The Hawaiian honeycreepers are a dramatic example of adaptive radiation but contrast with the four other songbird lineages that successfully colonized the Hawaiian archipelago and failed to undergo similar diversification. To explore the processes that produced the diversity dichotomy in this insular fauna, we compared clade age and morphological diversity between the speciose honeycreepers and the comparatively depauperate Hawaiian thrushes. Mitochondrial-DNA-based genetic distances between these Hawaiian clades and their continental sister taxa indicate that the ancestral thrush colonized the Hawaiian Islands as early as the common ancestor of the honeycreepers. This similar timing of colonization indicates that the marked difference in diversity between the Hawaiian honeycreeper and thrush clades is unlikely to result from differences in these clades' tenures within the archipelago. If time cannot explain the contrasting diversities of these taxa, then an intrinsic, clade-specific trait may have fostered the honeycreeper radiation. As the honeycreepers have diversified most dramatically in morphological characters related to resource utilization, we used principal components analyses of bill characters to compare the magnitudes of morphological variation in the ancestral clades from which the Hawaiian honeycreeper and thrush lineages are derived, the Carduelini and Turdinae respectively. Although the Carduelini share a more recent common ancestor and have a lower species diversity than the Turdinae, these finch-like relatives of the honeycreepers exhibit significantly greater variation in bill morphology than do the continental relatives of the Hawaiian thrushes. The higher magnitude of morphological variation in the non-Hawaiian Carduelini suggests that the honeycreepers fall within a clade exhibiting a generally high evolutionary flexibility in bill morphology. Accordingly, although the magnitude of bill variation among the honeycreepers is similar to that of the entire passerine radiation, this dramatic morphological radiation represents an extreme manifestation of a general clade-specific ability to evolve novel morphologies.
The tendency of animals and plants to independently develop similar features under similar evolutionary pressures - convergence - is a widespread phenomenon in nature. In plants, convergence has been suggested to explain the striking similarity in life form between the giant lobelioids (Campanulaceae, the bellflower family) of Africa and the Hawaiian Islands. Under this assumption these plants would have developed the giant habit from herbaceous ancestors independently, in much the same way as has been suggested for the giant senecios of Africa and the silversword alliance of Hawaii.
Phylogenetic analyses based on plastid (rbcL, trnL-F) and nuclear (internal transcribed spacer [ITS]) DNA sequences for 101 species in subfamily Lobelioideae demonstrate that the large lobelioids from eastern Africa the Hawaiian Islands, and also South America, French Polynesia and southeast Asia, form a strongly supported monophyletic group. Ancestral state reconstructions of life form and distribution, taking into account phylogenetic uncertainty, indicate their descent from a woody ancestor that was probably confined to Africa. Molecular dating analyses using Penalized Likelihood and Bayesian relaxed clock approaches, and combining multiple calibration points, estimate their first diversification at ~25-33 million years ago (Ma), shortly followed by several long-distance dispersal events that resulted in the current pantropical distribution.
These results confidently show that lobelioid species, commonly called 'giant', are very closely related and have not developed their giant form from herbaceous ancestors independently. This study, which includes the hitherto largest taxon sampling for subfamily Lobelioideae, highlights the need for a broad phylogenetic framework for testing assumptions about morphological development in general, and convergent evolution in particular.
The Hawaiian red algal flora is diverse, isolated, and well studied from a morphological and anatomical perspective, making it an excellent candidate for assessment using a combination of traditional taxonomic and molecular approaches. Acquiring and making these biodiversity data freely available in a timely manner ensures that other researchers can incorporate these baseline findings into phylogeographic studies of Hawaiian red algae or red algae found in other locations.
A total of 1,946 accessions are represented in the collections from 305 different geographical locations in the Hawaiian archipelago. These accessions represent 24 orders, 49 families, 152 genera and 252 species/subspecific taxa of red algae. One order of red algae (the Rhodachlyales) was recognized in Hawaii for the first time and 196 new island distributional records were determined from the survey collections. One family and four genera are reported for the first time from Hawaii, and multiple species descriptions are in progress for newly discovered taxa. A total of 2,418 sequences were generated for Hawaiian red algae in the course of this study - 915 for the nuclear LSU marker, 864 for the plastidial UPA marker, and 639 for the mitochondrial COI marker. These baseline molecular data are presented as neighbor-joining trees to illustrate degrees of divergence within and among taxa. The LSU marker was typically most conserved, followed by UPA and COI. Phylogenetic analysis of a set of concatenated LSU, UPA and COI sequences recovered a tree that broadly resembled the current understanding of florideophyte red algal relationships, but bootstrap support was largely absent above the ordinal level. Phylogeographic trends are reported here for some common taxa within the Hawaiian Islands and include examples of those with, as well as without, intraspecific variation.
