A comparative analysis of dispersal syndromes in terrestrial and semi‐terrestrial animals

Dispersal, the behaviour ensuring gene flow, tends to covary with a number of morphological, ecological and behavioural traits. While species‐specific dispersal behaviours are the product of each species’ unique evolutionary history, there may be distinct interspecific patterns of covariation between dispersal and other traits (‘dispersal syndromes’) due to their shared evolutionary history or shared environments. Using dispersal, phylogeny and trait data for 15 terrestrial and semi‐terrestrial animal Orders (> 700 species), we tested for the existence and consistency of dispersal syndromes across species. At this taxonomic scale, dispersal increased linearly with body size in omnivores, but decreased above a critical length in herbivores and carnivores. Species life history and ecology significantly influenced patterns of covariation, with higher phylogenetic signal of dispersal in aerial dispersers compared with ground dwellers and stronger evidence for dispersal syndromes in aerial dispersers and ectotherms, compared with ground dwellers and endotherms. Our results highlight the complex role of dispersal in the evolution of species life‐history strategies: good dispersal ability was consistently associated with high fecundity and survival, and in aerial dispersers it was associated with early maturation. We discuss the consequences of these findings for species evolution and range shifts in response to future climate change.     

Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes

Extant gars represent the remaining members of a formerly diverse assemblage of ancient ray-finned fishes and have been the subject of multiple phylogenetic analyses using morphological data. Here, we present the first hypothesis of phylogenetic relationships among living gar species based on molecular data, through the examination of gene tree heterogeneity and coalescent species tree analyses of a portion of one mitochondrial (COI) and seven nuclear (ENC1, myh6, plagl2, S7 ribosomal protein intron 1, sreb2, tbr1, and zic1) genes. Individual gene trees displayed varying degrees of resolution with regards to species-level relationships, and the gene trees inferred from COI and the S7 intron were the only two that were completely resolved. Coalescent species tree analyses of nuclear genes resulted in a well-resolved and strongly supported phylogenetic tree of living gar species, for which Bayesian posterior node support was further improved by the inclusion of the mitochondrial gene. Species-level relationships among gars inferred from our molecular data set were highly congruent with previously published morphological phylogenies, with the exception of the placement of two species, Lepisosteus osseus and L. platostomus. Re-examination of the character coding used by previous authors provided partial resolution of this topological discordance, resulting in broad concordance in the phylogenies inferred from individual genes, the coalescent species tree analysis, and morphology. The completely resolved phylogeny inferred from the molecular data set with strong Bayesian posterior support at all nodes provided insights into the potential for introgressive hybridization and patterns of allopatric speciation in the evolutionary history of living gars, as well as a solid foundation for future examinations of functional diversification and evolutionary stasis in a "living fossil" lineage.     

Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran?

