“Laughter” and “Smile” in Barbary Macaques (Macaca sylvanus)

In an observational study on semi-free Barbary macaques it was investigated whether the phylogenetic roots of human laughter and smile can be traced back to the genus Macaca. On the basis of morphological similarity a ‘relaxed open-mouth display’ as the phylogenetic precursor of the laughter, and a ‘silent bared-teeth display’ as the possible ancestor of the smile can be distinguished in the repertory of the Barbary macaque. Behavioural sequences from focal animal protocols were analyzed in order to establish message and meaning of both displays. Relaxed open-mouth display is regularly observed in the play interactions of juveniles. It is associated with partner-directed behaviour, it is frequently answered by a relaxed open-mouth display of the receiver, and accompanied by a special vocalization. Although up to 50% of the juvenile's play partners were higher ranking than themselves voluntary participation was the rule. Most characteristically, the behaviour patterns shown by both play partners are highly symmetrical and synchronized. Silent bared-teeth display is typically accompanied by evasive or submissive body movements, and occurs primarily in dyadic interactions, mainly by the lower ranking individual. It is not an unidirectional sign of a linear dominance hierarchy, though. Silent bared-teeth display is a frequent answer to aggressive behaviour shown by the receiver. After its performance, an increase of body contact between sender and receiver was observed. Behavioural sequences of senders and receivers are complementary, but lose their asymmetry after occurrence of the display. It is concluded that these results further support Van Hooff 's (1972) view that human laughter and smile have different phylogenetic roots: while silent bared-teeth display is a signal of submission and appeasement, relaxed open-mouth display is rightly called the ‘play face’, and is an expression of fun.     

Vicars,tramps and assembly of the New Zealand avifauna: a review of molecular phylogenetic evidence

The avifauna of New Zealand is taxonomically and ecologically distinctive, as is typical of island biotas. However, the potential for an old geological age of New Zealand has encouraged a popular notion of a ‘Moa’s ark’ based on the idea that much of the fauna was isolated when Zealandia broke from Gondwana c. 83 million years ago. Molecular phylogenetics has proved useful for exploring the relative importance of different biogeographical processes, revealing for example that ‘tramp’ species (widely dispersing taxa) have arrived in New Zealand even in the last few hundred years, and that some avian taxa have close phylogenetic relatives overseas (predominantly Australian), indicating their recent ancestors were tramps, too. Distinctive taxa with deep phylogenetic ancestry might be ‘vicars’ that owe their presence to vicariance, but lack of close morphological, taxonomic and phylogenetic affinity provides only tenuous evidence for this. Disproving the alternative possibility that apparent vicars are descended from tramps that dispersed in earlier times remains challenging, but molecular analyses have yielded startling insights. Among New Zealand’s iconic taxa, the world’s largest eagle shared a Pleistocene ancestor with a small Australian eagle, and giant, flightless moa are phylogenetic sisters of the much smaller, flying tinamous of South America. The New Zealand avifauna is neither isolated nor stable, but demonstrative of prolonged and ongoing colonization, speciation and extinction.     

Bias in phylogenetic measurements of extinction and a case study of end‐Permian tetrapods

Extinction risk in the modern world and extinction in the geological past are often linked to aspects of life history or other facets of biology that are phylogenetically conserved within clades. These links can result in phylogenetic clustering of extinction, a measurement comparable across different clades and time periods that can be made in the absence of detailed trait data. This phylogenetic approach is particularly suitable for vertebrate taxa, which often have fragmentary fossil records, but robust, cladistically‐inferred trees. Here we use simulations to investigate the adequacy of measures of phylogenetic clustering of extinction when applied to phylogenies of fossil taxa while assuming a Brownian motion model of trait evolution. We characterize expected biases under a variety of evolutionary and analytical scenarios. Recovery of accurate estimates of extinction clustering depends heavily on the sampling rate, and results can be highly variable across topologies. Clustering is often underestimated at low sampling rates, whereas at high sampling rates it is always overestimated. Sampling rate dictates which cladogram timescaling method will produce the most accurate results, as well as how much of a bias ancestor–descendant pairs introduce. We illustrate this approach by applying two phylogenetic metrics of extinction clustering (Fritz and Purvis's D and Moran's I) to three tetrapod clades across an interval including the Permo‐Triassic mass extinction event. These groups consistently show phylogenetic clustering of extinction, unrelated to change in other quantitative metrics such as taxonomic diversity or extinction intensity.     

