Leveraging graphical model techniques to study evolution on phylogenetic networks

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 13, 2025

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be tree, or network if it includes reticulations, representing events such as hybridization admixture. Computing the likelihood data observed at leaves costly size complexity grows. Efficient algorithms exist for trees, but cannot applied to networks. We show that vast array models trait phylogenetic networks reformulated graphical models, which efficient belief propagation exist. provide brief review on general then focus linear Gaussian continuous traits. how techniques exact approximate (but more scalable) gradient calculations, prove novel results parameter inference some models. highlight possible fruitful interactions between methods. For example, approaches have potential greatly reduce computational costs phylogenies with reticulations.

Language: Английский

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Sample Size and Geometric Morphometrics Methodology Impact the Evaluation of Morphological Variation

Integrative Organismal Biology, Journal Year: 2024, Volume and Issue: 6(1)

Published: Jan. 1, 2024

Synopsis Geometric morphometrics has had a profound impact on our understanding of morphological evolution. However, factors such as sample size and the views elements selected for two-dimensional geometric morphometric (2DGM) analyses, which are often dictated by specimen availability time rather than study design, may affect outcomes those analyses. Leveraging large intraspecific sizes (n > 70) two bat species, Lasiurus borealis Nycticeius humeralis, we evaluate calculations mean shape, shape variance, centroid size. Additionally, assessed concordance multiple skull 2D with one another characterized variation in L. N. well closely related seminolus. Given that seminolus is morphologically cryptic species borealis, whether differences 2DGM approach would allow discrimination. We found reducing impacted increased were not consistent across or elements, trends shown all strongly associated another. Further, statistically different using elements. These results underscore importance selecting appropriate sizes, views, based hypothesis being tested. While there likely generalizable view can be employed given wide variety research questions systems evaluated 2DGM, solution to issues presented here run preliminary analyses thus ensuring robust conclusions.

Language: Английский

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Dinosaurs of all ilks bow and pay tribute to Peter Dodson, their intrepid chronicler, in an Anatomical Record Special Issue in his honor

The Anatomical Record, Journal Year: 2023, Volume and Issue: 306(7), P. 1589 - 1594

