The Taxonomy and Phylogeny of Echinometra (Camarodonta: Echinometridae) from the Red Sea and Western Indian Ocean

The number of valid species in the genus Echinometra (Echinodermata, Echinoidea) and their associated identification keys have been debated in the scientific literature for more than 180 years. As the phylogeny and dispersal patterns of these species have been widely used as a prominent model for marine speciation, new insights into their taxonomy have the potential to deepen our understanding of marine speciation processes. In this study we examine Echinometra taxonomy, combining morphology and molecular tools. We present the taxonomy and phylogeny of Red Sea and Western Indian Ocean Echinometra. The currently available morphological keys were found to be limited in their ability to delineate all species within this genus. Nonetheless, morphological similarities between the Red Sea and Western Indian Ocean populations were high, and delimited them from the other species. These latter populations together formed a monophyletic clade, genetically distant from any of the other Echinometra species by more than 3%. Combining both traditional taxonomy and molecular evidence, we found that these populations were neither Echinometra mathaei nor E. oblonga, as previously considered. The morphological discrepancies of these populations, and their genetic divergence from the other Echinometra species, suggest that they should be considered as a new Echinometra species.     

More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data

Coral taxonomy and systematics continue to be plagued by a host of problems. Due to high phenotypic variability within species, morphological approaches have often failed to recognize natural taxa, and molecular techniques have yet to be applied to many groups. Here, we summarize the levels of paraphyly found for scleractinian corals and test, based on new data, whether paraphyly is also a significant problem in Faviidae, the second-most speciose hermatypic scleractinian family. Using both DNA sequence and morphological data we find that, regardless of analysis technique (maximum parsimony, maximum likelihood and Bayesian likelihood), many conventional taxonomic groups are not monophyletic. Based on two mitochondrial markers (COI and a noncoding region) that we amplified for 81 samples representing 41 faviid species and 13 genera, five genera that are represented by more than one species are paraphyletic, as is the family Faviidae. The morphological characters currently used to identify these corals similarly fail to recover many genera. Furthermore, trees based on both data types are incongruent, and total evidence analysis does little to salvage conventional taxonomic groupings. Morphological convergence, phenotypic variability in response to the environment, and recent speciation are likely causes for these conflicts, which suggest that the present classification of corals is in need of a major overhaul. We propose more detailed studies of problematic faviid taxa using standardized morphological, mitochondrial, and nuclear genetic markers to facilitate combining of data.     

Deceleration of morphological evolution in a cryptic species complex and its link to paleontological stasis

Morphological stasis or the absence of morphological change is a well-known phenomenon in the paleontological record, yet it is poorly integrated with neontological evidence. Recent evidence suggests that cryptic species complexes may remain morphologically identical due to morphological stasis. Here, we describe a case of long-term stasis in the Stygocapitella cryptic species complex (Parergodrilidae, Orbiniida, Annelida). Using phylogenetic methods and morphological data, we find that rates of morphological evolution in Stygocapitella are significantly slower than in closely related taxa (Nerillidae, Orbiniidae). Assessment of quantitative and qualitative morphology revealed the presence of four morphotypes with only subtle differences, whereas molecular data supports 10 reproductively isolated clades. Notably, estimates for the time of Stygocapitella species divergence range from ∼275 million years to ∼18 million years, including one case of two morphologically similar species that have diverged about 140 million years ago. These findings provide evidence for morphological deceleration and long-term morphological stasis in Stygocapitella, and that speciation is not necessarily accompanied by morphological changes. The deceleration of morphological divergence in Stygocapitella can be potentially linked to niche conservatism and tracking, coupled with the fluctuating dynamics of the interstitial environment, or genetic constraints due to progenetic evolution. Finally, we conclude that failing to integrate speciation without morphological evolution in paleontology may bias estimates of rates of speciation and morphological evolution.     

