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203 results for “Divergence times”
The implications of incongruence between gene tree and species tree topologies for divergence time estimation
<p>Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analysing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation.</p>
Figure 4. Approximate distributions and associated divergence times for A in Mitochondrial Dna Sequence Data Indicate Evidence For Multiple Species Within Peromyscus Maniculatus
Figure 4. Approximate distributions and associated divergence times for A) Peromyscus maniculatus-like ancestor; B) P. melanotis-like ancestor; C) P. gambelii/keeni/sejugis/sp.-like ancestor; D) P. polionotus-like ancestor; E) P. sonoriensis-like ancestor; F) P. labecula and P. maniculatus - like ancestor; G) P. keeni/sp.-like ancestor; and H) P. keeni-like, P. gambelii-like, P. sejugis-like, and P. sp.-like ancestors. Divergence times were estimated from the BEAST analysis (Version 2.4, Bouckaert et al. 2014) of the mitochondrial cytochrome-b gene dataset (see Fig. 3). Shading schemes that correspond to species distributions are shown in the inset.
Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris)
<p>The saturniid moth genus <em>Automeris</em> includes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru. <em>Automeri</em>s moths are cryptically colored and their forewings resemble dead leaves, with conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships within <em>Automeris</em> and between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny of <em>Automeris</em> to date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera, <em>Pseudautomeris</em> and <em>Leucanella</em>, as well as a morphologically distinct genus, <em>Molippa</em>. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to reconstruct a high-quality dataset for phylogenetic analysis. The resulting phylogeny supports <em>Automeris</em> as a paraphyletic genus, with <em>Leucanella</em> and <em>Pseudautomeris</em> nested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects of <em>Automeris</em> biology, including anti-predator defense mechanisms, ecological adaptations, geographical distribution patterns, and potential drivers of speciation.</p>
Fig. 6. Divergence times estimated from a in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism
Fig. 6. Divergence times estimated from a concatenated data set of per, COX1 and ITS2 sequences for the Lucilia bufornivora species group. Substitution model and relaxed clock models were unlinked for each gene. The tree was calibrated by setting the root to the node age corresponding to the split between Luciilinae and Calliphorinae subfamilies (~19 mya) as estimated by Wallman et al. (2005). Blue bars represent 95% highest posterior density (HPD) of each node age. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
FIGURE 1 in Divergence times of the Rhoadsia clade (Characiformes: Characidae)
FIGURE 1 | Maximum likelihood phylogeny (left) of representative members of family Characidae and Bayesian chronogram (right) of the subfamily Stethaprioninae. Only species names of the subfamily Stethaprioninae are displayed in both trees (full trees in Figs. S4 and S5). Nodes with ultrafast bootstrap support ≥95 are shown with a black dot (left). The nodes on the time tree depict the posterior distribution of the age estimates (right). Abbreviations of geological ages left to right, top to bottom: Ne = Neogene, Q = Quaternary, P = Paleocene, Eo = Eocene, Ol = Oligocene, Mi = Miocene, P = Pliocene.
Fig. 4. Maximum clade credibility and divergence time estimations from BEAST reconstruction using 89 specimens and 20 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 4. Maximum clade credibility and divergence time estimations from BEAST reconstruction using 89 specimens and 20 genes. Background colors represent the four Manilkarinae clades. Node labels are given as the mean of node age estimates for the main clades, including their 95% HPD and posterior probability (PP). The latter are only shown when PP <1. Epoch and ages in million years ago are represented at the bottom. Primary calibration points from fossils data are indicated with a red star, whereas clades constrained as monophyletic are labeled with an asterisk. RN: Réserves Naturelles; SF: Service Forestier.
Figure 4 in Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
Figure 4. Palaeogeographical reconstructions of New Zealand. Land is shaded in green, coastal areas in light yellow, shallow sea in light blue, and deep sea in dark blue. Inset shows present-day map of New Zealand: (1) the Wanganui Basin; (2) the Kuripapango Strait; (3) the Ruataniwha Strait; and (4) the Manawatu Strait. Row A maps are adapted from GNS Science reconstructions based on the studies by King et al. (1999) and King (2000). Row B maps are adapted from the work of Trewick & Bland (2012) and are focused on the area outlined in red on the present-day inset. Row C maps are adapted from the study by Bunce et al. (2009); the ~20 Mya map shows the entire landmass, and subsequent ones are focused on the area outlined in the black bounding box. Background grey shading denotes changing geological periods.
Figure 2 in Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
Figure 2. RAXML tree of Callaeidae mitogenomes, excluding the control region, showing different relationships and bootstrap support between Callaeidae (shaded green), Notiomystis cincta, Petroica spp. and Poodytes punctatus. Bootstrap support is shown at nodes.
