Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap

ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data

CRISPR/Cas9 gene editing technology has enabled lineage tracing for thousands of cells in vivo. However, most of the analysis of CRISPR/Cas9 lineage tracing data has so far been limited to the reconstruction of single-cell tree topologies, which depict lineage relationships between cells, but not the amount of time that has passed between ancestral cell states and the present. Time-resolved trees, known as chronograms, would allow one to study the evolutionary dynamics of cell populations at an unprecedented level of resolution. Indeed, time-resolved trees would reveal the timing of events on the tree, the relative fitness of subclones, and the dynamics underlying phenotypic changes in the cell population - among other important applications. In this work, we introduce the first scalable and accurate method to refine any given single-cell tree topology into a single-cell chronogram by estimating its branch lengths. To do this, we leverage a statistical model of CRISPR/Cas9 cutting with missing data, paired with a conservative version of maximum parsimony that reconstructs only the ancestral states that we are confident about. As part of our method, we propose a novel approach to represent and handle missing data - specifically, double-resection events - which greatly simplifies and speeds up branch length estimation without compromising quality. All this leads to a convex maximum likelihood estimation (MLE) problem that can be readily solved in seconds with off-the-shelf convex optimization solvers. To stabilize estimates in low-information regimes, we propose a simple penalized version of MLE using a minimum branch length and pseudocounts. We benchmark our method using simulations and show that it performs well on several tasks, outperforming more naive baselines. Our method, which we name 'ConvexML', is available through the cassiopeia open source Python package.

CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples

Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.

Allopatric mosaics in the Indo-West Pacific crab subfamily Chlorodiellinae reveal correlated patterns of sympatry, genetic divergence, and genitalic disparity

Molecular studies have revealed that many species once thought to be wide-ranging in the Indo-West Pacific contain allopatric mosaics of endemic lineages. These lineages provide compelling evidence that substantial time is needed to evolve isolating mechanisms sufficient to permit successful secondary sympatry, and that divergence is initiated in allopatry. In this context, questions arise regarding the nature, timing, and origin of isolating mechanisms that permit secondary sympatry. We present a phylogeny of the crab subfamily Chlorodiellinae which displays allopatric mosaics within species. These allopatric lineages typically do not have divergent male genitalia, while older sympatric lineages do. We tested the relationship between genetic distance (proxy for time), sympatry, and the divergence of male genitalic morphology. Our results suggest that male genitalic divergence is not involved in the initiation of speciation in chlorodielline crabs, having likely occurred only after isolation began in allopatry. However, morphological evolution of genitalia seemingly does play an important role in completing the process of speciation in these crabs.

Evolution of the germline mutation rate across vertebrates

The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself¹. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies². Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis³. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.

The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L

Selection together with variation in floral traits can act to mold floral form, often driven by a plant's predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical Costus. In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as dN/dS across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical Costus despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across Costus, while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the Costus inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical Costus.

Evolution of diverse host infection mechanisms delineates an adaptive radiation of lampsiline freshwater mussels centered on their larval ecology

North American watersheds contain a high diversity of freshwater mussels (Unionoida). During the long-lived, benthic phase of their life cycle, up to 40 species can co-occur in a single riffle and there is typically little evidence for major differences in their feeding ecology or microhabitat partitioning. In contrast, their brief parasitic larval phase involves the infection of a wide diversity of fish hosts and female mussels have evolved a spectrum of adaptations for infecting host fish with their offspring. Many species use a passive broadcast strategy: placing high numbers of larvae in the water column and relying on chance encounters with potential hosts. Many other species, including most members of the Lampsilini, have a proactive strategy that entails the use of prey-mimetic lures to change the behavior of the hosts, i.e., eliciting a feeding response through which they become infected. Two main lure types are collectively produced: mantle tissue lures (on the female’s body) and brood lures, containing infective larvae, that are released into the external environment. In this study, we used a phylogenomic approach (ddRAD-seq) to place the diversity of infection strategies used by 54 North American lampsiline mussels into an evolutionary context. Ancestral state reconstruction recovered evidence for the early evolution of mantle lures in this clade, with brood lures and broadcast infection strategies both being independently derived twice. The most common infection strategy, occurring in our largest ingroup clade, is a mixed one in which mimetic mantle lures are apparently the predominant infection mechanism, but gravid females also release simple, non-mimetic brood lures at the end of the season. This mixed infection strategy clade shows some evidence of an increase in diversification rate and most members use centrarchids (Micropterus & Lepomis spp.) as their predominant fish hosts. Broad linkage between infection strategies and predominant fish host genera is also seen in other lampsiline clades: worm-like mantle lures of Toxolasma spp. with sunfish (Lepomis spp.); insect larvae-like brood lures (Ptychobranchus spp.), or mantle lures (Medionidus spp., Obovaria spp.), or mantle lures combined with host capture (Epioblasma spp.) with a spectrum of darter (Etheostoma & Percina spp.) and sculpin (Cottus spp.) hosts, and tethered brood lures (Hamiota spp.) with bass (Micropterus spp.). Our phylogenetic results confirm that discrete lampsiline mussel clades exhibit considerable specialization in the primary fish host clades their larvae parasitize, and in the host infection strategies they employ to do so. They are also consistent with the hypothesis that larval resource partitioning of fish hosts is an important factor in maintaining species diversity in mussel assemblages. We conclude that, taking their larval ecology and host-infection mechanisms into account, lampsiline mussels may be legitimately viewed as an adaptive radiation.

