Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences

We infer phylogenetic relationships among isopod species of the genus Orthometopon distributed in the Greek area, comparing partial mitochondrial DNA sequences for cytochrome oxidase I (COI). All phylogenetic analyses produced topologically identical trees that revealed a well-resolved phylogeny. These trees support the monophyly of the genus Orthometopon , and suggest two clades that correspond to separate geographical regions (west and east of the mid-Aegean trench). However, the phylogenetic relationships among Greek populations of Orthometopon spp. are different from the presumed pattern on the basis of morphological evidence. The distinct geographical distribution of the major clades of the phylogenetic tree and its topology suggest a spatial and temporal sequence of phylogenetic separations, which coincide with some major palaeogeographical separations during the geological history of the Aegean Sea. The results stress the need for a reconsideration of the evolutionary history of Orthometopon species, which will help overcome difficulties encountered in classical taxonomy at the species level. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 707–715.     

A phylogeny of the families of fossil and extant tetraodontiform fishes (Acanthomorpha, Tetraodontiformes), Upper Cretaceous to Recent

A data matrix is presented of 210 morphological characters (mostly osteological, some external) for 20 extant taxa of the ten Recent families of tetraodontiform fishes and 36 fossil tetraodontiforms. The oldest of these are from the Upper Cretaceous (95 Mya); most are from the Lower to Middle Eocene (50–58 Mya). There are two outgroup taxa (a zeiform and a caproid). A cladistic analysis of this matrix for only the extant taxa produced two equally parsimonious trees that call into question the monophyly of some of the previously accepted major higher-level tetraodontiform clades. Inclusion in the analysis of the large number of available fossil taxa helps to resolve relationships between family level clades. The new phylogenetic hypothesis, together with stratigraphic and biogeographical data, is used to discuss scenarios of the origin and evolution of the major clades of the order.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 565−617.     

Polyploidy in fishes: patterns and processes

Fishes are the most speciose group of vertebrates, with more than 24 000 species. They are characterized by great diversity in ecology, morphology, life history, behaviour and physiology. Here, the phylogenetic patterns of orders in which polyploidy has been recorded are considered, with special reference to patterns of species richness and hybridization: these orders include such phylogenetically diverse taxa as the Lepidosireniformes (lungfish) and the Perciformes (perch). Examples, predominantly drawn from the Cyprinidae and Salmonidae, are used to illustrate attributes of polyploidy in fishes. It is concluded (i) that polyploidy may have been of considerable importance in the evolution of fishes, and (ii) that fishes, with their diverse life histories, represent a useful model system with which to test theories relating to the origin and consequences of polyploidy that have been derived from work on plants.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 431–442.     

Life history and ecology influences establishment success of introduced land birds

Despite the many studies that have investigated successful establishment of introduced bird species, very little is known about the patterns of success worldwide and the influence of life history and ecological traits. This study describes the analysis of non-native land bird introductions to test existing hypotheses of establishment success using a modern comparative approach to control for phylogenetic relatedness among taxa. I used randomization tests, permutational phylogenetic regressions, and across-taxa and sister-taxa comparisons to examine predicted correlates of introduction success. My analyses confirmed that the variability in establishment success among introduced land bird families is distributed in a manner significantly different from a random process, and that life history and ecological attributes are an important influence of introduction success. I found strong evidence, through a generalized linear model, that increased habitat generalism, lack of migratory tendency, and sexual monochromatism together explain significant variation in the successful establishment of introduced land bird species. This has resulted in a predictive equation for the novel introduction of land bird species.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76 , 465–480.     

