Evolutionary relationships, interisland biogeography, and molecular evolution in the Hawaiian violets (Viola: Violaceae)

The endemic Hawaiian flora offers remarkable opportunities to study the patterns of plant morphological and molecular evolution. The Hawaiian violets are a monophyletic lineage of nine taxa distributed across six main islands of the Hawaiian archipelago. To describe the evolutionary relationships, biogeography, and molecular evolution rates of the Hawaiian violets, we conducted a phylogenetic study using nuclear rDNA internal transcribed spacer sequences from specimens of each species. Parsimony, maximum likelihood (ML), and Bayesian inference reconstructions of island colonization and radiation strongly suggest that the Hawaiian violets first colonized the Maui Nui Complex, quickly radiated to Kaua'i and O'ahu, and recently dispersed to Hawai'i. The lineage consists of "wet" and "dry" clades restricted to distinct precipitation regimes. The ML and Bayesian inference reconstructions of shifts in habitat, habit, and leaf shape indicate that ecologically analogous taxa have undergone parallel evolution in leaf morphology and habit. This parallel evolution correlates with shifts to specialized habitats. Relative rate tests showed that woody and herbaceous sister species possess equal molecular evolution rates. The incongruity of molecular evolution rates in taxa on younger islands suggests that these rates may not be determined by growth form (or lifespan) alone, but may be influenced by complex dispersal events.     

Mitochondrial phylogeny of extant Hawaiian tree snails (Achatinellinae)

Hawaiian tree snails in the endemic subfamily Achatinellinae display a staggering variety of shell colors and banding patterns. Despite numerous attempts to classify this morphological variation, a conclusive phylogeny has not been proposed. To improve conservation efforts, we sought to better understand the species identities and phylogenetic relationships among the extant species of Achatinella and Partulina using partial mitochondrial 16S ribosomal DNA sequences. The reconstructed phylogeny showed a high degree of support for more recent branches, but gave little support to deeper nodes. The most confident branches challenge previous systematic arrangements of these snails, grouping species that previously had been placed into different subgenera. High levels of sequence divergence within some species may reflect the long-term isolation of subpopulations. Rapid rates of sequence divergence may have saturated base substitutions and contributed to the lack of resolution of higher-order relationships. We did not find support for the monophyly of the Achatinella species, nor thus for a single colonization of Oahu from Maui Nui.     

Origin of Hawaiian Polystichum (Dryopteridaceae) in the context of a world phylogeny

A genus-wide molecular phylogeny for Polystichum and allied genera (Dryopteridaceae) was reconstructed to address the biogeographic origin and evolution of the three Hawaiian Polystichum species, all endemic there. The analysis was based on the cpDNA sequences rbcL and the trnL-F spacer from a taxonomically and geographically diverse sample. Parsimony and Bayesian phylogenetic analyses of the combined data support a monophyletic Polystichum and corroborate recent hypotheses as to membership and sequence of origin of the major groups within the genus. The Hawaiian Polystichum species are polyphyletic; two separate lineages appear to have arrived independently from the Old World. The provenance of the diploid Polystichum hillebrandii is continental eastern Asia, while the source of the polyploid lineage comprising tetraploid P. haleakalense and octoploid P. bonseyi is likely continental Asia. From our results, the origin of the Hawaiian species of Polystichum, like many Hawaiian fern genera with several species, is the result of multiple migrations to the islands, rather than single migrations yielding nearly all the local diversity as in the angiosperms. This emerging pattern provides a modern test of the premise that propagule vagility has a central role in determining pattern of evolution.     

Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae,Cyprinidae, Teleostei) inferred from mitochondrial genome analysis

The distribution of freshwater taxa is a good biogeographic model to study pattern and process of vicariance and dispersal. The subfamily Leuciscinae (Cyprinidae, Teleostei) consists of many species distributed widely in Eurasia and North America. Leuciscinae have been divided into two phyletic groups, leuciscin and phoxinin. The phylogenetic relationships between major clades within the subfamily are poorly understood, largely because of the overwhelming diversity of the group. The origin of the Far Eastern phoxinin is an interesting question regarding the evolutionary history of Leuciscinae. Here we present phylogenetic analysis of 31 species of Leuciscinae and outgroups based on complete mitochondrial genome sequences to clarify the phylogenetic relationships and to infer the evolutionary history of the subfamily.     

