物种谱系不确定性对群落谱系格局指标的影响

物种谱系关系常被用于衡量群落谱系格局及推断格局背后的生态过程,但多数研究往往忽视谱系关系的不确定性及其可能对群落谱系格局造成的影响.为此,本文以浙江天童20 hm^2样地内150个树种为研究对象,采用这些物种叶绿体DNA的rbcL和matK碱基序列构建1棵一致系统发育树和反映谱系不确定性的999棵系统发育树,然后结合样地物种分布数据计算标准化净亲缘指数(NRI)和最近亲缘指数(NTI),最后运用独立置换零模型衡量样地群落谱系格局.结果表明:物种系统发育树在拓扑结构和物种谱系分支节点年龄上均存在较大的不确定性,谱系不确定性随着谱系分支节点年龄的减小而增大,也随物种间平均谱系距离的增加而增加;在样方尺度上,物种谱系的不确定性增加了标准化NRI和NTI指数的变异,但对两个指数的影响几乎独立;其对两指数的空间分布影响不同,且程度不一,其中标准化NRI受到的影响相对更大;在群落尺度上,物种谱系的不确定性增加了标准化NRI和NTI的变异,平均变异系数分别为0.37和0.077,表明群落水平的标准化NRI更易受到谱系不确定性的影响.这说明物种谱系不确定性会传递到常用的群落谱系格局指标中,且不同指标受影响的程度不同,进而影响对群落谱系格局的衡量及相关生态过程的推断.该结论也暗示以往不考虑谱系不确定性的研究中,非随机的群落谱系格局比例可能被高估.     

Phylogenetic clustering increases with succession for lianas in a Chinese tropical montane rain forest

Previous research found that phylogenetic clustering increased with disturbance for tropical trees, suggesting that community assembly is mainly influenced by abiotic factors during early succession. Lianas are an important additional component of tropical forests, but their phylogenetic community structure has never been investigated. Unlike tropical trees, liana abundance is often high in disturbed forests and diversity can peak in old secondary forest. Therefore, phylogenetic structure along a disturbance gradient might also differ from tropical tree communities. Here we determined phylogenetic community structure of lianas along a disturbance gradient in a tropical montane forest in China, using the net relatedness index (NRI) from 100 equivalent phylogenies with varying branch length that were constructed using DNA‐barcode sequences. Three additional phylogenetic indices were also considered for comparison. When NRI was used as index phylogenetic clustering of liana communities decreased with decreasing tree basal area, suggesting that liana competitive interactions dominate during early succession, which is in contrast to the pattern reported for trees. Liana communities in mature forests, on the other hand, were phylogenetic clustered, which could be caused by dispersal limitation and/or environmental filtering. The three additional phylogenetic indices identified different, sometimes contradicting predictors of phylogenetic community structure, indicating that caution is needed when generalizing interpretations of studies based on a single phylogenetic community structure index. Our study provides a more nuanced picture of non‐random assembly along disturbance gradients by focusing on a non‐tree forest component.     

What are “tippy” and “stemmy” phylogenies? Resolving a phylogenetic terminological tangle

Phylogenetic stemminess is one of the most popular metrics of tree shape among evolutionary biologists. The index was originally described by Fiala & Sokal (1985) as the proportion of the total length of the branches of a phylogenetic clade (including the subtending branch or “stem”) that is accounted for by the length of the subtending branch of the clade. Accordingly, phylogenies with high stemminess would show accumulation of speciation events toward the present, whereas those with low‐stemminess values would reflect the opposite pattern (i.e., speciation events skewed toward the root node, Fig.1).     

Are phylogenies resolved at the genus level appropriate for studies on phylogenetic structure of species assemblages?

Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages. Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants, researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera. However, whether the result of a study using species-level phylogenies generated in these ways is robust, compared to that based on phylogenies fully resolved at the species level, has not been assessed. Here, we use 1093 angiosperm tree assemblages (each in a 110 × 110 km quadrat) in North America as a model system to address this question, by examining six commonly used metrics of phylogenetic structure (phylogenetic diversity and phylogenetic relatedness) and six climate variables commonly used in ecology. Our results showed that (1) the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level (the mean of correlation coefficients is 0.973), and (2) the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny. Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.     

