Contrasting global‐scale evolutionary radiations: phylogeny,diversification, and morphological evolution in the major clades of iguanian lizards

Parallel evolutionary radiations in adjacent locations have been documented in many systems, but typically at limited geographical scales. Here, we compare patterns of evolutionary radiation at the global scale in iguanian lizards, the dominant clade of lizards. We generated a new time‐calibrated phylogeny including 153 iguanian species (based on mitochondrial and nuclear data) and obtained data on morphology and microhabitats. We then compared patterns of species diversification, morphological disparity, and ecomorphological relationships in the predominantly Old World and New World clades (Acrodonta and Pleurodonta, respectively), focusing on the early portions of these radiations. Acrodonts show relatively constant rates of species diversification and disparity over time. In contrast, pleurodonts show an early burst of species diversification and less‐than‐expected morphological disparity early in their history, and slowing diversification and increasing disparity more recently. Analyses including all species (with MEDUSA) suggest accelerated diversification rates in certain clades within both Acrodonta and Pleurodonta, which strongly influences present‐day diversity patterns. We also find substantial differences in ecomorphological relationships between these clades. Our results demonstrate that sister clades in different global regions can undergo very different patterns of evolutionary radiation over similar time frames. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Molecular phylogeny and biogeography of Astilbe (Saxifragaceae) in Asia and eastern North America

Phylogenetic analyses were conducted for Astilbe (Saxifragaceae), an Asian/eastern North American disjunct genus, using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid matK, trnL‐trnF and psbA‐trnH regions. The monophyly of Astilbe is well supported by both ITS and plastid sequences. Topological incongruence was detected between the plastid and the ITS trees, particularly concerning the placement of the single North American species, A. biternata, which may be most probably explained by its origin involving hybridization and/or allopolyploidy with plastid capture. In Astilbe, all species with hermaphroditic flowers constitute a well‐supported clade; dioecious species form a basal grade to the hermaphroditic clade. Astilbe was estimated to have split with Saxifragopsis from western North America at 20.69 Ma (95% HPD: 12.14–30.22 Ma) in the early Miocene. This intercontinental disjunction between Astilbe and Saxifragopsis most likely occurred via the Bering land bridge. The major clade of Astilbe (all species of the genus excluding A. platyphylla) was inferred to have a continental Asian origin. At least three subsequent migrations or dispersals were hypothesized to explain the expansion of Astilbe into North America, Japan and tropical Asian islands. The intercontinental disjunct lineage in Astilbe invokes a hybridization event either in eastern Asia or in North America. This disjunction in Astilbe may be explained by a Beringian migration around 3.54 Ma (95% high posterior density: 1.29–6.18 Ma) in the late Tertiary, although long‐distance dispersal from eastern Asia to North America is also likely. The biogeographical connection between continental Asia, Taiwan, the Philippines and other tropical Asian islands in Astilbe provides evidence for the close floristic affinity between temperate or alpine south‐western China and tropical Asia. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●● , ●●–●●.     

A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set

The first scolopocryptopid centipede known from the fossil record is a specimen of the subfamily Scolopocryptopinae in Miocene amber from Chiapas, southern Mexico. It is described here as Scolopocryptops simojovelensis sp. nov. , displaying a distinct combination of morphological characters compared to extant congeners. Anatomical details of the fossil specimen were acquired by non‐invasive 3D synchrotron microtomography using X‐ray phase contrast. The phylogenetic position of the new species is inferred based on a combination of morphological data with sequences for six genes (nuclear 18S and 28S rRNA, nuclear protein‐coding histone H3, and mitochondrial 12S rRNA, 16S rRNA, and protein‐coding cytochrome c oxidase subunit I) for extant Scolopendromorpha. The data set includes eight extant species of Scolopocryptops and Dinocryptops from North America, east Asia, and the Pacific, rooted with novel sequence data for other blind scolopendromorphs. The molecular and combined data sets, analysed in a parsimony/direct optimization framework, identified a stable pattern of two main clades within Scolopocryptopinae. North American and Asian species of Scolopocryptops are united as a clade supported by both morphological and molecular characters. Its sister group is a Neotropical clade in which the type species of Dinocryptops is nested within a paraphyletic assemblage of Scolopocryptops species; Dinocryptops is placed in synonymy with Scolopocryptops. The strength of support for the relationships of extant taxa from the molecular data allow the Chiapas fossil to be assigned with precision, despite ambiguity in the morphological data; the fossil is resolved as sister species to the extant Laurasian clade. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 768–786.     