The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

The pattern, timing and extent of the evolutionary radiation of anatomically modern birds (Neornithes) remains contentious: dramatically different timescales for this major event in vertebrate evolution have been recovered by the 'clock-like' modelling of molecular sequence data and from evidence extracted from the known fossil record. Because current synthesis would lead us to believe that fossil and nonfossil evidence conflict with regard to the neornithine timescale, especially at its base, it is high time that available data are reconciled to determine more exactly the evolutionary radiation of modern birds. In this review we highlight current understanding of the early fossil history of Neornithes in conjunction with available phylogenetic resolution for the major extant clades, as well as recent advancements in genetic methods that have constrained time estimates for major evolutionary divergences. Although the use of molecular approaches for timing the radiation of Neornithes is emphasized, the tenet of this review remains the fossil record of the major neornithine subdivisions and better-preserved taxa. Fossils allowing clear phylogenetic constraint of taxa are central to future work in the production of accurate molecular calibrations of the neornithine evolutionary timescale.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 141 , 153–177.     

Microanatomy of the amniote femur and inference of lifestyle in limbed vertebrates

The femoral microanatomy of 155 species of extant amniotes (57 species of mammals, 15 species of turtles, 56 species of lepidosaurs, and 27 species of birds) of known lifestyle is studied to demonstrate a possible link between some basic parameters of bone structure and specific lifestyles, as well as phylogenetic relationships between taxa. Squared change parsimony with random taxon reshuffling and pairwise comparisons reveal that most compactness and size parameters exhibit both phylogenetic and ecological signals. A discriminant analysis produces several inference models, including a ternary model (aquatic, amphibious, terrestrial) that yield the correct lifestyle in 88% of the cases. These models are used to infer the lifestyle of three extinct Permian temnospondyls: Eryops megacephalus, Acheloma dunni, and Trimerorhachis insignis. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 644–655.     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

The gall-inducing habit has evolved multiple times among the eriococcid scale insects (Sternorrhyncha: Coccoidea: Eriococcidae)

The habit of inducing plant galls has evolved multiple times among insects but most species diversity occurs in only a few groups, such as gall midges and gall wasps. This phylogenetic clustering may reflect adaptive radiations in insect groups in which the trait has evolved. Alternatively, multiple independent origins of galling may suggest a selective advantage to the habit. We use DNA sequence data to examine the origins of galling among the most speciose group of gall-inducing scale insects, the eriococcids. We determine that the galling habit has evolved multiple times, including four times in Australian taxa, suggesting that there has been a selective advantage to galling in Australia. Additionally, although most gall-inducing eriococcid species occur on Myrtaceae, we found that lineages feeding on Myrtaceae are no more likely to have evolved the galling habit than those feeding on other plant groups. However, most gall-inducing species-richness is clustered in only two clades ( Apiomorpha and Lachnodius  +  Opisthoscelis ), all of which occur exclusively on Eucalyptus s.s . The Eriococcidae and the large genus Eriococcus were determined to be non-monophyletic and each will require revision.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 441–452.     

Phylogenetic analysis of Russian Permian dicynodonts (Therapsida: Anomodontia): implications for Permian biostratigraphy and Pangaean biogeography

Dicynodont therapsids have been known from the Upper Permian of Eastern Europe since the beginning of the twentieth century, but the phylogenetic relationships of these taxa have not been examined cladistically. Here we present the results of a phylogenetic analysis that includes eight Permian dicynodonts from Russia as well as 18 taxa best known from southern Africa. Our results do not conflict with much of the established picture of Permian dicynodont phylogeny, but are consistent with several novel hypotheses. Most importantly, our analysis suggests that the genus Dicynodon is paraphyletic, and we question its use in correlating widely separated basins. However, we cannot strongly reject a monophyletic Dicynodon . Our results also indicate that the closest Permian relatives of Kannemeyeria lived in Russia, suggesting a Laurasian origin for the lineage that includes this important Triassic taxon. The phylogeny presented here also suggests a Laurasian origin for several other dicynodont clades, but a Gondwanan origin is equally likely given the data at hand. Regardless of where these groups originated, there appears to be some endemism among Late Permian dicynodont faunas. Although our understanding of dicynodont phylogeny is improving, this study emphasizes the disparity in sampling of the dicynodont record between Gondwana and Laurasia and the need for a large scale phylogenetic analysis of Permian and Triassic dicynodonts.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 139 , 157−212.     

