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Cranial variation in species and subspecies of kangaroo rats (Dipodomys, Dipodomyinae, Rodentia) according to geometric morphometrics
Abstract
Traditional Dipodomys (sub)species identification uses geography, phenotype, and external/skull measurements. Such measurements are correlated with size and thus redundant. I assessed the value of scaled cranial shape, based on two‐dimensional landmarks (analyzed using geometric morphometric methods) in distinguishing Dipodomys taxa, and in summarizing their variation. My dataset includes 601 adult specimens from 20 species (49 operational taxonomic units ‐ OTUs) across 190 localities. Cranial shape was highly useful in classifying Dipodomys taxa without considering geography. The auditory bulla was the most variable region—taxa differed in its hypertrophy, accompanied by different degrees of nearby structure crowding. Cranial shape was weakly allometric, with no significant sexual dimorphism. Weak size dimorphism was detected. (Sub)specific taxonomy is not reflective of shape variation, as the number of subspecies per species is not associated with disparity. Shape had significant phylogenetic signal, but subspecies did not always cluster with conspecifics and species did not always cluster according to phylogenetic relationship/taxonomy. Shape variation was correlated with climate, and species differed in morphological disparity and degree of specialization, which may contribute to divergence in shape variation patterns from phylogeny. D. deserti was the most specialized species, diverging greatly from the genus mean; D. heermanni was the least specialized. This study provides new insights into morphological variation of North American keystone species, several of conservation interest, for example, D. heermanni berkeleyensis , D. h. dixoni , D. nitratoides brevinasus , and D. n. nitratoides .
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Jumping mice (subfamily Zapodinae) occur across most of North America (Zapus and Napaeozapus) and in confined regions in China (Eozapus). Recent molecular phylogenies have revised their taxonomy, raising some subspecies to full species and synonymizing others. This taxonomic revision has implications for subspecies conservation and management, since Z. hudsonius preblei and Z. h. luteus are legally protected by the United States federal Endangered Species Act (ESA), while Z. h. campestris and Z. trinotatus orarius are conserved in parts of their range. Several molecular studies have either synonymized Z. h. preblei with Z. h. campestris (and Z. h. intermedius) or grouped it with Z. h. alascensis and Z. h. tenellus as a widely distributed “Northern” lineage, arguing against its continued legal protection. However, genetic differentiation is a proxy for historical but not always adaptive distinctiveness, and the ESA considers both for conservation (i.e., Evolutionarily Significant Units). This study uses geometric morphometrics to compare adaptive distinctiveness of jumping mice subspecies. This compares scaled cranial shape, leading to insights that differ from linear measurements. For broader insights, cranial morphology was compared within jumping mice and with the closely related birch mice. Subspecies pairs within the three traditionally accepted Zapus species were ranked in order morphometric distinctiveness. The most distinct pair was found to be Z. h. preblei vs. Z. h. alascensis, members of the same genetic lineage. Other morphometrically distinct subspecies pairs were parts of the same or different genetic lineages, some having been elevated to full species. Other members of especially distinct pairs include Z. princeps oregonus, Z. p. saltator, Z. p. cinereus, Z. p. minor, Z. p. pacificus, and Z. p. idahoensis. Other aspects of adaptive distinctiveness should be examined in these subspecies for validation and to prioritize conservation efforts.
Abstract Morphology‐based taxonomic research frequently applies linear morphometrics (LMM) in skulls to quantify species distinctions. The choice of which measurements to collect generally relies on the expertise of the investigators or a set of standard measurements, but this practice may ignore less obvious or common discriminatory characteristics. In addition, taxonomic analyses often ignore the potential for subgroups of an otherwise cohesive population to differ in shape purely due to size differences (or allometry). Geometric morphometrics (GMM) is more complicated as an acquisition technique but can offer a more holistic characterization of shape and provides a rigorous toolkit for accounting for allometry. In this study, we used linear discriminant analysis (LDA) to assess the discriminatory performance of four published LMM protocols and a 3D GMM dataset for three clades of antechinus known to differ subtly in shape. We assessed discrimination of raw data (which are frequently used by taxonomists); data with isometry (i.e., overall size) removed; and data after allometric correction (i.e., with nonuniform effects of size removed). When we visualized the principal component analysis (PCA) plots, we found that group discrimination among raw data was high for LMM. However, LMM datasets may inflate PC variance accounted in the first two PCs, relative to GMM. GMM discriminated groups better after isometry and allometry were removed in both PCA and LDA. Although LMM can be a powerful tool to discriminate taxonomic groups, we show that there is substantial risk that this discrimination comes from variation in size, rather than shape. This suggests that taxonomic measurement protocols might benefit from GMM‐based pilot studies, because this offers the option of differentiating allometric and nonallometric shape differences between species, which can then inform on the development of the easier‐to‐apply LMM protocols.