Molecular biogeography and diversification of the endemic terrestrial fauna of the Hawaiian Islands

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.     

Molecular phylogeny and biogeography of the endemic Hawaiian Succineidae (Gastropoda: Pulmonata)

The endemic Hawaiian Succineidae represent an important component of the exceptionally diverse land snail fauna of the Hawaiian Islands, yet they remain largely unstudied. We employed 663-bp fragments of the cytochrome oxidase I (COI) mitochondrial gene to investigate the evolution and biogeography of 13 Hawaiian succineid land snail species, six succineid species from other Pacific islands and Japan, and various outgroup taxa. Results suggest that: (1) species from the island of Hawaii are paraphyletic with species from Tahiti, and this clade may have had a Japanese (or eastern Asian) origin; (2) species from five of the remaining main Hawaiian islands form a monophyletic group, and the progression rule, which states that species from older islands are basal to those from younger islands, is partially supported; no geographic origin could be inferred for this clade; (3) succineids from Samoa are basal to all other succineids sampled (maximum likelihood) or unresolved with respect to the other succineid clades (maximum parsimony); (4) the genera Succinea and Catinella are polyphyletic. These results, while preliminary, represent the first attempt to reconstruct the phylogenetic pattern for this important component of the endemic Hawaiian fauna.     

Systematics and biology of the endemic water scavenger beetles of Hawaii (Coleoptera: Hydrophilidae, Hydrophilini)

Abstract.  Recent field surveys in the Hawaiian Islands have revealed an adaptive radiation of endemic water scavenger beetles (Coleoptera: Hydrophilidae). Phylogenetic analysis based on 55 adult morphological characters affirms that this endemic hydrophilid fauna is a monophyletic clade that incorporates the first well-supported transformation from an aquatic to terrestrial way of life within any lineage of the subfamily Hydrophilinae. The clade is prescribed to the genus Limnoxenus Motschulsky, where described members were previously placed. Five new species are described: L. waialeale sp.n. (Kauai), L. kauaiensis sp.n. (Kauai), L. oahuensis sp.n. (Oahu), L. punctatostriatus sp.n. (Kauai) and L. namolokama sp.n. (Kauai). Lectotypes are designated for the two previously described species L. semicylindricus (Eschscholtz) and L. nesiticus (Sharp). The Hawaiian lineage is a component of a larger clade that also includes the remaining four species of Limnoxenus from Europe, South Africa, and Australia, plus the monotypic genera Limnocyclus Balfour-Browne of New Caledonia and Hydramara Knisch of South America. The majority of the Hawaiian species exhibit vestigial wings, an extremely unusual condition in aquatic beetles. No other island-endemic members of the Hydrophilinae are known to be flightless, suggesting insularity per se is not responsible for this condition. L. nesiticus of Oahu has not been collected during the past 106 years, suggesting that it has been lost to anthropogenically mediated extinction.     

Tahitian tree snail mitochondrial clades survived recent mass extirpation

Oceanic islands frequently support endemic faunal radiations that are highly vulnerable to introduced predators [1]. This vulnerability is epitomized by the rapid extinction in the wild of all but five of 61 described Society Islands partulid tree snails [2], following the deliberate introduction of an alien biological control agent: the carnivorous snail Euglandina rosea[3]. Tahiti's tree snail populations have been almost completely extirpated and three of the island's eight endemic Partula species are officially extinct, a fourth persisting only in captivity [2]. We report a molecular phylogenetic estimate of Tahitian Partula mitochondrial lineage survival calibrated with a 1970 reference museum collection that pre-dates the predator's 1974 introduction to the island [4]. Although severe winnowing of lineage diversity has occurred, none of the five primary Tahitian Partula clades present in the museum samples is extinct. Targeted conservation measures, especially of montane refuge populations, may yet preserve a representative sub-sample of Tahiti's endemic tree snail genetic diversity in the wild.     

