Three-dimensional geometric morphometrics of Arvicanthis: implications for systematics and taxonomy

Arvicanthis is an African murid, found throughout sub-Saharan Africa, Sudan and Egypt. Although in the past 10 years several studies have been carried out to assess its systematics, there is still a need for a general revision of the genus. In this study the morphometric relationships between 71 populations throughout the range were investigated. A three-dimensional geometric morphometric approach was used to assess differences in the size and shape of the skull. These were related to the different biogeographical domains characterizing the range of the genus and to molecular and karyotypic phylogenies. Results agree only in part with phylogeny, and show a close relationship with the environmental backgrounds of each species. It is therefore suggested that the adaptation of Arvicanthis to local environment has played an important role in the phenotypic evolution of the skull. This leads to problems in taxonomic definitions based on morphometrics, which should not be used without comparison with other independently derived characters such as the DNA and the karyotype.     

几何形态测量法在生物形态学研究中的应用

形态分析是生物系统学及其多样性研究中很重要的一部分。随着统计学的发展,我们可以对非常复杂的数据进行分析,这在客观上导致了多变量形态测量的出现。在20世纪80年代,在数据收集和分析上产生了重要突破——标点和标点相对位置的几何信息的匹配,从而可以将多变量分析的标点集叠加到生物原始图上,它不仅仅是生成散点图,而是试图客观反映生物的形态性状。这项研究被称为几何形态测量法(geometricmorphometrics),Rohlf和Marcus(1993)称其为形态测量方法上的一次革命。文章简要介绍了该方法。     

分子系统学研究进展

分子系统学 ( molecular systematics)是近 30年发展起来的一门综合性前沿学科 ,它在分子水平上对生物进行遗传多样性、分类、系统发育和进化等方面的研究 ,其研究结果对于保护生物多样性 (尤其是遗传多样性 ) ,揭示生物进化历程及机理具有十分重要的意义。1　分子系统学的定义及发展简史分子系统学是通过检测生物大分子包含的遗传信息 ,定量描述、分析这些信息在分类、系统发育和进化上的意义 ,从而在分子水平上解释生物的多样性、系统发育及进化规律的一门学科。它以分子生物学、系统学、遗传学、分类学和进化论为理论基础 ,以分子生物学…     

叶蝉科昆虫分子系统发育的研究进展

从基因组DNA的提取、研究的基因片段、PCR引物选用、扩增条件以及叶蝉科不同阶元的分子系统发育分析等方面,综述叶蝉科(半翅目:叶蝉科)昆虫分子系统发育的研究进展。目前角顶叶蝉类的研究成果相对较多,大叶蝉亚科次之,其余类群的研究较少或无。线粒体基因与核基因序列联合分析以及线粒体全序列分析以及基因序列与形态数据相结合分析,分子鉴定叶蝉与共生菌之间的协同进化的研究,将是叶蝉分子系统学未来发展的主要研究手段。     

Leaf architecture of South American Nothofagus (Nothofagaceae) using traditional and new methods in morphometrics

Leaf morphology has been the subject of several studies in NoNothofagur especially in the context of the taxonomy and evolutionary relationships of taxa within the genus, which are still controversial. The leaf architecture of 8 dombgi , N. betuloides and N. nitida , dominant trees of temperate forest in southern South America, is compared using venation patterns, landmarks, and entire outlines. In terms of venation patterns N. dombgi and N. betuloides were more similar to each other than to N. nitida. Similar results were found when differences in shape were analysed by discriminant analyses of shape coordinates (landmarks) and Fourier coefficients (outlines). For both analyses, the fwst discriminant function separated N. nitida from the other two species; these were also distinguished but showed greater overlap with each other. This study, in concert with information from allozyme data confirms the hypothesis of a more ancestral position for N. nitida with N. dombgi and N. betuloides being more recently derived. In addition to differences in shape, the size component of leaf morphology indicated that whereas N. betuloides had the smallest leaves, N. dombgi spanned the greatest range and has the biggest leaves. Given that the data shown here were obtained from seedlings grown under common-garden conditions, differences in both shape and size, seem to be important components of leaf morphology that may warrant consideration in characterizing these and other species of Nothofagus.     