The UPA and COI markers were determined to be the most useful of the three and are recommended for inclusion in future algal biodiversity surveys. Molecular data for the survey provide the most extensive assessment of Hawaiian red algal diversity and, in combination with the morphological/anatomical and distributional data collected as part of the project, provide a solid baseline data set for future studies of the flora. The data are freely available via the Hawaiian Algal Database (HADB), which was designed and constructed to accommodate the results of the project. We present the first DNA sequence reference collection for a tropical Pacific seaweed flora, whose value extends beyond Hawaii since many Hawaiian taxa are shared with other tropical areas.
A controversial topic in evolutionary developmental biology is whether morphological diversification in natural populations can be driven by expansions and contractions of amino acid repeats in proteins. To promote adaptation, selection on protein length variation must overcome deleterious effects of multiple correlated traits (pleiotropy). Thus far, systems that demonstrate this capacity include only ancient or artificial morphological diversifications. The Hawaiian Islands, with their linear geological sequence, present a unique environment to study recent, natural radiations. We have focused our research on the Hawaiian endemic mints (Lamiaceae), a large and diverse lineage with paradoxically low genetic variation, in order to test whether a direct relationship between coding-sequence repeat diversity and morphological change can be observed in an actively evolving system.
Here we show that in the Hawaiian mints, extensive polyglutamine (CAG codon repeat) polymorphism within a homolog of the pleiotropic flowering time protein and abscisic acid receptor FCA tracks the natural environmental cline of the island chain, consequent with island age, across a period of 5 million years. CAG expansions, perhaps following their natural tendency to elongate, are more frequent in colonists of recently-formed, nutrient-rich islands than in their forebears on older, nutrient-poor islands. Values for several quantitative morphological variables related to reproductive investment, known from Arabidopsis fca mutant studies, weakly though positively correlate with increasing glutamine tract length. Together with protein modeling of FCA, which indicates that longer polyglutamine tracts could induce suboptimally mobile functional domains, we suggest that CAG expansions may form slightly deleterious alleles (with respect to protein function) that become fixed in founder populations.
In the Hawaiian mint FCA system, we infer that contraction of slightly deleterious CAG repeats occurred because of competition for resources along the natural environmental cline of the island chain. The observed geographical structure of FCA variation and its correlation with morphologies expected from Arabidopsis mutant studies may indicate that developmental pleiotropy played a role in the diversification of the mints. This discovery is important in that it concurs with other suggestions that repetitive amino acid motifs might provide a mechanism for driving morphological evolution, and that variation at such motifs might permit rapid tuning to environmental change.
Five species of Metrosideros (Myrtaceae) are recognized in the Hawaiian Islands, including the widespread M. polymorpha, and are characterized by a multitude of distinctive, yet overlapping, habit, ecological, and morphological forms. It remains unclear, despite several previous studies, whether the morphological variation within Hawaiian Metrosideros is due to hybridization, genetic polymorphism, phenotypic plasticity, or some combination of these processes. The Hawaiian Metrosideros complex has become a model system to study ecology and evolution; however this is the first study to use microsatellite data for addressing inter-island patterns of variation from across the Hawaiian Islands.
Ten nuclear microsatellite loci were genotyped from 143 individuals of Metrosideros. We took advantage of the bi-parental inheritance and rapid mutation rate of these data to examine the validity of the current taxonomy and to investigate whether Metrosideros plants from the same island are more genetically similar than plants that are morphologically similar. The Bayesian algorithm of the program structure was used to define genetic groups within Hawaiian Metrosideros and the closely related taxon M. collina from the Marquesas and Austral Islands. Several standard and nested AMOVAs were conducted to test whether the genetic diversity is structured geographically or taxonomically.
The results suggest that Hawaiian Metrosideros have dynamic gene flow, with genetic and morphological diversity structured not simply by geography or taxonomy, but as a result of parallel evolution on islands following rampant island-island dispersal, in addition to ancient chloroplast capture. Results also suggest that the current taxonomy requires major revisions in order to reflect the genetic structure revealed in the microsatellite data.