Palaeomorphology: fossils and the inference of cladistic relationships

Edgecombe, G.D. 2010. Palaeomorphology: fossils and the inference of cladistic relationships. —Acta Zoologica (Stockholm) 91 : 72–80 Twenty years have passed since it was empirically demonstrated that inclusion of extinct taxa could overturn a phylogenetic hypothesis formulated upon extant taxa alone, challenging Colin Patterson’s bold conjecture that this phenomenon ‘may be non‐existent’. Suppositions and misconceptions about missing data, often couched in terms of ‘wildcard taxa’ and ‘the missing data problem’, continue to cloud the literature on the topic of fossils and phylogenetics. Comparisons of real data sets show that no a priori (or indeed a posteriori) decisions can be made about amounts of missing data and most properties of cladograms, and both simulated and real data sets demonstrate that even highly incomplete taxa can impact on relationships. The exclusion of fossils from phylogenetic analyses is neither theoretically nor empirically defensible.     

“Ecological Armageddon” – more evidence for the drastic decline in insect numbers

The efficient use of nitrogen by crops can minimise environmental risks and maximise returns to farmers. Under organic farming systems, this can be achieved by adjusting the fertilisation management and/or using genetic variability. Seven durum wheat (Triticum durum) cultivars and three emmer (Triticum dicoccum) cultivars were assessed under an organic farming system over a non‐consecutive 4‐year period (2005–11) in Foggia (southern Italy). The objectives were to investigate the agronomic and qualitative characteristics, and to evaluate the agronomic efficiency and adaptability according to three N fertilisation levels (0, 40, 80 kg N ha^?1). A split‐plot design was used, with three replications in each year. Nine traits were investigated: heading time, plant height, seed yield, number of spikes m^?2, harvest index, specific weight, 1000‐seed weight, and protein and gluten contents. Increasing N to 80 kg ha^?1 increased plant height (+7.3%), seed yield (+22.1%), spike density (+16.6%), and protein (+9.8%) and gluten (+2.1%) contents. The emmer genotypes and the oldest durum wheat ‘Cappelli’ showed the highest protein and gluten contents (mean, 13.9%, 11.2%, respectively). The maximum N agronomic efficiency [AE(N)] and N recovery efficiency [RE(N)] were seen for the modern durum wheat cultivars under 40 kg ha^?1 N treatment: ‘Duilio’, ‘Iride’ and ‘Varano’. The significant correlation between AE(N) and RE(N) and the year of release of the durum wheat cultivars (r = 0.53, P < 0.05, F = 4.7 for AE(N) and r = 0.57, P < 0.01, F = 5.7 for RE(N), respectively; n = 14) showed that the genetic breeding of this species for high grain yield is associated with an increase in the efficiency of N fertiliser use under organic farming. The highly significant effect for the Genotype × Environment interaction (F = 18.1, P < 0.001) of seed yield indicate the possibility to select for stable genotypes across environments. Based on the additive main effects and multiplicative interaction analysis, and the yield stability index, the varieties ‘Iride’ and ‘Varano’ show high‐stability responses and good seed yields under all N fertiliser treatments. Therefore, these varieties can be recommended for organic farming systems in Mediterranean areas.     

