The birth of an endemic species flock: demographic history of the Bellamya group (Gastropoda,Viviparidae) in Lake Malawi

Changes in habitat stability may significantly shape evolutionary patterns and processes in ancient lakes. In the present study, we use a hierarchical combination of molecular phylogenetic and coalescent approaches to investigate the evolutionary history of the endemic species of the gastropod genus Bellamya in the African rift‐lake Malawi. By integrating our findings with reported palaeontological and palaeolimnological data, we demonstrate that all but one evolutionary lineage of the Pliocene Bellamya fauna in Lake Malawi became extinct. Coalescent analyses indicate that the modern radiation underwent both a sudden demographic and a spatial expansion after a genetic bottleneck. We argue that a reflooding of the lake after severe Pleistocene low stands offers a straightforward explanation for this pattern and may have triggered speciation processes in the modern endemic Bellamya radiation in Lake Malawi. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 130–143.     

The otic region of Doleserpeton (Temnospondyli) and its implications for the evolutionary origin of frogs

There is increasing evidence that the Palaeozoic temnospondyl amphibians had a frog‐like tympanic hearing system. For this reason, the otic region of Doleserpeton is described and compared with modern anurans. The otic capsules are expanded laterally and ventrally relative to other temnospondyls. The opisthotic has a bulbous ventral region resembling the ventrolateral ledge in modern frogs. Two lateral processes are located on the paroccipital process. Comparison with the condition in modern anurans with a tympanic hearing system shows that this may have been the attachment site for the tympanic annulus. Parts of the osseous labyrinth are also described. The inner ear shows numerous features resembling the condition found in frogs. These include strong evidence for the presence of a lissamphibian‐type perilymphatic duct most closely resembling that of anurans. This is the first time such a perilymphatic system has been described in any Palaezoic form. The posterior part of the braincase shows a jugular foramen closely associated with the perilymphatic foramen, as in anurans. Although the distribution of these traits among other temnospondyl groups remains little known, the sum of the evidence points to affinities between anurans and temnospondyls, and adds to the evidence for a close relationship between anurans and the Permian amphibamid Doleserpeton. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 738–751.     

Can phylogenetic signal,character displacement,or random phenotypic drift explain the morphological variation in the genus Geonoma (Arecaceae)?

Plant clades may exhibit little or wide morphological variation as a result of (1) the retention of ancestral characteristics or phylogenetic signal, (2) character displacement, or (3) random phenotypic drift or convergence. Understanding the taxonomy and systematics of many plant lineages has been challenging due to continuous intra‐ and interspecific morphological variation. To assess which evolutionary hypothesis could explain the morphological diversity in the genus Geonoma (Arecaceae), we performed a Mantel test between phylogenetic and morphological distances of 54 taxa, and tested for phylogenetic signal using Blomberg's K‐statistic on continuous variables, and a randomization of character states. To obtain a phylogenetic (patristic) distance matrix for Geonoma, we constructed a molecular phylogeny of tribe Geonomateae using three nuclear DNA regions. A positive relationship between the patristic and a 26‐discrete‐character distance matrix (R² = 0.55, P < 0.001) supported the phylogenetic signal hypothesis. The randomization test showed that signal was present in 16 characters. No relationship was evident using a 17‐quantitative‐variable distance matrix (R² = 0.07, P = 0.13), supporting the random drift hypothesis or convergence, and all 17 K‐values were close to 0, suggesting less phylogenetic signal than under the Brownian model. If most morphological variables traditionally used to classify Geonoma evolved randomly or convergently, it might explain Geonoma's challenging taxonomy. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 528–539.     

Do constructional constraints influence cyprinid (Cyprinidae: Leuciscinae) craniofacial coevolution?

Constraints on form may determine how organisms diversify. As a result of competition for the limited space within the body, investment in adjacent structures could represent an evolutionary compromise. For example, evolutionary trade‐offs resulting from limited space in the head could have influenced how the sizes of the jaw muscle, as well as the eyes, evolved in North American cyprinid fishes. To test the evolutionary independence of the size of these structures, we measured the mass of the three major adductor mandibulae muscles and determined the eye volume in 36 cyprinid species. Using a novel phylogeny, we tested the hypotheses that the sizes of these four structures were negatively correlated with each other during cyprinid evolution. We found that evolutionary change in the adductor mandibulae muscles was generally positively and/or not correlated, suggesting that competition for space among cyprinid jaw muscles has not influenced their evolution. However, there was a negative relationship between mass of adductor mandibulae 1 and eye volume, indicating that change in these physically adjacent structures is consistent with an evolutionary constructional constraint. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 136–146.     