Inference of a radiation in Mastus (Gastropoda, Pulmonata, Enidae) on the island of Crete

The Mediterranean land snail genus Mastus (Beck, 1837) is highly divergent. Thirty-two Mastus species have been recorded throughout the genus range, and 23 of them are endemic to the islands of the Aegean Sea and mainland Greece. Of these, all 16 Mastus species reported from Crete are endemic to this island. A robust molecular phylogenetic framework based on mitochondrial and nuclear genes (1623 bp) allowed us to explore the temporal diversification pattern of lineages, using molecular clock approaches. Our results showed an initial radiation in the evolutionary history of the Cretan lineage, followed by a subsequent slowdown of lineage splitting rate. Using a dated major vicariant event of the Aegean area, we estimated the absolute time of the radiation event and proposed a biogeographic scenario accounting for the observed pattern. Additionally, we tried to infer the processes that led to the divergence of the Cretan Mastus species, by applying comparative methods in phylogenetically informated context. Overall, our results favoured a nonecological radiation scenario in the Cretan Mastus species due to an allopatric divergence of secondary sexual characters.     

Sociality in theridiid spiders: repeated origins of an evolutionary dead end

Evolutionary "dead ends" result from traits that are selectively advantageous in the short term but ultimately result in lowered diversification rates of lineages. In spiders, 23 species scattered across eight families share a social system in which individuals live in colonies and cooperate in nest maintenance, prey capture, and brood care. Most of these species are inbred and have highly female-biased sex ratios. Here we show that in Theridiidae this social system originated eight to nine times independently among 11 to 12 species for a remarkable 18 to 19 origins across spiders. In Theridiidae, the origins cluster significantly in one clade marked by a possible preadaptation: extended maternal care. In most derivations, sociality is limited to isolated species: social species are sister to social species only thrice. To examine whether sociality in spiders represents an evolutionary dead end, we develop a test that compares the observed phylogenetic isolation of social species to the simulated evolution of social and non-social clades under equal diversification rates, and find that sociality in Theridiidae is significantly isolated. Because social clades are not in general smaller than their nonsocial sister clades, the "spindly" phylogenetic pattern-many tiny replicate social clades-may be explained by extinction rapid enough that a nonsocial sister group does not have time to diversify while the social lineage remains extant. In this case, this repeated origin and extinction of sociality suggests a conflict between the short-term benefits and long-term costs of inbred sociality. Although benefits of group living may initially outweigh costs of inbreeding (hence the replicate origins), in the long run the subdivision of the populations in relatively small and highly inbred colony lineages may result in higher extinction, thus an evolutionary dead end.     

Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus)

An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeographic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorphological divergence promotes the coexistence of lineages and that repeated, independent evolution of microhabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desmognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.     

Biogeography in the Death Valley region: evidence from springsnails (Hydrobiidae: Tryonia)

Allozyme and mitochondrial DNA variation were analysed to examine evolution of the nine species of springsnails (genus Tryonia) living in the Death Valley system (Owens and Amargosa basins) of southeastern California and southwestern Nevada. Both allozyme and mtDNA evidence indicate that this highly endemic fauna is non-monophyletic. Species from the upper Amargosa basin comprise a clade most closely related to snails living in the Colorado basin. Snails from the lower Amargosa basin (Death Valley trough) reflect a complex evolutionary history and two of these species are more closely related to an estuarine species from western California than to other snails of the region. These results indicate a commonality of pattern with the well-studied Death Valley pupfishes (Cyprinodon), which also are non-monophyletic and include species that are most closely related to Colorado basin congeners. These biogeographic patterns are interpreted within the context of a recently proposed model for the early history of the lower Colorado River.     

The ecological dynamics of clade diversification and community assembly

Clades diversify in an ecological context, but most macroevolutionary models do not directly encapsulate ecological mechanisms that influence speciation and extinction. A data set of 245 chordate, arthropod, mollusk, and magnoliophyte phylogenies had a majority of clades that showed rapid lineage accumulation early with a slowing more recently, whereas a small but significant minority showed accelerated lineage accumulation in their recent histories. Previous analyses have demonstrated that macroevolutionary birth-death models can replicate the pattern of slowing lineage accumulation only by a strong decrease in speciation rate with increasing species richness and extinction rate held extremely low or absent. In contrast, the metacommunity model presented here could generate the full range of patterns seen in the real phylogenies by simply manipulating the degree of ecological differentiation of new species at the time of speciation. Specifically, the metacommunity model predicts that clades showing decelerating lineage accumulation rates are those that have diversified by ecological modes of speciation, whereas clades showing accelerating lineage accumulation rates are those that have diversified primarily by modes of speciation that generate little or no ecological diversification. A number of testable predictions that integrate data from molecular systematics, community ecology, and biogeography are also discussed.     

