Diversity and evolution of microsporogenesis in Bromeliaceae

In this study, we explore the features of microsporogenesis in Bromeliaceae and, in particular, the diversity and evolution of additional callose deposits. Cytokinesis type, cell wall formation, tetrad form and patterns of additional callose deposition after intersporal wall formation were studied in 12 species of Bromeliaceae (each from a different genus) presenting four different aperture patterns. Microsporogenesis is highly conserved, with successive cytokinesis, centrifugal cell plate formation and predominantly tetragonal and decussate tetrads, as in many monocots, but five different patterns of additional callose deposition were recorded. The optimization of patterns of additional callose deposition on the phylogeny of Bromeliaceae reveals convergences. Additional callose deposition is a variable and labile feature of microsporogenesis in Bromeliaceae and is linked, to some extent, to aperture pattern. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 36–45.     

The conquest of fresh water by the palaemonid shrimps: an evolutionary history scripted in the osmoregulatory epithelia of the gills and antennal glands

Extant Palaemonidae occupy aquatic environments that have generated physiological diversity during their evolutionary history. We analyze ultrastructural traits in gills and antennal glands of palaemonid species from distinct osmotic niches, and employ phylogenetic comparative methods to ascertain whether transformations in their osmoregulatory epithelia have evolved in tandem, driven by salinity. Gill pillar cells exhibit apical evaginations whose surface density (S_v, μm² plasma membrane area/μm³ cytoplasmic volume) ranges from 6.3–7.1 in Palaemon, and 0.7–38.4 in Macrobrachium. In the septal cells, S_v varies from 8.9–10.0 in Palaemon, and 3.3–21.6 in Macrobrachium; mitochondrial volumes (V_mit) range from 43.3–46.8% in Palaemon and 34.9–53.4% in Macrobrachium. In the renal proximal tubule cells, apical microvilli S_v varies from 27.0–34.3 in Palaemon, and 38.3–47.8 in Macrobrachium; basal invagination S_v ranges from 18.7–20.0 in Palaemon and 30.8–40.8 in Macrobrachium. Septal cell S_v shows phylogenetic signal; evagination height/density, apical S_v, and V_mit vary independently of species relatedness. Salt transport capability by the gill and renal epithelia has increased during palaemonid evolution, reflecting amplified membrane availability for ion transporter insertion. These traits underpin the increased osmotic gradients maintained against the external media. Gill ultrastructure and osmotic gradient have evolved in tandem, driven by salinity at the genus level. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 673–688.     

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.     

Biogeographically dynamic genetic structure bridging two continents in the monotypic Central American rodent Ototylomys phyllotis

Central America is an ideal region in which to study patterns of historical divergence and population genetic differentiation, because of its extraordinarily dynamic biogeographical, tectonic, and climatic history. The rodent Ototylomys phyllotis is the only extant species of the genus Ototylomys and is distributed within this region from the Isthmus of Tehuantepec, Mexico, to central Costa Rica, offering an excellent opportunity to study spatial and temporal patterns of population structure of the species and to explain the ecological and evolutionary processes responsible for those patterns. We estimated the genetic diversity and structure within and between populations of O. phyllotis, times of divergence, and migration patterns using mitochondrial DNA and a comprehensive combination of phylogenetic and phylogeographical computational analyses. Our results support monophyly of the genus Ototylomys. We identified three major phylogeographical lineages within O. phyllotis that are linked to its diversification and coincide with the main geological features that shaped Middle America. The origin of the genus was before 3.35 Mya, prior to the Great American Biotic Interchange (GABI), and its initial occurrence was near the centre of its current distribution (Honduras/El Salvador), from which it later spread (3.20–2.84 Mya) following a series of GABI pulses. The species showed an initial northward dispersal to the Chiapas and Guatemala highlands (2.27 Mya) followed by diversification. A later dispersal (1.82 Mya) occurred toward both the south (Nicaragua, Costa Rica) and the north (Belize). The Yucatan peninsula was colonized (0.8 Mya) by individuals from Belize. Extremely high radiation and range expansion occurred throughout the entire range, the highest of which was in the Yucatan peninsula (0.125 Mya). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 593–610.     