The biogeography of Gunnera L.: vicariance and dispersal

Aim The genus Gunnera is distributed in South America, Africa and the Australasian region, a few species reaching Hawaii and southern Mexico in the North. A cladogram was used to (1) discuss the biogeography of Gunnera and (2) subsequently compare this biogeographical pattern with the geological history of continents and the patterns reported for other Southern Hemisphere organisms. Location Africa, northern South America, southern South America, Tasmania, New Zealand, New Guinea/Malaya, Hawaii, North America, Antarctica. Methods A phylogenetic analysis of twenty‐six species of Gunnera combining morphological characters and new as well as published sequences of the ITS region, rbcL and the rps16 intron, was used to interpret the biogeographical patterns in Gunnera. Vicariance was applied in the first place and dispersal was only assumed as a second best explanation. Results The Uruguayan/Brazilian Gunnera herteri Osten (subgenus Ostenigunnera Mattfeld) is sister to the rest of the genus, followed sequentially upwards by the African G. perpensa L. (subgenus Gunnera), in turn sister to all other, American and Australasian, species. These are divided into two clades, one containing American/Hawaiian species, the other containing all Australasian species. Within the Australasian clade, G. macrophylla Blume (subgenus Pseudogunnera Schindler), occurring in New Guinea and Malaya, is sister to a clade including the species from New Zealand and Tasmania (subgenus Milligania Schindler). The southern South American subgenus Misandra Schindler is sister to a clade containing the remaining American, as well as the Hawaiian species (subgenus Panke Schindler). Within subgenus Panke, G. mexicana Brandegee, the only North American species in the genus, is sister to a clade wherein the Hawaiian species are basal to all south and central American taxa. Main conclusions According to the cladogram, South America appears in two places, suggesting an historical explanation for northern South America to be separate from southern South America. Following a well‐known biogeographical pattern of vicariance, Africa is the sister area to the combined southern South America/Australasian clade. Within the Australasian clade, New Zealand is more closely related to New Guinea/Malaya than to southern South America, a pattern found in other plant cladograms, contradictory to some of the patterns supported by animal clades and by the geological hypothesis, respectively. The position of the Tasmanian G. cordifolia, nested within the New Zealand clade indicates dispersal of this species to Tasmania. The position of G. mexicana, the only North American species, as sister to the remaining species of subgenus Panke together with the subsequent sister relation between Hawaii and southern South America, may reflect a North American origin of Panke and a recolonization of South America from the north. This is in agreement with the early North American fossil record of Gunnera and the apparent young age of the South American clade.     

Phylogeny of <Emphasis Type="Italic">Gunnera</Emphasis>

 The phylogeny of the genus Gunnera is investigated for the first time. Twelve species representing the six currently recognised subgenera are analysed. Two chloroplast DNA regions, the rbcL gene and the rps16 intron, together provide 46 informative characters out of 2335. A combined analysis of both genes gives four most parsimonious trees, firmly establishing the east South American G. herteri as sister group to the rest of the genus. The African G. perpensa is sister group to two well-supported clades, one including the South American subgenera Misandra and Panke, the other the Australian/New Zealand/Malayan species of subgenera Milligania and Pseudogunnera. Thus, South America is a composite area for Gunnera, showing up at two different levels in the cladogram. Our analysis supports a close biogeographic relationship between Australia and New Zealand. The evolution of some morphological characters is discussed. Lastly, the unusual structure of some of the rbcL sequences is reported. Received July 6, 2000 Accepted October 24, 2000     