Ovipositor morphology correlates with life history evolution in agaonid fig wasps

The high adaptive success of parasitic Hymenoptera might be related to the use of different oviposition sites, allowing niche partitioning among co-occurring species resulting in life history specialization and diversification. In this scenario, evolutionary changes in life history and resources for oviposition can be associated with changes in ovipositor structure, allowing exploitation of different substrates for oviposition. We used a formal phylogenetic framework to investigate the evolution of ovipositor morphology and life history in agaonid wasps. We sampled 24 species with different life histories belonging to all main clades of Agaonidae including representatives of all described genera of non-pollinating fig wasps (NPFW). Our results show an overall correlation between ovipositor morphology and life history in agaonid fig wasps. Ovipositor morphologies seem to be related to constraints imposed by features of the oviposition sites since ovipositor morphology has experienced convergent evolution at least four times in Sycophaginae (Agaonidae) according to the resource used. Non-galling species have more distantly spaced teeth with uneven spacing, as opposed to the observed morphology of galling species. Our results suggest that the ancestral condition for ovipositor morphology was most likely the presence of one or two apical teeth. Regarding life history, ovary galling species that oviposit in receptive figs possibly represent the ancestral condition. Different ovipositor characteristics allow exploitation of new niches and may be related to resource partitioning and species co-existence in the fig-fig wasp system.     

Disentangling composite colour patterns in a poison frog species

A phylogenetic approach was performed to infer whether variation in conspicuous colour-patterns of a poison frog (Dendrobatidae: Dendrobates tinctorius ) has evolved neutrally or under selection. Colour and pattern were split into components that were separately analysed and subsequently re-grouped via principal component analysis. This revealed four different 'displayed' factors on the dorsal and lateral views versus one 'concealed' factor on the ventral view. Based on the assumption that current patterns of trait variation contain information about the evolutionary history of the phenotype, we correlated these trait components to a neutrally evolving gene fragment (cytochrome b ). The concealed factor was significantly correlated with the marker fragment, which identified it as having evolved under genetic drift. Noncorrelation of all displayed factors with the marker may indicate the evolution of colour patterns on dorsum and flanks under selection. In our example, colour pattern should therefore be regarded as a multicomponent signal system.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 433–444.     

Phylogeography of the freshwater crayfish Cherax destructor Clark (Parastacidae) in inland Australia: historical fragmentation and recent range expansion

The yabby, Cherax destructor Clark, is the most widespread species in the most widespread genus of Australian freshwater crayfish. It has a distribution that spans several distinct drainage basins and biogeographical regions within semiarid and arid inland Australia. Here we report a study designed to investigate patterns of genetic variation within the species and hypotheses put forward to account for its extensive distribution using DNA sequences from the mitochondrial 16S rRNA gene region. Results of phylogenetic analyses contradicted previous allozyme data and revealed relatively deep phylogenetic structure in the form of three geographically correlated clades. The degree of genetic divergences between clades (8–15 bp) contrasted with the relatively limited haplotype diversity within clades (1–3 bp). Network-based analyses confirmed these results and revealed genetic structure on both larger and more restricted geographical scales. Nevertheless some haplotypes and 1-step clades had large distributions, some of which crossed boundaries between river basins and aquatic biogeographical regions. Thus both older and more recent historical processes, including fragmentation on a larger geographical scale and more recent range expansion on a local scale, appear to be responsible for the observed pattern of genetic variation within C. destructor . These results support elements of alternative hypotheses previously put forward to account for the evolutionary history of C. destructor and the origin of its large distribution.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 539–550.     

Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia

The evolutionary history and biogeography of freshwater-dependent taxa in Australia is of intrinsic interest given the present-day aridity of this continent. Cherax is the most widespread and one of the most species-rich of Australia's nine freshwater crayfish genera. The phylogenetic relationships amongst 19 of the 23 Australian Cherax were established from mitochondrial DNA sequences representing the 12S rRNA and 16S rRNA gene regions. The relationships among species support an initial east–west separation, followed by a north–south divergence in eastern Australia. Molecular clock estimations suggest that these divergences date back to the Miocene. The phylogenetic relationships support endemic speciation within geographical regions and indicate that long-distance dispersal has not led to recent speciation as previously hypothesized. This new evolutionary scenario is consistent with the climatic history of Australia and the evolutionary history of other similarly distributed freshwater-dependent organisms in Australia.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 553–563.     