The concept of genus within the family Phytoseiidae (Acari: Parasitiformes): historical review and phylogenetic analyses of the genus Neoseiulus Hughes

Systematic studies on the family Phytoseiidae were first conducted at the beginning of the 20^th century but increased greatly after the Second World War. Various classifications have been proposed based on different characters such as: dorsal, ventral, and leg chaetotaxy; the shape of ventrianal and sternal shields; the shape of the insemination apparatus (spermatheca) and spermatodactylus; the number of teeth on the movable digit of chelicera; and dorsal and ventral adenotaxy. The genus concepts developed over the last five decades can be divided into two main categories or hypotheses. The first, supported mainly by Chant and McMurtry, focuses on dorsal and ventral chaetotaxy, and the genera so defined usually include a great number of species. The second category, proposed by Athias‐Henriot, considers the shape of the insemination apparatus as the key character, and the genera so defined usually include a limited number of species. From a diagnostic point of view, both classifications have a valid structure, but the question investigated herein was: which of the two classifications or hypotheses fits phylogenetic evolution? To answer this, we conducted molecular phylogenetic analyses (using the genes ITS and 12S rRNA) on the genus Neoseiulus, which has been subjected to classification based on the two main genus concepts. The results showed that the first hypothesis (Chant and McMurtry) leads to polyphyly of the genus Neoseiulus, while the second (Athias‐Henriot) leads to paraphyly of the genus. The results show that acarologists who first decided that the insemination apparatus was of evolutive importance could be correct as the shape of the insemination apparatus seems to better fit evolutive clades than dorsal and ventral chaetotaxy. The morphology of this organ, however, must be more accurately studied to better define homologies. The present paper investigates the two main hypotheses proposed until now for classification of Phytoseiidae and thereby opens the way for improved classification. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 253–273.     

A taxonomic revision of Encyclia (Orchidaceae: Laeliinae) in Costa Rica

A taxonomic revision of Encyclia (Orchidaceae) in Costa Rica is presented. The taxonomic history of the genus and its phylogenetic position are discussed. Characters of vegetative and floral morphology are described and their taxonomic significance is discussed. The genus is treated as comprising nine species in the country and a key to species is provided. Each taxon is described on the basis of Costa Rican material, illustrated in a composite plate, and its distribution within the country is assessed. Distribution maps for all the taxa are given. Overall distribution, derivation of name, synonymy, notes on species ecology and diagnostic features are presented for each taxon. The names Encyclia tonduziana and Epidendrum mooreanum are typified. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 395–448.     

Landscape and oceanic barriers shape dispersal and population structure in the island nematode Pristionchus pacificus

In this study evolutionary host plant patterns at ranks from order to species were analysed using spatial evolutionary and ecological vicariance analysis (SEEVA), based on a multigene phylogeny of 45 ascomycete fungal species. The objective was to understand speciation events and host associations in Ophiognomonia (Gnomoniaceae). Species of this genus are perithecial fungi that occur as endophytes, pathogens, and latent saprobes on plants in the families of Betulaceae, Fagaceae, Juglandaceae, Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae, and Sapindaceae. A second objective was to determine whether speciation events are influenced by host conservatism, host specialization, or host switching at different taxonomic host ranks. Host differences between sister clades were interpreted using the divergence index (D) from the SEEVA analysis, ranging from 0 for no divergence to 1 for maximum possible divergence. Several fungal subclades showed clear patterns of host order/family conservatism (D = 1.00) for hosts in Betulaceae, Fagaceae, Juglandaceae, and Rosaceae. Clear trends of host specialization at host genus and species ranks (D = 1.00) were suggested within these host families. Independent host jumps were observed for two species at the family rank and three at the order rank. As a result of this study, host specificity and specialization is hypothesized as a mechanism that can strongly contribute to speciation patterns in fungal pathogens. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 1–16.     

