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1.
Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.  相似文献   

2.
Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.  相似文献   

3.
Anguimorpha is a clade of limbed and limbless squamates with ca. 196 extant species and a known fossil record spanning the past 130 million years. Morphology‐based and molecule‐based phylogenetic analyses disagree on several key points. The analyses differ consistently in the placements of monstersaurs (e.g. Gila Monsters), shinisaurs (Crocodile Lizards), the anguid Anniella (American Legless Lizards), carusioids (Knobby Lizards), and the major clades within Varanus (Monitor Lizards). Given different data sources with such different phylogenetic hypotheses, Anguimorpha is an excellent candidate for a combined phylogenetic analysis. We constructed a data matrix consisting of 175 fossil and extant anguimorphs, and 2281 parsimony‐informative characters (315 morphological characters and 1969 molecular characters). We analysed these data using the computer program TNT using the “new technology search” with the ratchet. Our result is novel and shows similarities with both morphological and molecular trees, but is identical to neither. We find that a global combined evidence analysis (GCA) does not recover a holophyletic Varanoidea, but omission of fossil taxa reveals cryptic molecular support for that group. We describe these results and others from global morphological analysis, extant‐only morphological analysis, molecular data‐only analyses, combined evidence analysis of extant taxa, and GCA. © The Willi Hennig Society 2010.  相似文献   

4.
A revised infrageneric classification of Nothofagus (Fagaceae)   总被引:1,自引:0,他引:1  
HILL, R. S. & READ, J., 1991. A revised infrageneric classification of Nothofagus (Fagaceae). An examination of cupule morphology, leaf architecture and cuticular morphology of Nothofagus species demonstrates that the existing infrageneric classifications are inaccurate. Four subgenera are proposed, based on these characteristics as well as other morphological information. This analysis indicates that the traditional pollen groupings of Nothofagus closely reflect the infrageneric taxonomy. It is hypothesized that deciduousness is primitive in Nothofagus , and the evergreen habit has arisen more than once, and therefore the deciduous or evergreen habit is invalid as a primary taxonomic character.  相似文献   

5.
The 3400 species of Eumolpinae constitute one of the largest subfamilies of leaf beetles (Chrysomelidae). Their systematics is still largely based on late 19th century monographs and remains highly unsatisfactory. Only recently, some plesiomorphic lineages have been split out as separate subfamilies, including the southern hemisphere Spilopyrinae and the ambiguously placed Synetinae. Here we provide insight into the internal systematics of the Eumolpinae based on molecular phylogenetic analyses of three ribosomal genes, including partial mitochondrial 16S and nuclear 28S and complete nuclear 18S rRNA gene sequences. Sixteen morphological characters considered important in the higher-level systematics of Eumolpinae were also included in a combined analysis with the molecular characters. All phylogenetic analyses were performed using parsimony by optimizing length variation directly on the tree, as implemented in the POY software. The data support the monophyly of the Spilopyrinae outside the clade including all sampled Eumolpinae, corroborating their treatment as a separate subfamily within the Chrysomelidae. The systematic placement of the Synetinae remains ambiguous but consistent with considering it a different subfamily as well, since the phylogenetic analyses using all the available evidence show the representative sequence of the subfamily also unrelated to the Eumolpinae. The Megascelini, traditionally considered a separate subfamily, falls within the Eumolpinae. Several recognized taxonomic groupings within Eumolpinae, including the tribes Adoxini or Typophorini, are not confirmed by molecular data; others like Eumolpini seem well supported. Among the morphological characters analyzed, the presence of a characteristic groove on the pygidium (a synapomorphy of the Eumolpini) and the shape of tarsal claws (simple, appendiculate or bifid) stand out as potentially useful characters for taxonomic classification in the Eumolpinae.  相似文献   

6.
Previous phylogenetic analyses of the tribe Phyllotini, one of the largest components of the subfamily Sigmodontinae, have been based on a single source of evidence. In particular, morphological analyses were largely based on craniodental data, almost neglecting the potential phylogenetic information present in the postcranium. Despite the significant advances made in relation to the knowledge of phyllotine phylogeny in recent times, there are several unsolved issues that highlight the importance of a phylogenetic analysis that integrates multiple sources of evidence, including previously considered sources as well as new sources of data. We present here the first combined phylogenetic analysis (morphological and molecular) of phyllotines, which includes the widest taxon and character sampling to date. Our dataset includes 164 morphological characters, of which 83 are postcranial characters, plus 3561 molecular characters, scored for 52 species from 34 genera of Oryzomyalia. In this study 75 postcranial characters not previously considered in this group are thoroughly described, and their utility for solving the relationships within Phyllotini is evaluated by means of different complementary analyses. Phyllotini was retrieved as a monophyletic clade in the combined analysis, with a composition that matches that obtained in most other recent analyses. All genera of phyllotines were monophyletic and show high support values. Abrotrichini, Akodontini and Oryzomyini were also monophyletic. The inclusion of postcranial data appears to be of limited utility to solve the phylogenetic relationships within Phyllotini.  相似文献   

