影响开花植物物种多样化速率变化的因素探讨

开花植物(被子植物)是目前最为繁荣兴盛的陆地植物,是地球上种类最多、分布最广、适应性最强的优势植物类群。然而,物种多样性在开花植物的谱系中极端不均匀,同时其物种并非匀速增加,而是集中在某些时期快速扩张。这种现象暗示了开花植物的多样性受到某些因素的调控,而揭示影响开花植物多样化速率的机制便是这数十年来植物学家孜孜不倦努力的目标。该文介绍了当前的研究进展。研究显示,那些与类群分类相关的关键性状大多与多样化无关,而早期被视为决定因素的花性状,目前被认为影响较低或是需要多性状联合才产生实际影响。多倍化是一个受到高度关注的候选因素,被认为能提供物种扩张所需的遗传物质,在适当的情况或其他因素的参与下促成物种多样化。然而,许多研究也呈现各类的争议,这些悖论或许代表了多倍化不是决定因素,而是扮演着间接的角色。另外,环境的变异(温度、湿度、空间)也能提高多样性的发生。整体而言,影响开花植物多样化速率的原因,很可能是一种综合因素共同促成的结果,而每个植物类群多样化速率提升的原因亦可能不尽相同。因此,先分别对植物类群进行探讨,再进行整合,或许更能提供一个确实且普遍的模型。     

Phylogenomics and host-switching patterns of Philopteridae (Psocodea: Phthiraptera) feather lice

Philopteridae feather lice are a group of ectoparasitic insects which have intimate relationships with their avian hosts. Feather lice include an enormous number of described species; however, the relationships of major lineages have been clouded by homoplasious characters due to convergent evolution. In this study, a comprehensive phylogenomic analysis of the group is performed which includes 137 feather louse species. Several other analyses are also completed including dating analysis, cophylogenetic reconstructions, and ancestral character estimation to understand the evolution of complex morphological and ecological traits. Phylogenetic results recover high support for the placement of major feather louse lineages, but with lower support for long-branched enigmatic genera found at the base of the tree. The results of dating analyses suggest modern feather lice began to diversify approximately 49 million years ago following the adaptive radiation of their avian hosts. Cost-based cophylogenetic reconstructions recover a high frequency of host switching, while congruence-based methods indicate a significant level of congruence between host and parasite trees. Ancestral state reconstructions favour a generalist ancestor and water bird host at the root. The analyses completed provide insight into the evolution of a diverse group of ectoparasitic insects which infest a wide variety of avian hosts. The results represent the most comprehensive phylogenetic hypothesis of the group to date and provide a framework for future classification of the family into natural groupings.     

Linking the investigations of character evolution and species diversification

Variation in diversification rates is often studied by investigating traits related to species' ecology and life history. Often, however, it is unknown whether these traits evolve gradually or in punctuated bursts during speciation. Using phylogenetic data and species' present-day trait information, we present a novel approach to assessing the mode of character change while accounting for trait-dependent speciation and extinction. Our model, "Binary-State Speciation and Extinction-node enhanced state shift" (BiSSE-ness), estimates both the rate of change occurring along lineages and the probability of change occurring during speciation, as well as independent speciation and extinction rates for each character state. Using simulations, we found that BiSSE-ness is able to distinguish along-lineage and speciational change and accurately estimate the parameters associated with character change and diversification rates. We applied BiSSE-ness to an empirical primate data set and found evidence for along-lineage changes in primate mating systems and social behaviors, whereas shifts in habitat were associated with speciation. In cases where trait changes may be linked to the speciation process itself (e.g., niche-related traits), BiSSE-ness provides a suitable framework with which to simultaneously address questions regarding species diversification and character change.     

Behavioural evolution in penguins does not reflect phylogeny

Over the past two decades, behavioural biologists and ecologists have made effective use of the comparative method, but have often stopped short of adopting an explicitly phylogenetic approach. We examined 68 behaviour and life history (BLH) traits of 15 penguin species to: (i) infer penguin phylogeny, (ii) assess homology of behavioural characters, and (iii) evaluate hypotheses about character evolution and ancestral states. Parsimony analysis of the BLH dataset found either two shortest trees (characters coded as unordered) or a single shortest tree (characters coded as a combination of unordered and Dollo). The BLH data had significant structure. Kishino–Hasegawa tests indicated that BLH trees were significantly different from most previous estimates of penguin phylogeny. The BLH phylogeny generated from Dollo characters appeared to be less accurate than the tree derived from the completely unordered dataset. Dividing BLH data into display and non‐display traits resulted in no significant differences in level of homoplasy and no difference in the accuracy of phylogeny. Tests for homology of BLH traits were performed by mapping the characters onto a molecular tree. Assuming that independent gains are less likely than losses of character states, 65 of the 68 characters were likely to be homologous across taxa, and at least several characters appeared to have been stable since the origin of modern penguins around 30 Myr. Finally, the likely BLH traits of the most recent common ancestor of extant penguins were reconstructed from character states along the internal branch leading to the penguins. This analysis suggested that the “proto‐penguin” probably had a similar life history to current temperate penguins but few ritualized behaviours. A southern, cool‐temperate origin of penguins is suggested.     