Are phylogenies derived from family‐level supertrees robust for studies on macroecological patterns along environmental gradients?

Ecologists frequently use a supertree method to generate phylogenies in ecological studies. However, the robustness of research results based on phylogenies generated with a supertree method has not been well evaluated. Here, we use the angiosperm tree flora of North America as a model system to test the robustness of phylogenies generated with a supertree method for studies on the relationship between phylogenetic properties and environment, by comparing the relationship between phylogenetic metrics and environmental variables derived from a phylogeny reconstructed with a supertree method to that derived from a phylogeny resolved at species level. North America was divided into equal area quadrats of 12 100 km². Nine indices of phylogenetic structure were calculated for angiosperm tree assemblages in each quadrat using two phylogenies resolved at different levels (one resolved at the family level and the other resolved at the species level). Scores of phylogenetic indices were related to two major climatic variables (temperature and precipitation) using correlation and regression analyses. Scores of phylogenetic indices resulting from the two phylogenies are perfectly or nearly perfectly correlated. On average, there is no difference in the variation explained by the two climatic variables between scores of phylogenetic indices derived from the two phylogenies. Our study suggests that a phylogeny derived from a well resolved family-level supertree as backbone with genera and species attached to the backbone as polytomies is robust for studies investigating the relationship between phylogenetic structure and environment in biological assemblages at a broad spatial scale.     

Consequences of recombination on traditional phylogenetic analysis

We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.     

Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities

Conservation biologists and community ecologists have increasingly begun to quantify the phylogenetic diversity and phylogenetic dispersion in species assemblages. In some instances, the phylogenetic trees used for such analyses are fully bifurcating, but in many cases the phylogenies being used contain unresolved nodes (i.e. polytomies). The lack of phylogenetic resolution in such studies, while certainly not preferred, is likely to continue particularly for those analyzing diverse communities and datasets with hundreds to thousands of taxa. Thus it is imperative that we quantify potential biases and losses of statistical power in studies that use phylogenetic trees that are not completely resolved. The present study is designed to meet both of these goals by quantifying the phylogenetic diversity and dispersion of simulated communities using resolved and gradually ‘unresolved’ phylogenies. The results show that: (i) measures of community phylogenetic diversity and dispersion are generally more sensitive to loss of resolution basally in the phylogeny and less sensitive to loss of resolution terminally; and (ii) the loss of phylogenetic resolution generally causes false negative results rather than false positives.     

山西陵川南方红豆杉自然保护区鹅耳枥植物群落谱系结构特征

分析植物群落谱系结构,可以探究乔木层、灌木层和草本层物种对环境变化的响应情况。以山西陵川南方红豆杉自然保护区鹅耳枥群落为研究对象,采用样方法,分别从不同径级和不同坡向对鹅耳枥群落净谱系亲缘关系指数(Net relatedness index,NRI)和净最近种间亲缘关系指数(Nearest taxon index,NTI)进行研究,探讨了鹅耳枥群落沿着径级梯度形成群落谱系结构特征,进而分析了鹅耳枥群落构建的历史进程。结果表明:(1)该保护区鹅耳枥群落乔木层(26种)、灌木层(32种)和草本层(39种)谱系结构树可分为5个类群、5个类群和4个类群;乔木层(86.67%的样地,下同)和灌木层(73.33%)物种群落谱系结构呈谱系发散格局(NRI0,NTI0),但草本层(86.67%)物种群落谱系结构呈谱系聚集格局(NRI0,NTI0)。(2)鹅耳枥群落乔木层中,DBH在Ⅰ级至Ⅱ级间,NRI指数随着DBH的增大而减小,NTI指数随着DBH的增大而增大;在Ⅱ级至Ⅴ级之间,随着植物DBH增大NRI指数和NTI指数值均呈下降趋势;而且在不同DBH水平上群落NRI和NTI指数均差异显著(P0.05),说明随着径级的增大,群落谱系结构由谱系聚集变为谱系发散。(3)灌木层物种谱系结构在阴坡和阳坡均呈聚集型,乔木层阴坡物种的谱系结构呈发散型(NRI0,NTI0),乔木层阳坡和草本层阴阳坡群落均无法判定群落谱系结构是聚集还是发散。     

Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.     