Adaptive convergence in morphological characters has not been thoroughly investigated, and the processes by which phylogenetic relationships may be misled by morphological convergence remains unclear. We undertook a case study on the morphological evolution of viverrid-like feliformians (Nandinia, Cryptoprocta, Fossa, Eupleres, Prionodon) and built the largest morphological matrix concerning the suborder Feliformia to date. A total of 349 characters grouped into four anatomical partitions were used for all species of Viverridae and viverrid-like taxa plus representatives of the Felidae, Hyaenidae, Herpestidae, and one Malagasy mongoose. Recent molecular phylogenetic analyses suggest that viverrid-like morphotypes appeared independently at least three times during feliformian evolution. We thus used a synthetic molecular tree to assess morphological evolutionary patterns characterizing the viverrid-like taxa. We examined phylogenetic signal, convergence and noise in morphological characters using (a) tree-length distribution (g1), (b) partitioned Bremer support, (c) RI values and their distribution, (d) respective contributions of diagnostic synapomorphies at the nodes for each partition, (e) patterns of shared convergences among viverrid-like taxa and other feliformian lineages, (f) tree-length differences among alternative hypotheses, and (g) the successive removal of convergent character states from the original matrix. In addition, the lability of complex morphological structures was assessed by mapping them onto the synthetic molecular tree. The unconstrained morphological analysis yielded phylogenetic groupings that closely reflected traditional classification. The use of a synthetic molecular tree (constraint) combined with our thorough morphological investigations revealed the mosaics of convergences likely to have contributed to part of the historical uncertainty over viverrid classification. It also showed that complex morphological structures could be subjected to reversible evolutionary trends. The morphological matrix proved useful in characterizing several feliformian clades with diagnostic synapomorphies. These results support the removal from the traditionally held Viverridae of several viverrid-like taxa into three distinct families: Nandiniidae (Nandinia), Prionodontidae (Prionodon), and the newly defined Eupleridae (including Cryptoprocta, Fossa, Eupleres plus all "mongoose-like" Malagasy taxa). No clearly "phylogenetically misleading" data subsets could be identified, and the great majority of morphological convergences appeared to be nonadaptive. The multiple approaches used in this study revealed that the most disruptive element with regards to morphological phylogenetic reconstruction was noise, which blured the expression of phylogenetic signal. This study demonstrates the crucial need to consider independent (molecular) phylogenies in order to produce reliable evolutionary hypotheses and should promote a new approach to the definition of morphological characters in mammals. [Constrained analysis; convergence; evolutionary scenario; Feliformia; morphology; noise; phylogenetic signal; phylogeny; Viverridae.].     

Trophic convergence drives morphological convergence in marine tetrapods

Marine tetrapod clades (e.g. seals, whales) independently adapted to marine life through the Mesozoic and Caenozoic, and provide iconic examples of convergent evolution. Apparent morphological convergence is often explained as the result of adaptation to similar ecological niches. However, quantitative tests of this hypothesis are uncommon. We use dietary data to classify the feeding ecology of extant marine tetrapods and identify patterns in skull and tooth morphology that discriminate trophic groups across clades. Mapping these patterns onto phylogeny reveals coordinated evolutionary shifts in diet and morphology in different marine tetrapod lineages. Similarities in morphology between species with similar diets—even across large phylogenetic distances—are consistent with previous hypotheses that shared functional constraints drive convergent evolution in marine tetrapods.     

Evolutionary Patterns of Morphology and Behavior as Inferred from a Molecular Phylogeny of New World Emballonurid Bats (Tribe Diclidurini)

A molecular phylogeny of New World emballonurid bats based on parsimony and Bayesian analyses of loci from the three different nuclear genetic transmission pathways in mammals (autosomal, X, and Y chromosomes) is well supported and independently corroborated by each individual gene tree. This is in contrast to a single most parsimonious but poorly supported tree based on morphological data, which has only one intergeneric or higher relationship shared with the molecular phylogeny. Combining the morphological and molecular data partitions results in a tree similar to the molecular tree suggesting a high degree of homoplasy and low phylogenetic signal in the morphological data set. Behavioral data are largely incomplete and likewise produce a poorly resolved tree. Nonetheless, patterns of evolution in morphology and behavior can be investigated by using the molecular tree as a phylogenetic framework. Character optimization of the appearance of dorsal fur and preferred roosting sites maps consistently and are correlated on the phylogeny. This suggests an association of camouflage for bats with unusual appearance (two dorsal stripes in Rhynchonycteris and Saccopteryx, or pale fur in Cyttarops and Diclidurus) and roosting in exposed sites (tree trunks or under palm leaves). In contrast, the ancestral states for Old and New World emballonurids are typically uniform brown or black, and they usually roost in sheltered roosts such as caves and tree hollows. Emballonuridae is the only family of bats that has a sac-like structure in the wing propatagium, which is found in four New World genera. Mapping the wing sac character states onto the phylogeny indicates that wing sacs evolved independently within each genus and that there may be a phylogenetic predisposition for this structure. Ear orientation maps relatively consistently on the molecular phylogeny and is correlated to echolocation call parameters and foraging behavior, suggesting a phylogenetic basis for these character systems.     

