FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates

It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model‐based tests of state‐dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple nonparametric statistical test (“FiSSE”) to assess the effects of a binary character on lineage diversification rates. The method involves computing a test statistic that compares the distributions of branch lengths for lineages with and without a character state of interest. The value of the test statistic is compared to a null distribution generated by simulating character histories on the observed phylogeny. Our tests show that FiSSE can reliably infer trait‐dependent speciation on phylogenies of several hundred tips. The method has low power to detect trait‐dependent extinction but can infer state‐dependent differences in speciation even when net diversification rates are constant. We assemble a range of macroevolutionary scenarios that are problematic for likelihood‐based methods, and we find that FiSSE does not show similarly elevated false positive rates. We suggest that nonparametric statistical approaches, such as FiSSE, provide an important complement to formal process‐based models for trait‐dependent diversification.     

A preliminary classification of evolutionary radiations

Rapid increases in taxonomic diversity are generally described as adaptive or evolutionary radiations. Such radiations differ widely in the rate and extent of morphologic innovation, taxonomic diversification and phylogenetic breadth, suggesting that several patterns, and likely processes, are involved. At least four distinct patterns of evolutionary radiation can be identified: novelty events, which generate new morphological complexity (altering the body plan of the group under consideration) but not necessarily with the associated production of many lower taxa; broad diversification events involving many independent lineages that undergo diversification, generate many new species and are driven by new ecological opportunities; economic radiations of a limited group of ecologically (but not necessarily phylogenetically) related clades exploiting a limited new ecologic opportunity; and adaptive radiations that may occur at any taxonomic level, but involve a rapid increase in diversity within a single clade, including “true”; adaptive radiations. Many events produce simple diversity increases with no corresponding increase in genetic/developmental/morphological/behavioral sophistication, but the most evolutionarily interesting events add new levels of complexity.     

Macroevolution of hoverflies (Diptera: Syrphidae): the effect of using higher‐level taxa in studies of biodiversity,and correlates of species richness

We test a near‐complete genus level phylogeny of hoverflies (Diptera: Syrphidae) for consistency with a null model of clade growth having uniform probabilities of speciation and extinction among contemporaneous species. The phylogeny is too unbalanced for this null model. Importantly, the degree of imbalance in the phylogeny depends on whether the phylogeny is analysed at the genus level or species level, suggesting that genera ought not to be used uncritically as surrogates for species in large‐scale evolutionary analyses. Tests for a range of morphological, life‐history and ecological correlates of diversity give equivocal results, but suggest that high species‐richness may be associated with sexual selection and diet breadth. We find no correlation between species‐richness and either body size or reproductive rate.     

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data.     

Traits,trees and taxa: global dimensions of biodiversity in mammals

Measures of biodiversity encompass variation along several dimensions such as species richness (SR), phylogenetic diversity (PD) and functional/trait diversity (TD). At the global scale, it is widely recognized that SR and PD are strongly correlated, but the extent to which either tends to capture variation in TD is unclear. Here, we assess relationships among PD, SR and TD for a number of traits both across clades and regional assemblages of mammals. We also contrast results using two different measures of TD, trait variance and a new measure we refer to as trait bin filling (the number of orders of magnitude of variation that contain at least one species). When TD is defined as trait variance, PD is a much stronger correlate of TD than SR across clades, consistent with hypotheses about the conservation value of PD. However, when TD is defined as bin filling, PD and SR show similar correlations with TD across clades and space. We also investigate potential losses of SR, PD and TD if species that are currently threatened were to go extinct, and find that threatened PD is often a similar predictor of threatened TD as SR.     