New data on perittocrinids and hybocrinids (Crinoidea, Echinodermata) from the Middle Ordovician of the Baltic region

Age variation of radial plates of perittocrinids and aberrant cups of the hybocrinid genus Hoplocrinus from the Middle Ordovician of the St-Petersburg region are examined. Three patterns for the development of folds on the radial plates of perittocrinids are recognized. The differences between patterns are of species level. It is proposed here that the folded structures of perittocrinids (as well as the pore-structures of other pelmatozoans) were not only used for respiration, but also very likely for feeding. Tetracionocrinus transitor is a young individual of a species of the genus Perittocrinus or a paedomorphic species of this genus. The study of aberrant cups of Hoplocrinus suggests that its ancestor could have had biserial arms. Phylogenetic implications of this interpretation are discussed, and homologies within the phylum Echinodermata, reassessed. The three-armed genus Baerocrinus may be an aberrant form of a species of the genus Hoplocrinus.     

Floral evolution in Lithospermum (Boraginaceae): independent origins of similar flower types

In Lithospermum (Boraginaceae), floral diversity is quite large, with variation in individual quantitative and qualitative traits as well as suites of floral characteristics. The present study utilizes phylogenetic, morphometric and developmental methodologies to investigate patterns of floral evolution, of individual and suites of traits, in the genus and among related genera. The evolutionary patterns of eight quantitative and five qualitative traits were reconstructed, and morphometrics and the evolution of floral morphospace were examined in the genus. Floral developmental patterns were established with light and scanning electron microscopy. Phylogenetic analyses provided evidence that derived flower types have each evolved multiple times, with differences in the manner in which these flower types arose. Floral morphospace has increased throughout the evolution of Lithospermum. Floral developmental patterns and cell lengths of floral organs at anthesis provided evidence that, in Lithospermum, an increase in the length of the sexual organs of flowers involves both longer cells and a greater number of mitotic divisions, but an increase in the length of the corolla is primarily a result of a larger number of cell divisions. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 213–228.     

Resurrection in Carapa (Meliaceae): a reassessment of morphological variation and species boundaries using multivariate methods in a phylogenetic context

The taxonomy of the amphi‐Atlantic tree genus Carapa (Meliaceae) has long been controversial. Of the three species currently recognized in the genus, two are known to present substantial morphological variation that has been used in the past to distinguish several taxa, most of which are currently placed in synonymy. Here, a combination of field observations, univariate analyses of leaf, floral and seed characters and principal coordinate analyses of floral characters in the context of a molecular phylogenetic analysis was used to investigate the patterns of variation and delimit morphological species anew in the genus. These results support the recognition of 27 species in Carapa, of which 16 are previously described and 11 are new. In general, phylogenetically related species occurred in the same geographical area, but were morphologically distinct. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 186–221.     

Morphology and development of additional bony elements in the genus Brachycephalus (Anura: Brachycephalidae)

We describe the extra bony elements, plates, and osteoderms present in species of the genus Brachycephalus. Samples of eight species of Brachycephalus, including seven populations of Brachycephalus ephippium, were examined. The large additional elements associated with the skull (parotic plate) and vertebrae (vertebral and paravertebral plates) all comprise intramembranous bone, similar to that of the frontoparietal or nasal bones of the skull of most of frogs. Additionally, in the dermis of one unnamed species, we discovered and described true osteoderms. We discuss the morphological nature and diversity of theses elements and their importance as evidence of phylogenetic relationship within Brachycephalus. In summary, three distinct conditions of extra bony elements occur in the genus Brachycephalus: (1) bony plates may be present or absent in species of the genus; (2) a few, small bony plates may be developed and these may be represented by (a) paravertebral plates small and restricted to the distal ends of the transverse processes of the presacral IV, (b) parotic plates small and not covering the tops of the squamosals, and (c) ornamented spinal plates on all vertebrae; and (3) well‐developed bony plates may be present as (a) paravertebral plates forming a ‘bone‐shield’ on the dorsal surface of the trunk, ornamented, and visible through the integument, (b) parotic plates covering the tops of the squamosals, and (c) spinal plates associated with all vertebrae, and ornamented on vertebrate I–VI. Although the phenomenon of miniaturization may be associated with the appearance of new elements in at least some of the species in the genus, the traditional rule may not be universally applicable. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 752–767.     