Allometric and trophic effects on shell morphology of Pomacea canaliculata (Caenogastropoda,Ampullariidae) from a geometric morphometrics viewpoint

Pomacea canaliculata, an invasive apple snail native to South America, is a serious pest of aquatic crops in several parts of the world. The origin of inter-population variation in shell shape is thought to be both genetic and environmental but the reaction norms to specific environmental factors are still poorly understood. Our aims were to analyze the existence of direct and indirect (allometric) effects of food availability (FA) on the shape of young adults of P. canaliculata. Full sibling hatchlings were reared under different levels of FA. Nine landmarks and 10 semi-landmarks were determined on photographs of mature shells and analyzed using geometric morphometrics. In both sexes significant allometry was found: a decrease in the spire height in both sexes, and an increase of the aperture size in males and of the last whorl in females. When this allometric component was removed a relationship between size-corrected shape and FA was found only in females, which were more globose and had a larger aperture when grown under high FA. This effect may be explained by the faster growth of the reproductive organs and the thinner shells of the best fed females.     

Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence

Hantaviruses are considered one of the best examples of a long-termassociation between RNA viruses and their hosts. Based on theappearance of strong host specificity, it has been suggestedthat hantaviruses cospeciated with the rodents and insectivoresthey infect since these mammals last shared a common ancestor,approximately 100 million years ago. We tested this hypothesisof host–virus codivergence in two ways: 1) we used cophylogeneticreconciliation analysis to assess the fit of the virus treeonto that of the host and 2) we estimated the evolutionary ratesand divergence times for the Hantavirus genus using a BayesianMarkov Chain Monte Carlo method and similarly compared thesewith those of their hosts. Our reconciliation analysis providedno evidence for a history of codivergence between hantavirusesand their hosts. Further, the divergence times for the Hantavirusgenus were many orders of magnitude too recent to correspondwith the timescale of their hosts' speciation. We thereforepropose that apparent similarities between the phylogenies ofhantaviruses and their mammalian hosts are the result of a morerecent history of preferential host switching and local adaptation.Based on the presence of clade-defining amino acids in all genomicsegments, we propose that the patterns of amino acid replacementin these viruses are also compatible with a history of host-specificadaptation.     

Bias and error in estimates of mean shape in geometric morphometrics

Sampling experiments were performed to investigate mean square error and bias in estimates of mean shape produced by different geometric morphometric methods. The experiments use the isotropic error model, which assumes equal and independent variation at each landmark. The case of three landmarks in the plane (i.e., triangles) was emphasized because it could be investigated systematically and the results displayed on the printed page. The amount of error in the estimates was displayed as RMSE surfaces over the space of all possible configurations of three landmarks. Patterns of bias were shown as vector fields over this same space. Experiments were also performed using particular combinations of four or more landmarks in both two and three dimensions.It was found that the generalized Procrustes analysis method produced estimates with the least error and no pattern of bias. Averages of Bookstein shape coordinates performed well if the longest edge was used as the baseline. The method of moments (Stoyan, 1990, Model. Biomet. J. 32, 843) used in EDMA (Lele, 1993, Math. Geol. 25, 573) exhibits larger errors. When variation is not small, it also shows a pattern of bias for isosceles triangles with one side much shorter than the other two and for triangles whose vertices are approximately collinear causing them to resemble their own reflections. Similar problems were found for the log-distance method of Rao and Suryawanshi (1996, Proc. Nat. Acad. Sci. 95, 4121). These results and their implications for the application of different geometric morphometric methods are discussed.     