Snake diets and the deep history hypothesis

The structure of animal communities has long been of interest to ecologists. Two different hypotheses have been proposed to explain origins of ecological differences among species within present‐day communities. The competition–predation hypothesis states that species interactions drive the evolution of divergence in resource use and niche characteristics. This hypothesis predicts that ecological traits of coexisting species are independent of phylogeny and result from relatively recent species interactions. The deep history hypothesis suggests that divergences deep in the evolutionary history of organisms resulted in niche preferences that are maintained, for the most part, in species represented in present‐day assemblages. Consequently, ecological traits of coexisting species can be predicted based on phylogeny regardless of the community in which individual species presently reside. In the present study, we test the deep history hypothesis along one niche axis, diet, using snakes as our model clade of organisms. Almost 70% of the variation in snake diets is associated with seven major divergences in snake evolutionary history. We discuss these results in the light of relevant morphological, behavioural, and ecological correlates of dietary shifts in snakes. We also discuss the implications of our results with respect to the deep history hypothesis. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 476–486.     

Chromosomal fission accounts for small‐scale radiations in Zamia (Zamiaceae; Cycadales)

Zamia is unique among Cycadales in its diversity of morphology, ecology and chromosome numbers. The chromosome numbers in Zamia range from 16 to 28, excluding 20, manifest as both interspecific and intraspecific series. It has long been recognized that Robertsonian transformations (chromosomal fission or fusion) probably dominate karyotype evolution in Zamiaceae, although it has been debated whether chromosome numbers are increasing or decreasing. We re‐analyse published karyotypes of Zamia spp., relating both chromosome forms and sizes to recent phylogenetic data. We show that karyotype evolution is most probably moving towards increased asymmetry, with higher numbers of smaller chromosomes, thus supporting chromosomal fission. We also address additional hypotheses for increasing chromosome numbers, namely pericentric inversions and unequal translocations. Finally, we discuss the role of these chromosomal changes in evolutionary radiations. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 168–185.     

Life on the fly: phylogenetics and evolution of the helicopter damselflies (Odonata,Pseudostigmatidae)

Ingley, S.J., Bybee, S.M., Tennessen, K.J., Whiting, M.F. & Branham, M.A. (2012). Life on the fly: phylogenetics and evolution of the helicopter damselflies (Odonata, Pseudostigmatidae). —Zoologica Scripta, 41, 637–650. Helicopter damselflies (Odonata: Pseudostigmatidae) form a relatively small, yet highly specialized group of odonates, including the largest extant odonate (wingspan of ～190 mm). Pseudostigmatids are found throughout Central and South America, with the exception of one species that is found exclusively in East Africa. Pseudostigmatids oviposit exclusively in phytotelmata and forage on orb‐weaver spiders, which they pluck from webs. Pseudostigmatids also exhibit unique forms of both broad and narrow wings. Although the ecology of these behaviours and morphological features have been studied, their phylogenetic origins and evolutionary history are unknown. Here, we examine the origins of pseudostigmatid wing forms, oviposition in phytotelmata and spider feeding within a modern phylogenetic context, testing for single origins of each character. Phylogenetic analyses are based on 59 morphological characters and ～5 kb of sequence data. Our findings include a well‐supported monophyletic Pseudostigmatidae and Coryphagrion grandis as sister to the Neotropical genera. The genus Mecistogaster is paraphyletic, with Pseudostigma nested within the clade. The genus Microstigma is supported as monophyletic and forms a sister group relationship to the clade of Megaloprepus and Anomisma. The sister group relationship to Pseudostigmatidae is less clear. On the basis of this phylogenetic analysis, we propose three new tribes (Coryphagrionini, Microstigmatini and Mecistogastrini). As Pseudostigmatidae is monophyletic, the behaviour of gleaning spiders from webs appears to derive from a single origin. There are two origins of broad wings within Pseudostigmatidae. Oviposition in phytotelmata most certainly evolved multiple times within Coenagrionoidea. These findings provide new insights into pseudostigmatid evolution that can be used to generate hypotheses regarding behaviour and morphological adaptation in this unique and threatened group of damselflies.     

