Effects of an adaptive zone shift on morphological and ecological diversification in terapontid fishes

A fundamental goal of evolutionary ecology is understanding the processes responsible for contemporary patterns of morphological diversity and species richness. Transitions across the marine–freshwater interface are regarded as key triggers for adaptive radiation of many clades. Using the Australian terapontid fish family as a model system we employed phylogenetic analyses to compare the rates of ecological (dietary) and morphological evolution between marine and freshwater species of the family. Results suggested significantly higher rates of phenotypic evolution in key dietary and morphological characters in freshwater species compared to marine counterparts. Moreover, there was significant correlation between several of these dietary and morphological characters, suggesting an underlying ecomorphological aspect to these greater rates of phenotypic evolution in freshwater clades. Australia’s biogeographic history, which has precluded colonisation by many of the major ostariophysan fish families that make up much global freshwater fish diversity, appears to have provided the requisite ‘ecological opportunity’ to facilitate the radiation of invading marine-derived fish clades.     

中国榕小蜂触角感受器形态特征及进化适应性分析

【目的】榕树与传粉榕小蜂体系是协同进化、专性传粉的经典系统,每种榕树上一般还生活有种类丰富、数目众多的非传粉榕小蜂。在选择压力下,榕小蜂为在榕果内生存产生了明显的适应性形态。触角感受器是昆虫通讯系统的单元,其形态是反映生态和进化适应性的最佳特征之一。本文旨在对中国部分传粉和非传粉榕小蜂的触角感受器的形态多样性和进化适应性进行系统研究。【方法】对来源于海南和云南15种榕树上24种榕小蜂54个型的触角感受器形态进行了扫描电镜观察,基于现有的分子系统发育树,对传粉榕小蜂触角感受器的形态特征进行了性状演化分析,并对榕小蜂的形态特征进行了进化适应性分析。【结果】榕小蜂触角感受器普遍存在雌雄二型现象。雌蜂触角感受器种类有毛状、锥状、板状、刺状、钟形、腔锥状和栓锥状等,数目丰富,并且进果产卵的传粉雌蜂和果外产卵的非传粉雌蜂之间、进果产卵的传粉雌蜂和进果产卵的非传粉雌蜂之间在形态上存在差异。传粉雄蜂和不具有雄性多型现象的非传粉雄蜂触角感受器极为退化,具有雄性多型的非传粉雄蜂触角感受器形态在种内不具有显著差异。性状演化分析表明进化路径相当复杂,可能存在多次独立进化过程。触角感受器的形态类型与其进化适应性相关。【结论】榕小蜂触角感受器类型多样,形态变化丰富,并为适应榕果内的生存而产生了进化适应性特点。雌蜂和雄蜂在榕果内受到了完全不同的选择压力,行使不同的生态功能,从而产生了不同的适应性形态。不同的适应性形态可能与雌蜂不同的产卵行为、雄蜂不同的交配策略具有一定联系。该文是首次对中国榕小蜂触角感受器形态进行系统研究的报道,有助于更好地理解榕小蜂的形态特征、进化路线、行为策略和生态关系。     

Toward a DNA taxonomy of Alpine Rhithrogena (Ephemeroptera: Heptageniidae) using a mixed Yule-coalescent analysis of mitochondrial and nuclear DNA

Aquatic larvae of many Rhithrogena mayflies (Ephemeroptera) inhabit sensitive Alpine environments. A number of species are on the IUCN Red List and many recognized species have restricted distributions and are of conservation interest. Despite their ecological and conservation importance, ambiguous morphological differences among closely related species suggest that the current taxonomy may not accurately reflect the evolutionary diversity of the group. Here we examined the species status of nearly 50% of European Rhithrogena diversity using a widespread sampling scheme of Alpine species that included 22 type localities, general mixed Yule-coalescent (GMYC) model analysis of one standard mtDNA marker and one newly developed nDNA marker, and morphological identification where possible. Using sequences from 533 individuals from 144 sampling localities, we observed significant clustering of the mitochondrial (cox1) marker into 31 GMYC species. Twenty-one of these could be identified based on the presence of topotypes (expertly identified specimens from the species' type locality) or unambiguous morphology. These results strongly suggest the presence of both cryptic diversity and taxonomic oversplitting in Rhithrogena. Significant clustering was not detected with protein-coding nuclear PEPCK, although nine GMYC species were congruent with well supported terminal clusters of nDNA. Lack of greater congruence in the two data sets may be the result of incomplete sorting of ancestral polymorphism. Bayesian phylogenetic analyses of both gene regions recovered four of the six recognized Rhithrogena species groups in our samples as monophyletic. Future development of more nuclear markers would facilitate multi-locus analysis of unresolved, closely related species pairs. The DNA taxonomy developed here lays the groundwork for a future revision of the important but cryptic Rhithrogena genus in Europe.     

Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents

Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.     