“Explosive” adaptive radiations on islands remain one of the most puzzling evolutionary phenomena and the evolutionary genetic processes behind such radiations remain unclear. Rapid morphological and ecological evolution during island radiations suggests that many genes may be under fairly strong selection, although this remains untested. Here, we report that during a rapid recent diversification in the Hawaiian endemic plant genus Schiedea (Caryophyllaceae), 5 in 36 studied genes evolved under positive selection. Positively selected genes are involved in defence mechanisms, photosynthesis, and reproduction. Comparison with eight mainland plant groups demonstrates both the relaxation of purifying selection and more widespread positive selection in Hawaiian Schiedea. This provides compelling evidence that adaptive evolution of protein-coding genes may play a significant role during island adaptive radiations.
adaptive radiation; Hawaiian Islands; positive selection; relaxation of purifying selection; Schiedea
The analysis of molecular data within a historical biogeographical framework, coupled with ecological characteristics can provide insight into the processes driving diversification. Here we assess the genetic and ecological diversity within a widespread horseshoe bat Rhinolophus clivosus sensu lato with specific emphasis on the southern African representatives which, although not currently recognized, were previously described as a separate species R. geoffroyi comprising four subspecies. Sequence divergence estimates of the mtDNA control region show that the southern African representatives of R. clivosus s.l. are as distinct from samples further north in Africa than they are from R. ferrumequinum, the sister-species to R. clivosus. Within South Africa, five genetically supported geographic groups exist and these groups are corroborated by echolocation and wing morphology data. The groups loosely correspond to the distributions of the previously defined subspecies and Maxent modelling shows a strong correlation between the detected groups and ecoregions. Based on molecular clock calibrations, it is evident that climatic cycling and related vegetation changes during the Quaternary may have facilitated diversification both genetically and ecologically.
Genetic differentiation among nine populations of the endemic lizard Lacerta dugesii Milne-Edwards 1829 (Lacertidae) from four groups of islands constituting the Archipelago of Madeira, was investigated by protein electrophoresis at 23 enzyme loci. Among twenty polymorphic loci, the total genetic diversity was due primarily to intra-population variation. The allele and genotypic frequencies among populations showed some heterogeneity, allowing the species to present a structuring pattern compatible with their geographical clustering. Some evidence suggests that selection acting on some loci in different ecological conditions may be responsible for the clustering of the populations studied. There was no apparent isolation effect expected under an "island" model of population divergence, and no correlation was found between genetic and geographic distances among populations. Morphological variation of the proposed three L. dugesii subspecies is not congruent with the allozyme analysis. This most probably suggests a rapid colonization of the islands followed by a strong effect of selection operating over the morphological characters used to define the subspecies.
Lacerta dugesii; allozymes; morphology; geographical population structure
The divergence of Escherichia coli bacteria into metabolically distinct ecotypes has a similar genetic basis and similar evolutionary dynamics across independently evolved populations.
The causes and mechanisms of evolutionary diversification are central issues in biology. Geographic isolation is the traditional explanation for diversification, but recent theoretical and empirical studies have shown that frequency-dependent selection can drive diversification without isolation and that adaptive diversification occurring in sympatry may be an important source of biological diversity. However, there are no empirical examples in which sympatric lineage splits have been understood at the genetic level, and it is unknown how predictable this process is—that is, whether similar ecological settings lead to parallel evolutionary dynamics of diversification. We documented the genetic basis and the evolutionary dynamics of adaptive diversification in three replicate evolution experiments, in which competition for two carbon sources caused initially isogenic populations of the bacterium Escherichia coli to diversify into two coexisting ecotypes representing different physiological adaptations in the central carbohydrate metabolism. Whole-genome sequencing of clones of each ecotype from different populations revealed many parallel and some unique genetic changes underlying the derived phenotypes, including changes to the same genes and sometimes to the same nucleotide. Timelines of allele frequencies extracted from the frozen “fossil” record of the three evolving populations suggest parallel evolutionary dynamics driven at least in part by a co-evolutionary process in which mutations causing one type of physiology changed the ecological environment, allowing the invasion of mutations causing an alternate physiology. This process closely corresponds to the evolutionary dynamics seen in mathematical models of adaptive diversification due to frequency-dependent ecological interactions. The parallel genetic changes underlying similar phenotypes in independently evolved lineages provide empirical evidence of adaptive diversification as a predictable evolutionary process.