New crinoids from the Baltic region (Estonia): fossil tip‐dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the Flexibilia (Echinodermata)

This study documents previously unknown taxonomic and morphological diversity among early Palaeozoic crinoids. Based on highly complete, well preserved crown material, we describe two new genera from the Ordovician and Silurian of the Baltic region (Estonia) that provide insight into two major features of the geological history of crinoids: the early evolution of the flexible clade during the Great Ordovician Biodiversification Event (GOBE), and their diversification history surrounding the end‐Ordovician mass extinction. The unexpected occurrence of a highly derived sagenocrinid, Tintinnabulicrinus estoniensis gen. et. sp. nov., from Upper Ordovician (lower Katian) rocks of the Baltic palaeocontinent provides high‐resolution temporal, taxonomic and palaeobiogeographical constraints on the origin and early evolution of the Flexibilia. The Silurian (lower Rhuddanian, Llandovery) Paerticrinus arvosus gen. et sp. nov. is the oldest known Silurian crinoid from Baltica and thus provides the earliest Baltic record of crinoids following the aftermath of the end‐Ordovician mass extinction. A Bayesian ‘fossil tip‐dating’ analysis implementing the fossilized birth–death process and a relaxed morphological clock model suggests that flexibles evolved c. 3 million years prior to their oldest fossil record, potentially involving an ancestor–descendant relationship (via ‘budding’ cladogenesis or anagenesis) with the paraphyletic cladid Cupulocrinus. The sagenocrinid subclade rapidly diverged from ‘taxocrinid’ grade crinoids during the final stages of the GOBE, culminating in maximal diversity among Ordovician crinoid faunas on a global scale. Remarkably, diversification patterns indicate little taxonomic turnover among flexibles across the Late Ordovician mass extinction. However, the elimination of closely related clades may have helped pave the way for their subsequent Silurian diversification and increased ecological role in post‐Ordovician Palaeozoic marine communities. This study highlights the significance of studies reporting faunas from undersampled palaeogeographical regions for clade‐based phylogenetic studies and improving estimates of global biodiversity through geological time.     

MorphoBank: phylophenomics in the “cloud”

A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.     

Othenio Abel (1875–1946): the rise and decline of paleobiology in German paleontology

Othenio Abel is widely acclaimed as the founder of paleobiology; of the journal Palaeobiologica and of the Paleobiological Society in Vienna. His National–Socialist sympathies, which he shared with fellow paleobiologist Henry Fairfield Osborn from the American Museum of Natural History, resulted in his forced retirement from the University of Vienna in 1934. Abel secured subsequent employment at the University of Göttingen, later sought help from Nazi officials to create his own institute in Salzburg. A leader amongst German paleontologists, Abel supported efforts of the Deutsche Palaeontologische Gesellschaft to align paleobiology with Nazi ideology (‘National–Socialism is politically applied biology’) to secure more support for the discipline. Abel's paleobiology was neo-Lamarckian in nature, based on a ‘reaction theory’ of adaptation. Abel attempted to unify paleontology with biology under a universal law of nature – the Law of Biological Inertia – that itself was anchored in classical physics.     

Presence of punctae in the ‘plectorthoidean’ brachiopod Famatinorthis turneri (Middle Ordovician) from western Argentina: implications for early diversification of punctate orthides

Benedetto, J.L. 2013: Presence of punctae in the ‘plectorthoidean’ brachiopod Famatinorthis turneri (Middle Ordovician) from western Argentina: implications for early diversification of punctate orthides. Lethaia, Vol. 46, pp. 170–179. Famatinorthis Levy & Nullo is a distinctive orthide brachiopod of Dapingian age from the volcaniclastic rocks of the Famatina Range of western Argentina. Although it was originally classified among the plectorthoideans, a new collection from the La Escondida Formation has yielded exceptionally well‐preserved moulds of Famatinorthis turneri in which silicified infillings of punctae are clearly visible, leading to the reassignment of the genus to the dalmanellidines. In this paper, phylogenetic analyses are used to determine the evolutionary relationships of Famatinorthis, the Tremadocian linoporellid Lipanorthis, and other Ordovician Gondwanan genera. The placement of Plectorthoidea in the same major clade as linoporellids, and the separation of Dalmanellidina as an independent clade are the most important features of all shortest trees, supporting the idea that linoporellids may have originated from a plectorthoid ancestor. Cladistic analysis reveals that Lipanorthis lies close to the ancestry of the linoporellid lineage, and Famatinorthis clusters within the more derived taxa of the clade with which it shares a large septalium. It seems that the presence of endopunctae in the orthides does not necessarily indicate close phylogenetic relationships as it could have occurred at different times in different clades. If the homoplasic nature of endopunctae in the order Orthida is supported by further morphologic and phylogenetic studies, the fundamental division of orthides in non‐punctate (Orthidina) and punctate (Dalmanellidina) may need revision. □Brachiopods, Ordovician, Gondwana, Famatina, phylogeny, punctate orthides.     