Phylogeny,taxonomy, genetics and global heritage ranks of an imperilled,freshwater snail genus Lithasia (Pleuroceridae)

Numerous aquatic species are threatened with extinction from habitat elimination or modification. One particularly imperilled group is the freshwater gastropod family Pleuroceridae. Pleurocerids reach their greatest diversity in the southeastern United States, and many species are currently considered extinct, endangered or threatened. One issue hindering efforts to implement conservation management plans for imperilled pleurocerid species is that the taxonomy is in an abysmal state. The taxonomy of pleurocerids is currently based on late 19th- and early 20th-century studies, which used a typological or morphospecies concept. Most biologists today doubt the validity of many of the currently recognized species; however, this does not stop them from assigning conservation ranks in an attempt to determine which species are imperilled or currently stable. We conducted a phylogenetic analysis of the pleurocerid genus Lithasia using morphological and mitochondrial DNA sequence (mtDNA) data in an attempt to delimit species boundaries and test previous taxonomic schemes. We found that the current taxonomy of Lithasia does not reflect species diversity adequately within the genus, with two new undescribed species being discovered. The conservation status ranks of the new, undescribed species are imperilled and would have been overlooked had we relied on the conventional taxonomy. Additionally, the undescribed species' conservation ranks that were previously apparently secure became vulnerable due to being inappropriately assigned as members of formerly widely distributed species instead of the imperilled status they warrant and vice versa, as some taxa that were considered imperilled are now thought to be modestly stable. Our study suggests that conservation ranks should be considered suspect at best in taxonomically poorly known groups until the taxa are reviewed using modern systematic methods.     

Phylogenetic study of the species within the family Streptomycetaceae

Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

木灵藓科分类与系统学研究：历史、问题和展望

木灵藓科(Orthotrichaceae)是藓类植物中的第3大科。该科不仅种类多, 生态类型特殊, 而且是世界公认的多样化程度高、分类难度大、系统关系复杂的类群。当代木灵藓科植物分类系统学研究主要集中在该科的地区志编写和专属分类修订。目前, 除了热带美洲、热带非洲的变齿藓属(Zygodon)和火藓属(Schlotheimia)部分类群外, 木灵藓科主要类群的分类修订工作已基本完成, 但是有关亚科和属的划分和地位以及各属之间的关系等方面仍存在众多争议。木灵藓科分支系统学研究也不够系统全面, 有的仅应用了单个基因片段, 或者只涉及少数类群。因此, 需要基于更多的分子和形态学性状, 进一步开展世界木灵藓科植物的系统发育研究, 建立一个更趋自然的木灵藓科分类系统。     

欧洲水青冈(Fagus sylvatical L.)构筑型与形态多样性研究

通过对植物构件和构筑型的分析,可以了解植物的整体结构与系统演化关系。高等植物构筑型的研究以树木最为深入,植物学家对全球的树木进行了构筑模式的分类,并确定了２３个基本的构筑类型。植物的构筑型和其形态的多样性是密不可分的。构筑奕型确定了植物所属的整体形态类型,而对每种植物具体的形态多样性分析可以深入了解每种构筑型的数量特征及其形成过程。在概述了树木树筑型研究的基础上,系统说明了欧洲水青冈构筑才形态多样性分析的步骤和步骤和分析的意义。水青冈属（Fagus)为Ｔroll型构筑模式,处于不同生态条件下的同一种的不同种群之间,在形态、解剖、生理和遗传多样性方面都存在着差异。树木的形态多样性虽然主要受遗传因素的控制,但生态条件对其形态和遗传多样性也有非常显著的影响。在对树木进行构筑型分析时,道德要根据构筑要素（主要是形态与生长特性）确定它所属的构筑类型,其次是分析它的形态特征与环境条件的关系,进行进一步分析其遗传多样性。     

Possible links between phenotypic variability,habitats and connectivity in the killifish Aphaniops stoliczkanus in Northeast Oman

There is a significant gap in our knowledge of the intraspecific morphological variability in freshwater fish, although such data are crucial for understanding species diversity. Here we use the killifish Aphaniops stoliczkanus (Day, 1872; Aphaniidae: Cyprinodontiformes), which is a widespread but poorly known freshwater species in the Middle East, to investigate variability in morphological traits within and between its populations. As otolith morphology is known to evolve on ecological timescales and can signal the presence of cryptic lineages, a special focus lies on otolith variability. Based on samples from six populations in northern Oman, we found that variation in pigmentation, disparities in body shape and otolith variability can be associated with distinctive environmental conditions. The unique otolith shape of A. stoliczkanus from a hot sulphuric spring (Nakhal) suggests that a cryptic lineage may have emerged there. Our new data can serve as a benchmark for future studies on the diversity of Aphaniops and other Aphaniidae and help to clarify whether cryptic diversity is present in some lineages. Moreover, our data can serve as an actualistic model for studies on fossil fishes, in which morphological characters provide the only accessible data source for taxonomic and phylogenetic interpretations.     

Statistical evidence for common ancestry: Application to primates

Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA.     

Morphological and niche divergence of pinyon pines

The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.     

A new classification of Cyperaceae (Poales) supported by phylogenomic data

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology due to their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C₄ photosynthesis and holocentric chromosomes. Goetghebeur′s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower, and embryo characters, plus anatomical and other information. Since then, several family-level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family-wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal, and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time, we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes, and 10 subtribes, and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, and Oreobolinae.     

Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA

The Notothenioidei dominates the fish fauna of the Antarctic in both biomass and diversity. This clade exhibits adaptations related to metabolic function and freezing avoidance in the subzero Antarctic waters, and is characterized by a high degree of morphological and ecological diversity. Investigating the macroevolutionary processes that may have contributed to the radiation of notothenioid fishes requires a well-resolved phylogenetic hypothesis. To date published molecular and morphological hypotheses of notothenioids are largely congruent, however, there are some areas of significant disagreement regarding higher-level relationships. Also, there are critical areas of the notothenioid phylogeny that are unresolved in both molecular and morphological phylogenetic analyses. Previous molecular phylogenetic analyses of notothenioids using partial mtDNA 12S and 16S rRNA sequence data have resulted in limited phylogenetic resolution and relatively low node support. One particularly controversial result from these analyses is the paraphyly of the Nototheniidae, the most diverse family in the Notothenioidei. It is unclear if the phylogenetic results from the 12S and 16S partial gene sequence dataset are due to limited character sampling, or if they reflect patterns of evolutionary diversification in notothenioids. We sequenced the complete mtDNA 16S rRNA gene for 43 notothenioid species, the largest sampling to-date from all eight taxonomically recognized families. Phylogenetic analyses using both maximum parsimony and maximum likelihood resulted in well-resolved trees with most nodes supported with high bootstrap pseudoreplicate scores and significant Bayesian posterior probabilities. In all analyses the Nototheniidae was monophyletic. Shimodaira–Hasegawa tests were able to reject two hypotheses that resulted from prior morphological analyses. However, despite substantial resolution and node support in the 16S rRNA trees, several phylogenetic hypotheses among closely related species and clades were not rejected. The inability to reject particular hypotheses among species in apical clades is likely due to the lower rate of nucleotide substitution in mtDNA rRNA genes relative to protein coding regions. Nevertheless, with the most extensive notothenioid taxon sampling to date, and the much greater phylogenetic resolution offered by the complete 16S rRNA sequences over the commonly used partial 12S and 16S gene dataset, it would be advantageous for future molecular investigations of notothenioid phylogenetics to utilize at the minimum the complete gene 16S rRNA dataset.     

中国森林大型真菌重要类群多样性和系统学研究

大型真菌主要为担子菌门的真菌和少数为子囊菌门的真菌,该类真菌具有重要的经济价值和生态功能,主要生长在森林生态系统中.30年来作者对我国几乎所有类型森林生态中的大型真菌进行了系统调查和采集,共采集标本11.2万号.基于对这些材料的形态学及分子系统学研究,并结合生态学和生物地理学特征,共鉴定出中国森林大型真菌4 250种,...     

Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome B genes

The Gobioidei is a large suborder in the order Perciformes and consists of more than 2000 species belonging to about 270 genera. The vast number of species and their morphological specialization adapted to diverse habits and habitats makes the classification of the gobioid fishes very difficult.A comprehensive estimation of the evolutionary scenario of all gobioid fishes using only morphological information is difficult for two major reasons: first, in addition to wide ecological diversification, there is a trend towards specialization and degeneration of morphological characters among these species; second, an appropriate outgroup of gobioid fishes has not been recognized.Based upon nucleotide sequence comparisons of gobioid mitochondrial cytochrome b genes, we established the phylogenetic relationships of their differentiation into many groups of morphological and ecological diversity. The phylogenetic trees obtained show that most species examined have diverged from each other almost simultaneously or during an extremely short period of time.     

Levels of diversity in endomycorrhizal fungi (Glomales,Zygomycetes) and their role in defining taxonomic and non-taxonomic groups

Diversity in glomalean fungi is manifested at the molecular, morphological, and ecological levels. Characters at any of these levels can be ordered into hierarchical patterns defining taxonomic groups if they are conserved enough to be heritable through geologic time in all descendants of a common ancestor. At present, only morphological characters associated with mode of spore formation and in subcellular structure of spores are sufficiently stable and diverse to recognize at least 150 species. Ontogenetic comparisons indicate that species integrity, despite asexual reproduction, is the result of rigid internal constraints imposed on variation during the process of spore subcellular differentiation. Epigenetic factors dominate because the differentiation sequence is linear and each new stage is causally linked to preceding stages. Some morphological characters of the fungal mycelium also exist, but they define more inclusive groups at the family level and above. Most diversity in the mycorrhizae consists of life-history traits associated with abundance and architecture of fungal components, their rate of formation and longevity, and their cost in the symbiosis. These characters participate in processes at the molecular and ecological levels, so they are autonomous from morphological determinants. They often are labile or affected by external environmental conditions, so fewer stable taxonomic characters are likely to be discovered. Instead, molecular and ecological diversity has greater potential to define; (a) niche specificity of organisms/populations and (b) causal processes linked to host-fungus compatibility and mycorrhizal efficiency. Any taxonomic characters that relate to mycorrhizal functions will come only from comparative studies involving organisms from shared habitats rather than those having shared spore morphologies.     

The causes of species richness patterns across space, time, and clades and the role of "ecological limits"

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.