The causes and mechanisms of evolutionary diversification are central issues in biology. There is well-established theory that predicts that adaptive diversification can arise because of ecological interactions between individuals, such as competition or predation, but there are no empirical examples in which this process has been observed at the genetic level. We documented the genetic basis of adaptive diversification resulting from competition for resources in populations of the bacterium Escherichia coli. The populations diversified into two coexisting ecotypes representing different physiological adaptations. We found that similar but independently evolved phenotypes often shared mutations in the same gene and, in four cases, shared identical mutations at the same nucleotide position. Timelines of allele frequencies extracted from the frozen “fossil record” of three evolving populations showed parallel evolutionary dynamics, suggesting that mutations causing one type of physiology changed the ecological environment and allowed invasion of mutations causing an alternate physiology. The results provide empirical evidence of adaptive diversification as a predictable evolutionary process.
The endemic Hawaiian lobeliads are exceptionally species rich and exhibit striking diversity in habitat, growth form, pollination biology and seed dispersal, but their origins and pattern of diversification remain shrouded in mystery. Up to five independent colonizations have been proposed based on morphological differences among extant taxa. We present a molecular phylogeny showing that the Hawaiian lobeliads are the product of one immigration event; that they are the largest plant clade on any single oceanic island or archipelago; that their ancestor arrived roughly 13 Myr ago; and that this ancestor was most likely woody, wind-dispersed, bird-pollinated, and adapted to open habitats at mid-elevations. Invasion of closed tropical forests is associated with evolution of fleshy fruits. Limited dispersal of such fruits in wet-forest understoreys appears to have accelerated speciation and led to a series of parallel adaptive radiations in Cyanea, with most species restricted to single islands. Consistency of Cyanea diversity across all tall islands except Hawai `i suggests that diversification of Cyanea saturates in less than 1.5 Myr. Lobeliad diversity appears to reflect a hierarchical adaptive radiation in habitat, then elevation and flower-tube length, and provides important insights into the pattern and tempo of diversification in a species-rich clade of tropical plants.
community assembly; ecological saturation; island radiation; species richness
Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors.
Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species.
The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers (“Isolate Accession”), the first five of which correspond to the collection site (“Environmental Accession”). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.
HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/.
Algae; Biodiversity survey; Freshwater; Hawaii; Hawaiian Freshwater Algal Database; HfwADB
Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of geographical isolation on non-adaptive radiation and allopatric speciation brought about by genetic drift. The Aegean Archipelago forms a highly fragmented complex of mostly continental shelf islands that have become disconnected from each other and the mainland in relatively recent geological times (ca <5.2 Ma). These ecologically fairly homogenous islands thus provide a suitable biogeographic context for assessing the relative influences of past range fragmentation, colonization, gene flow and drift on taxon diversification. Indeed, recent molecular biogeographic studies on the Aegean Nigella arvensis complex, combining phylogenetic, phylogeographic and population level approaches, exemplify the importance of allopatry and genetic drift coupled with restricted gene flow in driving plant speciation in this continental archipelago at different temporal and spatial scales. While the recent (Late Pleistocene) radiation of Aegean Nigella, as well as possible instances of incipient speciation (in the Cyclades), is shown to be strongly conditioned by (palaeo)geographic factors (including changes in sea level), shifts in breeding system (selfing) and associated isolating mechanisms have also contributed to this radiation. By contrast, founder event speciation has probably played only a minor role, perhaps reflecting a migratory situation typical for continental archipelagos characterized by niche pre-emption because of a long established resident flora. Overall, surveys of neutral molecular markers in Aegean Nigella have so far revealed population genetic processes that conform remarkably well to predictions raised by genetic drift theory. The challenge is now to gain more direct insights into the relative importance of the role of genetic drift, as opposed to natural selection, in the phenotypic and reproductive divergence among these Aegean plant species.
Aegean palaeogeography; allopatric speciation; continental shelf islands; genetic drift; Nigella; non-adaptive radiation
The build-up of species locally within a region by allopatric speciation depends on geographically separated (allopatric) sister populations becoming reproductively incompatible followed by secondary sympatry. Among birds, this has happened frequently in remote archipelagos, spectacular cases including the Darwin's finches (Geospizinae) and Hawaiian honeycreepers (Drepanidinae), but similar examples are lacking in archipelagos nearer to continental landmasses. Of the required steps in the speciation cycle, achievement of secondary sympatry appears to be limiting in near archipelagos and, by extension, in continental regions. Here, I suggest that secondary sympatry might be prevented by apparent competition mediated through pathogens that are locally coevolved with one population of host and are pathogenic in sister populations. The absence of numerous pathogens in remote archipelagos might, therefore, allow sister populations to achieve secondary sympatry more readily and thereby accelerate diversification. By similar reasoning, species should accumulate relatively slowly within continental regions. In this essay, I explore the assumptions and some implications of this model for species diversification.
