skip to main content


Title: On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation
We consider species tree estimation from multiple loci subject to intralocus recombination. We focus on 𝑅∗, a summary coalescent-based method using rooted triplets. We demonstrate analytically that intralocus recombination gives rise to an inconsistency zone, in which correct inference is not assured even in the limit of infinite amount of data. In addition, we validate and characterize this inconsistency zone through a simulation study that suggests that differential rates of recombination between closely related taxa can amplify the effect of incomplete lineage sorting and contribute to inconsistency.  more » « less
Award ID(s):
1902892 2023239
NSF-PAR ID:
10326892
Author(s) / Creator(s):
Editor(s):
Pe'er, I. 
Date Published:
Journal Name:
Research in Computational Molecular Biology. RECOMB 2022.
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Murphy, William (Ed.)
    Abstract DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the “no intralocus-recombination” assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with 2 ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets. 
    more » « less
  2. Ruane, Sara (Ed.)
    Abstract Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation] 
    more » « less
  3. Abstract

    Despite widespread variation in life span across species, three clear patterns exist: sex differences in life span are ubiquitous, life span is commonly traded against reproduction, and nutrition has a major influence on these traits and how they trade‐off. One process that potentially unites these patterns is intralocus sexual conflict over the optimal intake of nutrients for life span and reproduction. If nutrient intake has sex‐specific effects on life span and reproduction but nutrient choice is genetically linked across the sexes, intralocus sexual conflict will occur and may prevent one or both sexes from feeding to their nutritional optima.

    Here we determine the potential for this process to operate in the decorated cricketGryllodes sigillatus. Using the Geometric Framework for Nutrition, we restrict male and female crickets to diets varying in the ratio of protein to carbohydrates and total nutrient content to quantify the effects on life span and daily reproductive effort in the sexes. We then use inbred lines to estimate the quantitative genetic basis of nutrient choice in males and females. We combine the nutrient effects and genetic estimates to predict the magnitude of evolutionary constraint for these traits in each sex. Finally, we present male and female crickets with a much broader range of diet pairs to determine how the sexes actively regulate their intake of nutrients.

    We show that protein and carbohydrate intake have contrasting effects on life span and reproduction in the sexes and that there are strong positive intersexual genetic correlations for the intake of these nutrients under dietary choice. This is predicted to accelerate the evolutionary response of nutrient intake in males but constrain it in females, suggesting they are losing the conflict. Supporting this view, males and females regulate nutrient intake to a common nutrient ratio that was not perfectly optimal for life span or reproduction in either sex, especially in females.

    Our findings show that intralocus sexual conflict over the optimal intake of nutrients is likely to be an important process generating sex differences in life span and reproduction and may help explain why females age faster and live shorter than males inG. sigillatus.

    A freePlain Language Summarycan be found within the Supporting Information of this article.

     
    more » « less
  4. Abstract

    Sex differences in animal coloration often result from sex‐dependent regulatory mechanisms. Still, some species exhibit incomplete sexual dimorphism as females carry a rudimentary version of a costly male trait, leading to intralocus sexual conflict. The underlying physiology and condition dependence of these traits can inform why such conflicts remain unresolved. In eastern fence lizards (Sceloporus undulatus), blue iridophore badges are found in males and females, but melanin pigmentation underneath and surrounding badges is male‐exclusive. We track color saturation and area of badges across sexual maturity, and their relationship to individual quality (body condition and immunocompetence) and relevant hormones (testosterone and corticosterone). Saturation and testosterone were positively correlated in both sexes, but hormone and trait had little overlap between males and females. Saturation was correlated with body condition and immunocompetence in males but not in females. Co‐regulation by androgens may have released females from resource allocation costs of color saturation, even when in high condition. Badge area was independent of testosterone, but associated with low corticosterone in females, indicating that a nonsex hormone underlies incomplete sexual dimorphism. Given the evidence in this species for female reproductive costs associated with ornamentation, this sex‐nonspecific regulation of an honest signal may underlie intralocus sexual conflict.

     
    more » « less
  5. Abstract

    Macrostructures preserved in deformed rocks are essential for the understanding of their evolution, especially when the deformation is weak and hard to discriminate in regional scale or purely through geophysical data. In order to resolve the inconsistency between NS trending fracture zones and NE oriented spreading fabrics of the South China Sea during the latest spreading stage, we analyzed macrostructures identifiable from the basalt and consolidated sediment samples of the Integrated Ocean Drilling Program (IODP) Sites U1431 and U1433. These two sites are close to the East and Southwest relict spreading ridges and provide critical information on the latest spreading stages. The structures in the basalt of both sites suggest two dominant orientations of NS and NE. At U1431, sediments show mainly WNW trending slickensides, different from that of basalt. At U1433, no structures were found in postspreading sediment. Thus, NE and NS trending structures in basalt are most possibly formed by seafloor spreading. Crosscutting relationship suggests that NE trending structures formed first, followed by NS and finally WNW trending structures. These observations are consistent with geophysical features. Magnetic anomalies and ocean bottom seismometer velocity suggest that the latest relict ridge of the East Subbasin coincides with the EW trending seamount chain. Located between the relict ridges of East and Southwest Subbasins, NS trending Zhongnan‐Liyue Fracture Zone had acted as the latest transform fault. Based on the above evidences, we proposed that the South China Sea may have experienced a short period of NS oriented spreading after earlier SE spreading. These results resolve the previous inconsistencies.

     
    more » « less