What can the mitochondrial genome reveal about higher‐level phylogeny of the molluscan class Cephalopoda?

We present the first analysis of cephalopod mitochondrial gene order and construct phylogenies based on gene order using Bayesian, distance, and parsimony analysis methods. Analyses included all species of cephalopod for which the whole mitochondrial genome has been sequenced. Where resolution was obtained, these analyses supported division of Neocoleoidea, in which all recent coleoid Cephalopoda can be placed, into Octopodiformes and Decapodiformes. For the same taxa, we also constructed a phylogeny in a maximum likelihood framework based on amino‐acid coded sequence data of all mitochondrial protein coding genes. As well as supporting Octopodiformes and Decapodiformes, amino‐acid analyses established support for Teuthoidea (Oegospida and Myopsida) to the exclusion of Sepiidae, and supported a monophyletic Oegopsida. Partial mitochondrial sequences of additional higher‐level taxa for which whole genome data were not available were subsequently included in the amino‐acid analysis to provide additional information on phylogeny. Spirulida was found to be basal amongst Decapodiformes. Mapping of morphological characters onto our phylogeny and consideration of palaeontological evidence suggests that our phylogeny reflects true evolutionary relationships. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 573–586.     

An integrative approach to species delineation incorporating different species concepts: a case study of Limnadopsis (Branchiopoda: Spinicaudata)

The unambiguous delineation and identification of species remain central problems in systematic and taxonomic studies. Species delineation depends on the data utilized and the species concept applied. In recent years, morphology‐based species delineation has been complemented by DNA sequence data, leading to an integrative taxonomy. Such integrative approaches, however, are hampered by the partial incongruence of the various data types with certain species concepts. In this study, we delineated Australian Limnadopsis species employing one mitochondrial (cytochrome c oxidase subunit I, COI) and one nuclear (elongation factor 1α, EF1α) marker and a morphological character apparently part of the specific mate recognition complex, and therefore potentially indicative of reproductive isolation. By integrating the data over various species concepts (e.g. the ‘biological’, ‘Hennigian’, ‘recognition’, ‘phylogenetic’ and ‘evolutionary’ species concepts), the delineation of most species becomes straightforward and unambiguous. Conflicts are particularly interesting as they reveal different aspects of speciation considering the various species concepts. Our study emphasizes the benefits of a truly integrative approach to taxonomy. By combining molecular data with morphological characters indicative of reproductive isolation, it is possible to delineate species integrating not only different data types, but also different underlying species concepts. Overall, 11 Limnadopsis species could be delineated, including all eight currently recognized species, and three so far undescribed species. Most species were congruently delineated under all species concepts. A strict application of the evolutionary species concept, however, would have further split L. parvispinus into two species on the basis of the COI data. In addition, Limnadopsis tatei is consistently split into two sympatrically occurring species under all applied species concepts. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 575–599.     

Tooth morphology of Echimyidae (Rodentia,Caviomorpha): homology assessments,fossils, and evolution

Echimyidae constitute the most important radiation of caviomorph rodents in the Neotropical region, represented by 20 extant genera and several extinct species. Both in extant and fossil forms, this diversity is reflected by a significant morphological variation found in crown structures of the cheek teeth. Different hypotheses of primary homology have been proposed for these structures, which, in turn, support diverse dental evolutionary hypotheses. In this contribution we inspect the main structures (cusps and lophids) of the lower deciduous teeth and molars in extinct and extant Echimyidae, and establish their topological correspondences. Comparisons with cusps and lophids of Erethizontidae are emphasized. We explore the testing of alternative primary hypotheses of lophid correspondences in a cladistic context. Following a ‘dynamic’ approach, we select the hypothesis of primary homology, which produced the more parsimonious results, and evaluate the evolutionary transformations of the dental characters analysed. In this context, the phylogenetic relationships of living Myocastor coypus (Molina, 1782) with the extinct Tramyocastor and Paramyocastor are tested. Our results indicate that pentalophodonty is the derived condition for the lower molars in Echimyidae, that trilophodonty evolved independently at least three times during the evolutionary history of these rodents, and that tetralophodonty represents the plesiomorphic condition. This study shows that dental evolution in echimyids can be better understood when occlusal structures are expressed as reliably comparable characters, and when fossils are taken into account. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 451–480.     

