Patterns of lineage diversification in rabbitfishes

Fishes of the tropical Indo-Pacific family Siganidae comprise 28 species, characterized by their body proportions and their colour patterns. A mitochondrial phylogeny of 20 Siganidae species was produced to infer their evolutionary history. Three distinct, major clades were found, that also correspond to the early radiation of the family into three major ecological types: fusiform species that also live in schools on the inshore reef flats (S. canaliculatus, S. fuscescens, S. luridus, S. rivulatus, S. spinus, S. sutor); deep-bodied species including brightly coloured ones whose adults live in pairs on the reef front (S. corallinus, S. doliatus, S. puellus, S. punctatus, S. unimaculatus, S. virgatus, S. vulpinus), and species that live in small schools in mangroves, estuaries and estuarine lakes (S. guttatus, S. javus, S. lineatus, S. randalli, S. vermiculatus); and a third clade including a cosmopolitan species, S. argenteus, the only species of the family known to possess a pelagic, prejuvenile stage and S. woodlandi, a recently described species from New Caledonia and morphologically close to S. argenteus. The partition of the genus into two sub-genera, Lo (erected for S. unimaculatus, S. vulpinus and three related species possessing a tubular snout) and Siganus (all the other species), had no phylogenetic rationale. The present results indicate that the tubular snout, which apparently results from ecological specialization, is a recent acquisition within the deep-body clade. The Western Indian Ocean endemic S. sutor appeared as the sister-species of the Red Sea endemic S. rivulatus within a well-supported subclade that also included S. canaliculatus and S. fuscescens. S. spinus did not appear as sister-species to S. luridus. S. lineatus haplotypes formed a paraphyletic group with S. guttatus, and an early isolation of Maldives S. lineatus was suggested. Unexpectedly, S. randalli did not appear as the sister-species of S. vermiculatus, but its haplotypes instead were embedded within the West Pacific S. lineatus haplogroup, suggesting recent introgression. Among currently-recognized sister-species with parapatric distribution, S. doliatus and S. virgatus haplotypes formed a single, unresolved haplogroup, as did S. unimaculatus and S. vulpinus. The occurrence of two distinct clades within S. fuscescens was confirmed.     

Spawning seasonality and body sizes at sexual maturity in the bluespine unicornfish,Naso unicornis (Acanthuridae)

We herein evaluate several reproductive metrics of Hawaiian Archipelagic populations of the bluespine unicornfish (Naso unicornis), an economically and ecologically important, broadly distributed tropical Pacific reef fish, based on multi-year, fishery-dependent and fishery-independent collections. Sex-specific spawning seasonality was characterized for fish collected mostly from Oahu (Main Hawaiian Islands, MHI) using a gonadosomatic index. Histological slides preparations were used to score gonad developmental phase and to classify individuals of either sex as immature or mature. Sex-specific median body lengths at maturity (L₅₀) were estimated by logistic fits of proportion mature versus length class. Spawning was highly seasonal in Hawaii, with a single brief (May–June) peak spawning period. Proportionate gonad-to-body weight values were relatively low, averaging only about 0.1 % and 0.6 % across all months of year and 0.16 % and 1.03 % during May–June for males and females, respectively. Median lengths at sexual maturity differed between the sexes. L₅₀ values for fish collected throughout all months of year were 30.1 ± 0.5 (standard error) cm Fork Length (FL) for males and 35.5 ± 0.7 cm FL for females. Spawning seasonality and L₅₀ estimates for bluespine unicornfish in Hawaii suggest that the species spawns several months earlier in the calendar year and matures at larger body lengths in Hawaii versus Guam, the Northern Mariana Islands, and Pohnpei in the Federated States of Micronesia. Estimated lengths at sexual maturity are compared to the minimum length (14 inches or 35.6 cm FL) mandated for this species in Hawaii: median size at maturity occurs at a length appreciably less than (males) or approximately equal to (females) minimum legal size. A likely disproportionately large contribution of old females to population replenishment is discussed relative to the minimum size limit.     