adaptive radiation; allopatry; island birds; parasites; speciation; sympatry
Lying in a shallow continental shelf cyclically affected by oscillating sea levels since the Miocene, the Seychelles islands are particularly interesting for evolutionary studies. Recent molecular studies are generating an emerging picture of the origin of its biota, yet very little is known regarding their phylogeographic structure or on the factors promoting diversification within the archipelago. Here we aimed to obtain a detailed depiction of the genetic structure and evolution of one of the most widespread vertebrate groups in the archipelago: the day-geckos of the genus Phelsuma. In parallel, we aimed to infer divergence times between species and subspecies, testing a long-standing hypothesis that argues for different time since sympatry between species as the cause of their different morphological differentiation across the archipelago.
Molecular data corroborated the existence of two main lineages, corresponding to the two currently recognized species. Divergences between species likely date back to the Mio-Pliocene, while more recent, Pleistocenic, divergences are suggested within each species. Populations from outer islands share mtDNA haplotypes with inner island populations, suggesting very recent dispersals (or introductions). We found no evidence of current gene flow between species, but results pointed to the possibility of gene flow between (now allopatric) subspecies. Time estimates suggest a synchronous divergence within each species (between island groups).
The geographic patterns of genetic variation agree with previous taxonomic subdivisions within each species and the origin of outer islands populations is clearly tracked. The similar intraspecific divergence time estimates obtained suggest that the differential body-size differentiation between species within each group of islands may be driven by factors other than character displacement proportional to time since sympatry, as previously suggested. These factors could include different habitats/resources available within each island group, niche differentiation and/or character displacement. We also bring again into consideration the hypothesis of body size being influenced by the distribution of native vegetation and social systems within this group, although it remains to be tested. Our results highlight not only the necessity of clarifying the role of ecology and interspecific interactions in this group’s morphological diversification and community assemblage, but also the importance of co-evolutionary mechanisms and their importance for appropriate conservation of island biodiversity. Further, we provide a detailed description of the phylogeographic structure of these taxa across these islands, which still remain poorly characterized in this respect.
Phelsuma; Seychelles; Phylogeography; Species-trees; Diversification; Morphological evolution; Character displacement; Biogeography
Species formation during adaptive radiation often occurs in the context of a changing environment. The establishment and arrangement of populations, in space and time, sets up ecological and genetic processes that dictate the rate and pattern of differentiation. Here, we focus on how a dynamic habitat can affect genetic structure, and ultimately, differentiation among populations. We make use of the chronology and geographical history provided by the Hawaiian archipelago to examine the initial stages of population establishment and genetic divergence. We use data from a set of 6 spider lineages that differ in habitat affinities, some preferring low elevation habitats with a longer history of connection, others being more specialized for high elevation and/or wet forest, some with more general habitat affinities. We show that habitat preferences associated with lineages are important in ecological and genetic structuring. Lineages that have more restricted habitat preferences are subject to repeated episodes of isolation and fragmentation as a result of lava flows and vegetation succession. The initial dynamic set up by the landscape translates over time into discrete lineages. Further work is needed to understand how genetic changes interact with a changing set of ecological interactions amongst a shifting mosaic of landscapes to achieve species formation.