Sympatric speciation in animals: the ugly duckling grows up

Sympatric speciation has become increasingly accepted in the past decade, as a result of new models substantiating its plausibility and new evidence that the conditions specified by the models are met in many natural populations. Retrospective phylogenetic and population genetic signatures of sympatric speciation have also been derived, and these are beginning to be tested. This new work has helped increase the acceptance of sympatric speciation as a plausible process, although it remains difficult to show conclusively that specific pairs of taxa have speciated through sympatric processes alone. It might be time for a re-evaluation of the geographical classification of speciation modes in favor of one based primarily on evolutionary mechanisms     

中国金粟兰属植物的形态多样性及地理分布

金粟兰属(Chloranthus Swartz)是研究被子植物起源和早期演化的关键类群之一,部分种类被广泛地栽培和使用。虽然前人已对该属植物的形态、地理分布、分类、系统发育、化石和化学成分等开展了丰富的研究,但是通过作者持续广泛的调查研究发现,以往对该属植物形态多样性、生活型和地理分布的认识仍不充分,且在该属植物中还存在分类观点不统一、名实混淆、沿用错误分类信息等问题。该研究在广泛查阅标本资料和长期野外调查的基础上,对金粟兰属植物的形态多样性、生活型和地理分布格局进行了较为全面的描述。结果表明:在形态方面,金粟兰属内花部器官尤其药隔形态在种间呈多样性而种内相对稳定,是物种划分最有效的分类性状,其中网脉金粟兰药隔形态变异较大,疑为复合群;在生活型方面,狭叶金粟兰与网脉金粟兰为常绿草本,区别于该属其他常绿亚灌木以及地上部分每年秋冬季节枯萎的多年生草本种类;在地理与生境分布方面,验证了金粟兰属内最近缘的4个长药隔草本物种间的确呈显著水平替代分布格局,而一直被认为只分布在湖北宜昌和重庆奉节等地的狭叶金粟兰却在贵州亦有分布。该研究结果不仅丰富了对中国金粟兰属植物的形态多样性、生活型、地理和生境分布特点等方面的认识,而且为正确划分和鉴别金粟兰属植物不同种类提供了更详实的依据,同时还为进一步深入研究该属植物物种的形成、演化和特殊分布格局的成因奠定基础,为这一类植物资源安全地可持续开发利用提供了保障。     

Latitudinal variation in genetic divergence of populations and the potential for future speciation

The increase in biological diversity with decreasing latitude is widely appreciated but the cause of the pattern is unknown. This pattern reflects latitudinal variation in both the origin of new species (cladogenesis) and the number of species that coexist. Here we address latitudinal variation in species origination, by examining population genetic processes that influence speciation. Previous data suggest a greater number of speciation events at lower latitudes. If speciation events occur more frequently at lower latitudes, we predicted that genetic divergence among populations within species, an important component of cladogenesis, should be greater among lower latitude populations. We tested this prediction using within-species patterns of mtDNA variation across 60 vertebrate species that collectively spanned six continents, two oceans, and 119 degrees latitude. We found greater genetic divergence of populations, controlling for geographic distance, at lower latitudes within species. This pattern remained statistically significant after removing populations that occur in localities previously covered by continental glaciers during the last glaciation. Results suggest that lower latitude populations within species exhibit greater evolutionary independence, increasing the likelihood that mutation, recombination, selection, and/or drift will lead to divergence of traits important for reproductive isolation and speciation. Results are consistent with a greater influence of seasonality, reduced energy, and/or glacial (Milankovitch) cycles acting on higher latitude populations, and represent one of the few tests of predictions of latitudinal variation in speciation rates using population genetic data.     

Investigating species boundaries in the Giliopsis group of Ipomopsis (Polemoniaceae): Strong discordance among molecular and morphological markers

As a first step in elucidating mechanisms of speciation in the Giliopsis group of Ipomopsis (Polemoniaceae), we examined patterns of morphological and genetic differentiation and crossability. This group comprises three species that diverged very recently: two perennials, I. guttata and I. tenuifolia, and one annual, I. effusa. Analysis of phenotypic variation established that the three species are distinct for floral characters, and this differentiation is maintained in a locality containing both perennial species. Next, we assessed the genealogical relationships with AFLPs. All sampled individuals of I. effusa clustered together, a result in accord with its genetic isolation. The perennials, which retain interfertility, were not resolved as sister taxa. Rather, individuals sampled from the single I. guttata population that is sympatric with I. tenuifolia were genetically more similar to I. tenuifolia samples than they were to conspecifics. This pattern may be due to substantial introgression of I. tenuifolia genomic regions that do not contribute to floral phenotype in I. guttata. Our result adds to mounting evidence that plant species, as defined by morphological characters, are often not genomically cohesive. Taken together, our data warrant caution in delimiting species with genetic markers alone, and, importantly, suggest that selection on species-diagnostic morphological characters can be sufficiently strong to counteract extensive gene flow.     