Food vacuole contents in the ciliate, Balantidium jocularum (Balantididae), a symbiont in the intestine of the surgeonfish, Naso tonganus (Acanthuridae)

During the past 16 years, the ciliate Balantidium jocularum has been collected from the intestines of many specimens of its fish host, Naso tonganus, all collected from the Great Barrier Reef near Lizard Island, Australia. Ciliates for this study of food consumption were isolated in 1988, 1989, 2003, and 2005. Nineteen specimens of B. jocularum were examined in the transmission electron microscope to determine the contents of both food vacuoles and a putative discharging cytoproct vacuole. Food vacuoles contained rod-shaped bacteria, tightly coiled spirilliform bacteria, and one or more euglenid flagellates. In several balantidia of somewhat different form than the type species of B. jocularum, the large bacterium, Epulopiscium fishelsoni, was observed in light microscope protargol preparations. Some putative phagolysosomes retained spirilliform bacteria that were apparently intact, and others contained partially digested flagellates. Food in a single discharging cytoproct vacuole consisted of normal appearing spirilliform bacteria, some other bacteria, and no flagellates. The results argue for non-selective ingestion of food and selective digestion; hence, somewhat inefficient food processing.     

Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco

Pleistocene glacial cycles are thought to have played a major role in the diversification of temperate and boreal species of North American birds. Given that coalescence times between sister taxa typically range from 0.1 to 2.0 Myr, it has been assumed that diversification occurred as populations were isolated in refugia over long periods of time, probably spanning one to several full glacial cycles. In contrast, the rapid postglacial range expansions and recolonization of northern latitudes following glacial maxima have received less attention as potential promoters of speciation. Here we report a case of extremely rapid diversification in the songbird genus Junco as a result of a single continent-wide range expansion within the last 10 000 years. Molecular data from 264 juncos sampled throughout their range reveal that as the yellow-eyed junco (Junco phaeonotus) of Mesoamerica expanded northward following the last glacial maximum, it speciated into the dark-eyed junco (Junco hyemalis), which subsequently diversified itself into at least five markedly distinct and geographically structured morphotypes in the USA and Canada. Patterns of low genetic structure and diversity in mitochondrial DNA and amplified fragment length polymorphism loci found in dark-eyed juncos relative to Mesoamerican yellow-eyed juncos provide support for the hypothesis of an expansion from the south, followed by rapid diversification in the north. These results underscore the role of postglacial expansions in promoting diversification and speciation through a mechanism that represents an alternative to traditional modes of Pleistocene speciation.     

Patterns of ontogenetic evolution in perianth diversification of Besseya (Scrophulariaceae)

Species of Besseya have perianth diversity centered largely in meristic variation, extreme corolla diminution, and corolla tube loss. Flowers of Besseya differ from those of their closest relative Synthyris in having a bilabiate corolla. The avenues of ontogenetic evolution that were important in creating these aspects of perianth diversity were explored by optimizing developmental transformations on cladograms. Three different evolutionary transformations were important in the diversification of calyx ontogenies in Besseya, including the derived reciprocal substitution of ontogenetic states in B. bullii, labile abaxial lobe expression in B. wyomingensis, and a heterotopic novel substitution in B. oblongifolia. The bilabiate corolla of Besseya arose via fractionation and localization of the zonal growth expressed in the more plesiomorphic Synthyris. Besseya plantaginea, B. ritteriana, and B. oblongifolia form a group characterized by diminished expression of the anterior corolla lobe. Four alternative scenarios equally explain the ontogenetic transformations underlying extreme corolla diminution and corolla tube loss. Corolla tube loss has been considered rare or impossible among angiosperms, but some alternative scenarios in Besseya demonstrate how this may have occurred via fractionation of zonal growth. Corolla tube loss may have arisen only indirectly from the sympetalous ancestors of Besseya following extreme corolla diminution and the reestablishment of a “full-size” corolla which had a novel developmental pattern that did not include the distribution of zonal growth present in ancestors.     

