Multiple merger gene genealogies in two species: Monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents

Probabilities of monophyly, paraphyly, and polyphyly of two-species gene genealogies are computed for modest sample sizes and compared for two different Λ coalescent processes. Coalescent processes belonging to the Λ coalescent family admit asynchronous multiple mergers of active ancestral lineages. Assigning a timescale to the time of divergence becomes a central issue when different populations have different coalescent processes running on different timescales. Clade probabilities in single populations are also computed, which can be useful for testing for taxonomic distinctiveness of an observed set of monophyletic lineages. The coalescence rates of multiple merger coalescent processes are functions of coalescent parameters. The effect of coalescent parameters on the probabilities studied depends on the coalescent process, and if the population is ancestral or derived. The probability of reciprocal monophyly tends to be somewhat lower, when associated with a Λ coalescent, under the null hypothesis that two groups come from the same population. However, even for fairly recent divergence times, the probability of monophyly tends to be higher as a function of the number of generations for coalescent processes that admit multiple mergers, and is sensitive to the parameter of one of the example processes.     

Slaying dragons: limited evidence for unusual body size evolution on islands

Aim Island taxa often attain forms outside the range achieved by mainland relatives. Body size evolution of vertebrates on islands has therefore received much attention, with two seemingly conflicting patterns thought to prevail: (1) islands harbour animals of extreme size, and (2) islands promote evolution towards medium body size (‘the island rule’). We test both hypotheses using body size distributions of mammal, lizard and bird species. Location World‐wide. Methods We assembled body size and insularity datasets for the world’s lizards, birds and mammals. We compared the frequencies with which the largest or smallest member of a group is insular with the frequencies expected if insularity is randomly assigned within groups. We tested whether size extremes on islands considered across mammalian phylogeny depart from a null expectation under a Brownian motion model. We tested the island rule by comparing insular and mainland members of (1) a taxonomic level and (2) mammalian sister species, to determine if large insular animals tend to evolve smaller body sizes while small ones evolve larger sizes. Results The smallest species in a taxon (order, family or genus) are insular no more often than would be expected by chance in all groups. The largest species within lizard families and bird genera (but no other taxonomic levels) are insular more often than expected. The incidence of extreme sizes in insular mammals never departs from the null, except among extant genera, where gigantism is marginally less common than expected under a Brownian motion null. Mammals follow the island rule at the genus level and when comparing sister species and clades. This appears to be driven mainly by insular dwarfing in large‐bodied lineages. A similar pattern in birds is apparent for species within orders. However, lizards follow the converse pattern. Main conclusions The popular misconception that islands have more than their fair share of size extremes may stem from a greater tendency to notice gigantism and dwarfism when they occur on islands. There is compelling evidence for insular dwarfing in large mammals, but not in other taxa, and little evidence for the second component of the island rule – gigantism in small‐bodied taxa.     

Lineages with long durations are old and morphologically average: an analysis using multiple datasets

Lineage persistence is as central to biology as evolutionary change. Important questions regarding persistence include: why do some lineages outlive their relatives, neither becoming extinct nor evolving into separate lineages? Do these long‐duration lineages have distinctive ecological or morphological traits that correlate with their geologic durations and potentially aid their survival? In this paper, I test the hypothesis that lineages (species and higher taxa) with longer geologic durations have morphologies that are more average than expected by chance alone. I evaluate this hypothesis for both individual lineages with longer durations and groups of lineages with longer durations, using more than 60 published datasets of animals with adequate fossil records. Analyses presented here show that groups of lineages with longer durations fall empirically into one of three theoretically possible scenarios, namely: (1) the morphology of groups of longer duration lineages is closer to the grand average of their inclusive group, that is, their relative morphological distance is smaller than expected by chance alone, when compared with rarified samples of their shorter duration relatives (a negative group morpho‐duration distribution); (2) the relative morphological distance of groups of longer duration lineages is no different from rarified samples of their shorter duration relatives (a null group morpho‐duration distribution); and (3) the relative morphological distance of groups of longer duration lineages is greater than expected when compared with rarified samples of their shorter duration relatives (a positive group morpho‐duration distribution). Datasets exhibiting negative group morpho‐duration distributions predominate. However, lineages with higher ranks in the Linnean hierarchy demonstrate positive morpho‐duration distributions more frequently. The relative morphological distance of individual longer duration lineages is no different from that of rarified samples of their shorter duration relatives (a null individual morpho‐duration distribution) for the majority of datasets studied. Contrary to the common idea that very persistent lineages are special or unique in some significant way, both the results from analyses of long‐duration lineages as groups and individuals show that they are morphologically average. Persistent lineages often arise early in a group's history, even though there is no prior expectation for this tendency in datasets of extinct groups. The implications of these results for diversification histories and niche preemption are discussed.     