Populations of broadly distributed species often exhibit geographic structuring, which is sometimes reflected in phenotype. The monotypic Indian gerbil ( Tatera indica ) is an example of a widely distributed species, with its range encompassing much of Asia. This study aims to determine if T. indica populations exhibit marked variation in skull morphology—this structure is particularly adaptable and thus could be amenable to show such variation. Furthermore, the potential drivers of skull variation are examined, including the role of climate and geography. To achieve these goals, 21 linear measurements were measured on the skulls of 509 specimens, coming from 111 different localities, across this species wide range. The specimens were then assigned into one of four broad geographic groups (≈ populations) based on their geographic proximity, and the overall and the pairwise differences in the 21 skull measurements among these groups were assessed. Specimens from Pakistan significantly differed from those belonging to the West Iran, East Iran, and India populations, which in turn did not significantly differ from each other. Pairwise bioclimatic and geographic distances between the localities explained a significant, yet small amount of variation in the measurements. Thus, while the Pakistani T. indica population was distinct in skull measurements, both climatic and non-climatic spatial factors seem not to account largely for its distinctiveness (from the other populations).
Recent phylogenetic studies amended the taxonomy of three-toed jerboas (subfamily Dipodinae), including raising subspecies to full species. Here, we use geometric morphometrics to compare scaled-shape differences in dipodine crania while considering their revised taxonomy. We sampled Dipus deasyi, D. sagitta halli, D. s. sowerbyi, Jaculus blanfordi blanfordi, J. hirtipes, J. jaculus, J. loftusi, J. orientalis gerboa, J. o. mauritanicus, and Stylodipus andrewsi. Crania were not sexually dimorphic. Common allometry explained some of the shape variation, e.g., reduced braincases in larger specimens. Most OTU pairs differed in both size and shape. Dipus and Stylodipus clustered together based on their cranial shape. Jaculus differed from the aforementioned genera by its larger tympanic bulla, broader braincase, larger infraorbital foramen, along with reduced molars and rostra. J. orientalis differed from other Jaculus by its broader face vs. reduced cranial vault. J. blanfordi (subgenus Haltomys) resembles members of the subgenus Jaculus more than its consubgener (J. orientalis). J. loftusi, previously considered a synonym of J. jaculus, clearly differed from the latter by its shorter rostrum, smaller infraorbital foramen, and more caudolaterally expanded tympanic bulla. J. hirtipes, another recent synonym of J. jaculus, resembled J. blanfordi more in scaled cranial shape than it did J. jaculus. D. s. halli and D. s. sowerbyi were indistinguishable, but they clearly differed from D. deasyi (recently raised to full species) with the later having a larger molar row, more inflated tympanic bulla, and shorter, slenderer rostrum. Ecological explanations for detected cranial shape differences are considered, including diet and habitat (particularly substrate).
Allactaginae is a dipodid subfamily consisting of four- and five-toed jerboas (Allactaga, Allactodipus, Orientallactaga, Pygeretmus, Scarturus) inhabiting Asian and North African open habitats. Recent molecular phylogenies upended our understanding of this group’s systematics across taxonomic scales. Cranial geometric morphometrics was used to examine variation across 219 specimens of 14 allactagine species (Allactaga major, A. severtzovi, Orientallactaga balikunica, O. bullata, O. sibirica, Pygeretmus platyurus, P. pumilio, P. shitkovi, Scarturus aralychensis, S. euphraticus, S. hotsoni, S. indicus, S. tetradactylus, S. williamsi) in light of their revised taxonomy. There was no significant sexual size nor shape dimorphism. Species significantly differed in cranial size and shape both overall and as species pairs. Species identity had a strong effect on both cranial size and shape. Only a small part of cranial shape variation was allometric, with no evidence of unique species allometries, and most specimens fit closely to the common allometric regression vector. Allactaga were the largest, followed by Orientallactaga, Scarturus, and finally Pygeretmus. PC1 separated O. bullata + O. balikunica + S. hotsoni (with inflated bullae along with reduced zygomatic arches and rostra) from A. major + A. severtzovi + O. sibirica (with converse patterns) while PC2 differentiated Orientallactaga (with enlarged cranial bases and rostra along with reduced zygomatic arches and foramina magna) from Scarturus + Pygeretmus (with opposite patterns). UPGMA clusters consisted of the four genera, but S. hotsoni clustered with O. bullata + O. balikunica and O. sibirica clustered with A. major + A. severtzovi, likely due to convergence and allometry, respectively.
Previous studies have demonstrated the pliability and adaptability of mammalian mandibles in response to different ecological demands such as food availability. The dwarf gerbil Gerbillus nanus has a wide distribution in Asia in which it encounters varied environments. These varied environments can house different food resources and it would be adaptively advantageous for the opportunistic rodents to have mandibles best suited for the most prevalent food resource. Geometric morphometric analysis was used to test this hypothesis by examining mandibular variation in 436 G. nanus specimens sampled from 44 localities. Based on this sample, mandibular morphology seems to be highly conserved in this species, with both size and shape being non-significantly different between pairs of geographic groups (i.e., locality clusters) and ecoregions. Mandibular size and shape are both not strongly predicted by 48 examined environmental variables. Despite this, the most variable aspect of mandibular shape was associated with its caudal regions, spanning from the coronoid process to the ventral mandibular border. These are regions of temporalis and masseter muscle attachments and thus mandibular variation could be associated with differential (potentially plastic) masticatory adaptations.