Explaining the distribution of breeding and dispersal syndromes in conifers

The evolution of plants exhibiting different sexes, or dioecy, is correlated with a number of ecological and life-history traits such as woody growth form and animal-dispersed seeds, but the underlying causes of these associations are unclear. Previous work in seed plants has suggested that the evolution of fleshy cones or seeds may favour dioecy. In this study, we use a well-sampled molecular phylogeny of conifers to show that although dioecy and fleshiness strongly co-occur at the species level, this relationship has not resulted from numerous separate origins of this trait combination or from differential rates of diversification. Instead, we suggest that two character combinations—the ancestral dry-monoecious condition and the derived fleshy-dioecious condition—have persisted in conifers longer than other combinations over evolutionary time. The persistence of these trait combinations appears to reflect differences in the rate of successful transition into and out of these character states over time, as well as the geographical restriction of species with rare combinations and their consequent vulnerability to extinction. In general, we argue that such persistence explanations should be considered alongside ‘key innovation’ hypotheses in explaining the phylogenetic distribution of traits.     

Comparing and contrasting life history variation in four aphid hyperparasitoids

1. In primary parasitoids, significant differences in life history and reproductive traits are observed among parasitoids attacking different stages of the same host species. Much less is known about hyperparasitoids, which attack different stages of primary parasitoids. 2. Parasitoids exploit hosts in two different ways. Koinobionts attack hosts that continue feeding and growing during parasitism, whereas idiobionts paralyse hosts before oviposition or attack non‐growing host stages, e.g. eggs or pupae. 3. Koino‐/idiobiosis in primary parasitoids are often associated with different expression of life history trade‐offs, e.g. endo‐ versus ectoparasitism, high versus low fecundity and short versus long life span. 4. In the present study, life history parameters of two koinobiont endoparasitic species (Alloxysta victrix; Syrphophagus aphidivorus), and two idiobiont ectoparasitic species (Asaphes suspensus; Dendrocerus carpenteri) of aphid hyperparasitoids were compared. These hyperparasitoids attack either the parasitoid larva in the aphid before it is killed and mummified by the primary parasitoid or the parasitoid prepupa or pupa in the dead aphid mummy. 5. There was considerable variation in reproductive success and longevity in the four species. The idiobiont A. suspensus produced the most progeny by far and had the longest lifespan. In contrast, the koinobiont A. victrix had the lowest fecundity. Other developments and life history parameters in the different species were variable. 6. The present results reveal that there was significant overlap in life history and reproductive traits among hyperparasitoid koinobionts and idiobionts, even when attacking the same host species, suggesting that selection for expression of these traits is largely association specific.     

Strong character incongruence and character choice in phylogeny of sea stars of the Asterinidae

Abstract. Historically, characters from early animal development have been a potentially rich source of phylogenetic information, but many traits associated with the gametes and larval stages of animals with complex life cycles are widely suspected to have evolved frequent convergent similarities. Such convergences will confound true phylogenetic relationships. We compared phylogenetic inferences based on early life history traits with those from mitochondrial DNA sequences for sea stars in the genera Asterina, Cryptasterina , and Patiriella (Valvatida: Asterinidae). Analysis of these two character sets produced phylogenies that shared few clades. We quantified the degree of homoplasy in each character set when mapped onto the phylogeny inferred from the alternative characters. The incongruence between early life history and nucleotide characters implies more homoplasy in the life history character set. We suggest that the early life history traits in this case are most likely to be misleading as phylogenetic characters because simple adaptive models predict convergence in early life histories. We show that adding early life history characters may slightly improve a phylogeny based on nucleotide sequences, but adding nucleotide characters may be critically important to improving inferences from phylogenies based on early life history characters.     

Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)

The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and Cichlinae (Heroini) exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.     