7.
We performed the first combined‐data phylogenetic analysis of ictalurids including most living and fossil species. We sampled 56 extant species and 16 fossil species representing outgroups, the seven living genera, and the extinct genus ?Astephus long thought to be an ictalurid. In total, 209 morphological characters were curated and illustrated in MorphoBank from published and original work, and standardized using reductive coding. Molecular sequences harvested from GenBank for one nuclear and four mitochondrial genes were combined with the morphological data for total evidence analysis. Parsimony analysis recovers a crown clade Ictaluridae composed of seven living genera and numerous extinct species. The oldest ictalurid fossils are the Late Eocene members of Ameiurus and Ictalurus. The fossil clade ?Astephus placed outside of Ictaluridae and not as its sister taxon. Previous morphological phylogenetic studies of Ictaluridae hypothesized convergent evolution of troglobitic features among the subterranean species. In contrast, we found morphological evidence to support a single clade of the four troglobitic species, the sister taxon of all ictalurids. This result holds whether fossils are included or not. Some previously published clock‐based age estimates closely approximate our minimum ages of clades.  相似文献   

8.
We examined the phylogenetic relationships between species and genera within the caddisfly subfamily Drusinae (Trichoptera: Limnephilidae) using sequence data from two mitochondrial loci (cytochrome oxidase 1, large subunit rRNA) and one nuclear gene (wingless). Sequence data were analysed for 28 species from five genera from the subfamily. We analysed individual and combined data sets using a Bayesian Markov Chain Monte Carlo and a maximum parsimony approach and compared the performance of each partition for resolving phylogenetic relationships at this level. In terms of resolution and phylogenetic utility wingless outperformed the two mitochondrial gene partitions. Using both Shimodaira-Hasegawa and expected likelihood weights tests we tested several hypotheses of relationships previously inferred based on adult morphological characters. The data did not support the generic concept, or many previously proposed species groupings, based on adult morphology. In contrast, the molecular data correlated with the morphology and feeding ecology of larvae. Using Bayesian ancestral character state reconstructions we inferred the evolution of feeding ecology and relevant larval morphological characters. Our analyses showed that within the subfamily Drusinae two derived feeding types evolved. One of these--grazing epilithic algae--is otherwise unusual in the Limnephilidae and may have promoted the high degree of diversity in the Drusinae.  相似文献   

9.
Cuticular organs have not been described systematically in harpacticoids until recently, and they have never been used as characters for reconstructing phylogenetic relationships in any crustacean group. We survey cuticular pores and sensilla on somites in ten Miraciidae species, belonging to six genera, from Korea, Australia, and Russia. Nine species belong to the subfamily Stenheliinae, while the outgroup belongs to the subfamily Diosaccinae. We aim to compare phylogenetic trees reconstructed for these harpactioids based on: 1) cuticular organs (with 76 characters scored, 71% of them phylogenetically informative); 2) traditionally used macro-morphological characters (66 scored, 77% of them informative); and 3) mtCOI DNA data. All analyses suggest that cuticular organs are useful characters for harpacticoid species delineation, although not as sensitive as some fast-evolving molecular markers. Reconstructed cladograms based on all three datasets show very high bootstrap values for clades representing distinct genera, suggesting that cuticular organs are suitable characters for studying phylogenetic relationships. Bootstrap values for the more basal nodes differ among the different cladograms, as do the sister-group relationships they suggest, indicating that cuticular organs probably have different evolutionary constraints from macro-morphological characters. Cuticular organs could be quite useful in the study of old museum specimens and fossil crustaceans.  相似文献   

10.
The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.  相似文献   

11.
A phylogenetic and systematic study of Orius species (Heteroptera: Anthocoridae) from Korea has been conducted using both morphological and molecular characters. Thirty morphological character states were coded for 10 strains of 9 species. Five molecular markers, partial cytochrome c oxidase I (COI), cytochrome b (CytB), 16S rRNA (16S), 18S rRNA (18S), and 28S rRNA (28S), from mitochondrial and nuclear genes, were tested. Phylogenetic analyses based on molecular data were conducted by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic (BP) analyses. Analysis of morphological data was performed using the parsimony programs NONA, and the combined dataset of morphological and molecular data was analyzed using BP analyses. The results of this study indicate that use of COI and CytB enabled relatively effective identification of species, whereas the sequences of 16S, 18S and 28S did not enable identification of closely related species such as Orius minutus and O. strigicollis. We discuss the usefulness of the five molecular markers for determining phylogenetic relationships and identifying the species.  相似文献   