The diversity of arthropods in homes across the United States as determined by environmental DNA analyses

We spend most of our lives inside homes, surrounded by arthropods that impact our property as pests and our health as disease vectors and producers of sensitizing allergens. Despite their relevance to human health and well‐being, we know relatively little about the arthropods that exist in our homes and the factors structuring their diversity. As previous work has been limited in scale by the costs and time associated with collecting arthropods and the subsequent morphological identification, we used a DNA‐based method for investigating the arthropod diversity in homes via high‐throughput marker gene sequencing of home dust. Settled dust samples were collected by citizen scientists from both inside and outside more than 700 homes across the United States, yielding the first continental‐scale estimates of arthropod diversity associated with our residences. We were able to document food webs and previously unknown geographic distributions of diverse arthropods – from allergen producers to invasive species and nuisance pests. Home characteristics, including the presence of basements, home occupants and surrounding land use, were more useful than climate parameters in predicting arthropod diversity in homes. These noninvasive, scalable tools and resultant findings not only provide the first continental‐scale maps of household arthropod diversity, but our analyses also provide valuable baseline information on arthropod allergen exposures and the distributions of invasive pests inside homes.     

净多样化速率和进化时间对虎耳草目科间物种多样性差异的影响

不同生物类群包含的物种数目常存在巨大差异,这是生态学和生物学研究中普遍观察到的现象。然而,这一现象产生的原因仍然是未解之谜。从宏观进化的角度,进化时间假说和多样化速率假说是两个比较流行的假说。进化时间假说认为类群的演化时间越长,积累的物种丰富度越高;而多样化速率假说认为类群的净多样化速率越快,则其物种丰富度越高。为验证这两个假说,该文以一棵包含1 539个物种化石定年的虎耳草目系统发育树为基础,通过宏观进化分析获取了虎耳草目内15个科的物种形成和灭绝速率,并计算了每个科的平均多样化速率。结果表明：(1)虎耳草目的物种多样化速率有着增加的趋势,并且多样化速率的增加主要出现在温带和高山类群,如茶藨子科、景天科和芍药科等。(2)采用系统发育广义最小二乘模型(PGLS)和线性回归模型(LM)结果表明,虎耳草目15个科的物种丰富度与科的分化时间和科内物种的最近共同祖先年龄都没有显著相关关系,而与净多样化速率显著正相关(R² =0.380,P<0.05)。该研究支持了多样化速率假说,认为不同科的净多样化速率的差异是导致虎耳草目科间物种数目差异的主要原因之一。全球气候变冷...     

Historical biogeography and the evolution of the latitudinal gradient of species richness in the Papionini (Primata: Cercopithecidae)

We apply historical biogeography techniques to the macaques, baboons and their relatives (Primata: Papionini) and relate the inferred history of range shifts, and associated evolutionary events, to the latitudinal distribution of extant species, which is strongly tropical. The results of reversible parsimony, weighted ancestral area and dispersal-vicariance analyses all agree that Central Africa was part of the range of the ancestor of the tribe. Tropical regions with high current species richness (Central Africa, South-east Asia, Indonesia) have: (1) had a relatively long history of occupation, (2) experienced both a greater number and a greater average rate of speciation events and (3) given rise to more dispersal events to other regions. However, nested sister-taxon comparisons across the tribe show no overall association between differences in latitude and differences in rates of cladogenesis. Our historical reconstructions are largely consistent with previous hypotheses and fossil data, and suggest that both the passage of time since colonization and rates of cladogenesis have enhanced tropical species richness. Historical biogeography may thus considerably aid understanding of this and other spatial problems in macroecology.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 235–246.     

Adaptive radiation and the evolution of nectarivory in a large songbird clade

The accumulation of exceptional ecological diversity within a lineage is a key feature of adaptive radiation resulting from diversification associated with the subdivision of previously underutilized resources. The invasion of unoccupied niche space is predicted to be a key determinant of adaptive diversification, and this process may be particularly important if the diversity of competing lineages within the area, in which the radiation unfolds, is already high. Here, we test whether the evolution of nectarivory resulted in significantly higher rates of morphological evolution, more extensive morphological disparity, and a heightened build‐up of sympatric species diversity in a large adaptive radiation of passerine birds (the honeyeaters, about 190 species) that have diversified extensively throughout continental and insular settings. We find that a large increase in rates of body size evolution and general expansion in morphological space followed an ancestral shift to nectarivory, enabling the build‐up of large numbers of co‐occurring species that vary greatly in size, compared to related and co‐distributed nonnectarivorous clades. These results strongly support the idea that evolutionary shifts into novel areas of niche space play a key role in promoting adaptive radiation in the presence of likely competing lineages.     