Biogeography and systematics of Hildenbrandia (Rhodophyta,Hildenbrandiales) in North America: inferences from morphometrics and rbcL and 18S rRNA gene sequence analyses

Morphometric analysis and phylogenetic analysis of sequences of the rbcL chloroplast gene (which codes for the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme) and the nuclear 18S ribosomal RNA (rRNA) gene were carried out on 26 specimens of marine and freshwater Hildenbrandia from North America. Nineteen marine specimens were collected from Alaska to Costa Rica on the Pacific coast and from Newfoundland to Connecticut on the Atlantic coast. Seven freshwater samples were collected from Texas, Costa Rica, St Lucia and Puerto Rico. Three groups of samples were distinguished by morphometric analysis: one containing all freshwater samples (H. angolensis Welwitsch ex West et West), one consisting of a marine sample with parallel tetrasporangial divisions (H. occidentalis Setchell ex Gardner) and one group with non-parallel tetrasporangial divisions (H. rubra (Sommerfelt) Meneghini. These groupings were partially incongruent with those obtained by analyses of the molecular data. Parsimony and distance analyses of the rbcL gene resulted in trees in which Atlantic and Pacific clades were largely resolved. However, an Alaskan sample was included in the Atlantic group, which may indicate a trans-Arctic invasion event. The freshwater samples were paraphyletic for the rbcL gene, among the marine collections, which supports the concept of multiple invasions establishing the freshwater populations in North America. The 18S rRNA gene sequence data indicate that the freshwater samples are monophyletic with the exception of the unresolved position of the H. occidentalis sample. The freshwater samples form a monophyletic clade when multiple outgroups are used. The rbcL data appear to be mutationally saturated above approximately 17% divergence, which makes interpretation of phylogenetic signal among distant groups difficult. This may be a result of the asexual reproduction of the alga.     

Phylogeny and adaptive diversity of rodents of the family Ctenomyidae (Caviomorpha): delimiting lineages and genera in the fossil record

Differentiation of genera of the modern (Late Miocene to Recent) South American rodent family Ctenomyidae would have been linked to the acquisition of disparate adaptations to digging and life underground. In accordance with this hypothesis, the delimitation of lineages and genera in the ctenomyid fossil record is evaluated here following an adaptation-rooted criterion that involves both an assessment of the monophyly and of the adaptive profiles of recognized clades. The application of such a criterion, including morphofunctional information, delimited four cohesive lineages among crown ctenomyids (i.e. euhypsodont species of the Late Miocene to Recent): Eucelophorus (Early Pliocene–Middle Pleistocene), Xenodontomys-Actenomys (Late Miocene–Pliocene), Praectenomys (Pliocene) and Ctenomys (including Paractenomys ; Pliocene–Recent); in addition, the results supported the status of Xenodontomys as a paraphyletic ancestor of Actenomys . The cladogenesis that gave rise to the crown group would have occurred immediately after the acquisition of euhypsodonty in a Xenodontomys simpsoni -like ancestor during the Late Miocene. This putative ancestor would have had fossorial habits and moderate digging specializations, an adaptive profile maintained in Xenodontomys-Actenomys . Eucelophorus and Ctenomys would have independently evolved subterranean habits at least since the Pliocene. Although the earliest history of the only living representative, Ctenomys , is known only fragmentarily, remains from Esquina Blanca (Uquía Formation), in north-western Argentina, suggest a minimum age of around 3.5 Ma (Early–Late Pliocene) for the differentiation of the genus. This date agrees with recent molecular estimates.     

Application of molecular genetics and geometric morphometrics to taxonomy and conservation of cave beetles in central Italy

Integration of molecular genetic techniques and geometric morphometrics represent a valuable tool in the resolution of taxonomic uncertainty and the identification of significant units for conservation. We combined mitochondrial DNA cytochrome c oxidase subunit II gene sequence data and geometric morphometric analysis to examine taxonomic status and identify units for conservation in four species of the hypogean beetle Duvalius (Coleoptera, Trechinae) using mainly museum specimens collected in central Italy. Previous taxonomic studies based on morphological traits described several subspecies often inhabiting geographically distinct caves. Phylogenetic analysis identified two well supported monophyletic lineages and a number of different clades with relatively small genetic differences, suggesting a short divergence time in line with known geological history of the study area. Geometric morphometrics, on the other hand, recovered a high level of distinctiveness among specimens. Both genetic and morphometric analyses did not entirely corroborate former taxonomic nomenclature, suggesting possible rearrangements and the definition of evolutionary significant units. Beetles of the genus Duvalius are protected by regional laws and the majority of taxa considered in this study inhabit caves located outside protected areas. Our study advocates the importance of devoting protection efforts to networks of cave ecosystems rather than single locations or species.     