Phylogenetics,character evolution,and distribution patterns of the greenbriers,Smilacaceae (Liliales), a near‐cosmopolitan family of monocots

Smilacaceae, composed of Smilax and Heterosmilax, are a cosmopolitan family of > 200 species of mostly climbing monocots with alternate leaves characterized by reticulate venation, a pair of petiolar tendrils and usually prickly stems. Although there has been a long history of studying Smilax since Linnaeus named the genus in 1753, the phylogenetic history of this dioecious family remains unclear. Here we present results based on nuclear ribosomal internal transcribed spacer (nrITS) and plastid matK and rpl16 intron DNA sequence data from 125 taxa of Smilacaceae. Our taxon sampling covers all sections of Smilax and Heterosmilax and major distribution zones of the family; species from Ripogonaceae and Philesiaceae are used as outgroups. Our molecular analysis indicates that phylogenetic relationships largely contradict the traditional morphological classification of the family, instead showing a conspicuous geographical pattern among the species clades. The previously recognized genus Heterosmilax was found to be embedded in Smilax. Species in the family are separated into primarily New World and Old World clades, except for a single species lineage, Smilax aspera, that is sister to the remaining species of the family, but with poor statistical support. Ancestral character state reconstructions and examination of distribution patterns among the clades provide important information for future taxonomic revisions and historical biogeography of the group. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 535–548.     

A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.     

Molecular phylogenetic analysis of Podostemaceae: implications for taxonomy of major groups

The river‐weed family Podostemaceae (c. 300 species in c. 54 genera) shows a number of morphological innovations to be adapted to its unusual aquatic habitat, and its unique or rare bauplan features have been reflected in the traditional (i.e. non‐molecular) classification recognizing numerous monotypic or oligospecific genera. The infrasubfamilial relationships of many genera remained unclear. The present study used molecular phylogenetic analysis of matK sequences for 657 samples (c. 132 species/c. 43 genera). The family was traditionally divided into three subfamilies (Podostemoideae, Tristichoideae and Weddellinoideae). American Podostemoideae were shown to be polyphyletic and divided into four clades, i.e. Ceratolacis, Diamantina, Podostemum and all other genera. Among the podostemoid clades, Diamantina was the first branching clade and a clade comprising Mourera and the Apinagia subclade was then sister to the remainder of the New World and Old World Podostemoideae with low statistic supports. The Old World Podostemoideae comprised four monophyletic clades, i.e. two African clades, one Madagascan clade and one Asian clade, although the relationships among these clades and American Ceratolacis and Podostemum were poorly resolved. African Podostemoideae were polyphyletic, with Saxicolella pro parte being weakly supported as sister to the remaining Old World Podostemoideae plus Ceratolacis and Podostemum. In contrast to the American and African clades, monophyly of four Asian subclades was well supported. Plants of Tristicha (Tristichoideae) and of Weddellina (Weddellinoideae), which are currently treated as monospecific, had great matK differentiation equivalent to at least interspecific variation. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 461–492.     

Rampant polyphyly indicates cryptic diversity in a clade of Neotropical flycatchers (Aves: Tyrannidae)

Polyphyletic arrangements in DNA phylogenies are often indicators of cryptic species diversity masked by erroneous taxonomic treatments that are frequently based on morphological data. Although mitochondrial (mt)DNA polyphyly is detected relatively rarely in phylogenetic studies, it has recently been found in a variety of tyrant‐flycatcher (Tyrannidae) groups. In the present study, we provide a DNA phylogeny for a mitochondrial and a nuclear locus with a complete species sampling in Zimmerius flycatchers, showing that the genus is characterized by multiple mtDNA polyphyly. Based on phylogenetic and life‐history information, we suggest the elevation of a number of taxa to species status, leading to a doubling of Zimmerius species‐level diversity compared to taxonomic treatments conducted before 2001. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, ●●, ●●–●●.     