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our “backbone-and-patch” approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level “patch” phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded (“DNA-only” trees) or imputed within taxonomic constraints using branch lengths drawn from local birth–death models (“completed” trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous “supertree” approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
It has been suggested that larger species of mammals tend to become long-faced when they diverge in size during an evolutionary radiation. However, whether this allometric pattern, reminiscent of ontogenetic changes in skull proportions, is indeed a rule has yet to be thoroughly tested. Using ~ 6000 adult specimens from 14 phylogenetically well separated and ecomorphologically distinctive lineages, 11 orders, and all superorders of the placentals, I tested each group for positive craniofacial allometry (CREA). The evidence supporting CREA is overwhelming, with virtually all analyses showing proportionally longer faces in bigger species. This corroborates previous studies in other groups, consolidates CREA as a pervasive morphological trend in placental evolution and opens important research avenues for connecting micro- and macro-evolution. If found in even more lineages of non-placental mammals, confirmed in birds, and possibly discovered in other tetrapods, CREA could become one of the most general rules of morphological evolution in land vertebrates.
Jirds (Meriones) are a mostly desert-adapted genus of gerbils, with a wide geographic range, through which it encounters various climatic conditions, which may influence their morphology. In this study, we quantified cranial morphometric variation both within and among seven jird species (M. meridianus, M. hurrianae, M. crassus, M. tristrami, M. persicus, M. libycus and M. vinogradovi), based on a two-dimensional landmark-based geometric morphometric analysis of 972 specimens, covering their entire geographic distribution. The aforementioned analysis was used to compare sexual dimorphism in size and shape within each species, as well as the relationship between size and shape (i.e. allometry) for each species. Despite greatly overlapping in morphospace (when examined visually), statistical analysis indicates significant differences in both size and shape among the seven examined jird species. UPGMA and CVA both show two main species clusters. Deformation grids indicate that these two clusters differ mostly in the relative size of the tympanic bulla, along with differences in the extent of nasal elongation, and the broadness of the zygomatic arch. Allometric changes in shape were analyzed in all species that show tan allometric relationship. Sexual dimorphism in shape and size was detected in only three of the seven jird species. A visual inspection of the data indicates high overlap in shape space, and that male skulls are significantly larger than female skulls. When specimens were divided by sex, we found significant allometry in six of the seven species (for both sexes). A factorial multivariate analysis of covariance (MANCOVA) indicated that even when taking size variation into account, the residual shape variation was also significantly different among the sexes of the examined species. The outcome of this study confirms the presence of cranial variation in the examined jirds, and that the patterns of sexual dimorphism and allometry vary considerably among jird species.
Residual randomization in permutation procedures (RRPP) is an appropriate means of generating empirical sampling distributions for ANOVA statistics and linear model coefficients, using ordinary or generalized least‐squares estimation. This is an especially useful approach for high‐dimensional (multivariate) data.
Here, we present an r package that provides a comprehensive suite of tools for applying RRPP to linear models. Important available features include choices for OLS or GLS coefficient estimation, data or dissimilarity matrix analysis capability, choice among types I, II, or III sums of squares and cross‐products, various effect size estimation methods, and an ability to perform mixed‐model ANOVA.
The lm.rrpp function is similar to the lm function in many regards, but provides coefficient and ANOVA statistics estimates over many random permutations. The S3 generic functions commonly used with lm also work with lm.rrpp . Additionally, a pairwise function provides statistical tests for comparisons of least‐squares means or slopes, among designated groups. Users have many options for varying random permutations. Compared to similar available packages and functions, RRPP is extremely fast and yields comprehensive results for downstream analyses and graphics, following model fits with lm.rrpp .
The RRPP package facilitates analysis of both univariate and multivariate response data, even when the number of variables exceeds the number of observations.
The taxonomy of Gerbillus, the most speciose gerbil genus, is highly debated. Of particular contention is the relationship of Dipodillus to Gerbillus; some consider it to be a closely related genus, while others synonymize it with Gerbillus—either with or without recognizing it as a subgenus. The main objective of this study is to test the validity of common taxonomic groupings within the Gerbillus-Dipodillus species complex, which was achieved by using geometric morphometrics to examine cranial and mandibular variation in 34 out of the 52 Gerbillus-Dipodillus species. Craniomandibular size and shape were highly correlated, indicating strong allometric patterns in shape variation. The common taxonomic groups were significantly different in craniomandibular size and shape, yet they did overlap considerably in morphospace. A notable exception was the extreme divergence of Monodia (G. mauritaniae) from all other species in the occlusal view of the mandible. Morphospace overlap is likely a consequence of both phylogenetic history and environmental adaptation. Only the ventral cranium was associated with climate, particularly in areas related to resource acquisition. Geographic distance was not significantly associated with craniomandibular morphometric distance, and the groups overlapped greatly in their geographic range. Cranial and mandibular regions differed in discrimination power—the ventral cranium had among the highest, while the dorsal cranium and the occlusal mandible had the lowest. Craniomandibular regions varied in association with climate, phylogeny, and size—previous studies suggest this difference may be a consequence of different genetic controls for shape variation.