Assessing astragalar morphology and biomechanics in western Palaearctic Bison populations with geometric morphometrics

Having arrived 1.8 Ma ago, bison prevailed in the bovid assemblages of the European subcontinent for more than 1.5 Ma. The current geometric morphometric study outlines a framework of ecomorphological differences among several Bison populations of the western Palaearctic, shown by inferences from the tibial and tarsal joint surfaces of their astragalus. Given the principal biomechanical role of this element in the locomotion mechanism, its anatomical features could be linked to diverse functional aspects. In terms of morphological affinity, it is possible to attribute the studied fossil Bison astragalar material to several morphological trends. Shape variation is not explained by size differences and is possibly associated with an open-close habitat gradient, as indicated by the presence of expanded or compressed astragali, respectively. This intragroup spatial and temporal phenotypic diversity among the examined populations could indicate a biogeographic segregation influenced by regional climatic and landscape heterogeneity in the European territory during Pleistocene. Furthermore, a relation to habitat-specific locomotor ecology could be supported, revealing forms with increased cursoriality, operating in open biomes and closed-country dwellers as well.     

Functional anatomy and adaptation of the third to sixth thoracic vertebrae in primates using three-dimensional geometric morphometrics

The morphology of the cranial thoracic vertebrae has long been neglected in the study of primate skeletal functional morphology. This study explored the characteristics of the third to sixth thoracic vertebrae among various positional behavioural primates. A total of 67 skeletal samples from four species of hominoids, four of cercopithecoids, and two of platyrrhines were used. Computed tomography images of the thoracic vertebrae were converted to a three-dimensional (3D) bone surface, and 104 landmarks were obtained on the 3D surface. For size-independent shape analysis, the vertebrae were scaled to the same centroid size, and the normalised landmarks were registered using the generalised Procrustes method. Principle components of shape variation among samples were clarified using the variance–covariance matrix of the Procrustes residuals. The present study revealed that the transverse processes were more dorsally positioned in hominoids compared to non-hominoids. The results showed that not only a dorsolaterally oriented but also a dorsally positioned transverse process in relation to the vertebral arch contribute to the greater dorsal depth in hominoids than in monkeys. The thoracic vertebrae of Ateles and Nasalis show relatively dorsoventrally low and craniocaudally long vertebrae with craniocaudally long zygapophyses and craniocaudally long base/short tip of the caudally oriented spinous process, accompanied by a laterally oriented and craniocaudally long base of the transverse process. Despite being phylogenetically separated, the vertebral features of Ateles (suspensory platyrrhine with its prehensile tail's aid) are similar to those of Nasalis (arboreal quadrupedal/jumping/arm-swing colobine). The morphology of the third to sixth thoracic vertebrae tends to reflect the functional adaptation in relation to positional behaviour rather than the phylogenetic characteristics of hominoids, cercopithecoids, and platyrrhines.

     

A comparison of phenetic and phylogenetic methods applied to the systematics of Oligochaeta

A comparative study of naidid subfamilies shows that a combination of ordination, Jaccard/Average Linkage cluster analysis and Wagner parsimony provides a useful basis for a rational phylogeny but that this does not differ markedly from the original proposed by Sperber nearly four decades ago. Hennig rules, modified by Wiley, permit a preliminary phylogeny and classification of the Annelida to be made by hand. An error in earlier versions suggested that the Dorydrilidae lacked prostate glands, and this is corrected.     