Environmental niche divergence between genetically distant lineages of an endangered water beetle

Historically, there has been considerable disagreement between researchers about the criteria used to discriminate among species. Decisions based on traditional morphological and genetic data alone can be potentially problematic, especially if the hypotheses are contradictory. Today, taxonomy is integrating new methods from different disciplines that study species' limits and evolution; this diverse range of evidence aids researchers in the recognition of species. Differences in niche characteristics could become a new and useful criterion in helping to decide the status of conflicting taxonomical entities. Ochthebius glaber (family Hydraenidae) is an endangered water beetle typical from southeast Iberian hypersaline streams that shows three clear discrete genetic units within its distribution range. However, there is no evidence to date that these lineages of O. glaber exhibit any adaptive morphological or ecological divergence. Using a modelling approach directed to generate niche representation from distributional data, we found a significant environmental niche divergence for allopatric lineages of O. glaber that followed an aridity gradient. Although we can not conclude firmly at present that the separate populations of O. glaber studied represent separate, reproductively isolated species, the present study complements and supports previous phylogeographic analyses through the inclusion of measures of another form of evolutionary change; in this case, ecological diversification. Despite the existence of some methodological limitations, also discussed in the present study, we emphasize the importance of recent conceptual advances that allow taxonomy to improve species delimitation practices through the integration of theory and methods from disciplines that study the origin and evolution of species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 891–903.     

A molecular characterization of the charismatic Faroe house mouse

Faroe house mice are a ‘classic’ system of rapid and dramatic morphological divergence highlighted by J. S. Huxley during the development of the Modern Synthesis. In the present study, we characterize these charismatic mice using modern molecular techniques, examining specimens from all Faroe islands occupied by mice. The aims were to classify the mice within the modern house mouse taxonomy (i.e. as either Mus musculus domesticus or Mus musculus musculus) using four molecular markers and a morphological feature, and to examine the genetic diversity and possible routes of colonization using mitochondrial (mt) control region DNA sequences and microsatellite data (15 loci). Mice on the most remote islands were characterized as M. m. domesticus and exhibited exceptionally low genetic diversity, whereas those on better connected islands were more genetically diverse and had both M. m. musculus and M. m. domesticus genetic elements, including one population which was morphologically M. m. musculus‐like. The mtDNA data indicate that the majority of the mice had their origins in south‐western Norway (or possibly southern Denmark/northern Germany), and probably arrived with the Vikings, earlier than suggested by Huxley. The M. m. musculus genetic component appears to derive from recent mouse immigration from Denmark. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 471–482.     