Ecological drivers of avian diversity in a subtropical landscape: Effects of habitat diversity,primary productivity and anthropogenic disturbance

Understanding the roles of ecological drivers in shaping biodiversity is fundamental for conservation practice. In this study, we explored the effects of elevation, conservation status, primary productivity, habitat diversity and anthropogenic disturbance (represented by human population density and birding history) on taxonomic, phylogenetic and functional avian diversity in a subtropical landscape in southeastern China. We conducted bird surveys using 1‐km transects across a total of 30 sites, of which 10 sites were located within a natural reserve. Metrics of functional diversity were calculated based on six functional traits (body mass, clutch size, dispersal ratio, sociality, diet and foraging stratum). We built simultaneous autoregression models to assess the association between the ecological factors and diversity of the local avian communities. Local avian diversity generally increased with increasing habitat diversity, human population density and primary productivity. We also detected phylogenetic and functional clustering in these communities, suggesting that the avian assemblages were structured mainly by environmental filtering, rather than interspecific competition. Compared with sites outside the natural reserve, sites within the natural reserve had relatively lower avian diversity but a higher level of phylogenetic heterogeneity.     

Geographical gradients in the biodiversity of Chinese freshwater molluscs: Implications for conservation

Aim

Large ‐ scale diversity patterns are generated by different but not mutually exclusive mechanisms. However, understanding of multiple facets of diversity and their determinants in the freshwater realm remains limited. Here, we characterized the geographical gradients, hotspots and spatial congruence of three facets of freshwater molluscan diversity and evaluated the relative importance of three different underlying mechanisms related to the energy, area/environmental heterogeneity and dispersal/historical hypotheses.

Location

China.

Methods

Species richness (SR), functional richness (FR) and taxonomic distinctness (TD, a proxy of phylogenetic diversity) were calculated for 212 drainage basins with a total of 313 molluscan species. Spatial congruence between the diversity facets was evaluated with Pearson correlation coefficient and overlap among hotspots. Multiple linear regression models and variation partitioning were used to assess the relative importance of different mechanisms.

Results

Hotspots of SR and FR were mainly concentrated in the Yangtze River and Huai River basins, while high TD values were patchily distributed across China. We found extremely low spatial congruence between TD and both SR and FR, while there was relatively high concordance between SR and FR. All diversity facets were best explained by the dispersal/historical hypothesis with strong unique effects, followed by the factors related to the energy hypothesis. The area/ environmental heterogeneity hypothesis was only weakly supported.

Main conclusions

We found a potentially strong influence of dispersal limitation and evolutionary history on the geographical diversity gradients of Chinese molluscs. This finding contrasts with the general finding that energy‐related factors are the strongest correlates of diversity patterns at large spatial scales. Moreover, our results do not support the idea that using any one diversity component as a surrogate of the others in developing conservation strategies. Instead, an integrative approach embracing multiple facets of diversity should be adopted in the conservation of freshwater biodiversity.

     

Area Networks for Conserving Iberian Insects: A Case Study of Dung Beetles (col., Scarabaeoidea)

Possibilities to create an efficient network of areas for the conservation of Iberian dung-beetle biodiversity were investigated. Data were taken from BANDASCA, a 15,740 record dung-beetle database with information for 101,996 specimens. The greatest species richness and phylogenetic diversity are found in the Iberian Central System cordilleras, while those of range-size rarity are in the southernmost corner of the Iberian Peninsula and in the coastal plains of the Guadalquivir basin. Additionally, broad regional score trends of these variables reach a maximum in a smaller northeastern, and a larger southeastern region (Baetic and sub-Baetic mountains). Major Central and Southern Spain dung-beetle hotspots contain many of the UTM grid cells which delimit the near-minimum-set of areas hosting maximum dung-beetle biodiversity scores. They are viewed as the nucleus of a potential network of reserves. A UTM grid cell (30TXK1) where Onthophagus albarracinus, an endemic and demographically rare species inhabits the Sierra of Albarracín and Montes Universales, was detected as an irreplaceable area. Because of recent land use changes and rapid human-induced habitat transformation threatening dung-beetle fauna, caution should be taken not to recommend an in memoriam network of areas no longer hosting a fauna extinct today. The abandoning of traditional herding management in Europe threatens the preservation of grasslands where dung-feeding beetles play a major ecological role in maintaining pasture quality and livestock health. A return to more traditional herding methods would require stable dung-beetle populations. Any insect conservation planning in Spain would benefit from more biogeographical information for other insect groups.     