Speciation; Shifting mosaic; Metapopulations; Founder events; Genetic revolutions; Adaptive radiation; Dispersal
Ribosomal DNA sequence data abounds from numerous studies on the dinoflagellate endosymbionts of corals, and yet the multi-copy nature and intragenomic variability of rRNA genes and spacers confound interpretations of symbiont diversity and ecology. Making consistent sense of extensive sequence variation in a meaningful ecological and evolutionary context would benefit from the application of additional genetic markers. Sequences of the non-coding region of the plastid psbA minicircle (psbAncr) were used to independently examine symbiont genotypic and species diversity found within and between colonies of Hawaiian reef corals in the genus Montipora. A single psbAncr haplotype was recovered in most samples through direct sequencing (∼80–90%) and members of the same internal transcribed spacer region 2 (ITS2) type were phylogenetically differentiated from other ITS2 types by substantial psbAncr sequence divergence. The repeated sequencing of bacterially-cloned fragments of psbAncr from samples and clonal cultures often recovered a single numerically common haplotype accompanied by rare, highly-similar, sequence variants. When sequence artifacts of cloning and intragenomic variation are factored out, these data indicate that most colonies harbored one dominant Symbiodinium genotype. The cloning and sequencing of ITS2 DNA amplified from these same samples recovered numerically abundant variants (that are diagnostic of distinct Symbiodinium lineages), but also generated a large amount of sequences comprising PCR/cloning artifacts combined with ancestral and/or rare variants that, if incorporated into phylogenetic reconstructions, confound how small sequence differences are interpreted. Finally, psbAncr sequence data from a broad sampling of Symbiodinium diversity obtained from various corals throughout the Indo-Pacific were concordant with ITS lineage membership (defined by denaturing gradient gel electrophoresis screening), yet exhibited substantially greater sequence divergence and revealed strong phylogeographic structure corresponding to major biogeographic provinces. The detailed genetic resolution provided by psbAncr data brings further clarity to the ecology, evolution, and systematics of symbiotic dinoflagellates.
Knowledge of the evolutionary history of plants that are ecologically dominant in modern ecosystems is critical to understanding the historical development of those ecosystems. Metrosideros is a plant genus found in many ecological and altitudinal zones throughout the Pacific. In the Hawaiian Islands, Metrosideros polymorpha is an ecologically dominant species and is also highly polymorphic in both growth form and ecology. Using 10 non-coding chloroplast regions, we investigated haplotype diversity in the five currently recognized Hawaiian Metrosideros species and an established out-group, Metrosideros collina, from French Polynesia. Multiple haplotype groups were found, but these did not match morphological delimitations. Alternative morphologies sharing the same haplotype, as well as similar morphologies occurring within several distinct island clades, could be the result of developmental plasticity, parallel evolution or chloroplast capture. The geographical structure of the data is consistent with a pattern of age progressive island colonizations and suggests de novo intra-island diversification. If single colonization events resulted in a similar array of morphologies on each island, this would represent parallel radiations within a single, highly polymorphic species. However, we were unable to resolve whether the pattern is instead explained by ancient introgression and incomplete lineage sorting resulting in repeated chloroplast capture. Using several calibration methods, we estimate the colonization of the Hawaiian Islands to be potentially as old as 3.9 (−6.3) Myr with an ancestral position for Kaua'i in the colonization and evolution of Metrosideros in the Hawaiian Islands. This would represent a more ancient arrival of Metrosideros to this region than previous studies have suggested.
chloroplast; Hawaiian Islands; Metrosideros; parallel evolution; plasticity; polymorphism
The Aerides–Vanda alliance is a complex group in the subtribe Aeridinae (subfamily Epidendroideae, Orchidaceae). Some phylogenetic systems of this alliance have been previously proposed based on molecular and morphological analyses. However, several taxonomic problems within this alliance as well as between it and its allies remain unsolved.
We utilized ITS and five plastid DNA regions in this phylogenetic analysis. Consensus trees strongly indicate that the Aerides–Vanda alliance is monophyletic, and the 14 genera of this alliance can be grouped into the following clades with 14 subclades: 1. Aerides, comprising two subclades: Rhynchostylis and Aerides; 2. Ascocentropsis; 3. Papilionanthe; 4. Vanda, comprising five subclades: Neofinetia, Christensonia, Seidenfadenia, Ascocentrum, and Vanda–Trudelia, in which Vanda and Trudelia form a subclade; 5. Tsiorchis, comprising three subclades: Chenorchis, Tsiorchis, and two species of Ascocentrum; 6. Paraholcoglossum; and 7. Holcoglossum. Among the 14 genera, only Ascocentrum is triphyletic: two species of the Ascocentrum subclade, an independent subclade Ascocentrum subclade in the Tsiorchis clade; the Ascocentrum subclade in the Vanda clade; and one species in the Holcoglossum clade. The Vanda and Trudelia species belong to the same subclade. The molecular conclusion is consistent with their morphological characteristics.
We elucidate the relationship among the 14 genera of the Aerides–Vanda alliance. Our phylogenetic results reveal that the Aerides–Vanda alliance is monophyletic, but it can be divided into 14 genera. The data prove that Ascocentrum is triphyletic. Plants with elongate-terete leaves and small flowers should be treated as a new genus, Pendulorchis. Saccolabium himalaicum (Ascocentrum himalaicum) should be transferred to Pendulorchis. Ascocentrum pumilum, endemic to Taiwan, should be transferred to Holcoglossum. A new combination, Holcoglossum pumilum, was also established. Trudelia should not be recognized as an independent genus. Two new species, Pendulorchis gaoligongensis and Holcoglossum singchianum, were described as well.