Calomys is one of the most polytypic and widely distributed genera of the Neotropical rodent fauna. The taxonomic hierarchy for the large and middle-sized morphotypes from the southern central Andes (SCA) (C. boliviae, C. callosus, C. fecundus, and C. venustus) has fluctuated repeatedly from synonyms or subspecies to valid species. As a first approach to the taxonomic resolution of the taxa complex of this genus inhabiting the SCA, we applied an integrative quantitative assessment of currently recognized species cranial discrimination through the analysis of geometric morphometrics. The morphometric analyses revealed the presence of 3 distinct species of Calomys in Northwestern and Central Argentina. We corroborated the presence of a large amount of intraspecific variation, with substantial overlap for the 3 species in the morphospace. The assessment indicates that 24% of skull size variation is due to differences among species. Calomys boliviae (including C. fecundus) was the largest among the studied species, whereas the differences were subtle between C. venustus and C. callosus. The relative contribution of interspecific differences to the total skull shape variation was lower than that of size and different among the cranial views -dorsal, ventral, and lateral- analyzed (between 8 and 16%). Moreover, static allometric size changes had a major effect on skull shape differences between species. So, including ecoregions and size-free shape variables improved significantly the amount of interspecific differentiation. We highlight the usefulness of morphometric assessments to clarify and contribute to the taxonomy of Neotropical mice.
The development and the present state of the “tps” series of software for use in geometric morphometrics on Windows-based computers are described. These programs have been used in hundreds of studies in mammals and other organisms.
The biologist examining samples of multicellular organisms in anatomical detail must already have an intuitive concept of morphological integration. But quantifying that intuition has always been fraught with difficulties and paradoxes, especially for the anatomically labelled Cartesian coordinate data that drive today’s toolkits of geometric morphometrics. Covariance analyses of interpoint distances, such as the Olson–Miller factor approach of the 1950’s, cannot validly be extended to handle the spatial structure of complete morphometric descriptions; neither can analyses of shape coordinates that ignore the mean form. This paper introduces a formal parametric quantification of integration by analogy with how time series are approached in modern paleobiology. Over there, a finding of trend falls under one tail of a distribution for which stasis comprises the other tail. The null hypothesis separating these two classes of finding is the random walks, which are self-similar, meaning that they show no interpretable structure at any temporal scale. Trend and stasis are the two contrasting ways of deviating from this null. The present manuscript introduces an analogous maneuver for the spatial aspects of ontogenetic or phylogenetic organismal studies: a subspace within the space of shape covariance structures for which the standard isotropic (Procrustes) model lies at one extreme of a characteristic parameter and the strongest growth-gradient models at the other. In-between lies the suggested new construct, the spatially self-similar processes that can be generated within the standard morphometric toolkit by a startlingly simple algebraic manipulation of partial warp scores. In this view, integration and “disintegration” as in the Procrustes model are two modes of organismal variation according to which morphometric data can deviate from this common null, which, as in the temporal domain, is formally featureless, incapable of supporting any summary beyond a single parameter for amplitude. In practice the classification can proceed by examining the regression coefficient for log partial warp variance against log bending energy in the standard thin-plate spline setup. The self-similarity model, for which the regression slope is precisely \documentclass[12pt]{minimal}
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\begin{document}$$-1,$$\end{document}-1, corresponds well to the background against which the evolutionist’s or systematist’s a-priori notion of “local shape features” can be delineated. Integration as detected by the regression slope can be visualized by the first relative intrinsic warp (first relative eigenvector of the nonaffine part of a shape coordinate configuration with respect to bending energy) and may be summarized by the corresponding quadratic growth gradient. The paper begins with a seemingly innocent toy example, uncovers an unexpected invariance as an example of the general manipulation proposed, then applies the new modeling tactic to three data sets from the existing morphometric literature. Conclusions follow regarding findings and methodology alike.
Schnell, G. D. (Department of Zoology and Stovall Museum, University of Oklahoma, Norman, Oklahoma 73019), T. L. Best (Natural
Sciences Research Institute, Natural History Museum, Eastern New Mexico University, Portales, New Mexico 88130), and M. L.
Kennedy (Department of Biology, Memphis State University, Memphis, Tennessee 38152) 1978. Interspecific morphologic variation
in kangaroo rats (Dipodomys): degree of concordance with genie variation. Syst. Zool. 27:34–48.—The 24 forms of kangaroo rats (Dipodomys) that have been recognized as species by one or more recent authors were studied using phenetic techniques. A total of 41
morphometric characters (4 skin, 16 skull, and 21 post-cranial) were measured for up to 10 males and 10 females of each species.
The standardized average measurements were analyzed and then measurements were divided by principal component I projections
based on unstandardized data to reduce the influence of overall size. Phenograms and three-dimensional principal component
models were produced and the results compared with the findings of previous authors, including those from allozyme analyses.
Several species pairs and groups involving a few species were stable throughout our studies and consistent with groups identified
in phylogenetic, specialization, or other classificatory schemes. These include: compactus and ordii; elephantinus and venustus; agilis, paralius, peninsularis, and antiquarius; nitratoides and merriami; and ornatus and phillipsii. However, marked morphologic gaps (other than those based on size) are not present between many of the species groups and
attempts to place species into such groups in classifications probably result in an indication of distinctness that goes beyond
what is found in nature. In terms of interspecific comparisons, there was no association between phenetic groups based on
morphologic data and those constructed using allozyme findings. When comparisons were made among previous classifications
and our results, the allozyme data produced the most divergent classifications. Overall, the associations between our morphologic
results and previous classifications were relatively weak, reflecting by and large the variance in arrangements of species
groups, rather than major differences within groups. Given the relative indistinctness of morphologic groups, it seems unlikely
that any one classification can accurately represent interspecific phenetic, cladistic, and/or phylogenetic affinities within
the genus.