New hominid fossils from Woranso‐Mille (Central Afar,Ethiopia) and taxonomy of early Australopithecus

The phylogenetic relationship between Australopithecus anamensis and Australopithecus afarensis has been hypothesized as ancestor‐descendant. However, the weakest part of this hypothesis has been the absence of fossil samples between 3.6 and 3.9 million years ago. Here we describe new fossil specimens from the Woranso‐Mille site in Ethiopia that are directly relevant to this issue. They derive from sediments chronometrically dated to 3.57–3.8 million years ago. The new fossil specimens are largely isolated teeth, partial mandibles, and maxillae, and some postcranial fragments. However, they shed some light on the relationships between Au. anamensis and Au. afarensis. The dental morphology shows closer affinity with Au. anamensis from Allia Bay/Kanapoi (Kenya) and Asa Issie (Ethiopia) than with Au. afarensis from Hadar (Ethiopia). However, they are intermediate in dental and mandibular morphology between Au. anamensis and the older Au. afarensis material from Laetoli. The new fossils lend strong support to the hypothesized ancestor‐descendant relationship between these two early Australopithecus species. The Woranso‐Mille hominids cannot be unequivocally assigned to either taxon due to their dental morphological intermediacy. This could be an indication that the Kanapoi, Allia Bay, and Asa Issie Au. anamensis is the primitive form of Au. afarensis at Hadar with the Laetoli and Woranso‐Mille populations sampling a mosaic of morphological features from both ends. It is particularly difficult to draw a line between Au. anamensis and Au. afarensis in light of the new discoveries from Woranso‐Mille. The morphology provides no evidence that Au. afarensis and Au. anamensis represent distinct taxa. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

“Lucy” (A.L. 288‐1) had five sacral vertebrae

A “long‐backed” scenario of hominin vertebral evolution posits that early hominins possessed six lumbar vertebrae coupled with a high frequency of four sacral vertebrae (7:12‐13:6:4), a configuration acquired from a hominin‐panin last common ancestor (PLCA) having a vertebral formula of 7:13:6‐7:4. One founding line of evidence for this hypothesis is the recent assertion that the “Lucy” sacrum (A.L. 288‐1an, Australopithecus afarensis) consists of four sacral vertebrae and a partially‐fused first coccygeal vertebra (Co1), rather than five sacral vertebrae as in modern humans. This study reassesses the number of sacral vertebrae in Lucy by reexamining the distal end of A.L.288‐1an in the context of a comparative sample of modern human sacra and Co1 vertebrae, and the sacrum of A. sediba (MH2). Results demonstrate that, similar to S5 in modern humans and A. sediba, the last vertebra in A.L. 288‐1an exhibits inferiorly‐projecting (right side) cornua and a kidney‐shaped inferior body articular surface. This morphology is inconsistent with that of fused or isolated Co1 vertebrae in humans, which either lack cornua or possess only superiorly‐projecting cornua, and have more circularly‐shaped inferior body articular surfaces. The level at which the hiatus' apex is located is also more compatible with typical five‐element modern human sacra and A. sediba than if only four sacral vertebrae are present. Our observations suggest that A.L. 288‐1 possessed five sacral vertebrae as in modern humans; thus, sacral number in “Lucy” does not indicate a directional change in vertebral count that can provide information on the PLCA ancestral condition. Am J Phys Anthropol 156:295–303, 2015. © 2014 Wiley Periodicals, Inc.     