The tale of the finch: adaptive radiation and behavioural flexibility

Darwin''s finches are a classic example of adaptive radiation. The ecological diversity of the Galápagos in part explains that radiation, but the fact that other founder species did not radiate suggests that other factors are also important. One hypothesis attempting to identify the extra factor is the flexible stem hypothesis, connecting individual adaptability to species richness. According to this hypothesis, the ancestral finches were flexible and therefore able to adapt to the new and harsh environment they encountered by exploiting new food types and developing new foraging techniques. Phenotypic variation was initially mediated by learning, but genetic accommodation entrenched differences and supplemented them with morphological adaptations. This process subsequently led to diversification and speciation of the Darwin''s finches. Their current behaviour is consistent with this hypothesis as these birds use unusual resources by extraordinary means. In this paper, we identify cognitive capacities on which flexibility and innovation depend. The flexible stem hypothesis predicts that we will find high levels of these capacities in all species of Darwin''s finches (not just those using innovative techniques). Here, we test that prediction, and find that while most of our data are in line with the flexible stem hypothesis, some are in tension with it.     

福安三种不同茶园节肢动物群落的消长动态调查

根据对福建福安的3种不同茶园（天香有机茶园、北门高山茶园和溪柄平地茶园）的节肢动物群落消长动态调查。并经多样性分析,结果获知：福安3种茶园节肢动物群落的物种丰富度（s）和多样性指数（H）的大小顺序依次为：天香（S=19．64,H=2．537）〉北门（S=18．01,H=2．502）〉溪柄（S=17．59,H=2．297）;而均匀度指数的大小顺序是：北门（J=0．621）〉天香（J=0．595）〉溪柄（J=0．559）。表明植被比较丰富、人为干扰较少的茶园,节肢动物群落的物种丰富度、多样性指数和均匀度指数较高,害、益虫群落易于保持较好的平衡状态,有利于减少（或不使用）化学农药、发展绿色无公害茶叶生产。     

The Erwin equation of biodiversity: From little steps to quantum leaps in the discovery of tropical insect diversity

Almost 40 years ago, Terry L. Erwin published a seemingly audacious proposition: There may be as many as 30 million species of insects in the world. Here, we translate Erwin's verbal argument into a diversity-ratio model—the Erwin Equation of Biodiversity—and discuss how it has inspired other biodiversity estimates. We categorize, describe the assumptions for, and summarize the most commonly used methods for calculating estimates of global biodiversity. Subsequent diversity-ratio extrapolations have incorporated parameters representing empirical insect specialization ratios, and how insect specialization changes at different spatial scales. Other approaches include macroecological diversity models and diversity curves. For many insect groups with poorly known taxonomies, diversity estimates are based on the opinions of taxonomic experts. We illustrate our current understanding of insect diversity by focusing on the six most speciose insect orders worldwide. For each order, we compiled estimates of the (a) maximum estimated number of species, (b) minimum estimated number of species, and (c) number of currently described species. By integrating these approaches and considering new information, we believe an estimate of 5.5 million species of insects in the world is much too low. New molecular methodologies (e.g., metabarcoding and NGS studies) are revealing daunting numbers of cryptic and previously undescribed species, at the same time increasing our precision but also uncertainty about present estimates. Not until technologies advance and sampling become more comprehensive, especially of tropical biotas, will we be able to make robust estimates of the total number of insect species on Earth.     