We examined the phylogenetic relationships among populations of the Mexican endemic and endangered Phillips' kangaroo rat, Dipodomys phillipsii (Rodentia: Heteromyidae), using mitochondrial (cytochrome-b and 12S ribosomal RNA) and nuclear (growth hormone receptor and interphotoreceptor retinoid-binding protein) genes for a total of 3,110 base pairs. Gene sequences were analyzed under maximum-likelihood and Bayesian models of phylogenetic inference. Analyses of the mitochondrial genes converged on essentially identical gene trees in which D. phillipsii is divided into 2 well-supported clades. The Mexican Plateau clade of D. phillipsii, formerly recognized as D. p. ornatus, is herein returned to full species status as D. ornatus. The southern clade of D. phillipsii retains the subspecies D. p. oaxacae, D. p. perotensis, and D. p. phillipsii. D. ornatus, D. phillipsii, D. elator, and D. merriami form a well-supported, but unresolved polytomy. Analyses of the nuclear genes show the same fundamental subdivision within D. phillipsii but do not provide additional resolution within the 4-species polytomy. Based on analyses of divergence times, we place the separation of these 4 species near the middle Pliocene, which suggests that the morphotectonic processes that gave rise to the Trans-Mexico Volcanic Belt may have influenced diversification in Mexican species of Dipodomys. Synonymies of D. phillipsii and D. ornatus are provided along with a key to the subspecies of D. phillipsi and D. ornatus.
Both nongeographic and geographic variation was assessed in southern banner-tailed kangaroo rats of the nominal species Dipodomys phillipsii and D. ornatus . Univariate and multivariate analyses were employed in consideration of geographic variation. D. ornatus is arranged as a subspecies of D. phillipsii, in which four races (phillipsii, ornatus, perotensis, and oaxacae) are recognized. Some observations on natural history also are included.
For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the
analysis of scientific images. We discuss the origins, challenges and solutions of these two programs,
and how their history can serve to advise and inform other software projects.
The genus Desmodillus is monospecific, consisting of only the Cape short-eared gerbil ( Desmodillus auricularis ). Despite being widely distributed across southern Africa, previous studies did not find evidence of intraspecific phenotypic geographic differentiation. The objectives of this study is to use geometric morphometrics to investigate if and how the skull of D. auricularis varies spatially. It examines the covariation of skull morphology with broad spatial (latitude and longitude) and climatic variables, based on a sample of 580 specimens from southern Africa (Botswana, Namibia, and South Africa). The results did not support the differentiation of D. auricularis populations into distinct geographically isolated phenotypic groups. However, there is strong evidence for clinal variation in skull morphology; the most prominent pattern being a decrease in size from the west (closest to the South Atlantic coast) to the east (towards the continent’s interior). Shape variation was not localized in any skull region and seem to be driven mostly by size (allometry), although it also covaried significantly with latitude and longitude. Statistically significant skull shape sexual dimorphism was also detected, with males having larger crania than females. Spatial clinal variation in skull morphology was mostly associated with differences in the aridity of the habitats relative to their distance from the coast as evidenced by precipitation-related bioclimatic variables—annual precipitation (BIO12), precipitation of driest month (BIO14), and precipitation of driest quarter (BIO17)—covarying the most with skull morphology. This could be driven by either the climate influencing local resources available to populations or by the climate directly instigating phenotypic climatic adaptations.
Molecular phylogenies support the monophyly of Desmodilliscus braueri and Pachyuromys duprasi as a clade basally split from all other gerbillines. While this monophyly supports their placement in a single tribe (Desmodilliscini), no morphological synapomorphies exist among desmodilliscines. This study compares the scale-independent cranial shapes of these two species using geometric morphometrics to determine how they differ and/or converge. Tribal synapomorphies, should they exist, may appear as interspecifically invariable cranial regions. No such invariable cranial regions were detected. The two species significantly differed in cranial size and shape. A small part of shape variation was allometric, with a weak unique allometric effect. No sexual size nor shape dimorphism was found. The sister taxa greatly differed in almost all cranial features, with Pachyuromys (when compared to Desmodilliscus ) having a larger-sized cranium, with a larger bulla and suprameatal triangle, a more posteriorly placed palatine foramina, and more anteriorly shifted (and reduced) rostral cranial structures, due to being crowded by the hypertrophied bulla. Cranial variation patterns are consistent with the literature. The extreme morphological divergence among these species is explained by the distant divergence time and ecological differences. Absence of cranial shape synapomorphies does not preclude synapomorphies in other craniodental morphological features (e.g., detailed morphology of the dentition and cranial foramina) or in other morphological structures, such as the postcranial skeleton.