Intraspecific variation within the diverse southern African murine rodents has not been extensively investigated, yet cryptic diversity is evident in several taxa studied to date. The Namaqua rock mouse, Micaelamys namaquensis Smith, 1834 is a widespread endemic murine rodent from the subregion. Currently, a single species with four subspecies is recognised, but in the past up to 16 subspecies were described. Thus, this species is a good candidate for the investigation of patterns and processes of diversification in a diverse but under-studied mammalian subfamily and geographic region. Here, we report genetic differentiation based on mitochondrial DNA (mtDNA) cytochrome b (cyt b) sequences among samples collected over an extensive coverage of the species' range.
Cytochrome b sequences of 360 widely sampled individuals identified 137 unique maternal alleles. Gene tree and phylogeographic analyses of these alleles suggest the presence of at least eight lineages or haplogroups (A-H), with varying degrees of intra-lineage diversity. This differentiation is in contrast with the most recent taxonomic treatment based on cranial morphometrics which only recognised four subspecies. The mtDNA diversity strongly supports earlier views that this taxon may represent a species complex. We further show statistical support for the association of several of these lineages with particular vegetation biomes of southern Africa. The time to the most recent common ancestor (TMRCA) dates to the Pliocene (~5 Mya) whereas coalescent-based divergence time estimates between lineages vary between 813 Kya [0.22 - 1.36] and 4.06 Mya [1.21 - 4.47]. The major diversification within lineages occurred during the Pleistocene. The identification of several regions of sympatry of distinct lineages offers future opportunities for the elucidation of the underlying speciation processes in the suggested species complex.
Similar to other African murine rodents, M. namaquensis radiated during the Pliocene and Pleistocene coinciding with major periods of aridification and the expansion of savanna habitats. The suggested species complex is represented by at least eight lineages of which the majority are confined to only one or a few neighbouring biomes/bioregions. Contrasting intra-lineage phylogeographic patterns suggest differences in adaptation and responses to Plio-Pleistocene climatic and vegetation changes. The role of ecological factors in driving speciation in the group needs further investigation.
The Hawaiian Archipelago is the most isolated island system on the planet and has been the subject of evolutionary research for over a century. The largest radiation of species in Hawaii is the Hawaiian Drosophilidae, a group of approximately 1000 species. Dispersal to isolated island systems like Hawaii is rare and the resultant flora and fauna shows high disharmony with mainland communities. The possibility that some lineages may have originated in Hawaii and subsequently ‘escaped’ to diversify on continental landmasses is expected to be rarer still. We present phylogenetic analysis of 134 partially sequenced mitochondrial genomes of Drosophilidae (approx. 1.3 Mb of sequence total) to address major aspects of adaptive radiation and dispersal in Hawaii. We show that the genus Scaptomyza, a group that accounts for approximately one-third of the species-level diversity of Drosophilidae in the Hawaiian Islands, originated in Hawaii, diversified there, and subsequently colonized a number of island and continental landmasses elsewhere on the globe. We propose that a combination of small body size, rapid generation time and unique ecological and physiological adaptations have allowed this genus to effectively disperse and diversify.
biogeography; phylogenetics; Hawaii; Scaptomyza; Drosophila
Background and Aims
Farfugium (Asteraceae) is a small genus that contains the two species F. japonicum and F. hiberniflorum and is distributed along a long archipelago in east Asia. The common taxon, F. japonicum, includes three varieties associated with a wide range of habitats, including forest understorey (sciophytes), coastal crag (heliophytes) and riverbed (rheophytes). Leaf shape is an important taxonomic character within this genus and is associated with the habitat.
Twenty populations that included all Farfugium taxa were collected throughout its range. Leaf morphology was measured to determine differences amongst the taxa. Phylogenetic analyses based on sequences of the internal transcribed spacer of nuclear rDNA and four plastid DNA regions (matK, trnL-trnF, trnH-psbA and rpl20-rps12) were conducted separately.