“Candidatus Phytoplasma asteris” and “Candidatus Phytoplasma mali” strains infecting sweet and sour cherry in the Czech Republic

A survey for phytoplasma diseases was conducted in a sweet and sour cherry germplasm collection and in cherry orchards within the Czech Republic during 2014–2015. Phytoplasmas were detected in 21 symptomatic trees. Multiple infections of cherry trees by diverse phytoplasmas of 16SrI and 16SrX groups and 16SrI‐A, 16SrI‐B, 16SrI‐L, 16SrX‐A subgroups were detected by restriction fragment length polymorphism (RFLP). Nevertheless, phylogenetic analysis placed subgroups 16SrI‐B and 16SrI‐L inseparable together onto one branch of phylogenetic tree. This is the first report of subgroups 16SrI‐A and 16SrI‐L in Prunus spp., and subgroup 16SrX‐A in sour cherry trees. Additionally, novel RFLP profiles for 16SrI‐A and 16SrI‐B‐related phytoplasmas were found in cherry samples. Phytoplasmas with these novel profiles belong, however, to their respective 16SrI‐A or 16SrI‐B phylogenetic clades.     

THE “PARADOX” DIATOM BACILLARIA PAXILLIFER (BACILLARIOPHYTA) REVISITED1

Defined by its unique colonial locomotion, Bacillaria paxillifer (O. F. Müll.) Hendey was recognized as a single, pandemic species by many phycologists. However, reinvestigation of colonies from different habitats revealed three distinct groups: (A) brackish/freshwater, (B) marine littoral, and (C) marine planktonic taxa. Groups differed in colony and cell form, raphe flanges (RFs), shape and position of transapical ribs (Tr's), and morphogenesis. Linear‐shaped species were restricted to group A: Tr's thickened principally to the interior. Lanceolate forms were confined to groups B and C: valve formation proceeded from an internal base layer to the exterior. The planktonic species differed in the shape of its raphe slit, and the transformation of girdle bands (GBs) into “winglets.” Taxa also differed in chloroplast shape and number. All species formed motile colonies. Siblings adhered via elastic fibrils secreted through their raphe. Raphe ribs were held in position by siliceous clamps (fibulae), anchored in an extra pair of axial ribs (fibular ribs) parallel to the raphe ribs. This raphe system resembled that of Cylindrotheca rather than the “canal raphe” of Nitzschia. Many valves were asymmetric along the apical axis due to protruding RFs shuttling in a 1:1 ratio within a colony, but raphe slits were mirror images, as were the growth direction of fibulae and position of plastids, with pyrenoids tilted in the same direction. Species possessed four open GBs per epitheca; the third band invariably bore an internal, organic ridge to aid in adhesion of the plasmalemma during cleavage. The results suggested that these taxa are a natural phylogenetic group, requiring precise determination of their taxonomic position.     

The recognition of ancestors

The recognition of ancestors is problematic using cladistic logic alone because monophyletic groups (clades) are defined by shared derived characters (synapomorphies) which their ancestors must have lacked. Nevertheless, ancestors possess three key attributes. They belong within a larger, paraphyletic group. They will be morphologically most similar to their immediate descendants, and they evolved before any and all of their descendants. Recognition of ancestors requires both morphological and stratigraphic data and, in practice, the task is to reduce the size of the paraphyletic group within which the ancestor must lie. All ancestor‐descendant relationships are phylogenetic hypotheses. Despite the legendary incompleteness of the fossil record, testing the validity of available data is far more difficult for character analysis than for stratigraphy.     

ORIGIN AND RECENT ENDEMIC DIVERGENCE OF A CASPIAN MYSIS SPECIES FLOCK WITH AFFINITIES TO THE “GLACIAL RELICT” CRUSTACEANS IN BOREAL LAKES