Phodopus is the smallest cricetine genus, consisting of the dwarf hamsters (Phodopus sungorus, Phodopus campbelli, and Phodopus roborovskii) of arid central and east Asia. Persistent taxonomic issues in this genus include (1) whether P. sungorus and P. campbelli are con- or heterospecific and (2) whether P. roborovskii is con- or heterogeneric with the aforementioned species. To shed new light on these questions, the crania of Phodopus species were compared to each other using geometric morphometrics. Furthermore, to determine what cranial traits are shared by Phodopus crania, they were compared to the more ‘typical’ small hamster Nothocricetulus migratorius. The three Phodopus species significantly differed in cranial size and shape from each other and from N. migratorius. A large part of shape variation was allometric with only weak evidence for unique allometries. All four species lacked sexual dimorphism in cranial size and shape. As a genus, Phodopus is characterized by small-sized crania, that are broad, short, and with flaring zygomatic arches. They also have reduced rostra and enlarged foramina magna. P. roborovskii was the most distinct Phodopus, characterized by its smaller-sized cranium, with greater breadth, a rounder braincase and orbit, a shorter incisive foramen and rostrum, a larger foramen magnum, and smaller bulla with a longer eustachian tube. The crania of P. sungorus and P. campbelli are very similar, but they do diverge in relatively minor (statistically nonsignificant) features, such as cranial roundness, as well as the size of the molar row, bulla, zygomatic arch, and incisive foramen. Shape differences conformed to phylogenetic distance and with habitat differences.
Half of the ten Australian hopping mice (Notomys) species have become extinct following the European colonization of Australia, and most of the rest are threatened. This makes the study of their present diversity paramount. While recent molecular phylogenies improved our understanding of the relationships among the species, detailed interspecific phenotypic comparisons are still lacking. This is the aim of the present study. Geometric morphometric methods were used to compare the crania of all five extant species (N. alexis, N. aquillo, N. cervinus, N. fuscus, and N. mitchellii) along with the extinct N. longicaudatus. While previous work (based on traditional approaches) find intragenerically conserved crania, the present study discovers significant differences in cranial size and shape among Notomys species, with the ventral view being more distinct than the dorsal view. There was no evidence of sexual dimorphism in cranial size nor shape, and only a weak allometric effect. Most aspects of cranial shape differed among the species. The extant species pair that differed in cranial shape the most was N. aquilo – N. cervinus, differing in the foramen magnum, tympanic bulla, orbit, incisive foramen, and rostrum, along with cranial width, potentially a consequence of N. cervinus’ phylogenetic position, and N. aquilo’s s ecological uniqueness.
The dwarf gerbil (Gerbillus nanus) is broadly distributed in Asia, with a range that encompasses altitudinally diverse terrain, including two major mountain ranges. Previous studies have shown this species to be generally varied across its geographic range, both genetically and morphologically. Physical barriers (e.g. mountains) and geographic distance (i.e. isolation by distance [IBD]) are expected to reduce dispersal rates, and consequently could lead to cranial morphological differentiation among populations. Adaptation to local environments is also expected to lead to cranial morphological differentiation among populations. Here, I test these hypotheses by examining variation in cranial shape and size across the geographic distribution of G. nanus using geometric morphometric analysis. Based on a sample of 473 specimens from throughout its distribution, G. nanus populations do not seem to show biologically meaningful variation in cranial shape. Cranial size, on the other hand, did show geographic variation—yet, this variation does not seem to show strong patterns of IBD nor adaptation to local environments, which could indicate that the geographic variation in the cranial size of G. nanus populations may be accounted for by factors unexamined in this study.
Superimposition methods for comparing configurations of landmarks in two or more specimens are reviewed. These methods show differences in shape among specimens as residuals after rotation, translation, and scaling them so that they align as well as possible. A new method is presented that generalizes Siegel and Benson's (1982) resistant-fit theta-rho analysis so that more than two objects can be compared at the same time. Both least-squares and resistant-fit approaches are generalized to allow for affine transformations (uniform shape change). The methods are compared, using artificial data and data on 18 landmarks on the wings of 127 species of North American mosquitoes. Graphical techniques are also presented to help summarize the patterns of differences in shape among the objects being compared.
The plateau zokor (Eospalax baileyi) is employed as an ideal model for examining the relationships between phenotypic and ecological adaptations to the underground conditions in which the skull morphology evolves to adapt to tunnel environment. We evaluated the influence of environmental factors (altitude, temperature, and precipitation) and geographical distance on the variations in skull morphology of a native subterranean rodent plateau zokor population. Thin-plate spline showed that the trend of morphological changes along the CV1 axis was as follows: the two zygomatic arch and the two postorbital processes moved down, the two mastoid processes and the tooth row moved upward, and the tympanic bulla grew longer. The changes along the CV2 axis were as follows: the nasal bone and the tooth row became longer, the distance between the two anterior tips of zygomatic arch lengthened, the infraorbital foramen became smaller, the whole posterior part of the skull became shorter, the zygomatic bone and the two posterior tips of zygomatic arch moved down, and the foramen magnum became bigger. Thus we found significant differences in the skull shape among the seven populations studied. Along with the reduction in the altitude and increase in the mean annual temperature and mean annual precipitation, the nasal bone became shorter, the distance between the two anterior tips of the zygomatic arch became shorter, the whole posterior part of the skull lengthened, the infraorbital foramen became smaller, the two mastoid processes moved upward, and the occipital bone moved down on the dorsal surface of the skull. On the ventral surface of the skull, with an increase in the altitude, mean annual temperature, and mean annual precipitation, the tympanic bulla became shorter, the tooth row moved down, and the foramen magnum became smaller. The morphological changes in the skull were significantly positively correlated with environmental factors. Finally, there was a significant positive correlation between the Procrustes distance matrix of the skull and the geographic distance matrix, which indicates that the evolution of the plateau zokor follows the distance isolation model, but it needs to be further explored from genetic perspectives.