Phylogeny and evolution of the South African genus Metalasia (Asteraceae–Gnaphalieae) inferred from molecular and morphological data

Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the ‘Metalasia clade’. A species‐level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA‐trnH, trnL‐trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well‐supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M. densa which appears to be an intricate species complex. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 173–198.     

The utility of leaf flavonoids as taxonomic markers for some Malaysian species of the tribe Shoreae (Dipterocarpaceae)

A flavonoid survey was carried out on 45 taxa from the genera Shorea, Hopea, Parashorea, Neobalanocarpus, and Dryobalanops of the tribe Shoreae in the Dipterocarpaceae. The study showed significant chemotaxonomic differences in leaf flavonoid aglycone patterns and the presence of tannins in these taxa. The flavonoid patterns are useful in the delimitation of some taxa. For example, the genus Parashorea is distinguished by the universal presence of kaempferol 3‐methyl ether, and the monotypic genus Neobalanocarpus is unique in not producing ellagic and gallo tannins. The presence of chalcones and flavone C‐glycosides supports the separation of the genus Hopea into two sections, section Dryobalanoides and section Hopea in Ashton's classification, which is based on the type of venation. The flavonoid distributions in this study show that they can be very useful for differentiating between the Balau group in the genus Shorea and some scaly barked Hopea species, particularly H. helferi (lintah bukit), H. nutans (giam), and H. ferrea (malut). © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 755–762.     

Phylogenetic relationships of the pygmy rice rats of the genus Oligoryzomys Bangs, 1900 (Rodentia: Sigmodontinae)

Sequences from two mitochondrial genes (cytochrome b and NADH1) were used to produce a molecular phylogeny for 12 named and two undescribed species of the genus Oligoryzomys. All analyses placed Oligoryzomys microtis as the most basal taxon, a finding consistent with previous studies that suggested the west‐central Amazon as a centre of origin for the tribe Oryzomyini to which Oligoryzomys belongs. Biogeographically, this suggests that Oligoryzomys had a South American origin, and later advanced northwards, entering Central America and Mexico more recently. Different analyses have provided consistent support for several additional clades that did not necessarily agree with the species groups hypothesized by previous studies. A molecular clock derived for these data suggests an origin for the genus of 6.67 Mya, with most speciation within the genus occurring between 3.7 and 1.5 Mya. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 551–566.     

Evolutionary history of the burnet moth genus Zygaena Fabricius, 1775 (Lepidoptera: Zygaenidae) inferred from nuclear and mitochondrial sequence data: phylogeny, host–plant association, wing pattern evolution and historical biogeography

Burnet moths of the genus Zygaena are a striking group of primarily diurnal Lepidoptera displaying an exceptional phenotypic plasticity. Previous attempts to elucidate the phylogenetic history of the group had been confounded by a perplexing pattern of characters or insufficient taxon sampling. In the present study, we infer a phylogeny of the genus Zygaena by analysing 5.4 kb of their nuclear and mitochondrial DNA. Eighty‐four of the 98 currently recognized species in this genus are considered, including representatives of all described species groups. RNA coding sequences are aligned with reference to zygaenoid moth specific secondary structure models of corresponding molecules. We conduct phylogenetic analyses within a Bayesian framework applying partition specific substitution parameters; covariation of paired sites in RNA gene sequences is accommodated by using doublet substitution models. The molecular data reveal that a considerable number of currently recognized species groups in Zygaena are not monophyletic. The traditional subgeneric classification proves to be artificial as well; Agrumenia and Zygaena (sensu stricto) are polyphyletic. Only the subgenus Mesembrynus can be confirmed as a monophyletic species cluster. Optimization of larval host–plant associations and forewing patterns on sampled trees of the Bayesian analyses suggest convergent evolution of similar wing pattern types in distantly related species clusters and a shift from cyanogenic to acyanogenic host‐plants. The phylogenetic results challenge the classic assumption that early species diversification in Zygaena took place in the Irano–Turkestanian region. Rather, the molecular data point to the western Mediterranean area as the geographical origin of the group and imply a subsequent colonization of the Middle East and Central Asia. We discuss the apparently convergent evolution of similar wing patterns in context with the chemical defence system of burnet moths and suggest a species group concept for the genus Zygaena that accounts for the recent findings. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92 , 501–520.     