Colocalization of synaptic GABAC-receptors with GABAA-receptors and glycine-receptors in the rodent central nervous system

Fast inhibition in the nervous system is preferentially mediated by GABA- and glycine-receptors. Two types of ionotropic GABA-receptor, the GABA_A-receptor and GABA_C-receptor, have been identified; they have specific molecular compositions, different sensitivities to GABA, different kinetics, and distinct pharmacological profiles. We have studied, by immunocytochemistry, the synaptic localization of glycine-, GABA_A-, and GABA_C-receptors in rodent retina, spinal cord, midbrain, and brain-stem. Antibodies specific for the α1 subunit of the glycine-receptor, the γ2 subunit of the GABA_A-receptor, and the ρ subunits of the GABA_C-receptor have been applied. Using double-immunolabeling, we have determined whether these receptors are expressed at the same postsynaptic sites. In the retina, no such colocalization was observed. However, in the spinal cord, we found the colocalization of glycine-receptors with GABA_A- or GABA_C-receptors and the colocalization of GABA_A- and GABA_C-receptors in approximately 25% of the synapses. In the midbrain and brain-stem, GABA_A- and GABA_C-receptors were colocalized in 10%–15% of the postsynaptic sites. We discuss the possible expression of heteromeric (hybrid) receptors assembled from GABA_A- and GABA_C-receptor subunits. Our results suggest that GABA_A- and GABA_C-receptors are colocalized in a minority of synapses of the central nervous system.     

The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics

Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.     

Molecular systematics and evolution in New Zealand: Applications to cryptic skink species

Abstract

The polymerase chain reaction (PCR) and DNA sequencing are being used for the study of the origin and evolution of New Zealand plants and animals. Here we describe methods for rapidly obtaining DNA sequences from small amounts of fresh and preserved tissue, and apply them to the problem ofresolving relationships among skinks of the Austrnlasian genus Leiolopisma. DNA extracted from frozen tail muscle was used for the main part of the study. Part ofthe mitochondrial12S ribosomal RNA gene was isolated using PCR. Direct sequencing of this 400 nucleotide region supports the separation of “L. nigriplantare” into several genetically distinct but morphologically similar species. The sequence data have also identified a potential case of hybridisation between two sympatric species in Otago, L. nigriplantare polychroma and L. maccanni. The data set supports the view that skinks have been in New Zealand very much longer than five million years.

From these results we expect that application of the PCR and other techniques in molecular biology will help solve many questions about the origins and evolution of New Zealand's biota, as well as help identify unique populations for conservation.     

Molecular systematics in the genus Mucor with special regards to species encountered in cheese

The genus Mucor, a member of the order Mucorales, comprises different species encountered in cheeses. Although fungi play a fundamental role in cheese manufacturing and ripening, the taxonomy of many fungal species found in cheese is poorly defined; indeed, this is the case for Mucor spp. In the present study, we assessed the phylogenetic relationships among 70 Mucor strains, including 36 cheese isolates, by using a five gene phylogenetic approach combined with morphological analyses. Overall, at least six species of Mucor were identified among the cheese isolates including a possible new taxon. The present study also suggests that the genus Mucor comprises undescribed taxa and needs to be properly defined.     

The problem of assessing landmark error in geometric morphometrics: theory, methods, and modifications

Geometric morphometric methods rely on the accurate identification and quantification of landmarks on biological specimens. As in any empirical analysis, the assessment of inter- and intra-observer error is desirable. A review of methods currently being employed to assess measurement error in geometric morphometrics was conducted and three general approaches to the problem were identified. One such approach employs Generalized Procrustes Analysis to superimpose repeatedly digitized landmark configurations, thereby establishing whether repeat measures fall within an acceptable range of variation. The potential problem of this error assessment method (the "Pinocchio effect") is demonstrated and its effect on error studies discussed. An alternative approach involves employing Euclidean distances between the configuration centroid and repeat measures of a landmark to assess the relative repeatability of individual landmarks. This method is also potentially problematic as the inherent geometric properties of the specimen can result in misleading estimates of measurement error. A third approach involved the repeated digitization of landmarks with the specimen held in a constant orientation to assess individual landmark precision. This latter approach is an ideal method for assessing individual landmark precision, but is restrictive in that it does not allow for the incorporation of instrumentally defined or Type III landmarks. Hence, a revised method for assessing landmark error is proposed and described with the aid of worked empirical examples.