The Heermann?s kangaroo rat (Dipodomys heermanni; Rodentia: Heteromyidae) is a Californian endemic primarily found in the dry, gravelly grassland and open chaparral habitats of the San Joaquin Valley. Current taxonomy (based on morphology and habitat use) recognizes nine subspecies within this kangaroo rat species. Management practices of D. heermanni primarily are based on this classification, but this taxonomy may not accurately reflect unique lineages in need of conservation. Using molecular and morphological data, we performed a phylogeographic assessment of D. heermanni across the full geographic range of the species. Phylogenetic and network analyses of mitochondrial data from over 90 museum specimens (representing all nine subspecies distributed across the range of the species) revealed no substantial genetic differentiation within D. heermanni. Similarly, a geometric morphometric analysis of the crania of over 200 adult D. heermanni museum specimens (again representing all subspecies across the geographic distribution of species) resulted in no apparent morphological clustering across geography. Our results indicate that recognition of none of the nine subspecies is warranted and that conservation and management practices of D. heermanni are in need of revision.
The dwarf gerbil (Gerbillus nanus) is broadly distributed in Asia, with a range that encompasses altitudinally diverse terrain, including two major mountain ranges. Previous studies have shown this species to be generally varied across its geographic range, both genetically and morphologically. Physical barriers (e.g. mountains) and geographic distance (i.e. isolation by distance [IBD]) are expected to reduce dispersal rates, and consequently could lead to cranial morphological differentiation among populations. Adaptation to local environments is also expected to lead to cranial morphological differentiation among populations. Here, I test these hypotheses by examining variation in cranial shape and size across the geographic distribution of G. nanus using geometric morphometric analysis. Based on a sample of 473 specimens from throughout its distribution, G. nanus populations do not seem to show biologically meaningful variation in cranial shape. Cranial size, on the other hand, did show geographic variation—yet, this variation does not seem to show strong patterns of IBD nor adaptation to local environments, which could indicate that the geographic variation in the cranial size of G. nanus populations may be accounted for by factors unexamined in this study.
After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use, and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.
Availability:
ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=apeFurther information may be found athttp://ape-package.ird.fr/.
This new edition to the classic book by ggplot2 creator Hadley Wickham highlights compatibility with knitr and RStudio. ggplot2 is a data visualization package for R that helps users create data graphics, including those that are multi-layered, with ease. With ggplot2, it's easy to:
• produce handsome, publication-quality plots with automatic legends created from the plot specification
• superimpose multiple layers (points, lines, maps, tiles, box plots) from different data sources with automatically adjusted common scales
• add customizable smoothers that use powerful modeling capabilities of R, such as loess, linear models, generalized additive models, and robust regression
• save any ggplot2 plot (or part thereof) for later modification or reuse
• create custom themes that capture in-house or journal style requirements and that can easily be applied to multiple plots
• approach a graph from a visual perspective, thinking about how each component of the data is represented on the final plot
This book will be useful to everyone who has struggled with displaying data in an informative and attractive way. Some basic knowledge of R is necessary (e.g., importing data into R). ggplot2 is a mini-language specifically tailored for producing graphics, and you'll learn everything you need in the book. After reading this book you'll be able to produce graphics customized precisely for your problems, and you'll find it easy to get graphics out of your head and on to the screen or page. New to this edition:<
• Brings the book up-to-date with ggplot2 1.0, including major updates to the theme system
• New scales, stats and geoms added throughout
• Additional practice exercises
• A revised introduction that focuses on ggplot() instead of qplot()
• Updated chapters on data and modeling using tidyr, dplyr and broom
Studies of the biostratigraphy and palaeoecology of fossil vertebrate assemblages require large samples of accurately identified specimens. Such analyses can be hampered by the inability to assign isolated and worn remains to specific taxa. Entoptychine gophers are a diverse group of burrowing rodents found in Oligo-Miocene deposits of the western United States. In both entoptychines and their extant relatives the geomyines, diagnostic characters of the occlusal surface of the teeth are modified with wear, making difficult the identification of many isolated fossil teeth. We use geometric morphometrics to test the hypothesis that tooth shape informs taxonomic affinities and expected levels of morphological variation across gopher taxa. We also incorporate data from microcomputer tomography to investigate changes in occlusal surface shape through wear within individuals. Our analyses demonstrate the usefulness of our approach in identifying extant geomyines to the genus, subgenus and species levels, and fossil entoptychines to the genus and, in some cases, the species level. Our results cast doubt on the validity of some species within Entoptychus and suggest future revisions to entoptychine taxonomy. The amounts of morphological divergence observed among fossil and extant genera are similar. Fossil species do not differ greatly from extant ones in that regard either. Further work evaluating the morphological variation within and across entoptychine species, including unworn teeth and osteological material, will allow revised analyses of the biostratigraphy and palaeoecology of important Oligo-Miocene mammalian assemblages of the western United States and help to infer the phylogenetic relationships and evolution of gophers.