The effect of paralogous lineages on the application of reconciliation analysis by cophylogeny mapping

Paralogy defines similarity caused by duplication rather than common descent and is well known in the case of paralogous gene copies within a single genome. The term is here extended to paralogous lineages of associates within a single host. The phylogenies of four genera within the Herpesviridae were reconciled with host phylogenies using cophylogenetic mapping. The observed correspondence for each pair of phylogenies was evaluated through randomization of the viral phylogeny and demonstrated to be greater than expected by chance. A simulation study was then carried out to assess the influence of paralogous lineages on the efficacy of reconciliation analysis. Combining viral taxa from different genera that infected common hosts introduced incongruence into the cophylogenies and reduced both the minimum and maximum observed number of codivergence events relative to the initial analysis of orthologous clades. However, at an average sample size this did not alter the fundamental significance of observed correspondence. With smaller sample sizes, the number of orthologous taxa selected at random from the pool of taxa was reduced. False-negative results then increased in proportion from 0.02 to 0.33. These results demonstrated that reconciliation analysis is robust under conditions of paralogy at "normal" sample sizes but is adversely affected by a combination of paralogy and low sample size. Consideration of phylogenies for Papillomavirus, Atadenovirus, and Mastadenovirus suggest that paralogous lineages may be a widespread phenomenon among DNA viruses and that duplication irrespective of host speciation is an important cause of viral diversification.     

Increased taxon sampling greatly reduces phylogenetic error

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.     

Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers

The Nymphaeales (water-lilies and relatives) represent one of the earliest branching lineages of angiosperms and comprise about 70 aquatic species. Here, we present a comprehensive study of phylogenetic relationships within the Nymphaeales from a dataset containing 24 representatives of the order, including all currently recognized genera and all subgenera of the genus Nymphaea , plus 5 outgroup taxa. Nine different regions of the chloroplast genome − comprising spacers, group II introns, a group I intron, and a protein coding gene − were analysed. This resulted in a character matrix of 6597 positions and an additional 369 characters obtained from coded length mutations. Maximum parsimony and Bayesian analyses of the complete dataset yielded congruent, fully resolved and well-supported trees. Our data confirm the monophyly of the Cabombaceae but do not provide convincing support for the monophyly of Nymphaeaceae with respect to Nuphar . Moreover, the genus Nymphaea is inferred to be paraphyletic with respect to Ondinea , Victoria and Euryale . In fact, the Australian endemic Ondinea forms a highly supported clade with members of the Australian Nymphaea subgenus Anecphya . In addition, Victoria and Euryale are inferred to be closely related to a clade comprising all night-blooming water-lilies ( Nymphaea subgenera Hydrocallis and Lotos ). An experimental approach showed taxon sampling to be of influence on the nodes reconstructed in core Nymphaeaceae. The results underscore that more diverse genera, if not clearly known to be monophyletic, should be represented by all major lineages.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 141–163.     

Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae)

We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously published morphological characters for a complimentary set of 24 species. The combined data set provided complete taxonomic coverage for this globally distributed clade of turtles, with incomplete data for a few taxa. Although our taxonomic sampling is complete, most of the modern taxa are representatives of old and very divergent lineages. Thus, due to biological realities, our sampling consists of one or a few representatives of several ancient lineages across a relatively deep phylogenetic tree. Our analyses of the combined data set converge on a set of well-supported relationships, which is in accord with many aspects of traditional softshell systematics including the monophyly of the Cyclanorbinae and Trionychinae. However, our results conflict with other aspects of current taxonomy and indicate that most of the currently recognized tribes are not monophyletic. We use this strong estimate of the phylogeny of softshell turtles for two purposes: (1) as the basis for a novel rank-free classification, and (2) to retrospectively examine strategies for analyzing highly homoplasious mtDNA data in deep phylogenetic problems where increased taxon sampling is not an option. Weeded and weighted parsimony, and model-based techniques, generally improved the phylogenetic performance of highly homoplasious mtDNA sequences, but no single strategy completely mitigated the problems of associated with these highly homoplasious data. Many deep nodes in the softshell turtle phylogeny were confidently recovered only after the addition of largely nonhomoplasious data from the nuclear intron.     

Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data

The complete nucleotide sequences of the mitochondrial (mt) genomes of three species of squamate lizards: Blanus cinereus (Amphisbaenidae), Anguis fragilis (Anguidae), and Tarentola mauritanica (Geckkonidae) were determined anew. The deduced amino acid sequences of all 13 mt protein-coding genes were combined into a single data set and phylogenetic relationships among main squamate lineages were analyzed under maximum likelihood (ML) and Bayesian Inference (BI). Within Squamata, the monophyly of Iguanidae, Anguimorpha, Amphisbaenia, Gekkota, Serpentes, and Acrodonta received high statistical support with both methods. It is particularly striking that this is the first molecular analysis that recovers the monophyly of Scincomorpha (including Scincidae, Xantusiidae, Cordylidae, and Lacertidae), although it is only supported in the Bayesian analysis, and it is sensitive to changes in the outgroup (see below). Phylogenetic relationships among the main squamate lineages could not be resolved with ML but received strong support with BI (above 95%). The newly reconstructed phylogeny of squamates does not support the Iguania-Scleroglossa split. Acrodonta and Serpentes form a clade, which is the sister group of the remaining squamate lineages. Within these, Gekkota were the first branching out, followed by Amphisbaenia, and a clade including Anguimorpha as sister group of Scincomorpha + Iguanidae. The recovered topology differed substantially from previously reported hypotheses on squamate relationships, and the relative effect of using different outgroups, genes, and taxon samplings were explored. The sister group relationship of Serpentes + Acrodonta, and their relative basal position within Squamata could be due to a long-branch attraction artifact. Phylogenetic relationships among Scincomorpha, Amphisbaenia, and Anguimorpha were found to be rather unresolved. Future improving of squamate phylogenetic relationships would rely on finding snake and acrodont species with slower mt evolutionary rates, ensuring thorough taxon coverage of squamate diversity, and incorporating more nuclear genes with appropriate evolutionary rates.     

Evolutionary trends in body size of parasitic flatworms

Evolutionary trends in body size have been identified within several lineages, but not all have followed Cope's rule, which states that average body size within a taxon tends to increase over time. In organisms such as parasites, space constraints may have shaped the evolution of body sizes, favouring small-bodied taxa capable of exploiting new niches. Here, the average adult body sizes of families in three groups of parasitic flatworms, the Digenea and two clades of Monogenea (Monopisthocotylea and Polyopisthocotylea), are related to their clade rank. Clade rank reflects the number of branching events, and thus the total path length, between an extant family and the root of the phylogenetic tree. Among families of Digenea, all of which are endoparasites of vertebrates, there was no trend in body size evolution. In contrast, the Monopisthocotylea and Polyopisthocotylea, which are (with the exception of Polystomatidae and Sphyranuridae) ectoparasites of fish, revealed significant negative relationships between family body size and clade rank, suggesting an evolutionary trend of decreasing size. In addition, an analysis of body size distributions in monogenean families also provides support, albeit weak, for this trend. From an ancestor parasitic on the skin of fishes, monogeneans have diversified by colonizing other microhabitats on their hosts, including such space-limited sites as the gaps between secondary gill lamellae. Using a conservative likelihood ratio test, however, a random walk, or null model of evolution could not be discarded in favour of the directional trends mentioned above. Nevertheless, these results suggest that body size has taken different evolutionary paths in endo- and ectoparasitic flatworms.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 181–189.     

