Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa

Klug, S. & Kriwet, J. (2010). Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa. —Zoologica Scripta, 39, 331–342. Dogfish sharks (Squaliformes) constitute a monophyletic group of predominantly deep‐water neoselachians, but the reasons and timing of their adaptation to this hostile environment remain ambiguous. Late Cretaceous dogfish sharks, which generally would be associated with deep‐water occur predominantly in shallow water environments. Did the end‐Cretaceous mass extinction event that eliminated large numbers of both terrestrial and aquatic taxa and clades including sharks trigger the evolutionary adaptation of present deep‐water dogfish sharks? Here, we construct, date, and analyse a genus‐level phylogeny of extinct and living dogfish sharks to bring a new perspective to this question. For this, eleven partial source trees of dogfish shark interrelationships were merged to create a comprehensive phylogenetic hypothesis. The resulting supertree is the most inclusive estimate of squaliform interrelationships that has been proposed to date containing 23 fossil and extant members of all major groups. ?Eoetmopterus represents the oldest dalatoid. ?Microetmopterus, ?Paraphorosoides, ?Proetmopterus and ?Squaliogaleus are stem‐group dalatoids in which bioluminescence most likely was not developed. According to our analyses, bioluminescence in dogfish sharks was already developed in the early Late Cretaceous indicating that these sharks adapted to deep‐water conditions most likely at about 100 Mya. The advantage of this reconstruction is that the fossil record is used directly for age node estimates rather than employing molecular clock approaches.     

Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times

This article reviews the most common methods used today for estimating divergence times and rates of molecular evolution. The methods are grouped into three main classes: (1) methods that use a molecular clock and one global rate of substitution, (2) methods that correct for rate heterogeneity, and (3) methods that try to incorporate rate heterogeneity. Additionally, links to the most important literature on molecular dating are given, including articles comparing the performance of different methods, papers that investigate problems related to taxon, gene and partition sampling, and literature discussing highly debated issues like calibration strategies and uncertainties, dating precision and the calculation of error estimates.     

Biology meets engineering: The structural mechanics of fossil and extant shark teeth

The majority of studies on the evolution and function of feeding in sharks have focused primarily on the movement of cranial components and muscle function, with little integration of tooth properties or function. As teeth are subjected to sometimes extreme loads during feeding, they undergo stress, strain, and potential failure. As attributes related to structural strength such as material properties and overall shape may be subjected to natural selection, both prey processing ability and structural parameters must be considered to understand the evolution of shark teeth. In this study, finite element analysis was used to visualize stress distributions of fossil and extant shark teeth during puncture, unidirectional draw (cutting), and holding. Under the loading and boundary conditions here, which are consistent with bite forces of large sharks, shark teeth are structurally strong. Teeth loaded in puncture have localized stress concentrations at the cusp apex that diminish rapidly away from the apex. When loaded in draw and holding, the majority of the teeth show stress concentrations consistent with well designed cantilever beams. Notches result in stress concentration during draw and may serve as a weak point; however they are functionally important for cutting prey during lateral head shaking behavior. As shark teeth are replaced regularly, it is proposed that the frequency of tooth replacement in sharks is driven by tooth wear, not tooth failure. As the tooth tip and cutting edges are worn, the surface areas of these features increase, decreasing the amount of stress produced by the tooth. While this wear will not affect the general structural strength of the tooth, tooth replacement may also serve to keep ahead of damage caused by fatigue that may lead to eventual tooth failure. J. Morphol., 2011. © 2010 Wiley‐Liss, Inc.     

tipdatingbeast: an r package to assist the implementation of phylogenetic tip‐dating tests using beast

Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to coestimate the timing of evolutionary events with rates of molecular evolution. In this context, beast , a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce tipdatingbeast , an r package built to assist the implementation of various phylogenetic tip‐dating tests using beast . tipdatingbeast currently contains two main functions. The first one allows preparing date‐randomization analyses, which assess the temporal signal of a data set. The second function allows performing leave‐one‐out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical data set and supply practical guidance for results interpretation.     

Occlusal pattern of cheek teeth in extant Spermophilus: A new approach to the identification of species

