scholarly journals Genomics Reveals the Origins of Historical Specimens

2021 ◽  
Author(s):  
Qian Cong ◽  
Jinhui Shen ◽  
Jing Zhang ◽  
Wenlin Li ◽  
Lisa N Kinch ◽  
...  
Keyword(s):  
Genomic Data ◽  
Species Concepts ◽  
Morphological Features ◽  
Phenotypic Traits ◽  
Museum Specimens ◽  
Biodiversity Research ◽  
Extant Species

Abstract Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computational protocols to overcome these challenges and applied our methods to resolve a series of long-standing controversies involving a group of butterflies. We deduced the geographical origins of several historical specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old specimens that serve as irreplaceable embodiments of species concepts cannot be confidently assigned to extant species or population due to the lack of diagnostic morphological features and clear documentation of the collection locality. The ability to determine where they were collected will resolve many on-going disputes. More broadly, we show the utility of applying genomics to historical museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

scholarly journals Genomics reveals the origins of ancient specimens

2019 ◽  
Author(s):  
Qian Cong ◽  
Jinhui Shen ◽  
Jing Zhang ◽  
Wenlin Li ◽  
Lisa N. Kinch ◽  
...  
Keyword(s):  
Dna Degradation ◽  
Species Concepts ◽  
Phenotypic Traits ◽  
Museum Specimens ◽  
Biodiversity Research

Centuries of zoological studies amassed billions of specimens in collections worldwide. Genomics of these specimens promises to rejuvenate biodiversity research. The obstacles stem from DNA degradation with specimen age. Overcoming this challenge, we set out to resolve a series of long-standing controversies involving a group of butterflies. We deduced geographical origins of several ancient specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old, poorly documented specimens that serve as irreplaceable embodiments of species concepts. The ability to figure out where they were collected will resolve many on-going disputes. More broadly, we show the utility of genomics applied to ancient museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

scholarly journals Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11602
Author(s):  
David T. Ledesma ◽  
Simon G. Scarpetta ◽  
Christopher J. Bell
Keyword(s):  
Morphological Variation ◽  
Phylogenetic Analyses ◽  
Morphological Features ◽  
Diagnostic Utility ◽  
Extensive Documentation ◽  
Extant Species ◽  
Traditionally Prepared ◽  
X Ray Computed ◽  
Cranial Osteology ◽  
First Time

Background There are limited data on intra- and interspecific osteological variation for many squamate clades. Those data are relevant for phylogenetic analyses that use osteological characters and for apomorphic identifications of fossils. We investigate whether morphological features in the skulls of extant gerrhonotine lizards can be used to distinguish taxa at the species- and genus-level and assess whether newly discovered intra- and interspecific osteological variation alters the utility of previously reported apomorphic features. We examined skulls of species belonging to the gerrhonotine genera Elgaria and Gerrhonotus. These genera contain 17 extant species, but the cranial osteology of only a few species was previously examined. As a result, intra- and interspecific osteological variation of these gerrhonotines is poorly understood. Methods We employed high-resolution x-ray computed tomography (CT) to scan 25 alcohol-preserved specimens. We provide data on the skulls of all eight species of Elgaria, four for the first time, and five species of Gerrhonotus, three for the first time. We examined 3-D reconstructed skulls of the scanned specimens as well as dry, traditionally prepared skeletons (when they were available). Results We found that the purported diagnostic utility of many previously described morphological features is impacted because of substantial morphological variation between and within species. We present an assessment of osteological differences that may be useful to differentiate species of Elgaria and Gerrhonotus, many of which are present on isolated cranial elements commonly recovered as fossils, including the premaxilla, maxilla, parietal, pterygoid, prootic, dentary, and surangular. We demonstrate the importance of documenting patterns of osteological variation using large sample sizes, and the utility of examining disarticulated cranial elements of the squamate skull to identify diagnostic morphology. This study adds to a growing body of literature suggesting that extensive documentation of morphological variation is needed to further our understanding of the phylogenetic and diagnostic utility of morphological features across vertebrate clades. Efforts in that direction likely will benefit from examination of disarticulated skeletal elements.

scholarly journals South American Nothochrysinae (Neuroptera, Chrysopidae): I. Description of Nothochrysa ehrenbergi sp. nov.