Mitochondrial DNA sequence evolution in sharks: rates, patterns, and phylogenetic inferences

Abundant representation of sharks in the fossil record makes this group a superb system in which to investigate rates and patterns of molecular evolution and to explore the strengths and weaknesses of phylogenetic inferences from molecular data. In this report, the molecular evolution of the cytochrome b gene in sharks is described and the information related to results from phylogenetic analysis of the data evaluated in the light of a phylogeny derived independently of the molecular data. Across divergent lineages of sharks there is evidence for significant substitution rate variation, departure from compositional equilibrium, and substantial homoplasy; nevertheless, the signal of evolutionary history is evident in patterns of shared transversions and amino acid replacements.      

iGTP: A software package for large-scale gene tree parsimony analysis

Background  

The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.     

Timing of organogenesis support basal position of turtles in the amniote tree of life

Background  

The phylogenetic position of turtles is the most disputed aspect in the reconstruction of the land vertebrate tree of life. This controversy has arisen after many different kinds and revisions of investigations of molecular and morphological data. Three main hypotheses of living sister-groups of turtles have resulted from them: all reptiles, crocodiles + birds or squamates + tuatara. Although embryology has played a major role in morphological studies of vertebrate phylogeny, data on developmental timing have never been examined to explore and test the alternative phylogenetic hypotheses. We conducted a comprehensive study of published and new embryological data comprising 15 turtle and eight tetrapod species belonging to other taxa, integrating for the first time data on the side-necked turtle clade.     

Phylogenetic relationships,evolution of broodcare behavior,and geographic speciation in the wrasse tribe Labrini

The family Labridae is a large assemblage of marine fish composed of about 580 species in 82 genera distributed in tropical and temperate marine waters around the world. Several subgroups, currently classified as tribes, have been identified in this large family, yet only a few phylogenetic analyses have been performed on labrid clades. We confirm monophyly of the labrid tribe Labrini and propose a phylogeny of the 23 species of the genera Acantholabrus, Centrolabras, Ctenolabrus, Labrus, Lappanella, Symphodus, Tautoga, and Tautogolabrus occurring in the eastern and western Atlantic and the Mediterranean. We analyzed a 577-bp segment of the mitochondrial 16S rDNA and a 506-bp segment of the mitochondrial control region in 22 species, for a total of up to 1069 bp per species. We used both parsimony and likelihood approaches under a variety of assumptions and models to generate phylogenetic hypotheses. The main features of the molecular phylogeny for the Labrini turned out to be the same for the two algorithms applied. The tree structure is similar to a previous, unpublished morphological phylogeny for a subset of labrine species. Estimated divergence times of the Labrini based on fossils and a molecular clock range from about 15 mya for the deepest splits to less than 1 mya for younger clades. Biogeographic patterns of the Symphodus species group and the genus Labrus are dominated by speciation events driven by the closing and opening of the Mediterranean Sea and periodic glaciation events during the past 1 million years. The Labrini are the only clade in the entire Labridae that exhibit nest-building and broodcare behavior. We use the phylogeny to show that similar broodcare behavior has evolved twice in the labrine fish and discuss scenarios for the evolution of broodcare from the diandric protogynous hermaphroditism found in ancestral labrines and many other wrasses.     

Phylogenetic uncertainty revisited: Implications for ecological analyses

Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximize the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade‐wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.     

Understanding phylogenetic incongruence: lessons from phyllostomid bats

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar‐feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species‐rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar‐feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well‐studied organisms such as phyllostomid bats.     

