Protection ◽  
Evolutionary Model ◽  
Morphological Characters ◽  
Anthropogenic Factors ◽  
Lineage Sorting ◽  
The North ◽  
Phylogenetic Resolution

When confronted with an adaptive radiation, considerable evidence is needed to resolve the evolutionary relationships of these closely related lineages. The North American genus Speyeria is one especially challenging radiation of butterflies due to potential signs of incomplete lineage sorting, ongoing hybridization, and similar morphological characters between species. Previous studies have found species to be paraphyletic and have been unable to disentangle taxa, often due to a lack of data and/or incomplete sampling. As a result, Speyeria remains unresolved. To achieve phylogenetic resolution of the genus, we conducted phylogenomic and population genomic analyses of all currently recognized North American Speyeria species, as well as several subspecies, using restriction-site-associated DNA sequencing (RADseq). Together, these analyses confirm the 16 canonical species, and clarify many internal relationships. However, a few relationships within Speyeria were poorly supported depending on the evolutionary model applied. This lack of resolution among certain taxa corroborates Speyeria is experiencing an ongoing adaptive radiation, with incomplete lineage sorting and lack of postzygotic reproductive barriers contributing to hybridization and further ambiguity. Given that many Speyeria taxa are under duress from anthropogenic factors, their legal protection must be viewed cautiously and on a case by case basis in order to properly conserve the diversity being generated.

scholarly journals Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

2021 ◽  
Author(s):  
Olena Meleshko ◽  
Michael D Martin ◽  
Thorfinn Sand Korneliussen ◽  
Christian Schröck ◽  
Paul Lamkowski ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Lineage Sorting ◽  
Rapid Radiation ◽  
Organellar Genomes ◽  
Genome Wide ◽  
Phylogenetic Discordance ◽  
Species Groups ◽  
Open Question

Abstract The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.

scholarly journals Reticulate Evolution, Ancient Chloroplast Haplotypes, and Rapid Radiation of the Australian Plant Genus Adenanthos (Proteaceae)

2021 ◽  
Vol 8 ◽  
Author(s):  
Francis J. Nge ◽  
Ed Biffin ◽  
Kevin R. Thiele ◽  
Michelle Waycott
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Plastid Dna ◽  
Lineage Sorting ◽  
Endemic Plant ◽  
Rapid Radiation ◽  
High Genetic Diversity ◽  
Chloroplast Haplotypes ◽  
Analytical Approaches

Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridization and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridization has previously been reported in the Australian endemic plant genus Adenanthos (Proteaceae). Like many Australian genera, Adenanthos is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for Adenanthos, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridization and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also results from extensive ancient introgression as well as recent chloroplast capture and introgression between extant Adenanthos species. The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localized populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in Adenanthos coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly.

scholarly journals Interspecific hybridization in North American Polygala (Polygalaceae)

2020 ◽  
Vol 14 (1) ◽  
pp. 47-56
Author(s):  
Kurt M. Neubig ◽  
J. Richard Abbott
Keyword(s):  
Interspecific Hybridization ◽  
North American ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Molecular Tools ◽  
Lineage Sorting ◽  
Sympatric Populations ◽  
Dna Sequence Data ◽  
Phylogenetic Studies ◽  
Species Pairs

As a part of ongoing systematic and phylogenetic studies in Polygalaceae, field collections of two pairs of North American species (Polygala balduinii and P. ramosa, and P. lutea and P. rugelii) had morphologically intermediate forms and grew sympatrically, and so were suspected to be interspecific hybrids. Although hybrids among plants are often invoked in taxonomic and floristic literature based on morphologic intermediacy, they are rarely documented and substantiated using molecular tools. We found that the morphologically intermediate individuals within intermixed populations of both species pairs did indeed share all of the variable nucleotide sites in nrITS among the parent species. Likewise, using plastid sequence data (trnL-F), we determined that in both species pairs, the parentage was bidirectional. Although some DNA inheritance phenomena (e.g. incomplete lineage sorting) can result in similar polymorphic DNA sequence data, the intermediacy in both morphology and sequence data within sympatric populations is more indicative of interspecific hybridization.

scholarly journals The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

2020 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Austin Mast ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Flowering Plant ◽  
Estimation Methods ◽  
Lineage Sorting ◽  
Tree Estimation ◽  
Perfect Storm

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

scholarly journals Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 455
Author(s):  
Na Ra Jeong ◽  
Min Jee Kim ◽  
Sung-Soo Kim ◽  
Sei-Woong Choi ◽  
Iksoo Kim
Keyword(s):  
Phylogenetic Analysis ◽  
First Generation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Mitochondrial Coi ◽  
Feeding Type ◽  
Pine Trees ◽  
Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

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