Influence of tree shape and evolutionary time‐scale on phylogenetic diversity metrics

During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro‐ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith's phylogenetic diversity (PD_Faith), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PD_Faith relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PD_Faith provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PD_Faith) we can obtain a better understanding of assemblage structure.     

Sensitivity of Ribosomal RNA Character Sampling in the Phylogeny of Rhabditida

Near-full-length 18S and 28S rRNA gene sequences were obtained for 33 nematode species. Datasets were constructed based on secondary structure and progressive multiple alignments, and clades were compared for phylogenies inferred by Bayesian and maximum likelihood methods. Clade comparisons were also made following removal of ambiguously aligned sites as determined using the program ProAlign. Different alignments of these data produced tree topologies that differed, sometimes markedly, when analyzed by the same inference method. With one exception, the same alignment produced an identical tree topology when analyzed by different methods. Removal of ambiguously aligned sites altered the tree topology and also reduced resolution. Nematode clades were sensitive to differences in multiple alignments, and more than doubling the amount of sequence data by addition of 28S rRNA did not fully mitigate this result. Although some individual clades showed substantially higher support when 28S data were combined with 18S data, the combined analysis yielded no statistically significant increases in the number of clades receiving higher support when compared to the 18S data alone. Secondary structure alignment increased accuracy in positional homology assignment and, when used in combination with paired-site substitution models, these structural hypotheses of characters and improved models of character state change yielded high levels of phylogenetic resolution. Phylogenetic results included strong support for inclusion of Daubaylia potomaca within Cephalobidae, whereas the position of Fescia grossa within Tylenchina varied depending on the alignment, and the relationships among Rhabditidae, Diplogastridae, and Bunonematidae were not resolved.     

Multi-scale phylogenetic structure in coastal dune plant communities across the globe

Aims Studies integrating phylogenetic history and large-scale community assembly are few, and many questions remain unanswered. Here, we use a global coastal dune plant data set to uncover the important factors in community assembly across scales from the local filtering processes to the global long-term diversification and dispersal dynamics. Coastal dune plant communities occur worldwide under a wide range of climatic and geologic conditions as well as in all biogeographic regions. However, global patterns in the phylogenetic composition of coastal dune plant communities have not previously been studied.Methods The data set comprised vegetation data from 18463 plots in New Zealand, South Africa, South America, North America and Europe. The phylogenetic tree comprised 2241 plant species from 149 families. We calculated phylogenetic clustering (Net Relatedness Index, NRI, and Nearest Taxon Index, NTI) of regional dune floras to estimate the amount of in situ diversification relative to the global dune species pool and evaluated the relative importance of land and climate barriers for these diversification patterns by geographic analyses of phylogenetic similarity. We then tested whether dune plant communities exhibit similar patterns of phylogenetic structure within regions. Finally, we calculated NRI for local communities relative to the regional species pool and tested for an association with functional traits (plant height and seed mass) thought to vary along sea–inland gradients.Important findings Regional species pools were phylogenetically clustered relative to the global pool, indicating regional diversification. NTI showed stronger clustering than NRI pointing to the importance of especially recent diversifications within regions. The species pools grouped phylogenetically into two clusters on either side of the tropics suggesting greater dispersal rates within hemispheres than between hemispheres. Local NRI plot values confirmed that most communities were also phylogenetically clustered within regions. NRI values decreased with increasing plant height and seed mass, indicating greater phylogenetic clustering in communities with short maximum height and good dispersers prone to wind and tidal disturbance as well as salt spray, consistent with environmental filtering along sea–inland gradients. Height and seed mass both showed significant phylogenetic signal, and NRI tended to correlate negatively with both at the plot level. Low NRI plots tended to represent coastal scrub and forest, whereas high NRI plots tended to represent herb-dominated vegetation. We conclude that regional diversification processes play a role in dune plant community assembly, with convergence in local phylogenetic community structure and local variation in community structure probably reflecting consistent coastal-inland gradients. Our study contributes to a better understanding of the globally distributed dynamic coastal ecosystems and the structuring factors working on dune plant communities across spatial scales and regions.     