Phylogeography and phylogenetic relationships of Malagasy tree and ground boas

Three species of boid snakes are recognized in Madagascar, namely the genus Sanzinia (one species and two subspecies) and the genus Acrantophis (two species). In the present study, we studied the patterns of genetic variation of these species across Madagascar using a fragment of the mitochondrial 16S rRNA gene in 77 specimens. To support the phylogenetic relationships of the lineages identified, three further gene fragments (cytochrome b, 12S rRNA and c‐mos) were analyzed in a reduced but representative set of samples. The results obtained corroborate that the genus Sanzinia includes two highly divergent mitochondrial lineages that evolved independently from each other on the east versus the west side of Madagascar. Each of these lineages presents a further subdivision that separates northern from southern groups. The nuclear marker showed no variation among the Malagasy boas, indicating either very low substitution rates in this gene or relatively recent speciation events coupled with high mitochondrial substitution rates. Because the broad geographic sampling detected no admixture among haplotypic lineages within Sanzinia, it is hypothesized that these may represent distinct species. Deviant haplotypes of snakes morphologically similar to Acrantophis dumerili indicate that this taxon may be a complex of two species as well. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 640–652.     

Molecular appraisal of Bunium and some related arid and subarid geophilic Apiaceae–Apioideae taxa of the Ancient Mediterranean

Bunium is unusual in Apiaceae in having a variable cotyledon number and broad infrageneric dysploidy. To test the monophyly of the genus, phylogenetic relationships among 39 Bunium species were investigated with DNA sequence data from nuclear (nrITS) and plastid (psbA‐trnH intergenic spacer) regions. Several other taxa with a similar ecology and geography were also included in the analyses. Our results suggest that Bunium is not monophyletic. Bunium spp. in the eastern part of the study area are more closely related to the Central Asian genera Elaeosticta, Galagania, Hyalolaena, Mogoltavia and Oedibasis than to those in the western part. Our study revealed that molecular, morphological (cotyledon number and width of fruit commissure) and karyological data reveal similar patterns in the taxa studied. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 149–170.     

Phylogeographic analysis of the nocturnal velvet ant genus Dilophotopsis (Hymenoptera: Mutillidae) provides insights into diversification in the Nearctic deserts

Understanding the history of diversification in the North American deserts has long been a goal of biogeographers and evolutionary biologists. Although it appears that a consensus is forming regarding the patterns of diversification in the Nearctic deserts in vertebrate taxa, little work has been done exploring the historical biogeography of widespread invertebrate taxa. Before a robust model of geobiotic change in the North American deserts can be proposed, it needs to be determined whether the same historical events affected vertebrate and invertebrate taxa in the same way. We explore the phylogeographic patterns in a widespread nocturnal wasp genus Dilophotopsis using two rDNA loci, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2). We use Bayesian phylogenetic analysis and haplotype network analysis to determine whether a consistent geographic pattern exists among species and populations within Dilophotopsis. We also used molecular dating techniques to estimate divergence dates of the major phylogenetic clades. Our analyses indicates that the species‐level divergences in Dilophotopsis occurred in the Neogene, and likely were driven by mountain building during the Miocene–Pliocene boundary (approximately 5 Mya) similar to the divergences in many vertebrate taxa. The population‐level divergences within species occurred during the Pleistocene (0.1–1.8 Mya). The present study shows that similar patterns of diversification exist in vertebrate and invertebrate taxa. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 360–375.