The shapes of neutral gene genealogies in two species: probabilities of monophyly,paraphyly, and polyphyly in a coalescent model

Abstract.— The genealogies of samples of orthologous regions from multiple species can be classified by their shapes. Using a neutral coalescent model of two species, I give exact probabilities of each of four possible genealogical shapes: reciprocal monophyly, two types of paraphyly, and polyphyly. After the divergence that forms two species, each of which has population size N , polyphyly is the most likely genealogical shape for the lineages of the two species. At ∼ 1.300 N generations after divergence, paraphyly becomes most likely, and reciprocal monophyly becomes most likely at ∼1.665 N generations. For a given species, the time at which 99% of its loci acquire monophyletic genealogies is ∼5.298 N generations, assuming all loci in its sister species are monophyletic. The probability that all lineages of two species are reciprocally monophyletic given that a sample from the two species has a reciprocally monophyletic genealogy increases rapidly with sample size, as does the probability that the most recent common ancestor (MRCA) for a sample is also the MRCA for all lineages from the two species. The results have potential applications for the testing of evolutionary hypotheses.     

Sample size for FDR-control in microarray data analysis

We consider identifying differentially expressing genes between two patient groups using microarray experiment. We propose a sample size calculation method for a specified number of true rejections while controlling the false discovery rate at a desired level. Input parameters for the sample size calculation include the allocation proportion in each group, the number of genes in each array, the number of differentially expressing genes and the effect sizes among the differentially expressing genes. We have a closed-form sample size formula if the projected effect sizes are equal among differentially expressing genes. Otherwise, our method requires a numerical method to solve an equation. Simulation studies are conducted to show that the calculated sample sizes are accurate in practical settings. The proposed method is demonstrated with a real study.     

Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates

Pleistocene climatic cycles altered species distributions in the Eastern Nearctic of North America, yet the degree of congruent demographic response to the Pleistocene among codistributed taxa remains unknown. We use a hierarchical approximate Bayesian computational approach to test if population sizes across lineages of snakes, lizards, turtles, mammals, birds, salamanders and frogs in this region expanded synchronously to Late Pleistocene climate changes. Expansion occurred in 75% of 74 lineages, and of these, population size trajectories across the community were partially synchronous, with coexpansion found in at least 50% of lineages in each taxonomic group. For those taxa expanding outside of these synchronous pulses, factors related to when they entered the community, ecological thresholds or biotic interactions likely condition their timing of response to Pleistocene climate change. Unified timing of population size change across communities in response to Pleistocene climate cycles is likely rare in North America.     

Recent rhinos do not lack character(s): neither do fossil rhinos!

Concepts, methods, and interest of phylogenetic reconstruction are briefly examined. As large data sets are considered and refutable results are proposed, there is no need to use the argument of authority concerning relationships between taxons. Cladistic analysis in vertebrate palaeontology has gained considerable strength in the last decade, based on sets of hundreds of anatomical characters. One example is selected, which concerns the rhino family, i.e. rhinocerotids. Although underrepresented in recent times, these perissodactyl mammals flourished throughout the Cenozoicera (4 recent genera vs. 50 fossil genera). The main results of a recent cladistic analysis of elasmotheriine rhinocerotids, based on 282 anatomical characters, are listed. Such results concern phylogenetics (monophyly of both elasmotheriines and recent rhinos; branching of elasmotheriines among rhinocerotids) and methodology (definition of a "branching group"; location and processing of homoplasy; influence of taxonomic sampling). The implications are both biostratigraphical and palaeobiogeographical (evolution of the diet and spatial distribution; intercontinental dispersals; ghost lineages and heuristic use of the phylogenetic tree). Finally, forthcoming developments of the available data set for rhinocerotids are examined: controversial phylogenetic relationships among recent rhinos will be refined (thanks to close extinct taxa) and an exhaustive phylogeny of fossil and recent rhinocerotids will be reconstructed (54 genera).     

Deterministic processes dominate nematode community structure in the Fynbos Mediterranean heathland of South Africa