Molecular phylogenetics and evolution of the endemic Hawaiian genus Adenophorus (Grammitidaceae)

Recent studies of the phylogeny of several groups of native Hawaiian vascular plants have led to significant insights into the origin and evolution of important elements of the Hawaiian flora. No groups of Hawaiian pteridophytes have been subjected previously to rigorous phylogenetic analysis. We conducted a molecular phylogenetic analysis of the endemic Hawaiian fern genus Adenophorus employing DNA sequence variation from three cpDNA fragments: rbcL, atpbeta, and the trnL-trnF intergenic spacer (IGS). In the phylogenetic analyses we employed maximum parsimony and Bayesian inference. Bayesian phylogenetic inference often provided stronger support for hypothetical relationships than did nonparametric bootstrap analyses. Although phylogenetic analyses of individual DNA fragments resulted in different patterns of relationships among species and varying levels of support for various clades, a combined analysis of all three sets of sequences produced one, strongly supported phylogenetic hypothesis. The primary features of that hypothesis are: (1) Adenophorus is monophyletic; (2) subgenus Oligadenus is paraphyletic; (3) the enigmatic endemic Hawaiian species Grammitis tenella is strongly supported as the sister taxon to Adenophorus; (4) highly divided leaf blades are evolutionarily derived in the group and simple leaves are ancestral; and, (5) the biogeographical origin of the common ancestor of the Adenophorus-G. tenella clade remains unresolved, although a neotropical origin seems most likely.     

Contrasting Phylogenetic and Diversity Patterns in Octodontoid Rodents and a New Definition of the Family Abrocomidae

Octodontoidea is the most species-rich clade among hystricomorph rodents. Based on a combined parsimony analysis of morphological and molecular data of extinct and extant species, we analyze the history of South American octodontoids and propose ages of divergence older than interpreted so far. Early Abrocomidae are recognized for the first time, and a new definition of the family is provided. Traditionally accepted fossil-based times of origin for the southern clades are reinterpreted as later stages of differentiation markedly uncoupled from the origin, differentiation implying specializations for open environments as shown in a morphospace of skull variation. Origin of crown groups is also strongly uncoupled from origin of clades as a consequence of extinction of deep lineages. In the resulting diversity pattern of modern southern clades of octodontoids, the combination of greater disparity, less content of evolutionary history, and lower taxonomic diversity, compared to their northern counterparts, appears at first counterintuitive. We propose that primary components of diversity derived from evolutionary transformation or anagenesis, on the one hand, and from cladogenesis and extinction, on the other, should not be considered associated, or at least not necessarily. Certain patterns of relationships between these distinct components could be driven by environmental dynamics. Like environments, octodontoid diversity would have been more stable in northern South America, whereas in the south, both strong adaptive change and extinction would have been triggered by emerging derived environments.     

Phylogenetic and biogeographic analysis of sphaerexochine trilobites

Background

Sphaerexochinae is a speciose and widely distributed group of cheirurid trilobites. Their temporal range extends from the earliest Ordovician through the Silurian, and they survived the end Ordovician mass extinction event (the second largest mass extinction in Earth history). Prior to this study, the individual evolutionary relationships within the group had yet to be determined utilizing rigorous phylogenetic methods. Understanding these evolutionary relationships is important for producing a stable classification of the group, and will be useful in elucidating the effects the end Ordovician mass extinction had on the evolutionary and biogeographic history of the group.

Methodology/Principal Findings

Cladistic parsimony analysis of cheirurid trilobites assigned to the subfamily Sphaerexochinae was conducted to evaluate phylogenetic patterns and produce a hypothesis of relationship for the group. This study utilized the program TNT, and the analysis included thirty-one taxa and thirty-nine characters. The results of this analysis were then used in a Lieberman-modified Brooks Parsimony Analysis to analyze biogeographic patterns during the Ordovician-Silurian.