Figure 3 in Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
Figure 3. BEAST chronogram of Callaeidae and 17 other passerines, based on a relaxed lognormal clock and fossil calibrations from the studies by Oliveros et al. (2019) and Scofield et al. (2017). Time scale is in millions of years. Mean divergence dates are shown in black at nodes; bars represent posterior probability intervals. Bayesian posterior probability is one unless specified by a red asterisk.
Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris)
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Data from: Ecological trait divergence over evolutionary time underlies the origin and maintenance of tropical spider diversity
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Data from: Robustness of divergence time estimation despite gene tree error: A case study of fireflies (Coleoptera: Lampyridae)
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The implications of incongruence between gene tree and species tree topologies for divergence time estimation
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Data from: Responses of activity rhythms to temperature cues evolve in Drosophila populations selected for divergent timing of eclosion
Even though the rhythm in adult emergence and rhythm in locomotor activity are two different rhythmic phenomena that occur at distinct life-stages of the fly life cycle, previous studies have hinted at similarities in certain aspects of the organisation of the circadian clock driving these two rhythms. For instance, the period gene plays an important regulatory role in both rhythms. In an earlier study, we have shown that selection on timing of adult emergence behaviour in populations of Drosophila melanogaster leads to the co-evolution of temperature sensitivity of circadian clocks driving eclosion. In this study, we were interested in asking if temperature sensitivity of the locomotor activity rhythm has evolved in our populations with divergent timing of adult emergence rhythm, with the goal of understanding the extent of similarity (or lack of it) in circadian organisation between the two rhythms. We found that in response to simulated jetlag with temperature cycles, late chronotypes (populations selected for predominant emergence during dusk) indeed re-entrain faster than early chronotypes (populations selected for predominant emergence during dawn) to 6-h phase-delays, thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time-cues). Additionally, we found that late chronotypes show higher plasticity of phases across regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of enhanced temperature sensitive activity/rest rhythms. Our results highlight remarkably similar organisation principles between emergence and activity/rest rhythms.
Local adaptation from afar: migratory bird populations diverge in the initiation of reproductive timing while wintering in sympatry
<p><span>The initiation of reproduction in many seasonally breeding animals is controlled by photoperiod and tends to be clinal: populations at higher latitudes breed later than those at lower latitudes, often reflecting a higher photoperiodic threshold. Migratory animals presumably time reproduction to match conditions at their breeding grounds at least in part by cues perceived</span> on their wintering grounds<span>. </span>We asked how closely related dark-eyed junco (<i>Junco hyemalis</i>) populations that overwinter in sympatry but breed in allopatry respond to their shared winter environment by comparing early spring indices of readiness to migrate and breed (baseline and elevated testosterone). We measured stable hydrogen isotopes from feathers grown the preceding year and claws grown during winter to estimate breeding and wintering latitudes, respectively. We predicted that if reproductive initiation is adapted to the emergence of resources at their respective breeding destinations, then birds migrating to higher latitudes (slate-colored junco; <i>J. h. hyemalis</i>) should delay breeding as compared to those migrating to lower latitudes (pink-sided junco; <i>J. h. mearnsi</i>) despite a common overwinter environment. We found higher testosterone in pink-sided juncos consistent with earlier reproductive initiation, suggesting local adaptation in reproductive phenology achieved through differential responses to predictive environmental cues.</p>
Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times
<p>Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data does not provide direct information about rates, but instead provides direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch. Often, the assumptions required for estimating rates for individual branches depend heavily on the implementation of multiple fossil calibrations in a single phylogeny. Here, we show that the basis of these assumptions is often critically undermined. First, we highlight that the temporal distribution of the fossil record often violates key assumptions of methods that use multiple fossil calibrations with relaxed clocks. With respect to "node calibration" methods, this conclusion is based on our inference that different fossil calibrations are unlikely to reflect the relative ages of different clades. With respect to the fossilised-birth-death-process, this conclusion is based on our inference that the fossil recovery rate is often highly heterogeneous. We then demonstrate that methods of divergence time estimation that use multiple fossil calibrations are highly sensitive to assumptions about the fossil record and among-branch-rate-variation. Given the problems associated with these assumptions, our results highlight that using multiple fossil calibrations with relaxed clocks often does little to improve the accuracy of divergence time estimates.</p> <p> </p>
Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element (UCE) data set (>3000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum-likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also result in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species-tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species-delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species-tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
<p>Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus <em>Arvicola</em>, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of <em>A. scherman</em> present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, <em>A. amphibius</em>, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.</p>
Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time
<p><span>The species studied in any evolutionary investigation generally constitute a 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 rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.</span></p>
Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity
<p>Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. Our results, presented as ancestral-state reconstructions, show that multicellularity arose independently twice in this clade. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae.</p>
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