Phylogenetic evidence for the evolution of ecological specialization in Timema walking‐sticks

We used phylogenetic and ecological information to study the evolution of host‐plant specialization and colour polymorphism in the genus Timema, which comprises 14 species of walking‐sticks that are subject to strong selection for cryptic coloration on their host‐plants. Phylogenetic analysis indicated that this genus consists of three main lineages. Two of the lineages include highly generalized basal species and relatively specialized distal species, and one of the lineages comprises four specialized species. We tested for phylogenetic conservatism in the traits studied via randomizing host‐plant use, and the four basic Timema colour patterns, across the tips of the phylogeny, and determining if the observed number of inferred changes was significantly low compared to the distribution of numbers of inferred changes expected under the null model. This analysis showed that (1) host‐plant use has evolved nonrandomly, such that more closely related species tend to use similar sets of hosts and (2) colour pattern evolution exhibits considerable lability. Inference of ancestral states using maximum parsimony, under four models for the relative ease of gain and loss of plant hosts or colour morphs, showed that (1) for all models with gains of host‐plants even marginally more difficult than losses, and for most optimizations with gains and losses equally difficult, the ancestral Timema were generalized, feeding on the chaparral plants Ceanothus and Adenostoma and possibly other taxa, and (2) for all models with gains of colour morphs more difficult than losses, the ancestral Timema were polymorphic for colour pattern. Generation of null distributions of inferred ancestral states showed that the maximum‐parsimony inference of host‐plant generalization was most robust for the most speciose of the three main Timema lineages. Ancestral states were also inferred using maximum likelihood, after recoding host‐plant use and colour polymorphism as dichotomous characters. Likelihood analyses provided some support for inference of generalization in host‐plant use at ancestral nodes of the two lineages exhibiting mixtures of generalists and specialists, although levels of uncertainty were high. By contrast, likelihood analysis did not estimate ancestral colour morph patterns with any confidence, due to inferred rates of change that were high with respect to speciation rates. Information from biogeography, floristic history and the timing of diversification of the genus are compatible with patterns of inferred ancestral host‐plant use. Diversification in the genus Timema appears to engender three main processes: (1) increased specialization via loss of host‐plants, (2) retention of the same, single, host‐plant and (3) shifts to novel hosts to which lineages were ‘preadapted’ in colour pattern. Our evidence suggests that the radiation of this genus has involved multiple evolutionary transitions from individual‐level specialization (multiple‐niche polymorphism) to population‐level and species‐level specialization. Ecological studies of Timema suggest that such transitions are driven by diversifying selection for crypsis. This paper provides the first phylogeny‐based evidence for the macroevolutionary importance of predation by generalist natural enemies in the evolution of specialization.     

A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches

Phylogenetic analysis of genomic data allows insights into the evolutionary history of pathogens, especially the events leading to host switching and diversification, as well as alterations of the life cycle (life-history traits). Hundreds, perhaps thousands, of malaria parasite species exploit squamate reptiles, birds, and mammals as vertebrate hosts as well as many genera of dipteran vectors, but the evolutionary and ecological events that led to this diversification and success remain unresolved. For a century, systematic parasitologists classified malaria parasites into genera based on morphology, life cycle, and vertebrate and insect host taxa. Molecular systematic studies based on single genes challenged the phylogenetic significance of these characters, but several significant nodes were not well supported. We recovered the first well resolved large phylogeny of Plasmodium and related haemosporidian parasites using sequence data for four genes from the parasites' three genomes by combining all data, correcting for variable rates of substitution by gene and site, and using both Bayesian and maximum parsimony analyses. Major clades are associated with vector shifts into different dipteran families, with other characters used in traditional parasitological studies, such as morphology and life-history traits, having variable phylogenetic significance. The common parasites of birds now placed into the genus Haemoproteus are found in two divergent clades, and the genus Plasmodium is paraphyletic with respect to Hepatocystis, a group of species with very different life history and morphology. The Plasmodium of mammal hosts form a well supported clade (including Plasmodium falciparum, the most important human malaria parasite), and this clade is associated with specialization to Anopheles mosquito vectors. The Plasmodium of birds and squamate reptiles all fall within a single clade, with evidence for repeated switching between birds and squamate hosts.     