Morphological hemiplasies in cladistic studies of phylogeny,with examples from birds

Cladograms usually include many evolutionary reversions, parallelisms, and convergences united under the term homoplasy. Recently, it has become evident that molecular traits that look like homoplasy may be in fact true homologies. The processes of independent sorting of genes, which provide the basis of these events, were recently termed hemiplasy. The present study demonstrates theoretical possibility of independent manifestation of true homology (synapomorphy) in remote lineages of phylogenetic tree, as morphological characters are analyzed; this phenomenon is similar in manifestation (but not in nature) to hemiplasy. In the case of “morphological hemiplasy,” characters that appeared only once in evolution may formally be treated by a cladist as parallelisms, since they occur in remote lineages of phylogenetic tree. It is proposed that “morphological hemiplasy” is responsible for a number of uncertain cases in avian phylogeny. Examples are provided by the ducklike bill in Paleogene Presbyornithidae and extant Anatidae and Anseranatidae (Anseriformes), the apomorphic structure of the flying apparatus in Paleogene Jungornithidae (Apodiformes) and extant Trochilidae, and “independent” development of a highly-modified zygodactyl foot in Zygodactylidae and Pici.     

HGT-Gen: a tool for generating a phylogenetic tree with horizontal gene transfer

Horizontal gene transfer (HGT) is a common event in prokaryotic evolution. Therefore, it is very important to consider HGT in the study of molecular evolution of prokaryotes. This is true also for conducting computer simulations of their molecular phylogeny because HGT is known to be a serious disturbing factor for estimating their correct phylogeny. To the best of our knowledge, no existing computer program has generated a phylogenetic tree with HGT from an original phylogenetic tree. We developed a program called HGT-Gen that generates a phylogenetic tree with HGT on the basis of an original phylogenetic tree of a protein or gene. HGT-Gen converts an operational taxonomic unit or a clade from one place to another in a given phylogenetic tree. We have also devised an algorithm to compute the average length between any pair of branches in the tree. It defines and computes the relative evolutionary time to normalize evolutionary time for each lineage. The algorithm can generate an HGT between a pair of donor and acceptor lineages at the same evolutionary time. HGT-Gen is used with a sequence-generating program to evaluate the influence of HGT on the molecular phylogeny of prokaryotes in a computer simulation study.

Availability

The database is available for free at http://www.grl.shizuoka.ac.jp/˜thoriike/HGT-Gen.html     

The Adaptive Evolution Database (TAED)

Background  

Developing an understanding of the molecular basis for the divergence of species lies at the heart of biology. The Adaptive Evolution Database (TAED) serves as a starting point to link events that occur at the same time in the evolutionary history (tree of life) of species, based upon coding sequence evolution analyzed with the Master Catalog. The Master Catalog is a collection of evolutionary models, including multiple sequence alignments, phylogenetic trees, and reconstructed ancestral sequences, for all independently evolving protein sequence modules encoded by genes in GenBank [1].     

Specificity and specialization of congeneric monogeneans parasitizing cyprinid fish

Patterns and likely processes connected with evolution of host specificity in congeneric monogeneans parasitizing fish species of the Cyprinidae were investigated. A total of 51 Dactylogyrus species was included. We investigated (1) the link between host specificity and parasite phylogeny; (2) the morphometric correlates of host specificity, parasite body size, and variables of attachment organs important for host specificity; (3) the evolution of morphological adaptation, that is, attachment organ; (4) the determinants of host specificity following the hypothesis of specialization on more predictable resources considering maximal body size, maximal longevity, and abundance as measures of host predictability; and (5) the potential link between host specificity and parasite diversification. Host specificity, expressed as an index of host specificity including phylogenetic and taxonomic relatedness of hosts, was partially associated with parasite phylogeny, but no significant contribution of host phylogeny was found. The mapping of host specificity into the phylogenetic tree suggests that being specialist is not a derived condition for Dactylogyrus species. The different morphometric traits of the attachment apparatus seem to be selected in connection with specialization of specialist parasites and other traits favored as adaptations in generalist parasites. Parasites widespread on several host species reach higher abundance within hosts, which supports the hypothesis of ecological specialization. When separating specialists and generalists, we confirmed the hypothesis of specialization on a predictable resource; that is, specialists with larger anchors tend to live on fish species with larger body size and greater longevity, which could be also interpreted as a mechanism for optimizing morphological adaptation. We demonstrated that ecology of host species could also be recognized as an important determinant of host specificity. The mapping of morphological characters of the attachment organ onto the parasite phylogenetic tree reveals that morphological evolution of the attachment organ is connected with host specificity in the context of fish relatedness, especially at the level of host subfamilies. Finally, we did not find that host specificity leads to parasite diversification in congeneric monogeneans.     