Aspects of the evolution of intralacustrine species flocks and of the origin of the Arctic or “glacial-relict” zoogeographical element in Eurasian inland waters were elucidated in an allozyme study of the crustacean genus Mysis. This element, of supposedly northern marine ancestry, is represented by vicarious taxa in the deeper parts of the Caspian Sea (an enclosed ancient basin) and in young boreal lakes. The three endemic Caspian Mysis species studied are very close genetically (Nei's D = 0.06), which suggests a recent intrabasin radiation and rapid morphological divergence. This is in contrast to the pattern in postglacial Holarctic boreal lakes, where the Mysis relicta group is represented by a set of morphologically uniform but probably much older sibling species (D = 0.3–0.6). The results provide a parallel to those on the recent diversification of some fish species flocks in ancient freshwater lakes. The situation is, however, unusual in that the Caspian sympatric Mysis flock is pelagic, and conditions promoting speciation through allopatric isolation or spatial segregation by trophic substrate specialization seem implausible. The monophyletic Caspian Mysis clade shows a relatively strong divergence from both the northern lacustrine and the Arctic marine congeners (D = 0.6–1.0); the phylogenetic branching order of these three zoogeographical groups is not conclusively resolved. The results contradict the prevailing hypothesis of a recent Pleistocene origin of the Caspian Arctic element by invasion from Eastern European continental proglacial lakes that drained south to the Caspian basin during the glacial maxima and served as refugia for the boreal lacustrine taxa.     

Sequence diversity of a domesticated transposase gene, <Emphasis Type="Italic">MUG1</Emphasis>, in <Emphasis Type="Italic">Oryza</Emphasis> species

MUG1 is a MULE transposon-related domesticated gene in plants. We assessed the sequence diversity, neutrality, expression, and phylogenetics of the MUG1 gene among Oryza ssp. We found MUG1 expression in all tissues analyzed, with different levels in O. sativa. There were 408 variation sites in the 3886 bp of MUG1 locus. The nucleotide diversity of the MUG1 was higher than functionally known genes in rice. The nucleotide diversity (π) in the domains was lower than the average nucleotide diversity in whole coding region. The π values in nonsynonymous sites were lower than those of synonymous sites. Tajima D and Fu and Li D* values were mostly negative values, suggesting purifying selection in MUG1 sequences of Oryza ssp. Genome-specific variation and phylogenetic analyses show a general grouping of MUG1 sequences congruent with Oryza ssp. biogeography; however, our MUG1 phylogenetic results, in combination with separate B and D genome studies, might suggest an early divergence of the Oryza ssp. by continental drift of Gondwanaland. O. longistaminata MUG1 divergence from other AA diploids suggests that it might not be a direct ancestor of the African rice species. These authors contributed equally to this work.     

TNT version 1.5, including a full implementation of phylogenetic morphometrics

Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.     

SHORT COMMUNICATION: Little evidence for Cope’s rule from Bayesian phylogenetic analysis of extant mammals

According to Cope’s rule, lineages tend to evolve towards larger body size, possibly because of selective advantages of being large. The status of Cope’s ‘rule’ remains controversial as it is supported in some but not all large‐scale fossil studies. Here, we test for Cope’s rule by Bayesian analyses of average body masses of 3253 extant mammal species on a dated phylogenetic tree. The data favour a model that does not assume Cope’s rule. When Cope’s rule is assumed, the best estimate of its strength is an average ancestor‐descendant increase in body size of only 0.4%, which sharply contrasts with the 9% bias estimated from fossil mammals. Thus, we find no evidence for Cope’s rule from extant mammals, in agreement with earlier analyses of existing species, which also did not find support for Cope’s rule.     

All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees

Objective

In mathematical phylogenetics, a labeled rooted binary tree topology can possess any of a number of labeled histories, each of which represents a possible temporal ordering of its coalescences. Labeled histories appear frequently in calculations that describe the combinatorics of phylogenetic trees. Here, we generalize the concept of labeled histories from rooted phylogenetic trees to rooted phylogenetic networks, specifically for the class of rooted phylogenetic networks known as rooted galled trees.

Results

Extending a recursive algorithm for enumerating the labeled histories of a labeled tree topology, we present a method to enumerate the labeled histories associated with a labeled rooted galled tree. The method relies on a recursive decomposition by which each gall in a galled tree possesses three or more descendant subtrees. We exhaustively provide the numbers of labeled histories for all small galled trees, finding that each gall reduces the number of labeled histories relative to a specified galled tree that does not contain it.

Conclusion

The results expand the set of structures for which labeled histories can be enumerated, extending a well-known calculation for phylogenetic trees to a class of phylogenetic networks.