Multilevel Control of Organelle DNA Sequence Length in Plants

We have compared the length of noncoding organelle DNA spacers in a broad sample of plant species characterized by different life history traits to test hypotheses regarding the nature of the mechanisms driving changes in their size. We first demonstrate that the spacers do not evolve at random in size but have experienced directional evolutionary trends during plant diversification. We then study the relationships between spacer lengths and other molecular features and various species attributes by taking into account population genetic processes acting within cell lineages. Comparative techniques are used to test these relationships while controlling for species phylogenetic relatedness. The results indicate that spacer length depends on mode of organelle transmission, on population genetic structure, on nucleotide content, on rates of molecular evolution, and on life history traits, in conformity with predictions based on a model of intracellular competition among replicating organelle genomes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

How traits shape trees: new approaches for detecting character state‐dependent lineage diversification

Biologists have long sought to understand the processes underlying disparities in clade size across the tree of life and the extent to which such clade size differences can be attributed to the evolution of particular traits. The association of certain character states with species‐rich clades suggests that trait evolution can lead to increased diversification, but such a pattern could also arise due other processes, such as directional trait evolution. Recent advances in phylogenetic comparative methods have provided new statistical approaches for distinguishing between these intertwined and potentially confounded macroevolutionary processes. Here, we review the historical development of methods for detecting state‐dependent diversification and explore what new methods have revealed about classic examples of traits that affect diversification, including evolutionary dead ends, key innovations and geographic traits. Applications of these methods thus far collectively suggest that trait diversity commonly arises through the complex interplay between transition, speciation and extinction rates and that long hypothesized evolutionary dead ends and key innovations are instead often cases of directional trends in trait evolution.     

Factors influencing diversification in angiosperms: at the crossroads of intrinsic and extrinsic traits

Recent studies indicate that both key innovations and available area influence species richness in angiosperms. Available area has been observed to have the greatest effect, however, and appears to alter the "carrying capacity" of a lineage rather than alter diversification rates. Here, we review and weigh the evidence of predictors of angiosperm diversification and further dissect how area can place ecological limits on diversification of angiosperms, specifically addressing the following: (1) theoretical mechanisms by which particular intrinsic and extrinsic traits may affect diversification in angiosperm families; (2) evidence that the amount of available area determines the ecological limits on lineages; and (3) geographical distribution of diversification hotspots in angiosperms, concentrating on the effects of zygomorphy, noncontiguous area, and latitude. While we found that dispersal to numerous noncontiguous areas is most important in spurring diversification, diversification of tropical and zygomorphic families appears to be elevated by the generation of more species per given area.     

Trait convergence and diversification arising from a complex evolutionary history in Hawaiian species of <Emphasis Type="Italic">Scaevola</Emphasis>

Species variation in functional traits may reflect diversification relating to convergence and/or divergence depending on environmental pressures and phylogenetic history. We tested trait-environment relationships and their basis in finer-scale evolutionary processes among nine extant Hawaiian species of Scaevola L. (Goodeniaceae), a taxon with a complex history of three independent colonizations by different phylogenetic lineages, parallel ecological specialization, and homoploid hybridization events in Hawai‘i. Using a wild population for each species, we evaluated traits related to plant function (morphology, leaf and wood anatomy, nutrient and carbon isotope composition). Hawaiian Scaevola species were distributed across coastal, dry forest and wet forest environments; multivariate environmental analysis using abiotic and biotic factors further showed that species from distantly related lineages inhabited similar environments. Many traits correlated with environment (based on the multivariate environmental analysis), considering both distantly related species and more closely related species. Scaevola species within shared habitats generally showed trait convergence across distantly related lineages, particularly among wet forest species. Furthermore, trait diversification through divergence was extensive among closely related Scaevola species that radiated into novel environments, especially in plant morphology and traits affecting water relations. Homoploid hybrid-origin species were “intermediate” compared to their ancestral parent species, and possessed trait combinations relevant for their current habitat. The diversity in functional traits reflected strong influences of both ecology and evolutionary history in native Hawaiian Scaevola species, and trait correspondence with environment was due to the combination of multiple processes within the taxon: trait pre-adaptation and filtering, evolutionary convergence, divergence, and hybridization.     