12.
The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence between existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony-based version of the Shimodaira-Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylogenetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. Also, marginal to insignificant incongruence was detected among data partitions using the ILD. Maximum parsimony analysis of all data partitions combined results in a single tree, and is a unique hypothesis of phylogenetic relationships in the Channichthyidae. In particular, this hypothesis resolves the phylogenetic relationships of at least two species (Channichthys rhinoceratus and Chaenocephalus aceratus), for which there was no consensus among the previous phylogenetic hypotheses. The combined data partition dataset provides substantial statistical power to discriminate among alternative hypotheses of channichthyid relationships. These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions.  相似文献   

13.
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.  相似文献   

14.
Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.  相似文献   

15.
大花忍冬复合群主要分布在中国南部及周边地区,是忍冬属的主要疑难类群之一,包含大花忍冬、灰毡毛忍冬、细毡毛忍冬、菰腺忍冬和锈毛忍冬5种。该复合群是中国南部金银花的重要野生替代资源。本研究通过形态和生境观察、叶表皮微形态扫描和分子系统学分析相结合的方法,探讨了大花忍冬复合群的种间关系。结果表明,分子系统学方法没有解决该复合群之间的关系,仅灰毡毛忍冬的区分较为明显,基于形态学证据大致可将大花忍冬复合群分为以下3小群:菰腺忍冬以其独有的蘑菇状腺体与其他4种显著不同,毛被长度也明显长于其他种类;锈毛忍冬与大花忍冬的毛被较稀疏,但锈毛忍冬的花冠筒较短,气孔特征独特;灰毡毛忍冬与细毡毛忍冬的叶背密覆柔毛,二者的上表皮角质膜结构有差异。该复合群的物种形成和传播机制仍待深入研究。  相似文献   

16.
17.
With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. “Thaliacea” is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic “Ascidiacea”. Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.  相似文献   

18.
Waterfowl (Aves, Anseriformes) constitute an ancient global radiation, and understanding the pattern and timing of their evolution requires a well-corroborated phylogeny including extant species and fossils. Following the molecular advances in avian systematics, however, morphology has often been held as misleading, yet congruence with molecular data has been shown to vary considerably among different skeletal parts. Here, we explore phylogenetic signal in discrete characters of the lacrimal/ectethmoid region of waterfowl, which is highly variable among species and constitutes a rich source of data. We do so by combining cladistic and multivariate approaches, and using phylogenetic comparative methods. We quantitatively recognize three major morphological types among lacrimal bones, and discuss homoplasy and potential synapomorphies of major clades using a molecular backbone tree. Our results clearly indicate that the lacrimal bone carries substantial phylogenetic signal and could be of systematic value at different levels of the phylogeny of waterfowl, feeding the exploration of other regions of the skull with this combined approach.  相似文献   

19.
We examine the phylogenetic relationships of more than 40 species of European satyrids representing six tribes (Coenonymphini, Erebiini, Maniolini, Satyrini, Melanargiini, and Lethini). The analyses are based on comparisons of morphological data and mitochondrial genes encoding the large ribosomal subunit (16S rDNA) and NADH dehydrogenase subunit 1 (ND1). The cladistic reassessment of systematics based on morphological characters differs from the view retained by Miller by a lack in resolution due to the low number of characters used. Furthermore, some level of incongruence about the monophyly of the tribes is found between topologies from morphological and molecular analyses. In the case of Aphantopus hyperantus, molecular data and reexamination of morphology of this taxon indicate that this species has to be included within Maniolini. Contrary to the other clades, Erebia displays a radiate systematic pattern which cannot be explained by a lack of variable or informative sites. The combined spatial and temporal specialization found in the Erebia species may explain the rapid diversification of this genus relative to other satyrids. Finally, the subfamily level as defined by Miller for the taxa presented in the data set (Satyrinae and Elymninae) is not consistent with the molecular data. Given the reassessment of satyrids as a subfamily within Nymphalidae (Satyrinae), it seems more appropriate to retain the tribes as valid taxonomic ranks only in Satyrinae.  相似文献   

20.
《Palaeoworld》2014,23(3-4):336-356
Lauraceae is among the largest and floristically most important woody plant families in subtropical and tropical zones. However, the Cenozoic fossil records of Lauraceae are mostly from mid-latitude regions. Here we described eight lauraceous species from the Oligocene of Ningming, Guangxi, South China on the basis of leaf compressions with cuticular structure, providing new evidence for high diversity of Lauraceae in the low latitude region of the northern hemisphere during the late Paleogene. The extant genera to which the Ningming Oligocene fossils are possibly closely related include Cinnamomum, Neolitsea, Litsea, Alseodaphne, Laurus, and Beilschmiedia. All of these extant genera except Laurus still exist in Guangxi today, whereas Laurus is currently distributed in the Mediterranean and adjacent regions. A cladistic analysis based on leaf architectural and leaf cuticular characters for Paleogene Lauraceae species in the world indicated a possible relationship between European and East Asian Paleogene species.  相似文献   

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