Systematics and biogeography of the New World species of Trichadenotecnum Enderlein (Insecta: Psocodea: 'Psocoptera': Psocidae)

The taxonomy of the New World species of the genus Trichadenotecnum is revised. A total of 44 species, including 29 new species, were treated. These species are classified into 12 monophyletic species groups, eight of them newly proposed here. Two species previously assigned to Trichadenotecnum , T. pichincha New & Thornton and T. sylvaticum Turner, are recognized as not belonging to this genus. Phylogenetic relationships among 16 previously and presently proposed species groups are estimated based on a data matrix of 58 morphological characters. Trees from these analyses support monophyly of Trichadenotecnum and the proposed species groups. The New World species were divided into three major clades. Based on the phylogenetic hypothesis and distributional pattern of the species groups, the biogeographical history of the New World Trichadenotecnum is discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 651–723.     

Phylogenetic relationships between parthenogens and their sexual relatives: the possible routes to parthenogenesis in animals

In theory, parthenogenetic lineages have low evolutionary potential because they inexorably accumulate deleterious mutations and do not generate much genotypic diversity. As a result, most parthenogenetic taxa occupy the terminal nodes of phylogenetic trees. The rate and mode of development of parthenogenesis are important factors to consider when assessing its costs and benefits since they determine both the level of genetic diversity and the ecological adaptability of the resulting lineages. The origin of parthenogenesis is polyphyletic in many taxa, suggesting that genetic systems maintaining sexuality are often labile. In addition, the loss of sex may be achieved in several ways, leading to parthenogenetic lineages with distinct genetic profiles. This could then influence not only the fate of such lineages in the long term, but also the outcome of competition with their sexual counterparts in the short term. In this paper, we review the possible evolutionary routes to parthenogenesis based on a survey of the phylogenetic relationships between sexual and parthenogenetic lineages in a broad range of animals. We also examine the different mechanisms by which parthenogenetic lineages could arise, and discuss the influence of these mechanisms on both the genetic properties and the ecological life styles of the resulting lineages.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 79 , 151–163.     

How to become a yucca moth: minimal trait evolution needed to establish the obligate pollination mutualism

The origins of obligate pollination mutualisms, such as the classic yucca–yucca moth association, appear to require extensive trait evolution and specialization. To understand the extent to which traits truly evolved as part of establishing the mutualistic relationship, rather than being pre‐adaptations, we used an expanded phylogenetic estimate with improved sampling of deeply‐diverged groups to perform the first formal reconstruction of trait evolution in pollinating yucca moths and their nonpollinating relatives. Our analysis demonstrates that key life‐history traits of yucca moths, including larval feeding in the floral ovary and the associated specialized cutting ovipositor, as well as colonization of woody monocots in xeric habitats, may have been established before the obligate mutualism with yuccas. Given these pre‐existing traits, novel traits in the mutualist moths are limited to the active pollination behaviours and the tentacular appendages that facilitate pollen collection and deposition. These results suggest that a highly specialized obligate mutualism was built on the foundation of pre‐existing interactions between early Prodoxidae and their host plants, and arose with minimal trait evolution. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 847–855.     

Microhabitat preferences drive phylogeographic disparities in two Australian funnel web spiders

Comparative phylogeography is underpinned by the assumption that sympatrically‐distributed taxa will have experienced similar environmental histories, resulting in broadly congruent spatial structuring of phylogenetic lineages, particularly if they inhabit similar niches. However, divergent local conditions, specifically those related to microhabitat, may produce significantly divergent systematic signatures of demographic histories. In the present study, we compare the phylogenetic and population genetic spatial patterns displayed by two species of niche‐separated (but sympatrically distributed) Australian funnel web spiders (Mygalomorphae: Hexathelidae). We demonstrate that an apparently minor disparity in habitat niche has led to divergent experiences of a common environmental history in the saproxylic Hadronyche cerberea and the ground‐burrowing Atrax sutherlandi. Furthermore, we take a crucial first step in documenting the molecular systematics of a group that has traditionally suffered from a dearth of research interest. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 805–819.     