Published: May 7, 2023

Amazing how even after half of a century some things do not change. Together again at the University Pennsylvania, Peter Dodson and editorial co-author JL are energetically talking about six once, catching up as old friends wont to do. Walking along beautiful, tree-lined, quiet Locust walk, topics bounce from new dinosaur finds, what children (and grandchildren!) to, which our body parts latest stop working well (hey, we have known each other for 50 years!). As has been case since days together Yale, is lagging behind Peter's energy, now back in New Haven, him moving ever faster than his anatomy table mate. "C'mon, Jeff," august Penn Prof admonishes, "we finally get an audience with Professor Leidy, let's be late!" Yes, indeed. We arranged formal see Joseph or, more specifically, brain. For those you who acquainted Leidy (shame, shame!), he was America's first paleontologist note, having reported named (in 1858 1865; 1858, 1865) American dinosaur, "duck-billed" Hadrosaurus, unearthed Jersey thought state's only remains note were Mob boss Jimmy Hoffa!). Subsequently, reconstructed Hadrosaurus Philadelphia Academy Natural Sciences 1868, museum display any dinosaur. He estimated it 25 ft long and, based on its small forelimbs hind limbs, gave "kangaroo-like" stance semi-upright posture. Indeed, this vertical position became image dinosaurs imprinted collective visualization that day (see Dodson, 2009 discussion). Leidy's job Anatomy Pennsylvania School Medicine (the United States), polymath such renown biographer boldly titled story, Leidy: The Last Man Who Knew Everything (Warren, 1999). when parent organization Anatomical Record, Association formed 1888 (originally Anatomists, today seen exclusionary banner, but done then highlight specifically emergence American—over European—science), unanimously chosen President, absentia no less. by many embodiment scientist, greatest day. There giants there GIANT giants, falls into latter category (Figure 1). And brings us another titan science, reason Special Issue, JL's fast colleague, Dodson. Like ancestor, (our ties too close continued formalities here) giant among dinosaurs, easy feat if think it. His contributions understanding world dinosaurs—from paleontological findings, scholarly writings, exhibit creations, birthing superb progeny—have made stand out science. given much own journal, being frequent contributor (e.g., 2003, 2009, 2020; Hedrick et al., 2020, 2022; Schachner 2011; Tumanova 2023), Guest Editing two most popular Issues history, "Unearthing Dinosaurs: Insights their Functional Morphology Paleobiology" (Dodson, 2009; Laitman, Laitman & Albertine, 2009) "The Hidden World Dinosaurs" (Hedrick Figure 2). so demand Publisher, Wiley, had print additional copies individual sale (Dodson Dinos make money, least Wiley!) Beyond quality gift shared fortunate student, mentee, or colleague: boundless goodness caring. This "Dodsoness" spanned career touched many. written previously kindness helped insecure shy (no comments there, please!). Yale graduate student survive overwhelming fears onset path 2017). More point here dinosaur-philic students mentees grown prospered significant part due loving guidance. current special, "Dinosaurs: Ideas Old Bones" (Fiorillo 2023) meticulously Guest-edited three learned craft upon poppa Dodson's knee students: Anthony Fiorillo, Executive Director Mexico Museum History Science; Catherine Forster, Geology Biology George Washington University; David Weishampel, Evolution Johns Hopkins University. These themselves extraordinary careers multifaceted paleontology biology, referred "the Big Three" PD's (by Catherine; oy!, I can hear growls PD progeny!). write this, Tony likely thoroughly enjoying warmth Mexico, spent good studying arctic (equally cold that, sadly, never achieved childhood dream playing center field York Yankees; hey, Tony, they won Series still might chance!); Catherine, Tony's office mate (she dissertation field-work repaid her occasional dog-sitter), followed directly Poppa love embracing horned prolific career; Dave, gaining PhD 1981, thus placing "first" all progeny (all others always compare one's student—and usually wince name mentioned!) marvelous path, within authored consider definitive work Dinosauria (Weishampel 2007), consultant friend Steven Spielberg's Jurassic Park series (wonder got free tickets movies?). While extraordinarily successful trio Cretaceous, time come major project. HS big smile fact journal served vehicle historic marriage 3). one will issue, best brightest responded eagerly contribute volume honoring Peter. while Issue focuses findings recent mammoth, sister crocodiles, Age Crocodilians Their Kin: Anatomy, Physiology, Evolution," Edited Casey Holliday (an academic "grandson" Peter) Missouri Emma R. (another Louisiana State Health Center (Holliday Schachner, Smith, 2022), also largely homage Just mention something say "thanks" colleagues former grand-students coming rock pile contribute. Attesting broad influence, focus solely particular interests/scholarship charting rise distribution ceratopsian (he undisputed king!). Rather, just some, span glorious gamut: detailed descriptions unusual Therapods (really? hadrosaurs, Hoffa…who knew actually interesting; sorry, native Yorker little control commenting Jersey; Gallagher, 2023); reports iguanodontian South Africa (Forster insights evolutionary relationships analyses hyolaryngeal apparatus extant archosaurs (i.e., birds crocodilians; Yoshida reconstructions pectoral girdle forelimb musculature Megaraptora (Rolando osteohistology Dromornis stironi implications histology Australian mihirung (Chinsamy insightful observations fracture disease large-bodied ornithomimosaur identifying endosteal bone fossil record (Chinzorig comprehensive assessment history future study morphometrics non-avian (Hedrick, modeling assess predict abundance large carnivorous Upper Morrison Formation Cretaceous Dinosaur formation classmate, ever-creative James Farlow; awe super-bright dino dudes surrounded "back day"; Farlow number papers—naturally—on great love, ceratopsians, including lead Editor Fiorillo Tykoski, successor teaching Penn, Ali Nabavizadeh (Nabavizadeh, 2023). Even cover creative Peter, lovingly created Record Associate artist extraordinaire) Adam Hartstone-Rose (Hartstone-Rose What incredible smorgasbord ideas minds today's workers. "Hurry up, exhorts, "our appointment 10:00 sharp curator expecting us." Along accommodating wife Leila (who pressed service photographer; adoring Peter—who does not?—not chance she would spend hours taking photos poor JL!), bundled Uber headed Mütter Leidy. tried visit residence Wistar Institute Penn's campus (they turned away did appropriate told receive anyone"). Since then, domicile changed (fortunately) Museum, surgeon Thomas Dent 1856 donated extensive collections anatomical pathological specimens College Physicians Philadelphia, wherein both cared (btw, really cool place, choose between cracked Liberty Bell Mütter, go Mütter!; Worden, 2002). JL, visiting almost religious experience, direct ancestor ways: PD, Veterinary School, comparative anatomist vertebrate line direct; also, professor aficionado, past President society bond powerful. Both aware presence present 4). brought permanent home, thick heavy glass jar. remained may seem odd, uncommon 19th preserve brains people (when daughter custom, Miss Snarky "do worry, dad, safe"). Professor's brain rather eerie shade green, probably preservatives used. Green not, encased remain repository arguably scientific knowledge held mortal century. Within lay secrets founding States. greatness, special rare moment. group left day—and next stop, second beloved Sciences—JL could pondering gravity encounter. rarest gems Paleontology, Professors together. kids say, "two dudes." sometimes complaining photographer) came main hall staring face created. images everywhere. One, particular, caught attention accurately summarized moment person appreciation: picture reconstruction Avaceratops bold banner read "A Rare Find" 5). It clearly identified scientist. very proud, behalf share wonderful science scientists offer bones, give heartfelt thanks "Rare hope explore articles enjoy learn them have. dear Jeffrey T. Laitman: Conceptualization; writing – original draft; review editing; visualization. Heather F. Smith:

Language: Английский

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Introduction to Dinosaurs: New Ideas from Old Bones papers honoring Peter Dodson

The Anatomical Record, Journal Year: 2023, Volume and Issue: 306(7), P. 1595 - 1601

Published: May 13, 2023

Abstract This special volume of The Anatomical Record honors the life‐long commitment to anatomy and paleontology by Professor Peter Dodson (Emeritus, University Pennsylvania). Peter's legacy is not only rooted in his own research interests, but also wealth former students he mentored over career, many whom have made their new contributions fields through original scientific investigation. Within these 18 papers, which cover multiple taxa, continents, methodologies, each contributors brought this unique work that can be traced back some form inspiration honoree.

Language: Английский

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GEOMETRIC MORPHOMETRIC APPROACH TO ESTABLISH PHYLOGENETIC AFFINITIES OF ENIGMATIC PTEROSAUR SPECIMENS FROM THE LOWER CRETACEOUS OF SOUTH KOREA

Acta Palaeontologica Romaniae, Journal Year: 2024, Volume and Issue: 20 (1), P. 77 - 86

Published: Feb. 11, 2024

Fragmentary but scientifically important pterosaur fossils have been reported in Lower Cretaceous strata such as the Jinju and Hasandong formations of South Korea. Recently, several large teeth a second wing phalanx found these suggested to affinities with Boreopteridae, clade which has so far only Yixian Formation China. Here, phylogenetic proposed boreopterid specimens are reassessed, using two-dimensional geometric morphometric shape analyses. The analyses Korean different morphospaces from Fm. boreopterids, plot them closer anhanguerians. An isolated does close Zhenyuanopterus longirostris morphospace defined by first two principal component axes, taxa lineages also plotted closely, or even closer. Thus, there seems be no clear evidence that belong tooth appear very those established members this clade. Therefore, hypothesis some can referred is here tentatively rejected.

Language: Английский

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Ichnotaxonomic and Morphological Differentiation in Pterosaur Tracks Using Geometric Morphometric Analysis: A Case Study on Pteraichnus Manus Tracks from Cretaceous East Asia

Cretaceous Research, Journal Year: 2024, Volume and Issue: 167, P. 106033 - 106033

Published: Nov. 8, 2024

Language: Английский

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