ZooKeys ◽  
2019 ◽  
Vol 866 ◽  
pp. 1-18
Author(s):  
Catherine A. Tauber
Keyword(s):  
New Species ◽  
Southern Hemisphere ◽  
New World ◽  
Morphological Features ◽  
South American ◽  
Late Oligocene ◽  
Extant Species ◽  
Nomina Dubia ◽  
A New Species

A new species, Nothochrysaehrenbergisp. nov., is described from Chile; it is the first species of Nothochrysa to be reported from the Southern Hemisphere and only the second from the New World. The genus now contains six extant species as well as two species known from late Oligocene and Miocene fossils. An updated catalog of the valid Nothochrysa species is presented, and three nomina dubia are discussed. The inclusion of the new species in Nothochrysa is well supported by morphological features. However, it and other species currently in the genus also share significant features with Archaeochrysa, an older genus of Nothochrysinae which is known only from the Eocene (Ypresian) to the late Oligocene. It therefore appears that N.ehrenbergi is among the least derived Nothochrysa species, and that the separation of Archaeochrysa from Nothochrysa is open to question and further examination.

scholarly journals Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2696 ◽  
Author(s):  
Victoria Sosa ◽  
Juan Francisco Ornelas ◽  
Santiago Ramírez-Barahona ◽  
Etelvina Gándara
Keyword(s):  
Cloud Forest ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Phenotypic Traits ◽  
Cloud Forests ◽  
Altitudinal Distribution ◽  
Ancestral Area ◽  
Divergence Time Estimates ◽  
Tree Ferns ◽  
Extant Species

BackgroundCloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remainedin situor expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence.MethodsHere we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences.ResultsBayesian trees retrievedCyathea, Alsophyla, GymnosphaeraandSphaeropterisin monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except forGymnosphaerathat was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations.ConclusionsOur data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors.

Notes on the chemistry of Maronea constans and Maronea polyphaea (Fuscideaceae)

2006 ◽  
Vol 38 (6) ◽  
pp. 595-598 ◽  
Author(s):  
Scott LaGreca
Keyword(s):  
Species Concepts ◽  
Morphological Features ◽  
Lichenized Fungi ◽  
Diagnostic Features ◽  
Generic Concept ◽  
Crustose Lichen

The crustose lichen genus Maronea A. Massal (Fuscideaceae) comprises about 12 species worldwide (Kantvilas 2001, 2004). The easily recognized, diagnostic features of this group of lichens are the lecanorine apothecia, Teloschistes-type ascus, and numerous spores per ascus, and these have contributed to a very stable generic concept over the years. As in many genera of lichenized fungi, however, differing species concepts have led to confusion over how many taxa are recognized. Many species, and varieties and forms of Maronea that were described on the basis of minor morphological features have since been synonymized (e.g. Harris 2006; Magnusson 1934).

scholarly journals Morphology captures diet and locomotor types in rodents

2017 ◽  
Vol 4 (1) ◽  
pp. 160957 ◽  
Author(s):  
Luis D. Verde Arregoitia ◽  
Diana O. Fisher ◽  
Manuel Schweizer
Keyword(s):  
Evolutionary History ◽  
Morphological Features ◽  
Museum Specimens ◽  
Museum Collections ◽  
Morphological Similarity ◽  
Closely Related Species ◽  
Phylogenetic Relatedness ◽  
Ecological Relevance ◽  
Ecological Literature ◽  
Close Relatives

To understand the functional meaning of morphological features, we need to relate what we know about morphology and ecology in a meaningful, quantitative framework. Closely related species usually share more phenotypic features than distant ones, but close relatives do not necessarily have the same ecologies. Rodents are the most diverse group of living mammals, with impressive ecomorphological diversification. We used museum collections and ecological literature to gather data on morphology, diet and locomotion for 208 species of rodents from different bioregions to investigate how morphological similarity and phylogenetic relatedness are associated with ecology. After considering differences in body size and shared evolutionary history, we find that unrelated species with similar ecologies can be characterized by a well-defined suite of morphological features. Our results validate the hypothesized ecological relevance of the chosen traits. These cranial, dental and external (e.g. ears) characters predicted diet and locomotion and showed consistent differences among species with different feeding and substrate use strategies. We conclude that when ecological characters do not show strong phylogenetic patterns, we cannot simply assume that close relatives are ecologically similar. Museum specimens are valuable records of species' phenotypes and with the characters proposed here, morphology can reflect functional similarity, an important component of community ecology and macroevolution.

scholarly journals A comparative morphological study of the sixth and seventh spinous processes of the cervical vertebrae in extinct and extant species of Equus.