Correlated evolution of self-incompatibility and clonal reproduction in Solanum (Solanaceae)

It has been suggested that clonality provides reproductive assurance in cross-fertilizing species subject to pollen limitation, relieving one of the main selective pressures favoring the evolution of self-fertilization. According to this hypothesis, cross-fertilizing species subject to pollen limitation should often be clonal. Here, we investigated the association between clonality and a genetic mechanism enforcing outcrossing, self-incompatibility, in Solanum (Solanaceae). We collected self-incompatibility and clonality information on 87 species, and looked for an association between these two traits. To account for the contribution of shared evolutionary history to this association, we incorporated phylogenetic information from chloroplast (NADH dehydrogenase subunit F) sequence data. We found that self-incompatibility is strongly associated with clonal reproduction: all self-incompatible species reproduce clonally, while the absence of clonality is widespread among self-compatible taxa. The observed correlation persists after taking into account shared phylogenetic history, assumptions about the evolutionary history of self-incompatibility, uncertainty associated with phylogeny estimation, and associations with life history (annual/perennial). Our results are consistent with the hypothesis that clonality provides reproductive assurance, and suggest that the consequences of clonal growth in the evolution of plant reproductive strategies may be more significant than previously thought.     

MORPHOMETRICS AND CLADISTICS: MEASURING PHYLOGENY IN THE SEA URCHIN ECHINOCARDIUM

A phylogenetic approach to the study of evolutionary patterns is based on taxic homologies (synapomorphies). In contrast, the recognition of evolutionary processes (namely heterochronies) involves analysis of the entire morphology. Recent developments in geometric morphometry permit analysis of morphological similarities grounded in operational homologies. Such morphometric techniques are explored (1) at the level of evolutionary processes, and (2) as a complement in exploration of phylogenetic relationships. To examplify this, we perform a two-part study of the ontogeny and phylogeny of the spatangoid sea urchin Echinocardium. First, a phylogenetic analysis of ten Recent species in the genus is performed on 18 informative characters of the test. Second, morphological divergences among the species are analyzed using procrustean (superimposition) methods based on 49 homologous points. An additive distance tree is built from a matrix of morphometric distances among adult specimens. This tree is fully congruent with the phyletic results. Ontogenetic processes are explored by inserting ontogenetic series into the analysis. A distance tree including the juvenile stages shows that the general evolutionary trend of the genus is peramorphic, but species-to-species comparisons attest that no general clinal trend exists. Our analysis emphasizes the importance of morphometric approaches in evolutionary studies (1) for the understanding of heterochronies; (2) to trace the morphological implications of phylogenetic patterns; and (3) to estimate the impact of homoplasies.     

Phylogeny, host-parasite relationship and zoogeography

Phylogeny is the evolutionary history of a group or the lineage of organisms and is reconstructed based on morphological, molecular and other characteristics. The genealogical relationship of a group of taxa is often expressed as a phylogenetic tree. The difficulty in categorizing the phylogeny is mainly due to the existence of frequent homoplasies that deceive observers. At the present time, cladistic analysis is believed to be one of the most effective methods of reconstructing a phylogenetic tree. Excellent computer program software for phylogenetic analysis is available. As an example, cladistic analysis was applied for nematode genera of the family Acuariidae, and the phylogenetic tree formed was compared with the system used currently. Nematodes in the genera Nippostrongylus and Heligmonoides were also analyzed, and the validity of the reconstructed phylogenetic trees was observed from a zoogeographical point of view. Some of the theories of parasite evolution were briefly reviewed as well. Coevolution of parasites and humans was discussed with special reference to the evolutionary relationship between Enterobius and primates.