Biology subjects

Parins-Fukuchi, C.

Publications and source records attributed to Parins-Fukuchi, C..

12 recordsLinked to original sources

bioRxiv2022

Compositional shifts associated with major evolutionary transitions in plants

O_LIHeterogeneity in gene trees, morphological characters, and composition has been associated with several major clades across the plant tree of life. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants in order to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. C_LIO_LIWe estimate mixed models of composition for both DNA and amino acids across a recent large scale transcriptomic dataset for plants. C_LIO_LIWe find shifts in composition across both DNA and amino acid datasets, with more shifts detected in DNA. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns. C_LIO_LICompositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes. C_LI Plain language summaryWe demonstrate that many nucleotide and amino acid compositional shifts in plants occur at the origins of major clades and while individual genes do not share the same composition they often shift in the same direction. We suggest that these patterns warrant further exploration as the signal of important biological processes during the evolution of plants.

evolutionary biology↗

bioRxiv2021

Gene duplications and genomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the Tree of Life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation1, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here we examine the relationship of various facets of genomic evolution--including gene and genome duplication, genome size, and chromosome number--with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.

evolutionary biology↗

bioRxiv2020

Phylogenomic conflict coincides with rapid morphological innovation

Evolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that phylogenomic conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between areas of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.

evolutionary biology↗

bioRxiv2020

Morphological and phylogeographic evidence for budding speciation: an example in hominins

Parametric phylogenetic approaches that attempt to delineate between distinct modes of speciation (splitting cladogenesis, budding cladogenesis, and anagenesis) between fossil taxa have become increasingly popular among comparative biologists. But it is not yet well-understood how clearly morphological data from fossil taxa speak to detailed questions of speciation mode as compared to the lineage diversification models that serve as their basis. In addition, the congruence of inferences made using these approaches with geographic patterns has not been explored. Here, I extend a previously introduced maximum-likelihood approach for the examination of ancestor-descendant relationships to accommodate budding speciation and apply it to a dataset of fossil hominins. I place these results in a phylogeographic context to better understand spatial dynamics underlying the hypothesized speciation patterns. The spatial patterns implied by the phylogeny hint at the complex demographic processes underlying the spread and diversification of hominins throughout the Pleistocene. I also find that inferences of budding are driven primarily by stratigraphic, versus morphological, data and discuss the ramifications for interpretations of speciation process in hominins specifically and from phylogenetic data in general.

evolutionary biology↗

bioRxiv2019

Mosaic evolution, constraint, and constructional opportunity in great apes

AbstractA major goal in post-synthesis evolutionary biology has been to better understand how complex interactions between traits drive movement along and facilitate the formation of distinct evolutionary pathways. I present analyses of a character matrix sampled across the haplorrhine skeleton that revealed several modules of characters displaying distinct patterns in macroevolutionary disparity. Comparison of these patterns to those in neurological development showed that early ape evolution was characterized by an intense regime of evolutionary and developmental flexibility. Shifting and reduced constraint in apes was met with episodic bursts in phenotypic innovation that built a wide array of functional diversity over a foundation of shared developmental and anatomical structure. Shifts in modularity drove dramatic evolutionary changes across the ape body plan in two distinct ways: 1) an episode of relaxed integration early in hominoid evolution coincided with bursts in evolutionary rate across multiple character suites; 2) the formation of two new trait modules along the branch leading to chimps and humans preceded rapid and dramatic evolutionary shifts in the carpus and pelvis. Changes to the structure of evolutionary mosaicism may correspond to enhanced evolvability that has a preadaptive effect by catalyzing later episodes of dramatic morphological remodeling.

evolutionary biology↗

bioRxiv2018

Phylogeny, ancestors and anagenesis in the hominin fossil record

Probabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary pattern by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary divergence. Recent methodological developments have integrated ancestral relationships into probabilistic phylogenetic methods. These new approaches rely on parameter-rich models and sophisticated inferential methods, potentially obscuring the respective contributions of data and models. In this study, we describe a simple likelihoodist approach that combines probabilistic models of morphological evolution and fossil preservation to reconstruct both cladogenetic and anagenetic relationships. By applying this approach to a dataset of fossil hominins, we demonstrate the capability of existing models to unveil evidence for anagenesis presented by morphological and temporal data. This evidence was previously recognized by qualitative assessments, but largely ignored by quantitative phylogenetic analyses. For example, we find support for directly ancestral relationships in multiple lineages: Sahelanthropus is ancestral to later hominins; Australopithecus anamensis is ancestral to Au. afarensis; Au. garhi is ancestral to Homo; H. antecessor is ancestral to H. heidelbergensis, which in turn is ancestral to both H. sapiens and H. neanderthalensis. These results show a benefit of accommodating direct ancestry in phylogenetics. By so doing, quantitative results align more closely with previous qualitative expectations.