Conclusions/Significance

The genus Sphaerexochus was found to be monophyletic, consisting of two smaller clades (one composed entirely of Ordovician species and another composed of Silurian and Ordovician species). By contrast, the genus Kawina was found to be paraphyletic. It is a basal grade that also contains taxa formerly assigned to Cydonocephalus. Phylogenetic patterns suggest Sphaerexochinae is a relatively distinctive trilobite clade because it appears to have been largely unaffected by the end Ordovician mass extinction. Finally, the biogeographic analysis yields two major conclusions about Sphaerexochus biogeography: Bohemia and Avalonia were close enough during the Silurian to exchange taxa; and during the Ordovician there was dispersal between Eastern Laurentia and the Yangtze block (South China) and between Eastern Laurentia and Avalonia.     

Natural history, biogeography, and endangerment of Hawaiian dry forest trees

We describe the floristic composition of Hawaiian dry forest trees and identify natural history characteristics and biogeographic variables that are associated with risk of endangerment. Hawaiian dry forests are comprised of 109 tree species in 29 families, with 90% of all species endemic, 10% indigenous, and 37% single-island endemics. Forty-five percent of Hawaiian dry forest taxa are at risk of endangerment. Dry forest taxa at risk have a significantly larger range size compared to taxa from other Hawaiian forest types. Dispersal mechanism was a significant predictor of a species occurrence in dry forest compared to other forest types based on logistic regressions clustered by lineage. Among dry forest taxa, hermaphroditic breeding systems, autochorous dispersal mechanisms, conspicuous flowers, and dry fruit were all more likely to be at risk of endangerment. When analyses were clustered by lineage using logistic regressions, only dispersal mechanism and flower size were significant predictors of risk and taxa with autochorous dispersal and conspicuous flowers were more likely to be at risk. The Big Island, Maui, Oahu, and Kauai all have remarkably similar numbers of dry forest taxa (63–65 species) and dry forest taxa at risk of endangerment. However, Big Island and Kauai have the highest number and percentage of single-island endemics. These results demonstrate patterns of endangerment specific to Hawaiian dry forests, the high levels of endangerment in this forest type, and the importance of prioritizing conservation in dry forest regions.     

Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders

Elevational variation in species richness is ubiquitous and important for conservation, but remains poorly explained. Numerous studies have documented higher species richness at mid-elevations, but none have addressed the underlying evolutionary and biogeographic processes that ultimately explain this pattern (i.e. speciation, extinction and dispersal). Here, we address the evolutionary causes of the mid-elevational diversity hump in the most species-rich clade of salamanders, the tropical bolitoglossine plethodontids. We present a new phylogeny for the group based on DNA sequences from all 13 genera and 137 species. Using this phylogeny, we find no relationship between rates of diversification of clades and their elevational distribution, and no evidence for a rapid 'species pump' in tropical montane regions. Instead, we find a strong relationship between the number of species in each elevational zone and the estimated time when each elevational band was first colonized. Mid-elevation habitats were colonized early in the phylogenetic history of bolitoglossines, and given similar rates of diversification across elevations, more species have accumulated in the elevational zones that were inhabited the longest. This pattern may be widespread and suggests that mid-elevation habitats may not only harbour more species, but may also contain more phylogenetic diversity than other habitats within a region.     

GAI homologues in the Hawaiian silversword alliance (Asteraceae-Madiinae): molecular evolution of growth regulators in a rapidly diversifying plant lineage

Accelerated evolution of regulatory genes has been proposed as an explanation for decoupled rates of morphological and molecular evolution. The Hawaiian silversword alliance (Asteraceae-Madiinae) has evolved drastic differences in growth form, including rosette plants, cushion plants, shrubs, and trees, since its origin approximately 6 MYA. We have isolated genes in the DELLA subfamily of putative growth regulators from 13 taxa of Hawaiian and North American Madiinae. The Hawaiian taxa contain two copies of DaGAI that form separate clades within the Madiinae, consistent with an allotetraploid origin for the silversword alliance. DaGAI retains conserved features that have previously been identified in DELLA genes. Selective constraint in the Hawaiian DaGAI copies remains strong in spite of rapid growth form divergence in the silversword alliance, although the constraint was somewhat relaxed in the Hawaiian copies relative to the North American lineages. We failed to detect evidence for positive selection on individual codons. Notably, selective constraint remained especially strong in the gibberellin-responsive DELLA region for which the gene subfamily is named, which is truncated or deleted in all identified dwarf mutants in GAI homologues in different angiosperm species. In contrast with the coding region, however, approximately 900 bp of the upstream flanking region shows variable rates and patterns of evolution, which might reflect positive selection on regulatory regions.