Analysing the history of the derelomine flower weevil–Carludovica association (Coleoptera: Curculionidae; Cyclanthaceae)

The evolutionary history of the interaction among species of derelomine flower weevils (Coleoptera: Curculionidae: Derelomini) and the Panama-hat palm Carludovica (Cyclanthaceae) is analysed with emphasis on the congruence of (1) topologies and (2) character state transformations in each of the Neotropical clades. For this purpose cladistic analyses are complemented with host plant records, natural history information and selected morphological studies of the associated taxa. The interaction is specialized, involving pollination, oviposition into the inflorescences and the predation of seeds (particularly within Systenotelus ). As results from a range of standard coevolutionary methods of analysis indicate, however, events of colonization, extinction and independent (non-reciprocal) speciation have been abundant throughout the history of the association. At the same time it is possible to specify the homology and succession of characters among species of derelomines and Carludovica and interpret them as reciprocal adaptations to attack and protect the seeds, respectively. It is argued that – in light of the limited evolutionary stability of many insect–plant interactions – the question of coevolution is most effectively addressed by combining information from the character- and topology-based approaches.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 483–517.     

Phylogenetic relationships in the subgenus Mus (genus Mus, family Muridae, subfamily Murinae): examining gene trees and species trees

Over eight kilobases (kb) of sequence from eight genes including two mitochondrial loci, Cyt b and 12S, and six nuclear loci, B2m , Zp3 , Tcp1, Sry, Smcx and Smcy , were used to investigate phylogenetic relationships among 11 taxa representing eight species within the rodent genus Mus . Particular attention was given to discerning relationships among species within the subgenus Mus including members of a Palearctic clade ( M. musculus , M. spicilegus , M. macedonicus and M. spretus ) and members of an Asian clade ( M. caroli , M. cookii and M. cervicolor ), as previous studies using different datasets have produced different topologies for taxa within these two groups. While parsimony analyses of the combined eight-gene dataset yielded a single, fully resolved tree, support values were lower for nodes resolving relationships within the Palearctic and Asian clades than they were elsewhere in the tree. In addition, a maximum likelihood analysis of the same eight-gene dataset yielded different topologies for both the Palearctic and the Asian clades. Both observations are indicative of clade instability. The nature of this instability was explored through a comparison with our previous study in which we included the two mitochondrial loci and only four of the six nuclear genes, and through an analysis of partitioned data, specifically mitochondrial vs. nuclear genes. This study underscores the importance of considering among-site rate variation in phylogeny reconstruction. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 653–662.     

Genetic variation and evolution in the genus Apodemus (Muridae: Rodentia)

Genetic variation was studied using protein electrophoresis of 28–38 gene loci in 1347 specimens of Apodemus agrar-ius, A. peninsulae, A. flavicollis, A. sylvaticus, A. alpicola, A. uralensis, A . cf. hyrcanicus, A. hermonensis, A. m. mystacinus and A. m. epimelas , representing 121 populations from Europe, the Middle East, and North Africa. Mean values of heterozygosity per locus for each species ranged from 0.02 to 0.04. Mean values of Nel's genetic distance ( D ) between the taxa ranged from 0.06 (between A. flavicollis and A. alpicola) to 1.34 (between A. uralensis and A. agrarius ). The highest values of D were found between A. agrarius and other Apodemus species (0.62-1.34). These values correspond to those generally observed between genera in small mammals. Our data show that A. agrarius and A. peninsulae are sister species, well-differentiated from other taxa. High genetic distance between A. m. mystacinus and A. m. epimelas leads us to consider them distinct species and sister taxa to other Western Palaearctic species of the subgenus Sylvaemus . The data also suggest a recent separation of members of the latter group from a common ancestor, and subsequent rapid radiation, making it difficult to infer phylogenetic relationships. Some taxonomic implications of the results are discussed further.© 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 395–419.