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sharon May-Davis ◽  
Robert Hunter ◽  
Wendy Brown
Keyword(s):  
Morphological Study ◽  
Cervical Vertebrae ◽  
Museum Specimens ◽  
Extant Species ◽  
Spinous Processes ◽  
Identification Of Species ◽  
Potential Use ◽  
Lateral Profile

The lateral profile of the 6th and 7th cervical spinous processes (CSPs) were examined in four extantspecies of Equus (n=33); E. caballus (n=26), E. przewalskii (n=3), E. quagga boehmi (n=1), E. asinus (n=3)and compared to pre-domesticated Equus specimens (n=66) representing three known species: E. occidentalis(n=56), E. mosbachensis (n=2), E. curvedins/insulatis (n=1) and unknown Equus species (n=7) from five museums.Six common morphological profiles were revealed: cuneate, curvate, falcate, rudimentary, scalenate,and truncate. For the 6th CSP, the distribution of these morphologies amongst extant Equus is: cuneate, onlyE. asinus; curvate, E. caballus and E. przewalskii always in combination with ligamentum lamina nuchae (lig.lamina nuchae) attachments from the 2nd through to 7th CSP inclusive; falcate, E. caballus and E. przewalskiialways in combination with lig. lamina nuchae attachments from the 2nd through to 7th CSP inclusive;rudimentary, E. caballus always associated with lig. lamina nuchae attachments from the 2nd through to 5thCSP inclusive; scalenate, E. caballus in association with lig. lamina nuchae attachments from the 2nd throughto 5th (n=11) or 7th (n=4) CSP inclusive; truncate, not present. The 6th CSP in museum specimens of Equusexhibits one of four profiles: cuneate (n=10), curvate (n=14), scalenate (n=11) and truncate (n=4). For the 7thCSP, the distribution of these morphologies amongst extant Equus is: curvate, E. caballus mostly associatedwith lig. lamina nuchae attachments from the 2nd through to 5th CSP inclusive, falcate, E. caballus mostly associatedwith lig. lamina nuchae attachments from the 2nd through to 7th CSP inclusive, scalenate, E. caballusassociated with lig. lamina nuchae attachments from the 2nd through to 5th CSP inclusive. Only Rancho LaBrea and Tar Pits Museum provided samples suitable for examination of the 7th CSP. These exhibited fourprofiles: curvate (n=7), falcate (n=11), scalenate (n=2), and truncate (n=7). These findings suggest that thelateral profile of the 6th CSP is of potential use in identification of species; attachments of the lig. lamina nuchaealter the morphology of the 6th and 7th CSP; and that attachments of the lig. lamina nuchae on the 2ndto 7th CSP were likely present in species of Equus prior to domestication.

scholarly journals Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models

2019 ◽  
Vol 116 (34) ◽  
pp. 16921-16926 ◽  
Author(s):  
Venelin Mitov ◽  
Krzysztof Bartoszek ◽  
Tanja Stadler
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Process ◽  
Automatic Generation ◽  
Likelihood Method ◽  
Single Type ◽  
Phenotypic Traits ◽  
Model Parameters ◽  
Mammal Species ◽  
Extant Species ◽  
Phylogenetic Models