evolutionary biology↗

bioRxiv2018

Detecting mosaic patterns in phenotypic disparity

Evolutionary biologists have long sought to understand the full complexity in pattern and process that shapes organismal diversity. Although phylogenetic comparative methods are often used to reconstruct complex evolutionary dynamics, they are typically limited to a single phenotypic trait. Extensions that accommodate multiple traits lack the ability to partition multidimensional datasets into a set of mosaic suites of evolutionarily linked characters. I introduce a comparative framework that identifies heterogeneity in evolutionary patterns across large datasets of continuous traits. Using a model of continuous trait evolution based on the differential accumulation of disparity across lineages in a phylogeny, the approach algorithmically partitions traits into a set of character suites that best explains the data, where each suite displays a distinct pattern in phylogenetic morphological disparity. When applied to empirical data, the approach revealed a mosaic pattern predicted by developmental biology. The evolutionary distinctiveness of individual suites can be investigated in more detail, either by fitting conventional comparative models or by directly studying the phylogenetic patterns in disparity recovered during the analysis. This framework can supplement existing comparative approaches by inferring the complex, integrated patterns that shape evolution across the body plan from disparate developmental, morphometric, and environmental sources of phenotypic data.

evolutionary biology↗

bioRxiv2018

Bayesian and likelihood placement of fossils on phylogenies from quantitative morphometrics

AO_SCPLOWBSTRACTC_SCPLOWJointly developing a comprehensive tree of life from living and fossil taxa has long been a fundamental goal in evolutionary biology. One major challenge has stemmed from difficulties in merging evidence from extant and extinct organisms. While these efforts have resulted in varying stages of synthesis, they have been hindered by their dependence on qualitative descriptions of morphology. Though rarely applied to phylogenetic inference, traditional and geometric morphometric data can improve these issues by generating more rigorous ways to quantify variation in morphological structures. They may also facilitate the rapid and objective aggregation of large morphological datasets. I describe a new Bayesian method that leverages quantitative trait data to reconstruct the positions of fossil taxa on fixed reference trees composed of extant taxa. Unlike most formulations of phylogenetic Brownian motion models, this method expresses branch lengths in units of morphological disparity, suggesting a new framework through which to construct Bayesian node calibration priors for molecular dating and explore comparative patterns in morphological disparity. I am hopeful that the approach described here will help to facilitate a deeper integration of neo- and paleontological data to move morphological phylogenetics further into the genomic era.

evolutionary biology↗

bioRxiv2017

What drives results in Bayesian morphological clock analyses?

Recently, approaches that estimate species divergence times using fossil taxa and models of morphological evolution have exploded in popularity. These methods incorporate diverse biological and geological information to inform posterior reconstructions, and have been applied to several high-profile clades to positive effect. However, there are important examples where morphological data are misleading, resulting in unrealistic age estimates. While several studies have demonstrated that these approaches can be robust and internally consistent, the causes and limitations of these patterns remain unclear. In this study, we dissect signal in Bayesian dating analyses of three mammalian clades. For two of the three examples, we find that morphological characters provide little information regarding divergence times as compared to geological range information, with posterior estimates largely recapitulating those recovered under the prior. However, in the cetacean dataset, we find that morphological data do appreciably inform posterior divergence time estimates. We supplement these empirical analyses with a set of simulations designed to explore the efficiency and limitations of binary and 3-state character data in reconstructing node ages. Our results demonstrate areas of both strength and weakness for morphological clock analyses, and help to outline conditions under which they perform best and, conversely, when they should be eschewed in favour of purely geological approaches.

paleontology↗

bioRxiv2017

Disparity, Diversity, And Duplications In The Caryophyllales

O_LIThe role whole genome duplication (WGD) plays in the history of lineages is actively debated. WGDs have been associated with advantages including superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates.\nC_LIO_LIUsing seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5,036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic niche and lineage diversification rate.\nC_LIO_LIThirteen putative WGDs and twenty-seven diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic niches.\nC_LIO_LIWhile we find that many diversification shifts occur after WGDs it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic niche, or rate of evolution.\nC_LI

evolutionary biology↗

bioRxiv2017

Continuous Characters Outperform Binary Discrete Characters In Phylogenetic Inference

The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behaviour is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximise phylogenetic information in morphological datasets by preserving larger variation in state space compared to many discretisation schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.

evolutionary biology↗

bioRxiv2017

Missing the point (estimate): Bayesian and likelihood phylogenetic reconstructions of morphological characters produce generally concordant inferences. A comment on Puttick et al.

Puttick et al. [1] performed a simulation study to compare accuracy among methods of inferring phylogeny from discrete morphological characters. They report that a Bayesian implementation of the Mk model [2] was most accurate (but with low resolution), while a maximum likelihood (ML) implementation of the same model was least accurate. They conclude by strongly advocating that Bayesian implementations of the Mk model should be the default method of analysis for such data. While we appreciate the authors attempt to investigate the accuracy of alternative methods of analysis, their conclusion is based on an inappropriate comparison of the ML point estimate, which does not consider confidence, with the Bayesian consensus, which incorporates estimation credibility into the summary tree. Using simulation, we demonstrate that ML and Bayesian estimates are concordant when confidence and credibility are comparably reflected in summary trees, a result expected from statistical theory. We therefore disagree with the conclusions of PEA and consider their prescription of any default method to be poorly founded. Instead, we recommend caution and thoughtful consideration of the model or method being applied to a morphological dataset.

evolutionary biology↗