Modes of speciation and the neutral theory of biodiversity

Hubbell's neutral theory of biodiversity has generated much debate over the need for niches to explain biodiversity patterns. Discussion of the theory has focused on its neutrality assumption, i.e. the functional equivalence of species in competition and dispersal. Almost no attention has been paid to another critical aspect of the theory, the assumptions on the nature of the speciation process. In the standard version of the neutral theory each individual has a fixed probability to speciate. Hence, the speciation rate of a species is directly proportional to its abundance in the metacommunity. We argue that this assumption is not realistic for most speciation modes because speciation is an emergent property of complex processes at larger spatial and temporal scales and, consequently, speciation rate can either increase or decrease with abundance. Accordingly, the assumption that speciation rate is independent of abundance (each species has a fixed probability to speciate) is a more natural starting point in a neutral theory of biodiversity. Here we present a neutral model based on this assumption and we confront this new model to 20 large data sets of tree communities, expecting the new model to fit the data better than Hubbell's original model. We find, however, that the data sets are much better fitted by Hubbell's original model. This implies that species abundance data can discriminate between different modes of speciation, or, stated otherwise, that the mode of speciation has a large impact on the species abundance distribution. Our model analysis points out new ways to study how biodiversity patterns are shaped by the interplay between evolutionary processes (speciation, extinction) and ecological processes (competition, dispersal).     

Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia)

Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.     

Cryptic species as a window into the paradigm shift of the species concept

The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new “species” paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category—which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a “process” counterpart to the long‐studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance‐based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large‐scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.     

The genetics and ecology of sympatric speciation: A case study

Mating occurs on the larval host plant in allRhagoletis species (Diptera: Tephritidae). We show how this attribute, when coupled with certain differences in other biological traits, strongly influences the mode of speciation. In species of thesuavis species group, host shifts have never occurred during speciation, and larvae feed in the husks of any walnut species(Juglans spp.), which are highly toxic. Taxa are allopatric or parapatric and exhibit deep phylogenetic nodes suggesting relatively ancient speciation events. Traits responsible for species and mate recognition, particularly in parapatric species, are morphologically distinct and strongly sexually dimorphic. All aspects of their biology, genetics and distribution are consistent with a slow rate of allopatric speciation followed by morphological divergence in secondary contact. In contrast, speciation in thepomonella species group has always involved a shift to a new, usually unrelated, non-toxic host, and all taxa within these groups are sympatric, monophagous and morphologically indistinguishable from one another. Phylogenetic nodes are very shallow, indicating recent sympatric speciation. Sympatric divergence is promoted by genetic variation which allows a portion of the original species to shift to a new habitat or host. Evidence suggests that changes in a few key loci responsible for host selection and fitness on a new host may initiate host shifts. By exploiting different habitats, competition for resources between diverging populations is reduced or avoided. We provide evidence that in phytophagous and parasitic insects sufficient intrinsic barriers to gene flow can evolve between sister populations as they adapt to different habitats or hosts to allow each population to establish independent evolutionary lineages in sympatry.     

AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae)

? Premise of the study: Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. ? Methods: We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. ? Key results: We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. ? Conclusions: Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.     

Deep genetic divergences among morphologically similar and parapatric Skistodiaptomus (Copepoda: Calanoida: Diaptomidae) challenge the hypothesis of Pleistocene speciation

We used mitochondrial [cytochrome c oxidase subunit I (CO I ), cytochrome b , and 16S] and nuclear [internal transcribed spacer (ITS) phylogenies of Skistodiaptomus copepods to test hypotheses of Pleistocene divergence and speciation within the genus. Mitochondrial (mt)DNA sequence divergences do not support hypotheses for Pleistocene speciation and instead suggest much more ancient speciation events in the genus. Skistodiaptomus oregonensis and Skistodiaptomus pygmaeus (i.e. two morphologically similar and parapatric species) exhibited uncorrected mtDNA sequence divergences exceeding 20%. Similarly, we identified three divergent clades of Skistodiaptomus pallidus that exhibited mtDNA sequence divergences exceeding 15%, suggesting that even intraspecific divergence within this morphospecies predates the Pleistocene. We found clear evidence of CO I pseudogenes in S. pygmaeus , but their presence did not lead to significant overestimates of sequence divergences for this gene. Substitution saturation and strong purifying selection have most likely led to underestimates of sequence divergences and divergence times among Skistodiaptomus . The widespread phenomenon of morphological stasis among genetically divergent copepod groups indicates that speciation often occurs with little or no morphological change. Instead, morphological evolution may occur idiosyncratically after speciation and create discordant patterns of morphological similarity, shared ancestry and divergence time. Cryptic species complexes are therefore common in copepods, and morphological species concepts underestimate their true species diversity.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 150–165.     

