Assessing rapid relaxed-clock methods for phylogenomic dating

Phylogenetic relationships versus environmental impacts on the distribution and traits of Laureae (Lauraceae) species within and outside karst tiankengs

PREMISE

A karst tiankeng, a unique sinkhole-like terrain with a rare and distinctive habitat, is often likened to an isolated island because of its limited contact with the external environment. This distinctive landscape potentially shapes the evolution and distribution of the associated plant species. However, the relative contributions of environmental impacts versus phylogenetic relationships in shaping plant adaptations to the tiankeng environment remain unclear. We analyzed trait divergence within Laureae, a dominant group in a tiankeng forest, to discern whether trait variations among Laureae populations within and outside the tiankeng were shaped predominantly by environmental influences or phylogenetic heritage.

METHODS

We reconstructed a phylogenetic tree for Laureae within and beyond the Baise Tiankengs using plastid genomes to estimate dispersal times, trace ancestral distributions, and model distributional shifts under various climatic scenarios. We also compared leaf and fruit traits of plants within and outside the tiankeng.

RESULTS

The uplift of the Qinghai-Tibet Plateau affected the climate in South China, shaping Laureae traits. A discernible phylogenetic signal indicated environmental factors significantly drive trait variations in Laureae in the tiankeng. A markedly smaller leaf length/width ratio endows the Laureae populations in the tiankeng with enhanced resilience to colder microclimates compared to populations in surrounding areas. Maximum and minimum leaf length/width ratios were also significantly lower in the tiankeng.

CONCLUSIONS

These findings advance our understanding on biodiversity and plant trait divergence inside tiankengs, underscoring the importance of preserving unique habitats and restoring vegetation in these terrains.

The complete mitogenome of Amazonian Brachyplatystoma filamentosum and the evolutionary history of body size in the order Siluriformes

The order Siluriformes (catfish) is one of the largest groups of fish. Diversity in the body size among its species, which range from a few centimeters to 4 meters, makes Siluriformes an interesting group to investigate the body size evolution. Here, we present the complete mitogenome of Brachyplatystoma filamentosum (Piraíba), the largest Amazonian catfish, to explore the evolutionary history of Siluriformes and their body size dynamics. The Piraíba's mtDNA is 16,566 bp long, with a GC content of 42.21% and a D-loop of 911 bp. Phylogenetic analysis was conducted using protein-coding sequences, tRNAs, and rRNAs from mtDNA of Piraíba and 137 other Siluriformes species. Time-calibrated maximum likelihood trees estimated the origin of the order Siluriformes to be ~118.4 Ma, with the Loricarioidei suborder diversifying first, followed by Diplomystoidei and Siluroidei. The Siluroidei suborder experienced rapid expansion around 94.1 Ma. Evolutionary dynamics revealed 16 positive and 11 negative directional body size changes in Siluriformes, with no global trend toward larger or smaller sizes, and with Piraíba showing a significant size increase (5.65 times over 40.8 Ma). We discuss how biological, ecological and environmental factors could have shaped the evolution of body size in this group.

A new forest lizard fauna from Caribbean islands (Squamata, Diploglossidae, Celestinae)

The taxonomy of Neotropical forest lizards (Diploglossidae) has been the subject of controversy because of a paucity of diagnostic characters and genetic data. Recent molecular studies have produced phylogenies that are highly supported but have few individuals represented for each species. These studies have corrected generic names and defined new genera and subfamilies in Diploglossidae. However, they have shown that multiple species are not monophyletic or have high levels of genetic divergence, indicating the need to define new species. Three subfamilies, 12 genera, and 56 species of diploglossid lizards are currently recognized; 25 of these are in the subfamily Celestinae. We conducted a systematic revision of Caribbean celestine forest lizards (from the Cayman Islands, Jamaica, and Hispaniola) using DNA sequence data from 372 individuals, supplemented by both conventional and unconventional morphological characters from 958 preserved specimens. In some cases, we obtained DNA sequence data from museum specimens, including types, nearly 200 years old. We propose and use a new species delimitation method based on time of divergence. We define 17 new species, elevate 17 subspecies, and elevate one species from synonymy, resulting in 35 newly recognized species. Additionally, we synonymize two pairs of previously recognized subspecies and one pair of species. This increases the number of celestine species from 25 to 59 and raises the total number of diploglossids to 90 species. Of those, 63 occur on Caribbean islands and all are endemic to those islands. Fourteen Caribbean celestine species (24%) are Critically Endangered, 17 species (29%) are Endangered, and 1 species (2%) is Vulnerable, resulting in a proportion of threatened species (54%) more than twice as high as the average for reptiles, based on IUCN Redlist criteria. Three of the Critically Endangered species are possibly extinct because of human activities during the last two centuries. Several of the surviving species are near extinction and in need of immediate protection. Extensive forest loss on Caribbean islands has led to the decline of Caribbean forest lizards, which rely on forests as their primary habitat. In addition to deforestation, the introduction of the Small Indian Mongoose is in part responsible for the decline of Caribbean diploglossid lizards. That invasive predator was introduced as a biological control of rats in sugar cane fields in the late 19th Century (1872-1900), immediately resulting in a mass extinction of reptiles. The ground-dwelling and diurnal habits of diploglossids have made them particularly susceptible to mongoose predation.