A mixed branch length model of heterotachy improves phylogenetic accuracy

Evolutionary relationships are typically inferred from molecular sequence data using a statistical model of the evolutionary process. When the model accurately reflects the underlying process, probabilistic phylogenetic methods recover the correct relationships with high accuracy. There is ample evidence, however, that models commonly used today do not adequately reflect real-world evolutionary dynamics. Virtually all contemporary models assume that relatively fast-evolving sites are fast across the entire tree, whereas slower sites always evolve at relatively slower rates. Many molecular sequences, however, exhibit site-specific changes in evolutionary rates, called "heterotachy." Here we examine the accuracy of 2 phylogenetic methods for incorporating heterotachy, the mixed branch length model--which incorporates site-specific rate changes by summing likelihoods over multiple sets of branch lengths on the same tree--and the covarion model, which uses a hidden Markov process to allow sites to switch between variable and invariable as they evolve. Under a variety of simple heterogeneous simulation conditions, the mixed model was dramatically more accurate than homotachous models, which were subject to topological biases as well as biases in branch length estimates. When data were simulated with strong versions of the types of heterotachy observed in real molecular sequences, the mixed branch length model was more accurate than homotachous techniques. Analyses of empirical data sets confirmed that the mixed branch length model can improve phylogenetic accuracy under conditions that cause homotachous models to fail. In contrast, the covarion model did not improve phylogenetic accuracy compared with homotachous models and was sometimes substantially less accurate. We conclude that a mixed branch length approach, although not the solution to all phylogenetic errors, is a valuable strategy for improving the accuracy of inferred trees.     

Phylogenetic clustering and overdispersion for alpine plants along elevational gradient in the Hengduan Mountains Region,southwest China

To better understand the elevational pattern of phylogenetic structure shown by alpine taxa and the underlying causes, we analyzed the phylogenetic structure of each elevational belt of alpine plants in the Hengduan Mountains Region, measured by net related index (NRI) and net nearest taxon index (NTI). We found both the indices of phylogenetic diversity indicated that alpine plants tended to show phylogenetic overdispersion at low elevational belts, implying that the distribution of alpine plants in these belts was mainly determined by interspecific competition. Alpine plants at higher elevational belts tended to phylogenetic clustering indicated by NRI, and NTIrevealed phylogenetic clustering at the belts between 4300 m and 5500 m, which presumably suggested environment filtering and rapid speciation. Above 5500 m,NTI indicated that the phylogenetic structure became random again, perhaps due to the low intensity of filtering and the large distances between plants at the top of the scree slopes. We concluded that phylogenetic structure was, indeed, influenced by the environmental filter, interspecies interaction, rapid speciation during the uplift of the Qinghai–Tibet Plateau, and distance between plants.     

The phylogenetic structure of primate communities: variation within and across continents

Aim Our goals are: (1) to examine the relative degree of phylogenetic overdispersion or clustering of species in communities relative to the entire species pool, (2) to test for across‐continent differences in community phylogenetic structure, and (3) to examine the relationship between species richness and community phylogenetic structure. Location Africa, Madagascar, Asia, and the Neotropics. Methods We collected species composition and phylogenetic data for over 100 primate communities. For each community, we calculated two measures of phylogenetic structure: (1) the net relatedness index (NRI), which provides a measure of the mean pairwise phylogenetic distance among all species in the community; and (2) the nearest taxon index (NTI), which measures the relative phylogenetic distance among the closest related species in a community. Both measures are relative to the phylogeny of the species in the entire species pool. The phylocom package uses a randomization procedure to test whether the NRI and NTI values are higher or lower than expected by chance alone. In addition, we used a Kruskal–Wallis test to examine differences in NRI and NTI across continents, and linear regressions to examine the relationship between species richness and NRI/NTI. Results We found that the majority of individual primate communities in Africa, Asia and the Neotropics consist of member species that are neither more nor less closely related than expected by chance alone. Yet 37% of Malagasy communities contain species that are more distantly related to each other compared with random species assemblages. Also, we found that the average degree of relatedness among species in communities differed significantly across continents, with African and Malagasy communities consisting of more distantly related taxa compared with communities in Asia and the Neotropics. Finally, we found a significant negative relationship between species richness and phylogenetic distance among species in African, Asian and Malagasy communities. The average relatedness among species in communities decreased as community size increased. Main conclusions The majority of individual primate communities exhibit a phylogenetic structure no different from random. Yet there are across‐continent differences in the phylogenetic structure of primate communities that probably result from the unique ecological and evolutionary characteristics exhibited by the endemic species found on each continent. In particular, the recent extinctions of numerous primates on Madagascar are likely responsible for the low levels of evolutionary relatedness among species in Malagasy communities.     

