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opencc-zeroJan 2020View details →

Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times

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.

opencc-zeroJan 2024View details →

Fossil calibrated molecular phylogenies of Southern cave weta

Aim: The biota of continents and islands are commonly considered to have a source-sink relationship, but small islands can harbour distinctive taxa. The distribution of four monotypic genera within the southern subfamily Macropathinae on young oceanic islands indicates a role for long-distance dispersal and extinction. We used molecular dating to estimate the timing of the southern radiation and infer potential processes involved. Location: Subantarctic islands, South Africa, South America, Australia, Aotearoa/New Zealand. Taxon: Southern hemisphere camel crickets subfamily Macropathinae within the Orthopteran family Rhaphidophoridae (Cave crickets/camel crickets/cave weta/tokoriro). Methods: Phylogenetic relationships were inferred from whole mtDNA genomes and nuclear sequences (45S cassette; four histones). We used a fossil and one palaeogeographic event to calibrate a molecular clock analysis. Results: We confirm that neither the Australian nor Aotearoa/New Zealand Rhaphidophoridae fauna are monophyletic. The Macropathinae radiation may have begun in the late Jurassic but trans-oceanic dispersal is required to explain the distribution of some lineages within the subfamily Macropathinae. Dating the most recent common ancestor of seven island endemic species with their nearest mainland relative suggests that each existed long before land surface on their island home was available. Main conclusions: If our molecular clock analysis is a good time estimate, then our data from the island endemic species suggest a failure to sample mainland species (New Zealand, Australia, or elsewhere) due to either extinction or lack of investment into taxonomy and species discovery.

opencc-zeroMay 2024View details →

Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity

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.

publicMay 2024View details →

Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity

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publicJan 2024View details →

Fossil calibrated molecular phylogenies of Southern cave weta

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publicJan 2020View details →

Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times

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dryad32/100

Fossilization processes have little impact on tip-calibrated divergence time analyses

The importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian Total-Evidence Dating methods which utilise fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non-random distribution of missing data. The impact of non-random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip-calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimise the impact of taphonomy on divergence time estimation.

opencc-zeroJun 2021View details →

dryad32/100

Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.

Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.

opencc-zeroDec 2010View details →

FIGURES 3–4 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

FIGURES 3–4. Wing venation of (A) Pareronia Bingham, 1907 (Pieridae), and (B) Hasora Moore, 1881 (Hesperiidae). See text for explanation.

FIGURE 22 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

FIGURE 22. Fossils marked on phylogenetic tree of "redefined" butterflies (Heikkilä et al. 2011), with family trees according to Simonsen et al. (2011, Papilionidae), Warren et al. (2009, Hesperiidae), Wahlberg et al. (2014, Pieridae), Wahlberg et al. (2005, Lycaenidae), and Espeland et al. (2015, Riodinidae).

FIGURE 2 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

FIGURE 2. Apomorphies, their placement on a tree, and the assignment of calibration points. See text for explanation.

FIGURES 11–13 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

FIGURES 11–13. Ƒanessa pluto Heer, 1849. Figures copied from (1875), Plate II, figures 1, 17 and 7, respectively. (A), copied by Scudder from original description by Heer; (B) and (C), figures sent to Scudder by Mr. Brunner de Wattenwyl, made after the same object. Note differences in wing shape and other details. Figs 14–16. Thaites ruminiana Scudder, 1875. Figures copied from Scudder (1875), Plate III, figures 9, 1 and 3, respectively. (A), underside of fossil; (B), reconstruction of venation; (C), reconstruction of markings. In (A) two separate subcostal veins have been drawn in the forewing, an impossible configuration in Lepidoptera, and apparently a mistake, corrected in (B) and (C). Fig. 17. Cyllo sepulta Boisduval, 1841, wing venation after Scudder (1875). Fig. 18. Butterfly fossil recorded by Wangrin (1939), but shown to be a fraud by Ansorge (2015). Photo kindly provided by J. Ansorge, Horst, Germany (see text for explanation).

FIGURE 23 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

FIGURE 23. Distribution of land, epicontinental seas (flooded continental areas) and oceans during the middle Paleocene (Thanetian Stage) at 60 Mya. From Smith, A.G., Smith, D.G. & Funnell, B.M. (1994); with permission of Cambridge University Press and University of East Anglia.

FIGURE 1 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

FIGURE 1. Localities of fossil butterflies plotted ion a modern map. See Table 1 for further, complementary information.

FIGURE 5 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

FIGURE 5. Ƒanessa amerindica Miller & Brown, 1989, holotype, collections of Invertebrate Paleontology, University of Florida. Photo by Roger Portell. Fig. 6. Pseudoneorina coulleti Nel & Descimon, 1984. France, Dép. Alpes-de-Haute- Provence, Dauphin, specimen in coll. M. Henrotay; photo by courtesy of M. Henrotay. Fig. 7. Archaeolycorea ferreirai Martins-Neto, 1989. Fig. 4A of original description. Fig. 8. Oligodonta florissantensis Brown, 1976, holotype, collections of Invertebrate Paleontology, University of Florida. Photo by courtesy of Akito Kawahara. Fig. 9. Neorinella garciae Martins- Neto, Kucera-Santos, de Moraes Vieira & de Campos Fragoso, 1993. Fig. 3A of original description. Fig. 10. Protocoeliades kristenseni de Jong, 2016, holotype, Zoologisk Museum, Copenhagen, Denmark. Photo by Department of Paleobiology, National Museum of Natural History, Washington DC, USA.

Figure 4 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

Figure 4. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 28 concatenated individual mtDNA gene sequences, i.e. 14 from female-type (12 protein-coding and 2 rRNA genes) and 14 (12 protein-coding and 2 rRNA genes) from male-type mitochondria. Values for branch support above each node represent Bayesian posterior probabilities percentage/ maximum likelihood bootstrap.

Figure 3 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

Figure 3. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 14 concatenated individual mtDNA gene sequences (12 protein-coding and 2 rRNA genes). Values for branch support above each node represent Bayesian posterior probabilities percentage/maximum likelihood bootstrap support. *Supported values ≥ 95 are represented by an asterisk.

Figure 1 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

Figure 1. Recent multi-locus phylogenetic hypotheses on Gonideinae sensu Pfeiffer et al. (2019). Vertical bars indicate subfamilies recognized in respective publications. Note that Froufe et al. (2020) adopted a new systematic framework with three instead of two family-group levels, and thus, traditional tribes (ending -ini) are considered subtribes (ending -ina) in that study.

Figure 6 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

Figure 6. Relationship between (A) mean Ka/Ks and substitution rate (μ) per female-type (full circles) and male-type (empty circles) mtDNA protein-coding gene; and (B) differences between male- and female-type K a /K s and μ per proteincoding mtDNA gene.

Figure 2 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

Figure 2. Gene maps of the F- and M-type mitochondrial genomes of Lens contradens, Physunio superbus, Hyriopsis bialata and Rectidens sumatrensis. Genes positioned inside the circle are encoded on the heavy strand, and genes outside the circle are encoded on the light strand. Colour codes: small and large ribosomal RNAs (red); transfer RNAs (purple); M-orf, F-specific open reading frame (yellow); M-orf, M-specific open reading frame (yellow); protein-coding genes (green).