Testing concordance in species boundaries using acoustic,morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea,Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species‐specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 285–303.     

AFLP analysis shows high incongruence between genetic differentiation and morphology‐based taxonomy in a widely distributed tortoise

Morphology has traditionally been used to diagnose the taxa of various taxonomic ranks. However, there is growing evidence that morphology is not always able to reveal cryptic taxa, and that pronounced morphological variation could reflect phenotypic plasticity rather than evolutionary divergence. Spur‐thighed tortoises (the Testudo graeca complex), distributed in the western Palaearctic region, are characterized by high morphological variability and complicated taxonomy, which are under debate. Previous molecular studies using mainly mitochondrial DNA (mtDNA) sequences have revealed incongruence between genetic differentiation and morphology‐based taxonomy, suggesting that morphological variability is the result of phenotypic plasticity and stabilizing selection, which masks the true genealogies. In the present study, we used a range‐wide sampling and nuclear Amplified fragment length polymorphism (AFLP) markers to investigate genetic differentiation within the T. graeca complex. We found that spur‐thighed tortoises are differentiated into four geographically well‐defined AFLP groups: Balkans–Middle Eastern, western Mediterranean, Caucasian and central‐eastern Iranian. Compared with the distribution of mtDNA lineages, the groups are largely concordant, although the AFLP markers are less sensitive and distinguish fewer groups than do mtDNA sequences. The AFLP groups show an allopatric or parapatric distribution. The AFLP differentiation conflicts with the previously proposed morphology‐based taxonomy of the complex, suggesting that local adaptation to different environmental conditions may have led to the great extent of morphological variation within the same lineages. We propose a re‐evaluation of the taxa that were confirmed genetically using a thorough morphological analysis corrected for phenotypic plasticity. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Effects of changing climate on species diversification in tropical forest butterflies of the genus Cymothoe (Lepidoptera: Nymphalidae)

Extant clades may differ greatly in their species richness, suggesting differential rates of species diversification. Based on phylogenetic trees, it is possible to identify potential correlates of such differences. Here, we examine species diversification in a clade of 82 tropical African forest butterfly species (Cymothoe), together with its monotypic sister genus Harma. Our aim was to test whether the diversification of the Harma–Cymothoe clade correlates with end‐Miocene global cooling and desiccation, or with Pleistocene habitat range oscillations, both postulated to have led to habitat fragmentation. We first generated a species‐level phylogenetic tree for Harma and Cymothoe, calibrated within an absolute time scale, and then identified temporal and phylogenetic shifts in species diversification. Finally, we assessed correlations between species diversification and reconstructed global temperatures. Results show that, after the divergence of Harma and Cymothoe in the Miocene (15 Mya), net species diversification was low during the first 7 Myr. Coinciding with the onset of diversification of Cymothoe around 7.5 Mya, there was a sharp and significant increase in diversification rate, suggesting a rapid radiation, and correlating with a reconstructed period of global cooling and desiccation in the late Miocene, rather than with Pleistocene oscillations. Our estimated age of 4 Myr for a clade of montane species corresponds well with the uplift of the Eastern Arc Mountains where they occur. We conclude that forest fragmentation caused by changing climate in the late Miocene as well as the Eastern Arc Mountain uplift are both likely to have promoted species diversification in the Harma–Cymothoe clade. Cymothoe colonized Madagascar much later than most other insect lineages and, consequently, had less time available for diversification on the island. We consider the diversification of Cymothoe to be a special case compared with other butterfly clades studied so far, both in terms of its abrupt diversification rate increase and its recent occurrence (7 Myr). It is clear that larval host plant shift(s) cannot explain the difference in diversification between Cymothoe and Harma; however, such a shift(s) may have triggered differential diversification rates within Cymothoe. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, ●● , ●●–●●.     