In many ecosystems, the factors that determine landscape-scale community structure of soil nematodes are poorly understood. We were interested in discovering whether deterministic or stochastic factors dominate nematode community variation. We used a novel metagenetic approach to investigate variation in nematode community structure in the Fynbos vegetation of South Africa. We compared 23 samples of soil nematode communities from five different Fynbos landscapes. Nematode DNA was 454-pyrosequenced for the 18S rRNA gene. We investigated the community structure, diversity, and the relative role of both deterministic (niche-based) and neutral processes may play in delimiting the nematode phylogenetic community structure in different Fynbos vegetation types. Nematode diversity showed no relationship to any measured soil parameter. The phylogenetic signal showed that more closely related types of nematodes in the Fynbos tended to co-occur more often than would be expected by chance, demonstrating that (a) closely related lineages occupy similar niches spatially and (b) community variation is influenced more by determinism than stochasticity. The standardised beta mean nearest taxon distance (ses.βMNTD) index showed no association with vegetation type. Both ses.NTI (nearest taxon index) and ses.βMNTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of nematode communities. Furthermore, at local scale, the ses.NTI was significantly higher than null expectations, indicating that co-occurrence of related nematode lineages is determined by the differences in environmental conditions across the sites. We conclude that in the Fynbos there is niche overlap between closely related types of nematodes, that nematode speciation tends to occur conservatively into closely related niches, and that the phylogenetic community structure reveals that deterministic (rather than stochastic) processes are more important in delimiting the community assembly.     

Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake Tanganyika Cichlid Fish: Nuclear Sequences Are Less Homoplasious But Also Less Informative Than Mitochondrial DNA

Over 200 described endemic species make up the adaptive radiation of cichlids in Lake Tanga-nyika. This species assemblage has been viewed as both an evolutionary reservoir of old cichlid lineages and an evolutionary hotspot from which the modern cichlid lineages arose, seeding the adaptive radiations in Lakes Victoria and Malawi. Here we report on a phylogenetic analysis of Lake Tanganyika cichlids combining the previously determined sequences of the mitochondrial ND2 gene (1047 bp) with newly derived sequences of the nuclear RAG1 gene (∼700 bp of intron 2 and ∼1100 bp of exon 3). The nuclear data—in agreement with mitochondrial DNA—suggest that Lake Tanganyika harbors several ancient lineages that did not undergo rampant speciation (e.g., Bathybatini, Trematocarini). We find strong support for the monophyly of the most species-rich Tanganyikan group, the Lamprologini, and we propose a new taxonomic group that we term the C-lineage. The Haplochromini and Tropheini both have an 11-bp deletion in the intron of RAG1, strongly supporting the monophyly of this clade and its derived position. Mapping the phylogenetically informative positions revealed that, for certain branches, there are six times fewer apomorphies in RAG1. However, the consistency index of these positions is higher compared to the mitochondrial ND2 gene. Nuclear data therefore provide, on a per–base pair basis, less but more reliable phylogenetic information. Even if in our case RAG1 has not provided as much phylogenetic information as we expected, we suggest that this marker might be useful in the resolution of the phylogeny of older groups. Reviewing Editor: Dr. Rafael Zardoya     

A molecular phylogeny of chafers revisits the polyphyly of Tanyproctini (Scarabaeidae,Melolonthinae)

Tanyproctini (Melolonthinae) is a large group of chafers within the pleurostict Scarabaeidae that shows an enormous morphological diversity and variation. However, their morphology based definition appears to be mainly based on presumably plesiomorphic characters. Here, we investigate the phylogeny of this interesting lineage with a three‐gene data set using partial gene sequences of 28S rRNA, cytochrome c oxidase I (cox1) and 16S rRNA (rrnL). Our data set comprised 191 species of all major lineages of pleurostict scarabs. Combined analyses of the 2,070 base pairs alignment with maximum‐likelihood and Bayesian tree inference always recovered Tanyproctini to be highly polyphyletic. Tests of an alternative topology with constrained monophyly of Tanyproctini using CONSEL and IQ‐TREE were not found to be more likely than the unconstrained tree topology. Instead, Tanyproctini was split into six independent lineages under the current taxon sampling that were scattered throughout diverse parts of the pleurostict tree. The fact that numerous smaller chafer lineages exist beside several evolutionary successful and large lineages, highlights the complexity of the pleurosticts’ evolutionary history. The resulting tree topologies imply the need for a thorough revision of tribal classification within Melolonthinae lineages to accommodate the polyphyly of Tanyproctini. However, a revision of classification would be premature due to low support of most relevant branches, instable tree topologies among different tree searches, and due to a still very incomplete representation of Tanyproctini lineages.     

Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae)

Family level molecular phylogenetic analyses of cichlid fishes have generally suffered from a limited number of characters and/or poor taxonomic sampling across one or more major geographic assemblage, and therefore have not provided a robust test of early intrafamilial diversification. Herein we use both nuclear and mitochondrial nucleotide characters and direct optimization to reconstruct a phylogeny for cichlid fishes. Representatives of major cichlid lineages across all geographic assemblages are included, as well as nearly twice the number of characters as any prior family‐level study. In a strict consensus of 81 equally most‐parsimonious hypotheses, based on the simultaneous analysis of 2222 aligned nucleotide characters from two mitochondrial and two nuclear genes, four major subfamilial lineages are recovered with strong support. Etroplinae, endemic to Madagascar (Paretroplus) and southern Asia (Etroplus), is recovered as the sister taxon to the remainder of Cichlidae. Although the South Asian cichlids are monophyletic, the Malagasy plus South Asian lineages are not. The remaining Malagasy lineage, Ptychochrominae, is monophyletic and is recovered as the sister group to a clade comprising the African and Neotropical cichlids. The African (Pseudocrenilabrinae) and Neotropical (Cichlinae) lineages are each monophyletic in this reconstruction. The use of multiple molecular markers, from both mitochondrial and nuclear genes, results in a phylogeny that in general exhibits strong support, notably for early diversification events within Cichlidae. Results further indicate that Labroidei is not monophyletic, and that the sister group to Cichlidae may comprise a large and diverse assemblage of percomorph lineages. This hypothesis may at least partly explain why morphological studies that have attempted to place Cichlidae within Percomorpha, or that have tested cichlid monophyly using only “labroid” lineages, have met with only limited success. © The Willi Hennig Society 2004.     

The biogeographic history of ruminant faunas determines the phylogenetic structure of their assemblages at different scales

Phylogenetic community structure may help us understand how macroecological and macroevolutionary processes shape assemblages at large geographical scales. In this paper, we test hypotheses linking the formation of large‐scale assemblages, evolutionary processes and macroecology. To provide new insight into ruminant biogeography and evolution, phylogenetic community structure metrics were calculated for faunal assemblages at four hierarchical levels. Phylogenetic relatedness indices (net relatedness index and nearest taxon index) were determined for 59 ruminant assemblages at the landscape scale and scale of their respective climate domains (continuous biome stretches). Species pools at the global and biogeographic realm levels were used to construct null observation models. Significantly, assemblages were selected if they were distributed across biogeographic realms and represented all the world's biomes. Non‐random patterns were also tested for biogeographic realms within the global ruminant species pool. By examining ruminant assemblages at different scales we were able to observe that ruminant faunas show a distribution mainly limited within the boundaries of their biogeographic realms. However, the diversification of some clades was found to be restricted to extremely arid domains in the Sahara and Arabia. The random patterns featured by other extreme climate domains could reflect phylogenetically heterogeneous filling by less biome‐restricted lineages outside Africa.     

Using phylogeographic analyses of gene trees to test species status and processes

A gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra- and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.     

The mitochondrial nad2 gene as a novel marker locus for phylogenetic analysis of early land plants: a comparative analysis in mosses

The mitochondrial nad2 gene is established as a novel marker locus for phylogenetic analyses among early land plants. The potential of this gene for phylogenetic resolution was checked with a broad taxon sampling of 42 mosses (Bryopsida, including the enigmatic genus Takakia) to allow both a comparative analysis with the recently explored nad5 gene and the fusion of independent data sets. The mitochondrial gene sequences provide valuable phylogenetic information on the relationships of classically defined orders and their respective monophylies. The more rapidly diverging sequences of a group I intron in nad5 and of a group II intron in nad2 add information for fine resolution. Although both genes provide phylogenetic information in the same taxonomic range (above family level), the combined sequence alignment results in an approximate doubling in the number of nodes with significant bootstrap support (>90). According to our data, Buxbaumiales are a paraphyletic taxon in a key position between the earliest branching taxa (Sphagnales, Takakiales, Andreaeales, Polytrichales, and Tetraphidales) and all other orders, possibly to be placed in the subclass Bryidae. A dichotomy in the latter recalls two previously suggested superorders Hypnanae and Dicrananae. Both genes independently question the monophyly of the orders Dicranales and Neckerales and reject the inclusion of the genera Schistostega, Timmia, and Encalypta among Eubryales.