Karyologic evidence of diversification of the genus Thrichomys (Rodentia,Echimyidae)

Karyologic analysis of Thrichomys specimens from different Brazilian localities, in Pantanal, Cerrado and Caatinga biomes, shows different chromosome complements. The 2n = 34, FN = 64 karyotype is found in Mato Grosso do Sul state; the 2n = 30, FN = 54 karyotype in Bahia, Pernambuco, Piauí and Ceará states; the 2n = 30, FN = 56 karyotype in Goiás and Tocantins states, the 2n = 28, FN = 50 karyotype in Minas Gerais state, the 2n = 28, FN = 52 and 2n = 26, FN = 48 karyotypes in Bahia state. Comparisons of G-band patterns allowed the identification of homologies shared by all karyotypes and show that the two karyotypes with the lowest diploid number (2n = 26 and 2n = 28) belong to two different evolutionary lineages. The most proper names for each karyomorphic population are: Thrichomys pachyurus for 2n = 34; Thrichomys apereoides apereoides for 2n = 28, FN = 50; Thrichomys apereoides laurentius for 2n = 30, FN = 54 and Thrichomys inermis for 2n = 26. Two karyotypes (2n = 28, FN = 52 and 2n = 30, FN = 56) could not be attributed to any subspecies. These different karyomorphotypes are allopatric and/or parapatric.     

Evolutionary diversification of the lizard genus Bassiana (Scincidae) across Southern Australia

Background

Relatively recent (Plio-Pleistocene) climatic variations had strong impacts on the fauna and flora of temperate-zone North America and Europe; genetic analyses suggest that many lineages were restricted to unglaciated refuges during this time, and have expanded their ranges since then. Temperate-zone Australia experienced less severe glaciation, suggesting that patterns of genetic structure among species may reflect older (aridity-driven) divergence events rather than Plio-Pleistocene (thermally-mediated) divergences. The lizard genus Bassiana (Squamata, Scincidae) contains three species that occur across a wide area of southern Australia (including Tasmania), rendering them ideally-suited to studies on the impact of past climatic fluctuations.

Methodology/Principal Findings

We performed molecular phylogenetic and dating analyses using two partial mitochondrial genes (ND2 and ND4) of 97 samples of Bassiana spp. Our results reveal a pattern of diversification beginning in the Middle Miocene, with intraspecific diversification arising from 5.7 to 1.7 million years ago in the Upper Miocene-Lower Pleistocene.

Conclusions/Significance

In contrast to the temperate-zone Northern Hemisphere biota, patterns of evolutionary diversification within southern Australian taxa appear to reflect geologically ancient events, mostly relating to east-west discontinuities imposed by aridity rather than (as is the case in Europe and North America) relatively recent recolonisation of northern regions from unglaciated refugia to the south.     

Molecular phylogenetics and diversification of the genus Sporophila (Aves: Passeriformes)

The evolutionary affinities within and among many groups of nine-primaried oscines remain unresolved. One such group is Sporophila, a large genus of New World tanager-finches. Our study focused particularly on clarifying the relationship between this genus and a closely related one, Oryzoborus, and on examining the phylogenetic affinities of the "capuchinos," a group of 11 Sporophila species that share a similar male plumage coloration pattern. Our phylogenetic analyses, based on 498 bp of mitochondrial DNA sequence, indicated that: (1) Oryzoborus is embedded within a well-supported clade containing all Sporophila species, which strongly suggests that both genera should be merged, (2) the species of capuchinos comprise a monophyletic group, implying that the plumage patterns common to all probably arose only once, and (3) the capuchinos clade is comprised of two sub-clades, one including two species that are distributed in northern South America and the other one containing eight species that are present south of the Amazon River. Mean sequence divergence among the southern capuchinos species was extremely low, suggesting a rapid radiation within the last half-million years that may be related to the high level of sexual selection present in the genus and might have been promoted by marine ingressions and egressions that occurred in some southern coastal regions of South America in the Late Pleistocene.     