A guide to using S environments to perform statistical analyses providing both an introduction to the use of S and a course in modern statistical methods. The emphasis is on presenting practical problems and full analyses of real data sets.
Herein the taxonomy of the family is reviewed and diagnoses of Recent species and accounts of all currently recognized Recent species and subspecies are provided. The objective is to present a current taxonomy for the family rather than a systematic review. Unfortunately, there have been no comprehensive reviews for most genera for 80 years or more and the current taxonomy of many species clearly is unsatisfactory, as is the understanding of the relationships between most of the described fossil and Recent taxa.
Interspecific morphometric variation among 19 species of kangaroo rats (genus Dipodomys) was examined using discriminant-function analysis. Discriminant functions I, II, and III accounted for 53.0, 18.3, and 12.6%, respectively, of the discrimination in males, and 48.9, 19.7, and 13.0%, respectively, of the discrimination in females. Geographic samples were classified to the correct species for 99.6% of the samples. Magnitude of intraspecific variation was related to the size of a species' geographic distribution. Samples segregated into three major aggregations. The first contained the majority of taxa and consisted of smaller species. The second aggregation comprised most of the larger taxa (D. ingens, D. nelsoni, D. spectabilis). Samples of D. deserti were the sole members of the third aggregation. Morphologically similar taxa often were allopatric (e.g., D. californicus, D. elator, D. heermanni, D. panamintinus, D. phillipsii) or had different microhabitat preferences where syntopic (e.g., D. merriami, D. ordii). Other taxa that had generally similar body sizes and overlapping geographic distributions were morphometrically distinct (e.g., D. microps and D. ordii, D. merriami and D. microps, D. compactus and D. ordii). These more subtly defined morphometric differences probably are reflections of adaptations allowing superficially similar species to occupy the same geographic region.
Electrophoretic and morphologic variation was examined among two populations of Dipodomys merriami from Baja California, one population of Dipodomys nitratoides from southern California, and Dipodomys insularis from San José Island, Baja California. Analysis of allozyme variation resulted in a mean genetic distance of 0.07 among the two populations of D. merriami and D. insularis. Analyses of morphologic variation among these populations indicated that D. insularis is distinct from populations of D. merriami and D. nitratoides using bacular, cranial, and external characters. Although D. insularis is geographically isolated and is statistically significantly different in several morphologic characters from D. merriami, we recommend placement of D. insularis as a subspecies of D. merriami based upon their allozymic similarities and because other species of Dipodomys exhibit similar degrees of intraspecific geographic variation in morphologic characters.
Genic and morphometric variation was examined among populations of Dipodomys agilis, D. elephantinus, and D. venustus from the Pacific coastal ranges of central and southcentral California to ascertain their systematic relationships. Genic data separated D. agilis from D. elephantinus and D. venustus on the basis of six unique alleles, and the two populations of D. agilis were separated from one another by three fixed alleles. D. elephantinus and D. venustus were not separated from each other by any fixed allelic differences, although D. venustus had one allele at a polymorphic locus that was not present in D. elephantinus. Multivariate analyses of external and cranial characters placed both populations of D. venustus close together, the two populations of D. agilis were well separated from D. venustus and each other, and D. elephantinus was placed apart from D. venustus. This study indicates that D. agilis is not conspecific with D. elephantinus or D. venustus. Although D. elephantinus differs from D. venustus in several morphometric characters, none can reliably differentiate between them. D. elephantinus is considered to be a subspecies of D. venustus because these taxa are nearly identical genetically, karyotypically, and in bacular morphology. In addition, the degrees of differences in external and cranial characters are similar to those observed among populations of other species of Dipodomys.
A sample of 2,360 skulls representing 21 of the 22 recognized species of Dipodomys were examined for the presence and structure of the interparietal. The interparietal is basically formed from four ossification centers. These often fuse during the early stages of development. The median components are the equivalent of the interparietal of other animals while the antero-lateral components are possibly equivalent of the tabular bones of reptiles and primitive mammals.
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.
2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.
3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.
4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
Fossils of the Heteromyidae usually are distinguished using quantitative dental characters because of a lack of diagnostic qualitative characters. However, utility of these characters in addressing taxonomic questions is unclear. Teeth of 19 extant species of kangaroo rats (Dipodomys) were measured to determine if quantitative characters provided reliable separation of taxa and to what extent morphometric analyses revealed meaningful higher level relationships. A discriminant analysis correctly allocated >70% of specimens to their a priori species groups. Dimensions that were best able to separate taxa, as judged from a canonical variate analysis, were lengths of premolars and 1st lower molar. Squared Mahalanobis distances, canonical variate analysis, principal component analysis, cluster analysis, and minimum spanning trees supported morphological groupings including: D. nelsoni and D. spectabilis; D. compactus and D. ordii; D. merriami and D. nitratoides; and the 5 species D. agilis, D. heermanni, D. panamintinus, D. simulons, and D. stephensi. D. deserti and D. elator differed in their dental morphology from all other taxa. Overall, results closely paralleled those of previous workers, suggesting that quantitative dental characters can reliably distinguish heteromyid taxa and perhaps help elucidate higher level taxonomic relationships.