Impact of habitat diversification on arthropod communities： A study in the fields of Chinese cabbage, Brassica chinensis

Field trials were carried out from June to August in 2004 at Wuyishan （Wuyi Mountains）, Fujian province, China, to determine the effects of habitat diversification on arthropod communities. Two Chinese cabbage, Brassica chinensis, field 1 （F1） and field 2 （F2） surrounded by diverse vegetable cultivars were selected, while a monoculture of Chinese cabbage served as the control field （CK）. The results showed that： （i） when comparing insect abundance of each order between different habitats, significantly higher numbers of lepidopterous insects （39.76% from the each order） and lower densities of Hymenoptera （19.82%） were found in CK than in F1 and F2; （ii） compared with CK, F1 and F2 had a lower percentage of species richness and an abundance of herbivorous insects, but increased richness, abundance and biodiversity of predatory insects; （iii） no differences were observed in neutral insects＇ guild between different fields; and （iv） the dominant species for each guild depends on the habitat types and sampling dates. This study suggests that intercropping could conceivably be used in these habitats to increase the population of natural predators, thus achieving desirable and ecologically friendly results in vegetable fields.     

Genetic diversity of Couratari multiflora and Couratari guianensis (Lecythidaceae): consequences of two types of rarity in central Amazonia

We quantified the within-population genetic variation of Couratari multiflora and C. guianensis, two tree species found in terra firme forests of central Amazonia. Both species have some ecological features in common, but they differ in population abundance across their geographic ranges. While C. multiflora has been found only in low-density populations in all sites studied to date, C. guianensis is relatively common in some sites and very scarce in others. In a 400-ha plot, we found 41 and 29 adults of C. multiflora and C. guianensis, respectively. Twenty-two saplings of C. guianensis and 103 seedlings of C. multiflora were also examined. The mean expected heterozygosities (H_em) of seedlings and adults of C. multiflora were 0.431 and 0.436, and the mean fixation indices (F_m), 0.114 and 0.176, respectively. For C. guianensis, saplings and adults presented H_em equal to 0.425 and 0.429, and the F_m were 0.393 and 0.527, respectively. These low-density populations of two congeneric species did not differ in terms of genetic diversity, but rather they differed in terms of mean observed heterozygosity (H_om), and therefore F_m. The species with variable population density had lower H_om and greater F_m relative to the species that is always found in low-density.     

Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification

Competition can drive macroevolutionary change, for example during adaptive radiations. However, we still lack a clear understanding of how it shapes diversification processes and patterns. To better understand the macroevolutionary consequences of competition, as well as the signal left on phylogenetic data, we developed a model linking trait evolution and species diversification in an ecological context. We find four main results: first, competition spurs trait diversity but not necessarily species richness; second, competition produces slowdowns in species diversification even in the absence of explicit ecological limits, but not in phenotypic diversification even in the presence of such limits; third, early burst patterns do not provide a reliable way of testing for adaptive radiations; and fourth, looking for phylogenetic signal in trait data and support for phenotypic models incorporating competition is a better alternative. Our results clarify the macroevolutionary consequences of competition and could help design more powerful tests of adaptive radiations in nature.     

A multiple peak adaptive landscape based on feeding strategies and roosting ecology shaped the evolution of cranial covariance structure and morphological differentiation in phyllostomid bats

We explored the evolution of morphological integration in the most noteworthy example of adaptive radiation in mammals, the New World leaf‐nosed bats, using a massive dataset and by combining phylogenetic comparative methods and quantitative genetic approaches. We demonstrated that the phenotypic covariance structure remained conserved on a broader phylogenetic scale but also showed a substantial divergence between interclade comparisons. Most of the phylogenetic structure in the integration space can be explained by splits at the beginning of the diversification of major clades. Our results provide evidence for a multiple peak adaptive landscape in the evolution of cranial covariance structure and morphological differentiation, based upon diet and roosting ecology. In this scenario, the successful radiation of phyllostomid bats was triggered by the diversification of dietary and roosting strategies, and the invasion of these new adaptive zones lead to changes in phenotypic covariance structure and average morphology. Our results suggest that intense natural selection preceded the invasion of these new adaptive zones and played a fundamental role in shaping cranial covariance structure and morphological differentiation in this hyperdiverse clade of mammals. Finally, our study demonstrates the power of combining comparative methods and quantitative genetic approaches when investigating the evolution of complex morphologies.