Deciphering the products of evolution at the species level: the need for an integrative taxonomy

Progress in molecular techniques together with the incorporation of phylogenetic analyses of DNA into taxonomy have caused an increase in the number of species’ discoveries in groups with morphological characters that are difficult to study or in those containing polytypic species. But some emerged criticisms plead for a taxonomic conservatism grounded either on the requirement of providing evidences of morphological distinctiveness or reproductive barriers to erect new species names. In a case study of taxonomic research on Neotropical frogs, we combine several lines of evidence (morphological characters, prezygotic reproductive isolation and phylogenetic analyses of mitochondrial DNA) to test the status of 15 nominal species and to assess the degree of agreement of the different lines of evidence. Our study reveals that morphology alone is not sufficient to uncover all species, as there is no other single line of evidence independently. Full congruence between lines of evidence is restricted to only four out of the 15 species. Five species show congruence of two lines of evidence, whereas the remaining six are supported by only one. The use of divergence in morphological characters seems to be the most conservative approach to delineate species boundaries because it does not allow the identification of some sibling reciprocally monophyletic species differing in their advertisement calls. The separate analysis of differences in advertisement calls (evidence of reproductive isolation) or of phylogenetic data alone also shows limitations, because they do not support some morphological species. Our study shows that only an integrative approach combining all sources of evidence provides the necessary feedback to evaluate the taxonomic status of existing species and to detect putative new ones. Furthermore, the application of integrative taxonomy enables the identification of hypotheses about the existence of species that will probably be rejected or changed, and those that can be expected to persist.     

Hybrid Speciation in a Marine Mammal: The Clymene Dolphin (Stenella clymene)

Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow.     

What is speciation and how should we study it?

To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology.     

Evolution of blind beetles in isolated aquifers: a test of alternative modes of speciation

Evidence is growing that not only allopatric but also sympatric speciation can be important in the evolution of species. Sympatric speciation has most convincingly been demonstrated in laboratory experiments with bacteria, but field-based evidence is limited to a few cases. The recently discovered plethora of subterranean diving beetle species in isolated aquifers in the arid interior of Australia offers a unique opportunity to evaluate alternative modes of speciation. This naturally replicated evolutionary experiment started 10-5 million years ago, when climate change forced the surface species to occupy geographically isolated subterranean aquifers. Using phylogenetic analysis, we determine the frequency of aquifers containing closely related sister species. By comparing observed frequencies with predictions from different statistical models, we show that it is very unlikely that the high number of sympatrically occurring sister species can be explained by a combination of allopatric evolution and repeated colonisations alone. Thus, diversification has occurred within the aquifers and likely involved sympatric, parapatric and/or microallopatric speciation.     

Evolutionary history of the Drosophila bipectinata species complex

Groups of recently diverged species offer invaluable glimpses into the history and genetic basis of speciation and phenotypic evolution. In this report, we combine phylogenetic and population-genetic approaches to reconstruct the evolutionary history of the Drosophila bipectinata species complex. This complex is a group of four closely related, largely sympatric species--D. bipectinata, D. parabipectinata, D. malerkotliana and D. pseudoananassae. Using the sequences of one mitochondrial and six nuclear loci, we show that D. bipectinata and D. parabipectinata are the two most closely related species, and that together with D. malerkotliana they form a monophyletic clade to which D. pseudoananassae is a relatively distant outgroup. Genetic divergence among D. bipectinata, D. parabipectinata and D. malerkotliana is extremely low, and we estimate that these species diverged only 283,000-385,000 years ago. We also find that mitochondrial DNA shows evidence of recent gene flow across species boundaries. Despite the low genetic divergence, species of the bipectinata complex show an unusually high degree of morphological differentiation. This contrast underscores the importance of understanding the genetic basis of functional differentiation among closely related species.