Phylogeny of South American Bufo (Anura: Bufonidae) inferred from combined evidence

Despite the considerable research that has focused on the evolutionary relationships and biogeography of the genus Bufo, an evolutionary synthesis of the entire group has not yet emerged. In the present study, almost 4 kb of DNA sequence data from mitochondrial (12S, tRNA^Val, and 16S) and nuclear (POMC; Rag-1) genes, and 83 characters from morphology were analysed to infer a phylogeny of South American toads. Phylogenies were reconstructed with parsimony and maximum likelihood and Bayesian model-based methods. The results of the analysis of morphological data support the hypothesis that within Bufo , some skull characters (e.g. frontoparietal width), correlated with the amount of cranial ossification, are prone to homoplasy. Unique and unreversed morphological synapomorphies are presented that can be used to diagnose recognized species groups of South American toads. The results of all phylogenetic analyses support the monophyly of most species groups of South American Bufo . In most DNA-only and combined analyses, the South American (minus the B. guttatus and part of the ' B. spinulosus ' groups), North American, Central American, and African lineages form generally well-supported clades: ((((((((South America) (North America + Central America)) Eurasia) Africa) Eurasia) South America) West Indies) South America). This result confirms and extends prior studies recovering South American Bufo as polyphyletic. The biogeographical results indicate that: (1) The origin of Bufo predates the fragmentation of Gondwana; (2) Central and North American species compose the sister group to a large, 'derived' clade of South American Bufo ; and (3) Eurasian species form the sister group to the New World clade.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 407–452.     

Phylogenetics of Escallonia (Escalloniaceae) based on plastid DNA sequence data

Escallonia (Escalloniaceae) is a New World genus of c. 39 species distributed mainly in the South American highlands. Plastid DNA sequence data from the intergenic spacers trnS‐trnG and 3′ trnV‐ndhC and the ndhF gene for 32 species were used to examine the relationships among species and related genera and to analyse the relationship between phylogeny and the geographical distribution of the species. Maximum parsimony and Bayesian inference were employed to analyse the data. The sister relationship of Escallonia to Forgesia and Valdivia was corroborated. We recovered five strongly supported clades that are geographically structured, suggesting that the evolutionary history of the genus may be linked to historical processes, including the uplift of mountainous systems in South America. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 442–451.     

Testing the monophyly and position of the North American shrubby desert genus Leucophyllum (Scrophulariaceae: Leucophylleae)

Leucophyllum is one of the most remarkable endemic genera of North American deserts, with its simultaneous bloom of showy purple flowers. With Eremogeton and probably Capraria it forms part of tribe Leucophylleae. Leucophyllum has 16 species distributed mostly throughout the Chihuahuan and Tehuacán deserts. The three genera were sampled to investigate the phylogenetic relationships among them and to test the monophyly of Leucophyllum, based on plastid DNA (trnL‐F, rps16) and nuclear ribosomal (nr)DNA (internal transcribed spacer) sequences. Bayesian inference and maximum‐likelihood analyses confirmed that tribe Leucophylleae is monophyletic and formed by the three Neotropical genera. Separate (plastid DNA and nrDNA) and combined analyses retrieved Leucophyllum as paraphyletic, with L. mojinense as the sister species to the rest of the species in the tribe and Capraria spp. nested in one of two clades of Leucophyllum. Further monographic work is needed to identify the defining characters and limits of the genera, but we suggest that L. mojinense, with its different vegetative architecture, distinctive flowers and dissimilar distribution could be placed in its own genus. Each of the two clades in Leucophyllum could be considered a genus in its own right, and Capraria and Eremogeton can be recognized as independent genera, as they are at present. Leucophyllum ambiguum, the type species of the genus, belongs to one of the clades so the species of the other could be considered members of a new genus. The only diagnostic character detected at present is a ventricose corolla tube in one of the clades in Leucophyllum and a pressed corolla tube in the other. © 2013 The Linnean Society of London     

Molecular phylogenetics,character evolution and systematics of the genus Micranthes (Saxifragaceae)

With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66.