Discrete characters of the occlusal surface (additional cusps) have been studied to elaborate a new approach to the identification of the Ground Squirrel species Spermophilus odessanus, S. suslicus, S. pygmaeus, S. citellus, and S. xanthoprymnus. Data on the presence/absence of the additional cusps have been represented as star plots and, in addition, have been studied using discriminant function analysis. The species‐specific sets of the characters (patterns of bunodonty) have been revealed and are of high diagnostic value. The Citellus‐set is defined by the presence of mesostyles and the rareness of the metastylids, paraconules and metaconules, hypostyles and protostyles. The Pygmaeus‐set is characterized by the presence of additional cusps in the lower cheek teeth. The Odessanus‐oriented set is found in the Spermophilus pygmaeus, S. odessanus, and S. suslicus. The relatively high frequency of additional cusps of the metaloph and the paraloph is characteristic for this set. The Plesiomorphic‐set (characters shared by all the studied species and for this reason regarded herein as ancestral) is found in S. xanthoprymnus. The patterns of bunodonty serve as diagnostic criteria only as a whole: the shape of a star plot (relations among the character frequencies), rather than certain character values, is indicative. An optimal level of identification of species is possible based on the combination of the discrete characters mentioned and on the size parameters of the third upper molar. The occlusal sets are intended to remain stable during the time of species existence and seem to correspond to trends in specialization. The functional meaning of the sets can be explained by the dependence between the presence/absence of the discrete characters and the shape of the crown and its main lophs. Each pattern is likely to correspond to a trophic niche, and this niche corresponds to the species. J. Morphol. 277:814–825, 2016. © 2016 Wiley Periodicals, Inc.     

A palaeontological and phylogenetical analysis of squaliform sharks (Chondrichthyes: Squaliformes) based on dental characters

Squaliformes comprise the major proportion of modern deep-water sharks, yet their fossil history and phylogenetic relationships are still poorly understood. New analyses have been undertaken, however, and new living and fossil species have been discovered during the past 10 years. A cladistic analysis involving 29 dental characters has been made and most living and fossil genera are included. On the basis of their dental morphology, the monophyly of the Squaliformes can be supported if the fossil genus Protospinax is excluded. The traditional phylogenetic positions of most living genera, Protosqualus, Cretascymnus and Eoetmopterus, are confirmed despite the fact that the Oxynotidae, Etmopterinae, Palaeomicroides, Proetmopterus and Microetmopterus have some atypical phylogenetic relationships within the Squaliformes. The addition of the palaeontological data in a phylogenetic tree including fossil and living Squaliformes demonstrates some gaps in the fossil record. Nevertheless, and as a consequence of that stratigraphy-phylogeny inference, two particular events can be pinpointed in the history of the Squaliformes: the first one occurs after the major Cenomanian-Turonian anoxic event and the second one after the Cretaceous/Tertiary crisis. The first radiation involves the majority of the living Squaliformes (Somniosinae, Centrophorinae, most of the Etmopterinae, Oxynotinae) in deep-sea waters, the second, the more epipelagic sharks (most of the Dalatiidae), suggesting a secondary adaptation to more shallow environments.     

From extant to extinct: locomotor ontogeny and the evolution of avian flight

Evolutionary transformations are recorded by fossils with transitional morphologies, and are key to understanding the history of life. Reconstructing these transformations requires interpreting functional attributes of extinct forms by exploring how similar features function in extant organisms. However, extinct-extant comparisons are often difficult, because extant adult forms frequently differ substantially from fossil material. Here, we illustrate how postnatal developmental transitions in extant birds can provide rich and novel insights into evolutionary transformations in theropod dinosaurs. Although juveniles have not been a focus of extinct-extant comparisons, developing juveniles in many groups transition through intermediate morphological, functional and behavioral stages that anatomically and conceptually parallel evolutionary transformations. Exploring developmental transitions may thus disclose observable, ecologically relevant answers to long puzzling evolutionary questions.     

New crinoids from the Baltic region (Estonia): fossil tip‐dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the Flexibilia (Echinodermata)

This study documents previously unknown taxonomic and morphological diversity among early Palaeozoic crinoids. Based on highly complete, well preserved crown material, we describe two new genera from the Ordovician and Silurian of the Baltic region (Estonia) that provide insight into two major features of the geological history of crinoids: the early evolution of the flexible clade during the Great Ordovician Biodiversification Event (GOBE), and their diversification history surrounding the end‐Ordovician mass extinction. The unexpected occurrence of a highly derived sagenocrinid, Tintinnabulicrinus estoniensis gen. et. sp. nov., from Upper Ordovician (lower Katian) rocks of the Baltic palaeocontinent provides high‐resolution temporal, taxonomic and palaeobiogeographical constraints on the origin and early evolution of the Flexibilia. The Silurian (lower Rhuddanian, Llandovery) Paerticrinus arvosus gen. et sp. nov. is the oldest known Silurian crinoid from Baltica and thus provides the earliest Baltic record of crinoids following the aftermath of the end‐Ordovician mass extinction. A Bayesian ‘fossil tip‐dating’ analysis implementing the fossilized birth–death process and a relaxed morphological clock model suggests that flexibles evolved c. 3 million years prior to their oldest fossil record, potentially involving an ancestor–descendant relationship (via ‘budding’ cladogenesis or anagenesis) with the paraphyletic cladid Cupulocrinus. The sagenocrinid subclade rapidly diverged from ‘taxocrinid’ grade crinoids during the final stages of the GOBE, culminating in maximal diversity among Ordovician crinoid faunas on a global scale. Remarkably, diversification patterns indicate little taxonomic turnover among flexibles across the Late Ordovician mass extinction. However, the elimination of closely related clades may have helped pave the way for their subsequent Silurian diversification and increased ecological role in post‐Ordovician Palaeozoic marine communities. This study highlights the significance of studies reporting faunas from undersampled palaeogeographical regions for clade‐based phylogenetic studies and improving estimates of global biodiversity through geological time.     