Phylogenetic comparative methods are widely used to understand and quantify the evolution of phenotypic traits, based on phylogenetic trees and trait measurements of extant species. Such analyses depend crucially on the underlying model. Gaussian phylogenetic models like Brownian motion and Ornstein–Uhlenbeck processes are the workhorses of modeling continuous-trait evolution. However, these models fit poorly to big trees, because they neglect the heterogeneity of the evolutionary process in different lineages of the tree. Previous works have addressed this issue by introducing shifts in the evolutionary model occurring at inferred points in the tree. However, for computational reasons, in all current implementations, these shifts are “intramodel,” meaning that they allow jumps in 1 or 2 model parameters, keeping all other parameters “global” for the entire tree. There is no biological reason to restrict a shift to a single model parameter or, even, to a single type of model. Mixed Gaussian phylogenetic models (MGPMs) incorporate the idea of jointly inferring different types of Gaussian models associated with different parts of the tree. Here, we propose an approximate maximum-likelihood method for fitting MGPMs to comparative data comprising possibly incomplete measurements for several traits from extant and extinct phylogenetically linked species. We applied the method to the largest published tree of mammal species with body- and brain-mass measurements, showing strong statistical support for an MGPM with 12 distinct evolutionary regimes. Based on this result, we state a hypothesis for the evolution of the brain–body-mass allometry over the past 160 million y.

Kiwigaster gen. nov. (Hymenoptera: Braconidae) from New Zealand: the first Microgastrinae with sexual dimorphism in number of antennal segments

Zootaxa ◽  
2011 ◽  
Vol 2932 (1) ◽  
pp. 24 ◽  
Author(s):  
J. L. FERNANDEZ-TRIANA ◽  
D. F. WARD ◽  
J. B. WHITFIELD
Keyword(s):  
New Species ◽  
New Zealand ◽  
Sexual Dimorphism ◽  
Phylogenetic Analyses ◽  
Morphological Features ◽  
Extant Species ◽  
Males And Females ◽  
One New Species

A new and morphologically unusual genus of microgastrine Braconidae, Kiwigaster Fernandez-Triana, Whitfield and Ward, with one new species, K. variabilis Fernandez-Triana and Ward, is described from New Zealand, where it is widespread. A number of morphological features mark it as unique among Microgastrinae, the most striking being the males and females having different numbers of antennal flagellomeres (females 17, males 18). Other unusual characters suggest this may be the most early-diverging extant species of the subfamily, although comprehensive phylogenetic analyses have yet to be conducted. Nothing is yet known about its host(s) or other aspects of its biology.

scholarly journals Hydrodynamic Simulations of the Performance Landscape for Suction-Feeding Fishes Reveal Multiple Peaks for Different Prey Types

2020 ◽  
Vol 60 (5) ◽  
pp. 1251-1267 ◽  
Author(s):  
Karin H Olsson ◽  
Christopher H Martin ◽  
Roi Holzman
Keyword(s):  
Prey Capture ◽  
Mechanistic Model ◽  
Prey Type ◽  
Kinematic Parameter ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Suction Feeding ◽  
Multiple Peaks ◽  
Feeding Performance ◽  
Extant Species

Abstract The complex interplay between form and function forms the basis for generating and maintaining organismal diversity. Fishes that rely on suction-feeding for prey capture exhibit remarkable phenotypic and trophic diversity. Yet the relationships between fish phenotypes and feeding performance on different prey types are unclear, partly because the morphological, biomechanical, and hydrodynamic mechanisms that underlie suction-feeding are complex. Here we demonstrate a general framework to investigate the mapping of multiple phenotypic traits to performance by mapping kinematic variables to suction-feeding capacity. Using a mechanistic model of suction-feeding that is based on core physical principles, we predict prey capture performance across a broad range of phenotypic trait values, for three general prey types: mollusk-like prey, copepod-like prey, and fish-like prey. Mollusk-like prey attach to surfaces, copepod-like prey attempt to escape upon detecting the hydrodynamic disturbance produced by the predator, and fish-like prey attempt to escape when the predator comes within a threshold distance. This approach allowed us to evaluate suction-feeding performance for any combination of six key kinematic traits, irrespective of whether these trait combinations were observed in an extant species, and to generate a multivariate mapping of phenotype to performance. We used gradient ascent methods to explore the complex topography of the performance landscape for each prey type, and found evidence for multiple peaks. Characterization of phenotypes associated with performance peaks indicates that the optimal kinematic parameter range for suction-feeding on different prey types are narrow and distinct from each other, suggesting different functional constraints for the three prey types. These performance landscapes can be used to generate hypotheses regarding the distribution of extant species in trait space and their evolutionary trajectories toward adaptive peaks on macroevolutionary fitness landscapes.

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