Biogeography of ITS Variation in the Helenium autumnale (Asteraceae) Species Complex

2021 ◽  
Vol 46 (1) ◽  
pp. 235-247
Author(s):  
Skip Williams ◽  
Kelly Bezold ◽  
John S. Knox ◽  
Maryanne C. Simurda
Keyword(s):  
Species Complex ◽  
Incomplete Lineage Sorting ◽  
Its Sequences ◽  
Fine Scale ◽  
Lineage Sorting ◽  
Biogeographic Patterns ◽  
Dna Evidence ◽  
Base Site ◽  
Canadian Provinces ◽  
Central Usa

Abstract—We used ITS sequences as species barcodes to evaluate 127 samples of 12 Helenium species from the eastern and central USA, focusing on a species complex of H. autumnale (76 sequences from 11 U.S. states and two Canadian provinces), the federally “threatened” H. virginicum, now recommended for delisting (30 sequences from three U.S. states), and H. flexuosum (11 sequences from four U.S. states). ITS sequences confirmed most species identifications and supported the presence of the first population of the “threatened” endemic Missouri-Virginia disjunct, Helenium virginicum, in Indiana. Because the Indiana plants grow in a restored wetland, have a cpDNA haplotype previously known only from Missouri, with a morphology similar to Missouri variants, and an herbarium search for additional populations in Indiana found none, it is unclear whether the Indiana population is natural or planted. The presence of a putative sister lineage to H. virginicum thought to exist on the Bruce Peninsula, Ontario, Canada, was not supported after sequencing 36 plants with the sister morphology that grew there along 18 km of beach fens and finding they had H. autumnale sequences. Fine-scale biogeographic patterns of intraspecific sequence variation were found mostly in H. autumnale, with centers of different base site polymorphisms found in northern North America and the Missouri Ozarks. As in a previous study, we found DNA evidence of hybridization between Helenium species in Missouri. We offer hypotheses to explain the biogeography of North American Helenium, focusing on the three species that compose the H. autumnale species complex and suggesting that H. autumnale may be a compilospecies showing incomplete lineage sorting. We encourage exploration of more Helenium species and their conspecific populations in search of fine-scale ITS base site polymorphisms to reveal emerging lineages and resolve the origins and evolutionary implications of these biogeographic patterns.

Gradual evolution of male genitalia in a sibling species complex of millipedes (Diplopoda : Spirobolida : Rhinocricidae : Anadenobolus)

2003 ◽  
Vol 17 (6) ◽  
pp. 711 ◽  
Author(s):  
Jason E. Bond ◽  
David A. Beamer ◽  
Marshal C. Hedin ◽  
Petra Sierwald
Keyword(s):  
Male Genitalia ◽  
Species Complex ◽  
Unusual Case ◽  
Incomplete Lineage Sorting ◽  
Rapid Change ◽  
Nuclear Gene ◽  
Lineage Sorting ◽  
Gradual Evolution ◽  
Copulatory Structure

Jamaican millipedes in the Anadenobolus species complex provide an unusual case study of arthropods having undergone speciation in the absence of conspicuous divergence of male genitalia. Using landmark-based morphometrics, we examined shape deformation of the male anterior copulatory device in three genetically divergent yet morphologically cryptic species. A multivariate analysis of variance and relative warp analysis of nonuniform components show that although male genitalic shape is statistically different among species, many specimens are 'misplaced' in morphological space, perhaps consistent with a condition analogous to incomplete lineage sorting. A simulation of neutral nuclear gene coalescence suggests that such incomplete sorting is expected, given the depth of mtDNA divergences observed across species. The pronounced contrast between deep molecular v. incomplete genitalic divergence is at odds with the paradigm of selection-driven rapid change in male copulatory structure during arthropod speciation. Alternatively, we suggest that male genitalic divergence is evolving neutrally or in concert with other components of the genome (pleiotropy). Although we recognise the empirical validity of rapid genitalic divergence via sexual selection or sexual conflict, such models must be empirically tested using multiple lines of evidence. Accepting the rapid and divergent hypothesis without such multiple evidence scrutiny may result in a gross underestimation of evolutionary diversity and, subsequently, the misinterpretation of processes shaping genitalic change.

scholarly journals Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10896
Author(s):  
José Cerca ◽  
Angel G. Rivera-Colón ◽  
Mafalda S. Ferreira ◽  
Mark Ravinet ◽  
Michael D. Nowak ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Cryptic Species ◽  
Species Complex ◽  
Population Genomics ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Population Level ◽  
Similar Species ◽  
Lineage Sorting ◽  
Amplification Method

Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.

Taxonomic resolution of the Tetratheca hirsuta (Elaeocarpaceae) species complex using an integrative approach

2017 ◽  
Vol 30 (1) ◽  
pp. 1 ◽  
Author(s):  
E. M. Joyce ◽  
R. Butcher ◽  
M. Byrne ◽  
P. F. Grierson ◽  
M. Hankinson ◽  
...  
Keyword(s):  
Species Complex ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Taxonomic Resolution ◽  
Integrative Approach ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Molecular Phylogenetic ◽  
Slow Evolution

The Tetratheca hirsuta Lindl. species complex from south-west Western Australia is one of the last unresolved complexes in this Australian endemic genus, and comprises the highly variable T. hirsuta, two rare, phrase-named taxa, and the closely allied T. hispidissima Steetz. An integrative approach, incorporating multivariate morphometric analysis and molecular phylogenetic and phenetic analyses of nrDNA (ETS) and cpDNA (ndhF–trnL, rpl16, trnS–trnG5ʹ2S), was used to investigate taxonomic boundaries within the complex. Morphological data showed clear divergence within the complex, and allowed several taxonomically uncertain individuals to be assigned. Phenetic and phylogenetic analyses of ETS showed substantial congruence with morphology, indicating that the groups recognised through morphometric analyses are also genetically divergent. By comparison, the chloroplast regions yielded incongruent gene trees, perhaps owing to incomplete lineage sorting, hybridisation or slow evolution of cpDNA. The present results support the recognition of the following four taxa: a morphologically and geographically expanded T. hispidissima, which is highly divergent from the remainder of the complex, and a closer grouping of T. hirsuta subsp. boonanarring Joyce & R.Butcher subsp. nov., T. hirsuta subsp. viminea (Lindl.) Joyce comb. et stat. nov. and T. hirsuta subsp. hirsuta.

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.

scholarly journals Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

2020 ◽  
Author(s):  
Fernando Lopes ◽  
Larissa R Oliveira ◽  
Amanda Kessler ◽  
Yago Beux ◽  
Enrique Crespo ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Molecular Data ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Data Types ◽  
High Coverage ◽  
Sea Lions ◽  
The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

The Auk ◽  
2019 ◽  
Vol 136 (4) ◽  
Author(s):  
Catalina Palacios ◽  
Silvana García-R ◽  
Juan Luis Parra ◽  
Andrés M Cuervo ◽  
F Gary Stiles ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Incomplete Lineage Sorting ◽  
Lineage Sorting ◽  
Phenotypic Differences ◽  
Adaptive Mechanisms ◽  
The Face ◽  
Gloger’S Rule ◽  
Divergence With Gene Flow ◽  
Neutral Markers

Abstract Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

scholarly journals Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

2022 ◽  
Author(s):  
XiaoXu Pang ◽  
Da-Yong Zhang
Keyword(s):  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
Tree Methods ◽  
The Impact

The species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

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