Major evolutionary events in the origin and diversification of the fern genus Polystichum (Dryopteridaceae)

Recent advances in molecular systematics of the ferns make it possible to address long-standing questions about classification of the major fern genera, such as the worldwide genus Polystichum (Dryopteridaceae), comprising at least 200 species. In this study we examined rbcL sequences and morphological characters from 55 fern taxa: 34 were from Polystichum and 21 were from other genera in the Dryopteridaceae. We found that Phanerophlebia, possibly including Polystichopsis, is the sister group to Polystichum sensu lato (s.l.), including Cyrtomium. Polystichum as commonly recognized is paraphyletic. Our results lead us to suggest recognizing the clade of earliest diverging Polystichum species as a distinct genus (Cyrtomidictyum) and to continue to recognize Cyrtomium as a separate genus, leaving a monophyletic Polystichum sensu stricto (s.s.). We resolved a tropical American clade and an African clade within Polystichum s.s. However, the resemblance between the once-pinnate, bulb-bearing calciphilic species found in Asia and the West Indies appears to be the result of convergent evolution. Optimizing our morphological character transformations onto the combined phylogeny suggests that the common ancestor of Polystichum s.l. and Phanerophlebia had evolved the common features of the alliance, including ciliate petiole-base scales, once-pinnate fronds, ultimate segments with scarious tips, peltate indusia, and microscales.     

Alkaloid diversification in the genus Palicourea (Rubiaceae: Palicoureeae) viewed from a (retro-)biogenetic perspective

Phytochemistry Reviews - The species-rich genus Palicourea (Rubiaceae: Palicoureeae) is source of an intriguing diversity of alkaloids derived from tryptamine and its precursor tryptophan. So far...     

Evolutionary diversification of the gall midge genus Asteromyia (Cecidomyiidae) in a multitrophic ecological context

Gall-forming insects provide ideal systems to analyze the evolution of host–parasite interactions and understand the ecological interactions that contribute to evolutionary diversification. Flies in the family Cecidomyiidae represent the largest radiation of gall-forming insects and are characterized by complex trophic interactions with plants, fungal symbionts, and predators. We analyzed the phylogenetic history and evolutionary associations of the North American cecidomyiid genus Asteromyia, which is engaged in a complex and perhaps co-evolving community of interactions with host-plants, fungi, and parasitoids. Mitochondrial gene trees generally support current classifications, but reveal extensive cryptic diversity within the eight named species. Asteromyia likely radiated after their associated host-plants in the Astereae, but species groups exhibit strong associations with specific lineages of Astereae. Evolutionary associations with fungal mutualists are dynamic, however, and suggest rapid and perhaps coordinated changes across trophic levels.     

Recent evolutionary diversification of a protist lineage

Here, we have identified a protist (dinoflagellate) lineage that has diversified recently in evolutionary terms. The species members of this lineage inhabit cold-water marine and lacustrine habitats, which are distributed along a broad range of salinities (0–32) and geographic distances (0–18 000 km). Moreover, the species present different degrees of morphological and sometimes physiological variability. Altogether, we analysed 30 strains, generating 55 new DNA sequences. The nuclear ribosomal DNA (nrDNA) sequences (including rapidly evolving introns) were very similar or identical among all the analysed isolates. This very low nrDNA differentiation was contrasted by a relatively high cytochrome b (COB) mitochondrial DNA (mtDNA) polymorphism, even though the COB evolves very slowly in dinoflagellates. The 16 Maximum Likelihood and Bayesian phylogenies constructed using nr/mtDNA indicated that the studied cold-water dinoflagellates constitute a monophyletic group (supported also by the morphological analyses), which appears to be evolutionary related to marine-brackish and sometimes toxic Pfiesteria species. We conclude that the studied dinoflagellates belong to a lineage which has diversified recently and spread, sometimes over long distances, across low-temperature environments which differ markedly in ecology (marine versus lacustrine communities) and salinity. Probably, this evolutionary diversification was promoted by the variety of natural selection regimes encountered in the different environments.     