Data-driven guidelines for phylogenomic analyses using SNP data

Premise

There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full "locus") in phylogenomic analyses and subsequent comparative methods.

Methods

Using genotyping-by-sequencing data from 22 Glycine species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.

Results

Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90-100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution.

Discussion

Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.

Challenges in Assembling the Dated Tree of Life

The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.

Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock

Relaxing the molecular clock using models of how substitution rates change across lineages has become essential for addressing evolutionary problems. The diversity of rate evolution models and their implementations are substantial, and studies have demonstrated their impact on divergence time estimates can be as significant as that of calibration information. In this review, we trace the development of rate evolution models from the proposal of the molecular clock concept to the development of sophisticated Bayesian and non-Bayesian methods that handle rate variation in phylogenies. We discuss the various approaches to modeling rate evolution, provide a comprehensive list of available software, and examine the challenges and advancements of the prevalent Bayesian framework, contrasting them to faster non-Bayesian methods. Lastly, we offer insights into potential advancements in the field in the era of big data.

Molecular timetrees using relaxed clocks and uncertain phylogenies

A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.

Speciation across the Earth driven by global cooling in terrestrial orchids

Although climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localized climate or the accumulation of species with time. Focused analyses of highly speciose clades are needed in order to disentangle the consequences of climate change, geography, and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Using a phylogeny of 1,475 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is dependent on historic global cooling, not time, tropical distributions, elevation, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are over 700 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that terrestrial orchids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >2.5 million georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the Earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the long-term impacts of global climate change on biodiversity.

When lizards try out a more plant-based lifestyle: The macroevolution of mutualistic lizard-plant-interactions (Squamata: Sauria/Lacertilia)

Pollination and seed dispersal of plants by animals are key mutualistic processes for the conservation of plant diversity and ecosystem functioning. Although different animals frequently act as pollinators or seed dispersers, some species can provide both functions, so-called 'double mutualists', suggesting that the evolution of pollination and seed dispersal may be linked. Here, we assess the macroevolution of mutualistic behaviours in lizards (Lacertilia) by applying comparative methods to a phylogeny comprising 2,838 species. We found that both flower visitation (potential pollination) (recorded in 64 species [2.3% of total] across 9 families) and seed dispersal (recorded in 382 species [13,5% of total] across 26 families) have evolved repeatedly in Lacertilia. Furthermore, we found that seed dispersal activity pre-dated flower visitation and that the evolution of seed dispersal activity and flower visitation was correlated, illustrating a potential evolutionary mechanism behind the emergence of double mutualisms. Finally, we provide evidence that lineages with flower visitation or seed dispersal activity have higher diversification rates than lineages lacking these behaviours. Our study illustrates the repeated innovation of (double) mutualisms across Lacertilia and we argue that island settings may provide the ecological conditions under which (double) mutualisms persist over macroevolutionary timescales.

Assessing the relative performance of fast molecular dating methods for phylogenomic data

Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.

Phylogenomic data resolve the historical biogeography and ecomorphs of Neotropical forest lizards (Squamata, Diploglossidae)

Few studies have been conducted on the biogeography and phylogenetic relationships of Neotropical forest lizards (Diploglossidae) because of incomplete taxon sampling, conflicting datasets, and low statistical support at phylogenetic nodes. Here, we enhance a recent nine-gene dataset with a genomic dataset of 3,232 loci and 642,775 aligned base pairs. The resulting phylogeny includes 30 diploglossid species, 10 of the 11 genera, and the three subfamilies. It shows significant support for all supra-specific taxa in either maximum likelihood or Bayesian analyses or both. With this well-supported phylogeny, we further investigate the historical biogeography of the group and how diploglossids reached the Caribbean islands. Our analyses indicate that Antillean diploglossid lizards originated from at least two overwater dispersals from South America. Our tests for the strength of convergent evolution between morphologically similar taxa support the recognition of a soil and a tree ecomorph. In addition, we propose grass, ground, rock, and swamp ecomorphs for species in this family based on ecological and morphological data and analyses.