Biogeography explains cophylogenetic patterns in toucan chewing lice

Historically, comparisons of host and parasite phylogenies have concentrated on cospeciation. However, many of these comparisons have demonstrated that the phylogenies of hosts and parasites are seldom completely congruent, suggesting that phenomena other than cospeciation play an important role in the evolution of host-parasite assemblages. Other coevolutionary phenomena, such as host switching, parasite duplication (speciation on the host), sorting (extinction), and failure to speciate can also influence host-parasite assemblages. Using mitochondrial and nuclear protein-coding DNA sequences, I reconstructed the phylogeny of ectoparasitic toucan chewing lice in the Austrophilopterus cancellosus subspecies complex and compared this phylogeny with the phylogeny of the hosts, the Ramphastos toucans, to reconstruct the history of coevolutionary events in this host-parasite assemblage. Three salient findings emerged. First, reconstructions of host and louse phylogenies indicate that they do not branch in parallel, and their cophylogenetic history shows little or no significant cospeciation. Second, members of monophyletic Austrophilopterus toucan louse lineages are not necessarily restricted to monophyletic host lineages. Often, closely related lice are found on more distantly related but sympatric toucan hosts. Third, the geographic distribution of the hosts apparently plays a role in the speciation of these lice. These results suggest that for some louse lineages biogeography may be more important than host associations in structuring louse populations and species, particularly when host life history (e.g., hole nesting) or parasite life history (e.g., phoresis) might promote frequent host switching events between syntopic host species. These findings highlight the importance of integrating biogeographic information into cophylogenetic studies.     

Explosive radiation of a bacterial species group

The current diversity of life on earth is the product of macroevolutionary processes that have shaped the dynamics of diversification. Although the tempo of diversification has been studied extensively in macroorganisms, much less is known about the rates of diversification in the exceedingly diverse and species-rich microbiota. Decreases in diversification rates over time, a signature of explosive radiations, are commonly observed in plant and animal lineages. However, the few existing analyses of microbial lineages suggest that the tempo of diversification in prokaryotes may be fundamentally different. Here, we use multilocus and genomic sequence data to test hypotheses about the rate of diversification in a well-studied pathogenic bacterial lineage, Borrelia burgdorferi sensu lato (sl). Our analyses support the hypothesis that an explosive radiation of lineages occurred near the origin of the clade, followed by a sharp decay in diversification rates. These results suggest that explosive radiations may be a general feature of evolutionary history across the tree of life.     

Co-phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities

Comparative microevolutionary studies of multiple parasites occurring on a single host species can help shed light on the processes underlying parasite diversification. We compared the phylogeographical histories, population genetic structures and population divergence times of three co-distributed and phylogenetically independent ectoparasitic insect species, including an amblyceran and an ischnoceran louse (Insecta: Phthiraptera), a hippoboscid fly (Insecta: Diptera) and their endemic avian host in the Galápagos Islands. The Galápagos hawk (Aves: Falconiformes: Buteo galapagoensis) is a recently arrived endemic lineage in the Galápagos Islands and its island populations are diverging evolutionarily. Each parasite species differed in relative dispersal ability and distribution within the host populations, which allowed us to make predictions about their degree of population genetic structure and whether they tracked host gene flow and colonization history among islands. To control for DNA region in comparisons across these phylogenetically distant taxa, we sequenced ~1 kb of homologous mitochondrial DNA from samples collected from all island populations of the host. Remarkably, the host was invariant across mitochondrial regions that were comparatively variable in each of the parasite species, to degrees consistent with differences in their natural histories. Differences in these natural history traits were predictably correlated with the evolutionary trajectories of each parasite species, including rates of interisland gene flow and tracking of hosts by parasites. Congruence between the population structures of the ischnoceran louse and the host suggests that the ischnoceran may yield insight into the cryptic evolutionary history of its endangered host, potentially aiding in its conservation management.     

Angiosperm diversification through time

The extraordinary diversity of angiosperms is the ultimate outcome of the interplay of speciation and extinction, which determine the net diversification of different lineages. We document the temporal trends of angiosperm diversification rates during their early history. Absolute diversification rates were estimated for order-level clades using ages derived from relaxed molecular clock analyses that included or excluded a maximal constraint to angiosperm age. Diversification rates for angiosperms as a whole ranged from 0.0781 to 0.0909 net speciation events per million years, with dates from the constrained analysis. Diversification through time plots show an inverse relationship between clade age and rate, where the younger clades tend to have the highest rates. Angiosperm diversity is found to have mixed origins: slightly less than half of the living species belong to lineages with low to moderate diversification rates, which appeared between 130 and 102 Mya (Barremian-uppermost Albian; Lower Cretaceous). Slightly over half of the living species belong to lineages with moderate to high diversification rates, which appeared between 102 and 77 Mya (Cenomanian-mid Campanian; Upper Cretaceous). Terminal lineages leading to living angiosperm species, however, may have originated soon or long after the phylogenetic differentiation of the clade to which they belong.     

Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade

The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. 'beetles'), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.