Leaf morphology was significantly different amongst taxa, but morphological variations were partly explained by adaptation to certain environmental conditions that each population inhabited. Molecular phylogenies for the nDNA internal transcribed spacer and cpDNA were consistent in classifying F. hiberniflorum and the Taiwanese var. formosanum, whilst suggesting polyphyletic origins for the rheophyte, sciophyte and heliophyte taxa. All samples from the southern Ryukyus (Japan) and Taiwan clustered into a monophyletic group, which corroborates the land configuration theory involving Quaternary land-bridge formation and subsequent fragmentation into islands. The incongruence between the two DNA datasets may imply traces of introgressive hybridization and/or incomplete lineage sorting.
The occurrence of rheophyte, sciophyte and heliophyte plants within Farfugium may be attributable to their isolation on islands and subsequent adaptation to the riparian, coastal crag and forest understorey environments, following their migration over the Quaternary land-bridge formation along their distribution range. Nearly identical DNA sequences coupled with highly divergent morphologies amongst these taxa suggest that diversification was rapid.
Habitat radiation; heliophyte; leaf shape; rheophyte; Ryukyu Islands; sciophyte
Backgroud and Aims
The Caesalpinia hintonii group comprises six species of endemic shrubs or trees, C. epifanioi, C. hintonii, C. laxa, C. macvaughii, C. melanadenia and C. oyamae, found in scattered patches of seasonally dry forest in the Río Balsas depression and the neighbouring Tehuacán–Cuicatlán valley, which are part of the Mexican morphotectonic province of Sierra Madre del Sur. An evaluation is made of phylogeographic patterns and genetic diversity with a phylogenetic analysis of the C. hintonii complex in order to study the dynamics of speciation in this endemic group of legumes.
A phylogeographic study based on four highly variable non-coding plastid regions (trnL intron, trnL-F intergenic spacer, trnH-psbA intergenic spacer, and accD-psaI intergenic spacer) was carried out for the Caesalpinia hintonii complex. Five of the six taxa of the C. hintonii complex were included.
Key Results and Conclusions
The plastid analyses involving multiple accessions of each taxon from throughout their ranges resolved C. epifanioi and C. hintonii as well-supported clusters, but C. oyamae has two unexpectedly divergent lineages. Two well-supported geographic clades: eastern (C. epifanioi, C. melanadenia and C. oyamae) and western (C. hintonii and C. macvaughii) were established. The analyses performed provide evidence of recent morphostatic radiation in C. oyamae resulting from isolation and local adaptation. This pattern of genetic differentiation without morphological divergence may be a model that fits many groups of tropical woody taxa inhabiting similarly dry forests subjected to shifting selection.
Caesalpinia hintonii complex; legumes; Mesoamerica; Mexico; plant phylogeography; population differentiation; seasonally dry forest
Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages.
Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups.
Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation.
Hawaii; Hybridization; Lineage sorting; Microsatellite; Pritchardia; Radiation
Oceanic islands have played a central role in biogeography and evolutionary biology. Here, we review molecular studies of the endemic terrestrial fauna of the Hawaiian archipelago. For some groups, monophyly and presumed single origin of the Hawaiian radiations have been confirmed (achatinelline tree snails, drepanidine honeycreepers, drosophilid flies, Havaika spiders, Hylaeus bees, Laupala crickets). Other radiations are derived from multiple colonizations (Tetragnatha and Theridion spiders, succineid snails, possibly Dicranomyia crane flies, Porzana rails). The geographic origins of many invertebrate groups remain obscure, largely because of inadequate sampling of possible source regions. Those of vertebrates are better known, probably because few lineages have radiated, diversity is far lower and morphological taxonomy permits identification of probable source regions. Most birds, and the bat, have New World origins. Within the archipelago, most radiations follow, to some degree, a progression rule pattern, speciating as they colonize newer from older islands sequentially, although speciation often also occurs within islands. Most invertebrates are single-island endemics. However, among multi-island species studied, complex patterns of diversification are exhibited, reflecting heightened dispersal potential (succineids, Dicranomyia). Instances of Hawaiian taxa colonizing other regions are being discovered (Scaptomyza flies, succineids). Taxonomy has also been elucidated by molecular studies (Achatinella snails, drosophilids). While molecular studies on Hawaiian fauna have burgeoned since the mid-1990s, much remains unknown. Yet the Hawaiian fauna is in peril: more than 70 per cent of the birds and possibly 90 per cent of the snails are extinct. Conservation is imperative if this unique fauna is to continue shedding light on profound evolutionary and biogeographic questions.
arthropods; birds; dispersal; Hawaii; snails; speciation