The fossil record and estimating divergence times between lineages: Maximum divergene times and the importance of reliable phylogenies

Summary Bounded estimates on divergence times between lineaes are crucial to the calculation of absolute rates of molecular evolution. Upper (minimum) bounds on divergence times are easily estimated based on earliest fossil finds. Lower (maximum) bounds are more difficult to estimate; the age of putative ancestors may be used, though in practice it is virtually impossible to distinguish ancestors from primitive sister groups, which do not, of logical necessit, consitute lower bounds on divergence times. Two relatively new approaches to estimating lower bounds directly assess the incompleteness of the fossil record. The first uses taphonomic control groups to distinguish real absences from nonpreservation, while the second, and probably more powerful, uses the quality of the fossil recored to estimate confidence intervals on the bases of stratigraphic ranges. For some groups, especially vertebrates, the inclusion or exclusion of problematic fossils can dramaticaly affect estimated lower bounds on divergence times, often swamping the uncertainties due to the incompleteness of the fossil record and/or corelation and dating errors. When datable paleogeographic events reflect ancient divisions of faunas, a lower bound on the divergence time of speices within a fauna can be established based on the geologic, rather than fossil, record. The fossil records of hominids, eutherianmammals, echinoids, and geese are used as examples.This article was presented at the C.S.E.O.L. Conferrence on DNA-DNA Hybridization and Evolution, Lake Arrowhead, California, May 11–14, 1989     

Comment on Rieux and Balloux: calibration from tip‐dating can compromise topological accuracy and evolutionary inference

We contribute to the recent review of Rieux & Balloux, 2016, Mol. Ecol., 25, 1911 on inferences from tip‐dated phylogenies by developing their discussion on the influence of population size (N_e) under panmixia for the estimation of substitution rate (μ). We highlight how phylogenetic trees inferred with tip‐dated sequences under large panmictic N_e tend to erroneously enforce an age‐based coalescent pattern on the posterior distribution of trees, which in turn results in systematically inflated estimates of μ. We discuss the consequences of this and suggest how to accommodate the issue in the short term and long term.     

Phylogeny of snout butterflies (Lepidoptera: Nymphalidae: Libytheinae): combining evidence from the morphology of extant, fossil, and recently extinct taxa

Snout butterflies (Nymphalidae: Libytheinae) are morphologically one of the most unusual groups of Lepidoptera. Relationships among libytheines remain uncertain, especially in the placement of the recently extinct Libythea cinyras and two fossils, L. florissanti , and L. vagabunda . The aim of this study is to present the first phylogenetic hypothesis of Libytheinae utilizing all available morphological data from extant and extinct species. Forty-three parsimony-informative characters were coded, and the all-taxa analysis resulted in six most parsimonious trees (length 92 steps, CI = 0.66, RI = 0.82). The subfamily was resolved as monophyletic and was split into Old World and New World clades. Inclusion of extinct species with considerable missing data had little effect on relationships of extant taxa, although Bremer support values and jackknife frequencies generally decreased if extinct species were included. In order to preserve the monophyly of extant genera, two fossils are assigned to Libytheana for the first time ( L. florissanti comb. n. and L. vagabunda comb. n.). This study demonstrates the value of morphological data in phylogenetic analysis, and highlights the contribution that can be made by scoring extinct taxa and including them directly into the analysis.     

Inflorescence bracts of fossil and extant Tilia in North America,Europe, and Asia: patterns of morphologic divergence and biogeographic history

The enlarged inflorescence bract diagnostic of extant Tilia has an extensive Tertiary fossil record in the Northern Hemisphere. Diversity of bract morphology, and the extent of adnation between peduncle and bract, is reviewed for fossil and extant species of Tilia. An extinct type of bract with an orbicular outline and palmate venation is documented by the fossil species Tilia circularis (Chaney) comb. nov. from the early Oligocene of Oregon and is designated Type A. Living species of the genus have elongate bracts with predominately pinnate venation that are borne in two basic configurations: Type B, with the peduncle fused only to the extreme base of the bract lamina, as in extant Tilia endochrysea Hand.-Mzt. of southern China; and Type C with the peduncle fused medially along the basal one-third of the bract lamina, as in most extant species. Bracts of Type B were widely distributed in the Tertiary of western North America (late Eocene to Miocene) and Europe (early Miocene to Pliocene), while those of Type C are known in the fossil condition only from the middle and late Tertiary of Asia and Pliocene of Europe. The bracts of T. circularis, like those of type B, are borne on relatively long stalks and have the peduncle fused only at the extreme base. The fossil record supports recognition of the following characters as apomorphic in Tilia bract evolution: bracts sessile, peduncle adnate to the upper surface of the bract, and pinnate bract venation.     