Molecular phylogeny of sea snakes reveals a rapidly diverged adaptive radiation

Evolutionary relationships within and between the marine hydrophiine sea snake groups have been inferred primarily using morphological characters, and two major groups traditionally are recognized. The Aipysurus group comprises nine species in two genera, and the taxonomically chaotic Hydrophis group comprises as many as 40 species, of which 27 are generally allocated to the genus Hydrophis and 13 to ten additional genera. In addition to these two major groups are three putatively ‘primitive’ monotypic genera, Hydrelaps darwiniensis, Ephalophis greyi and Parahydrophis mertoni. The present study investigated the evolutionary relationships of 23 representative species of marine hydrophiines, comprising 15 species from the Hydrophis group, six species from the Aipysurus group, and H. darwiniensis and P. mertoni, to address two broad aims. First, the aim was to provide a robust phylogeny for sea snakes to test previous phylogenetic hypotheses based on morphology, and thus provide some taxonomic stability to the group. Second, there was interest in evaluating the hypothesis that the Hydrophis group might represent a rapidly diverged adaptive radiation. A large mitochondrial DNA data set based on the cytochrome b gene (1080 bp, 401 parsimony informative) and the 16S rRNA gene (510 bp, 57 parsimony informative) was assembled and these data were analysed using parsimony, maximum‐likelihood and Bayesian approaches. All analyses yielded virtually the same optimal tree, confirming that hydrophiine sea snakes comprise at least three lineages. The Aipysurus group formed a strongly supported and well‐resolved monophyletic clade. The Hydrophis group also formed a strongly supported clade; however, resolution among the genera and species was very poor. Hydrelaps darwiniensis and P. mertoni formed a sister clade to the Hydrophis lineage. Our phylogeny was used to test the validity of previous taxonomic and phylogenetic hypotheses, and to demonstrate that the genus Hydrophis is not monophyletic. Genetic diversity relative to phenotypic diversity is four to seven times greater in the Hydrophis lineage compared with the Aipysurus lineage. The topology of our phylogenetic hypothesis, combined with the levels of genetic divergence relative to morphological diversity, demonstrate that the Hydrophis lineage represents a rapidly diverged adaptive radiation. The data are consistent with the hypothesis that this adaptive radiation may be due to historical sea level fluctuations that have isolated populations and promoted speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 523–539.     

Morphological and molecular taxonomy of a new Daptonema (Nematoda,Xyalidae) with comments on the systematics of some related taxa

A new species of Daptonema is described based upon morphological characters and 18S rRNA sequence. Daptonema matrona sp. nov. was collected in Pina Basin (north‐eastern Brazil). It differs from all other species of the genus by the presence of reduced cephalic setae and straight spicules. These features require an adaptation of the generic diagnosis. Moreover, the females are characterized by intra‐uterine development of the offspring, considered herein as their major autapomorphic feature. Molecular systematic analyses supported Daptonema matrona sp. nov. as a distinct genetic and evolutionary lineage. The data also indicate hypotheses of taxonomic synonymies amongst some related taxa from Xyalidae as well as the paraphyly of Daptonema. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 1–15.     

On the evolutionary and ontogenetic origins of tool‐oriented behaviour in New Caledonian crows (Corvus moneduloides)

New Caledonian crows (Corvus moneduloides) are prolific tool users in captivity and in the wild, and have an inherited predisposition to express tool‐oriented behaviours. To further understand the evolution and development of tool use, we compared the development of object manipulation in New Caledonian crows and common ravens (Corvus corax), which do not routinely use tools. We found striking qualitative similarities in the ontogeny of tool‐oriented behaviour in New Caledonian crows and food‐caching behaviour in ravens. Given that the common ancestor of New Caledonian crows and ravens was almost certainly a caching species, we therefore propose that the basic action patterns for tool use in New Caledonian crows may have their evolutionary origins in caching behaviour. Noncombinatorial object manipulations had similar frequencies in the two species. However, frequencies of object combinations that are precursors to functional behaviour increased in New Caledonian crows and decreased in ravens throughout the study period, ending 6 weeks post‐fledging. These quantitative observations are consistent with the hypothesis that New Caledonian crows develop tool‐oriented behaviour because of an increased motivation to perform object combinations that facilitate the necessary learning. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 870–877.     

Patterns of diversification in two species of short‐tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests

The small‐sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 527–539.     

The archeology of modern human origins

Two competing hypotheses have long dominated specialist thinking on modern human origins. The first posits that modern people emerged in a limited area and spread from there to replace archaic people elsewhere. Proponents of this view currently favor Africa as the modern human birthplace.^1–5 The second suggests that the evolution of modern humans was not geographically restricted, but invlved substantial continuity between archaic and modern populations in all major regions of the occupied world.^6–7 Based solely on the fossil record, both hypotheses are equally defensible, but the spread-and-replationships scenario is far more strongly supported by burgeoning data on the genetic relationships and diversity of living humans.^8–16 These data impy that there was a common ancestor for all living humans in Africa between 280,000 and 140,000 year ago, and that Neanderthals and other archaic humans who inhabited Eurasia during the same interval contributed few, if any, genes to living peiple. I argue here that the spread-and-replacement hypothesis is also more compatible with a third line of evidence: the spread-and-replacement hypothesis is also more compatible with a third line of evidence: the archeological record for human behavioral evolution.