Climatic correlates of phylogenetic relatedness of woody angiosperms in forest communities along a tropical elevational gradient in South America

Aims This study assesses the relationship between phylogenetic relatedness of angiosperm tree species and climatic variables in local forests distributed along a tropical elevational gradient in South America. In particular, this paper addresses two questions: Is phylogenetic relatedness of plant species in communities related to temperature variables more strongly than to water variables for tropical elevational gradients? Is phylogenetic relatedness of plant species in communities driven by extreme climatic conditions (e.g. minimum temperature (MT) and water deficit) more strongly than by climatic seasonal variability (e.g. temperature seasonality and precipitation seasonality)?Methods I used a set of 34 angiosperm woody plant assemblages along an elevational gradient in the Andes within less than 5 degrees of the equator. Phylogenetic relatedness was quantified as net relatedness index (NRI) and nearest taxon index (NTI) and was related to major climatic variables. Correlation analysis and structure equation modeling approach were used to assess the relationships between phylogenetic relatedness and climatic variables.Important findings Phylogenetic relatedness of angiosperm woody species in the local forest communities is more strongly associated with temperature-related variables than with water-related variables, is positively correlated with mean annual temperature (MAT) and MT, and is related with extreme cold temperature more strongly than with seasonal temperature variability. NTI was related with elevation, MAT and MT more strongly than was NRI. Niche convergence, rather than niche conservatism, has played a primary role in driving community assembly in local forests along the tropical elevational gradient examined. Negative correlations of phylogenetic relatedness with elevation and higher correlations of phylogenetic relatedness with elevation and temperature for NTI than for NRI indicate that evolution of cold tolerance at high elevations in tropical regions primarily occurred at recent (terminal) phylogenetic nodes widely distributed among major clades.     

Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.     

Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas

Identifying the main determinants of tropical marine biodiversity is essential for devising appropriate conservation measures mitigating the ongoing degradation of coral reef habitats. Based on a gridded distribution database and phylogenetic information, we compared the phylogenetic structure of assemblages for three tropical reef fish families (Labridae: wrasses, Pomacentridae: damselfishes and Chaetodontidae: butterflyfishes) using the net relatedness (NRI) and nearest taxon (NTI) indices. We then related these indices to contemporary and historical environmental conditions of coral reefs using spatial regression analyses. Higher levels of phylogenetic clustering were found for fish assemblages in the Indo‐Australian Archipelago (IAA), and more particularly when considering the NTI index. The phylogenetic structure of the Pomacentridae, and to a lower extent of the Chaeotodontidae and Labridae, was primarily associated with the location of refugia during the Quaternary period. Phylogenetic clustering in the IAA may partly result from vicariance events associated with coral reef fragmentation during the glacial periods of the Quaternary. Variation in the patterns among fish families further suggest that dispersal abilities may have interacted with past habitat availability in shaping the phylogenetic structure of tropical reef fish assemblages.     

A likelihood approach to estimating phylogeny from discrete morphological character data

Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. An important modification of standard Markov models involves making the likelihood conditional on characters being variable, because constant characters are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence data), likelihood ratio tests, and Bayesian analyses.     

PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments

We present PhyloMeasures, a new software package including both a C++ and R version, that provides very fast computation of popular phylogenetic diversity measures. PhyloMeasures introduces two major advances over existing methods. First, it uses efficient algorithms for calculating basic phylogenetic metrics (such as Faith's PD and the mean pairwise distance, MPD) and two‐sample measures (such as common branch length, CBL, and the unique fraction) that are designed to perform well even on very large trees. Second, it computes exact richness‐standardised versions of these measures (such as the widely used net relatedness index, NRI) by efficiently evaluating analytical expressions for the mean and variance of the basic measures, rather than by the slow and inexact randomization techniques that are the current standard. Together, these lead to massive improvements in performance compared to the current state of the art. For example, running on a standard laptop, PhyloMeasures functions can provide the NRI for 20 samples from a tree of 100 000 tips in about 1.5 s, compared to an estimated 37 d using standard resampling approaches. This will allow analyses on larger data sets than were previously possible.