ESTIMATION OF CELL LINEAGE TREES BY MAXIMUM-LIKELIHOOD PHYLOGENETICS

CRISPR technology has enabled cell lineage tracing for complex multicellular organisms through insertion-deletion mutations of synthetic genomic barcodes during organismal development. To reconstruct the cell lineage tree from the mutated barcodes, current approaches apply general-purpose computational tools that are agnostic to the mutation process and are unable to take full advantage of the data's structure. We propose a statistical model for the CRISPR mutation process and develop a procedure to estimate the resulting tree topology, branch lengths, and mutation parameters by iteratively applying penalized maximum likelihood estimation. By assuming the barcode evolves according to a molecular clock, our method infers relative ordering across parallel lineages, whereas existing techniques only infer ordering for nodes along the same lineage. When analyzing transgenic zebrafish data from McKenna, Findlay and Gagnon et al. (2016), we find that our method recapitulates known aspects of zebrafish development and the results are consistent across samples.

Differences in developmental potential predict the contrasting patterns of dental diversification in characiform and cypriniform fishes

Morphological diversification during adaptive radiation may depend on factors external or internal to the lineage. We provide evidence for the latter in characiform fishes (tetras and piranhas), which exhibit extensive dental diversity. Phylogenetic character mapping supported regain of lost teeth as contributing to this diversity. To test for latent potential for dentition that would facilitate its evolutionary expansion, we overexpressed a tooth initiation signal, the tumour necrosis factor pathway ligand ectodysplasin, in a model characiform, the Mexican tetra (Astyanax mexicanus). This manipulation resulted in extensive ectopic dentition, in contrast with its previously reported limited effect in the zebrafish (Danio rerio). Tooth location in the order Cypriniformes, to which the zebrafish belongs, is much more restricted than in characiforms, a pattern that may be explained by differences in the retention of ancestral developmental potential. Our results suggest that differences in evolvability between lineages may lead to contrasting patterns of diversification.

Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics

One of the two major clades of the endemic American Amaryllidaceae subfam. Amaryllidoideae constitutes the tetraploid-derived (n = 23) Andean-centered tribes, most of which have 46 chromosomes. Despite progress in resolving phylogenetic relationships of the group with plastid and nrDNA, certain subclades were poorly resolved or weakly supported in those previous studies. Sequence capture using anchored hybrid enrichment was employed across 95 species of the clade along with five outgroups and generated sequences of 524 nuclear genes and a partial plastome. Maximum likelihood phylogenetic analyses were conducted on concatenated supermatrices, and coalescent-based species tree analyses were run on the gene trees, followed by hybridization network, age diversification and biogeographic analyses. The four tribes Clinantheae, Eucharideae, Eustephieae, and Hymenocallideae (sister to Clinantheae) are resolved in all analyses with > 90 and mostly 100% support, as are almost all genera within them. Nuclear gene supermatrix and species tree results were largely in concordance; however, some instances of cytonuclear discordance were evident. Hybridization network analysis identified significant reticulation in Clinanthus, Hymenocallis, Stenomesson and the subclade of Eucharideae comprising Eucharis, Caliphruria, and Urceolina. Our data support a previous treatment of the latter as a single genus, Urceolina, with the addition of Eucrosia dodsonii. Biogeographic analysis and penalized likelihood age estimation suggests an origin in the Cauca, Desert and Puna Neotropical bioprovinces for the complex in the mid-Oligocene, with more dispersals than vicariances in its history, but no extinctions. Hymenocallis represents the only instance of long-distance vicariance from the tropical Andean origin of its tribe Hymenocallideae. The absence of extinctions correlates with the lack of diversification rate shifts within the clade. The Eucharideae experienced a sudden lineage radiation ca. 10 Mya. We tie much of the divergences in the Andean-centered lineages to the rise of the Andes, and suggest that the Amotape-Huancabamba Zone functioned as both a corridor (dispersal) and a barrier to migration (vicariance). Several taxonomic changes are made. This is the largest DNA sequence data set to be applied within Amaryllidaceae to date.

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements' variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.

Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO

Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special features, including sampled ancestors in which we sequence a genotype along with its direct descendants, and polytomies in which multiple descendants arise simultaneously. These features are apparent after identifying zero-length branches in the tree. However, current maximum-likelihood based approaches are not capable of revealing such zero-length branches. In this paper, we find these zero-length branches by introducing adaptive-LASSO-type regularization estimators for the branch lengths of phylogenetic trees, deriving their properties, and showing regularization to be a practically useful approach for phylogenetics.

Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing

We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33× genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2-fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

A Penalized Likelihood Framework for High-Dimensional Phylogenetic Comparative Methods and an Application to New-World Monkeys Brain Evolution

Working with high-dimensional phylogenetic comparative data sets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits $p $ approaches the number of species $n $ and because some computational complications occur when $p $ exceeds $n$. Alternative phylogenetic comparative methods have recently been proposed to deal with the large $p $ small $n $ scenario but their use and performances are limited. Herein, we develop a penalized likelihood (PL) framework to deal with high-dimensional comparative data sets. We propose various penalizations and methods for selecting the intensity of the penalties. We apply this general framework to the estimation of parameters (the evolutionary trait covariance matrix and parameters of the evolutionary model) and model comparison for the high-dimensional multivariate Brownian motion (BM), Early-burst (EB), Ornstein-Uhlenbeck (OU), and Pagel's lambda models. We show using simulations that our PL approach dramatically improves the estimation of evolutionary trait covariance matrices and model parameters when $p$ approaches $n$, and allows for their accurate estimation when $p$ equals or exceeds $n$. In addition, we show that PL models can be efficiently compared using generalized information criterion (GIC). We implement these methods, as well as the related estimation of ancestral states and the computation of phylogenetic principal component analysis in the R package RPANDA and mvMORPH. Finally, we illustrate the utility of the new proposed framework by evaluating evolutionary models fit, analyzing integration patterns, and reconstructing evolutionary trajectories for a high-dimensional 3D data set of brain shape in the New World monkeys. We find a clear support for an EB model suggesting an early diversification of brain morphology during the ecological radiation of the clade. PL offers an efficient way to deal with high-dimensional multivariate comparative data.

A penalized likelihood approach to estimate within-household contact networks from egocentric data

Acute infectious diseases are transmitted over networks of social contacts. Epidemic models are used to predict the spread of emergent pathogens and compare intervention strategies. Many of these models assume equal probability of contact within mixing groups (homes, schools, etc.), but little work has inferred the actual contact network, which may influence epidemic estimates. We develop a penalized likelihood method to infer contact networks within households, a key area for disease transmission. Using egocentric surveys of contact behavior in Belgium, we estimate within-household contact networks for six different age compositions. Our estimates show dependency in contact behavior and vary substantively by age composition, with fewer contacts occurring in older households. Our results are relevant for epidemic models used to make policy recommendations.

Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion

Dating the divergence in a phylogenetic tree is a fundamental step in evolutionary analysis. Some extensions and improvements of the penalised likelihood method originally presented by Sanderson are introduced. The improvements are the introduction of alternative models, including one with non-correlated rates of molecular substitution ("relaxed" model), a completely reworked fitting algorithm that considers the high-dimensionality of the optimisation problem, and the development of a new information criterion for model selection in the presence of a penalised term. It is also shown that the strict clock model is a special case of the present approach. An extensive simulation study was conducted to assess the statistical performance of these improvements. Overall, the different estimators studied here appeared as unbiased though their variance varied depending on the fitted and the simulated models and on the number of calibration points. The strict clock model gave good estimates of branch lengths even in the presence of heterogeneous substitution rates. The correlated model gave the best estimates of substitution rates whatever the model used to simulate the data. These results, which are certainly the first from an extensive simulation study of a molecular dating method, call for more comparison with alternative methods, as well as further work on the developments introduced here.

Biologically inspired phylogenetic models strongly outperform the no common mechanism model

But Tuffley and Steel (1997) introduced a model called No Common Mechanism (NCM), in which characters may-but are not required to-vary their relative rates independently, both within and between branches. Because the independent variation is taken only as a possibility, not as a requirement, NCM would apply to almost any situation, and so may be accepted as realistic. This is useful because Tuffley and Steel also showed that maximum likelihood under NCM selects the same trees as does parsimony. With the realistic NCM in the background, then, most parsimonious trees have greatest power to explain available observations. -Farris (2008).

General heterotachy and distance method adjustments

Heterotachy is a general term to describe positions in a sequence that evolve at different rates in different lineages. Kolaczkowski and Thornton (2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.) recently described an intriguing heterotachy model that leads to topological bias for likelihood-based methods and parsimony methods. In this article, we show that heterotachy can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each site. Motivated by this idea, we propose a pairwise alpha heterotachy adjustment model, which gives us much improved topological estimation in the settings by Kolaczkowski and Thornton (2004).