A comprehensive phylogeny of extinct and extant Rhizomyinae (Rodentia): evidence for multiple intercontinental dispersals

The subfamily Rhizomyinae is known from the Late Oligocene up to the present. Today this group comprises six species, which live in southern Asia and eastern Africa. Despite the current moderate diversity of the rhizomyines, they had a greater diversification and wider distribution in the past: from Asia, their land of origin, to Africa, which they entered during the Early Miocene. So far 33 fossil species can be referred to this group. A cladistic analysis involving fossil and living species has been carried out. Prokanisamys spp. turned out to be the most basal taxa of the ingroup. This analysis calls into question the monophyly of several genera, and allows the proposal of a phylogenetic definition of the tribes Tachyoryctini and Rhizomyini. It also provides information about the origin of the African rhizomyines and allows inferring multiple dispersal phenomena from Asia to Africa in Early and Late Miocene times.     

Horizon annealing: a collection‐based approach to automated sequencing of the fossil record

Sheets, H.D., Mitchell, C.E., Izard, Z.T., Willis, J.M., Melchin, M.J. & Holmden, C. 2012: Horizon annealing: a collection‐based approach to automated sequencing of the fossil record. Lethaia, Vol. 45, pp. 532–547. A number of different approaches to quantitative biochronology have been proposed and used to construct high‐resolution time‐scales for a range of uses. We present a new approach, horizon annealing, which uses simulated annealing to optimize the sequencing of collection horizons. Temporal sequences of events produced by this method are compared with those produced by graphic correlation, CONOP and RASC for a series of previously studied exemplar data sets. Horizon annealing produces results similar to other methods, but it does have properties (the ordination of collections and the avoidance of some local minima) that make it useful for high‐resolution studies, particularly those based on capture‐mark‐recapture methods requiring detailed presence–absence data for individual collections and taxa. □ Chronostratigraphy, graphic correlation, graptolite, rate of evolution, CONOP9.     

Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses

Background  

Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae: Geogale). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed.     

Origin and divergence of Afro-Indian Picrodendraceae: linking pollen morphology,dispersal modes,fossil records,molecular dating and paleogeography

The pantropical Picrodendraceae produce mostly spheroidal to slightly oblate, echinate pollen grains equipped with narrow circular to elliptic pori that can be hard to identify to family level in both extant and fossil material using light microscopy only. Fossil pollen of the family have been described from the Paleogene of America, Antarctica, Australia, New Zealand, and Europe, but until now none have been reported from Afro-India. Extant pollen described here include representatives from all recent Picrodendraceae genera naturally occurring in Africa and/or Madagascar and south India and selected closely related tropical American taxa. Our analyses, using combined light microscopy and scanning electron microscopy, show that pollen of the Afro-Indian genera encompass three morphological types: Type 1, comprising only Hyaenanche; Type 2, including Aristogeitonia, Mischodon, Oldfieldia and Voatamalo; Type 3, comprising the remaining two genera, Androstachys and Stachyandra. Based on the pollen morphology presented here it is evident that some previous light microscopic accounts of spherical and echinate fossil pollen affiliated with Arecaceae, Asteraceae, Malvaceae, and Myristicaceae from the African continent could belong to Picrodendraceae. The pollen morphology of Picrodendraceae, fossil pollen records, a dated intra-familial phylogeny, seed dispersal modes, and the regional Late Cretaceous to early Cenozoic paleogeography, together suggest the family originated in the Americas and dispersed from southern America across Antarctica and into Australasia. A second dispersal route is believed to have occurred from the Americas into continental Africa via the North Atlantic Land Bridge and Europe.     

Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.

Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.     

A systematic approach to infer biological relevance and biases of gene network structures

The development of high-throughput technologies has generated the need for bioinformatics approaches to assess the biological relevance of gene networks. Although several tools have been proposed for analysing the enrichment of functional categories in a set of genes, none of them is suitable for evaluating the biological relevance of the gene network. We propose a procedure and develop a web-based resource (BIOREL) to estimate the functional bias (biological relevance) of any given genetic network by integrating different sources of biological information. The weights of the edges in the network may be either binary or continuous. These essential features make our web tool unique among many similar services. BIOREL provides standardized estimations of the network biases extracted from independent data. By the analyses of real data we demonstrate that the potential application of BIOREL ranges from various benchmarking purposes to systematic analysis of the network biology.