Late Miocene diversification of the genus Hydrochus (Coleoptera, Hydrochidae) in the west Mediterranean area

We provide a reconstruction of the phylogenetic relationships, the geographical and temporal origin, and the mode of diversification of the Mediterranean species of the aquatic beetle family Hydrochidae (Coleoptera, Hydrophiloidea). A total of ca. 3KB of sequence data of three mitochondrial and two nuclear genes were used to reconstruct the phylogeny of 62 specimens of 21 species of Hydrochus, including all western Mediterranean species but one. We estimated the times of divergence using Bayesian methods and an evolutionary rate of 0.0115 substitutions/site/MY, and used an ultrametric calibrated tree to construct a Lineage Through Time (LTT) plot to test alternative models of diversification. A well resolved, well supported phylogeny showed that all western Mediterranean Hydrochus formed a clade, sister to a group including species with a central and eastern European distribution. The origin of the western Mediterranean clade was estimated to be at ca. 13MY, and the speciation events took place between this time and the end of the Messinian, at about 5.3MY. The LTT plot best fitted a model with a shift in the rate of diversification at ca. 8 MY, with a single speciation event (originating two Iberian endemics) subsequent to this period. We conclude that most of the western Mediterranean species of Hydrochidae, including the Ibero-Maghrebian endemics, are ancient elements likely to have remained in the same geographical area since their Miocene origin. Our results add to a growing body of evidence showing the importance of Mediterranean long-term, Tertiary refugia as both cradles and museums of diversity.     

Out-of-Africa origin and dispersal-mediated diversification of the butterfly genus Junonia (Nymphalidae: Nymphalinae)

The relative importance of dispersal and vicariance in the diversification of taxa has been much debated. Within butterflies, a few studies published so far have demonstrated vicariant patterns at the global level. We studied the historical biogeography of the genus Junonia (Nymphalidae: Nymphalinae) at the intercontinental level based on a molecular phylogeny. The genus is distributed over all major biogeographical regions of the world except the Palaearctic. We found dispersal to be the dominant process in the diversification of the genus. The genus originated and started diversifying in Africa about 20 Ma and soon after dispersed into Asia possibly through the Arabian Peninsula. From Asia, there were dispersals into Africa and Australasia, all around 5 Ma. The origin of the New World species is ambiguous; the ancestral may have dispersed from Asia via the Beringian Strait or from Africa over the Atlantic, about 3 Ma. We found no evidence for vicariance at the intercontinental scale. We argue that dispersal is as important as vicariance, if not more, in the global diversification of butterflies.     

Molecular phylogeny and diversification of the "Haenydra" lineage (Hydraenidae, genus Hydraena), a north-Mediterranean endemic-rich group of rheophilic Coleoptera

Hydraena is the largest genus within the water beetle family Hydraenidae, with ca. 1000 species distributed worldwide. Within this large genus some monophyletic groups of species are recognised, among them the "Haenydra" lineage, including ca. 90 species distributed in the western Palaearctic from the Iberian peninsula to Iran. Species of "Haenydra" have often very restricted distributions, and are typical of clean small rivers and streams. We obtained ca. 2.5Kb of mitochondrial and nuclear protein-code and ribosomal markers of 101 specimens of 69 species of "Haenydra", and used Bayesian and Maximum Likelihood phylogenetic methods to reconstruct their phylogeny and diversification history. We found a derived phylogenetic position of the "Haenydra" lineage within the genus Hydraena, as sister to the species of the Hydraenabisulcata group. Within "Haenydra" three main lineages were recognised, with poorly resolved relationships among them: the Hydraena iberica, Hydraena gracilis and Hydraena dentipes lineages, the former restricted to the Iberian peninsula but the latter two distributed through the whole north-Mediterranean area. A Bayesian relaxed molecular clock approach using a combined mitochondrial rate of 2% divergence per MY estimated the origin of "Haenydra" in the Tortonian, ca. 8Mya, and the main diversification and the origin of most extant species in the Pliocene and Pleistocene. We did not found evidence of a phylogenetic connection between the western and eastern species that could be traced to the Messinian salinity crisis, with dispersal only at small geographical scales (e.g. the colonisation of Corsica and Sardinia from NW Italy and SW France). The H. gracilis and H. iberica lineages were estimated to have diversified under a pure birth model with a speciation rate of 0.64 and 0.23 species/MY respectively, while the H. dentipes lineage was estimated to have a decreasing diversification rate with time, with an average rate of 0.29 sp/MY.     

Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin

We carried out a phylogeograhic and population genetic analysis of fishes of the taxonomically contentious genus Symphysodon from the Amazon basin in order to test hypotheses of relationships among taxonomic units, and potential processes driving diversification within this genus. We sampled 334 individuals of the genus Symphysodon from 24 localities that span the complete geographic distribution of this genus. The sampling scheme included all known phenotypic groups, species and subspecies. Analyses were based on 474 bp of the mitochondrial control region and 1443 bp of the exon 3 of RAG1 gene. We observed 102 mtDNA haplotypes defined by 89 segregating sites, and 5 nuDNA alleles defined by three segregating sites. Maximum-likelihood, Bayesian-inference and statistical parsimony analyses revealed three well defined monophyletic groups. These clades corresponded to the 'green' and 'blue' groups of Symphysodon aequifasciatus, and to a previously morphologically unrecognized clade from the Xingu River drainage. These three clades were nested within a paraphyletic assemblage consisting of the 'brown' group of S. aequifasciatus and of both described subspecies of S. discus, the 'Heckel' and the 'abacaxi' discus. Nuclear allele sharing was observed among groups, but there were significant differences in frequencies. We inferred several processes including past fragmentation among groups, and restricted gene flow with isolation by distance within the paraphyletic 'brown+Heckel+abacaxi' groups, and suggest that differences among the 'blue', 'Heckel' and 'brown' groups are potentially maintained by differences in water chemistry preferences. We further inferred colonization of the western Amazon basin by an ancestor of the 'green' clade. The 'green' group was the only group with a pattern of haplotype distribution consistent of a demographic expansion, and the divergence of this clade from other groups of discus was consistent with recent geologic evidence on the breach of the Purus Arch which separates western Amazon from eastern Amazon. We further hypothesized that the differentiation of the 'Xingu' clade could be due to vicariance events resulting from Pleistocene sea level, and thus Amazon River level fluctuations. We discuss the bearings of our results on the current taxonomy of this group, and on the biological reality of the different forms, subspecies and species of Symphysodon concluding that we are probably observing a process of diversification, and therefore taxonomy will remain contentious.     

Patterns of introduction and diversification of Vanilla planifolia (Orchidaceae) in Reunion Island (Indian Ocean)

The cultivated species Vanilla planifolia is a typical example of a crop introduced from its area of origin (America) to new regions where natural pollinators are absent. Although the Vanilla cultivars are exclusively vegetatively propagated, a high degree of phenotypic variation is observed among the cultivars in their introduction areas such as Reunion Island. To test several hypotheses explaining this variation-different introduction events, somatic mutations and sexual reproduction (through manual pollination)-we used AFLP markers to elucidate the patterns of introduction of V. planifolia. Most of the accessions cultivated in the world were derived from a single accession, possibly the Mexican cultivar Mansa. The patterns of diversification of this cultivated species were also studied and compared with other cultivated (V. tahitensis) and wild (V. pompona and V. bahiana) species. Except for one particular phenotype ('Aiguille'), which may come from sexual reproduction, cultivated accessions exhibit very low levels of genetic diversity. They have evolved by the accumulation of point mutations through vegetative multiplication. The genetic diversity revealed could not explain the phenotypic diversity, which may be related to epigenetics or polyploidy. This new understanding of the basis of genetic diversity of vanilla may assist to improve management of genetic resources.