Patterns Of Phylogenetic Structure Research Articles

From clustering to overdispersion: a north to south gradient in the patterns of phylogenetic structure in North American hummingbird assemblages

From clustering to overdispersion: a north to south gradient in the patterns of phylogenetic structure in North American hummingbird assemblages

Macroevolutionary patterns in European vegetation

AbstractQuestionHabitat‐specific species pools are shaped by ecological and evolutionary processes such as speciation, extinction, and migration. However, their role is poorly known because of the lack of robust data on species pools across a large number of plant community types and large areas. Here, we analyse a unique dataset of species pools of diagnostic species for all European vegetation types, asking: (a) what are the patterns of phylogenetic structure and phylogenetic beta‐diversity across European vegetation types and biomes; (b) what are the drivers of these patterns; and (c) is there a signal of niche conservatism at the level of biomes and broad categories of vegetation types?LocationEurope, Canary Islands, Madeira, Azores, Cyprus, Caucasus, Iceland and Greenland.MethodsWe built a dataset comprising 10,804 vascular plant species (almost 85% of the European flora) assigned to 106 vegetation types representing all European vegetated habitats, grouped into 11 biomes. This dataset represented habitat‐specific species pools. We analysed the phylogenetic structure of the species pools and related it to distribution range sizes of individual vegetation types, their successional status, levels of disturbance and environmental stress.ResultsIn European vegetation, phylogenetic overdispersion is associated with late‐successional habitats: several forest types, aquatic vegetation, and rock‐cliff vegetation serve as depositories of relict lineages. In contrast, phylogenetic clustering is typical of early successional and disturbed vegetation in anthropogenic, coastal and saline habitats, and in open‐canopy Mediterranean vegetation. The phylogenetic similarity of vegetation types is higher within than between broad categories of vegetation types and biomes.ConclusionsThe variable phylogenetic structure of European vegetation types is a heritage of evolutionary processes in the Tertiary and Quaternary. Habitat‐specific species pools of different vegetation types and biomes have been formed by different evolutionary processes as indicated by the observation that certain clades are significantly associated with certain vegetation types or biomes, hence indicating the phylogenetic niche conservatism.

Review of Brazilian jawfishes of the genus Opistognathus with descriptions of two new species (Teleostei, Opistognathidae)

A new species of jawfish, Opistognathusthionyisp. n., is described from the Vitória-Trindade Chain and Fernando de Noronha Archipelago off Brazil, a disjunct distribution of ca. 1,800 km. Opistognathusthionyi and its allopatric Caribbean sister-species, Opistognathusmaxillosus, both have a wide, fan-like upper margin of the subopercular flap and mostly over-lapping meristic data. The new species differs from O.maxillosus in having the darkest spot on the spinous dorsal fin, when present, between spines 2–5, versus always present between spines 6–9, the buccal area surrounding the esophageal opening pale versus very dark and fewer oblique scale rows in longitudinal series (45–52 vs. 69–85). A second new species, Opistognathusvicinussp. n., known from Brazil’s mainland, has completely over-lapping meristic values with its allopatric Caribbean sister-species O.whitehursti, but differs in lacking vomerine teeth and a supramaxilla and retaining the juvenile color pattern of the latter species in adults. Diagnoses, photographs, an identification key, and distributional maps are given for all Brazilian species of Opistognathus.Molecular phylogenetic analysis of partial cytochrome c oxidase subunit-I sequences indicates that specimens of the two allopatric pairs, O.thionyi – O.maxillosus and O.vicinus – O.whitehursti, form reciprocally monophyletic groups that differ from each other on average by 9 to 11%, with less than 1% average pair-wise genetic distance within-species. Similar patterns of phylogenetic structure were observed between reciprocally monophyletic (predominately allopatric) groups within nominal species of Opistognathusaurifrons, suggesting the possibility of at least two additional undescribed species from the Brazilian Province.

Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones.

Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden. Three major patterns emerged. (1) Phylogenetic diversity (PD) was significantly different between arthropod communities on hybrids and Fremont cottonwood when pooled by tree type. (2) Mean phylogenetic distance (MPD) and net relatedness index (NRI) indicated that communities on hybrid trees were significantly more phylogenetically overdispersed than communities on either parental tree type. (3) Community distance (D pw) indicated that communities on hybrids were significantly different than parental species. Our results show that arthropod communities on parental and hybrid cottonwoods exhibit significantly different patterns of phylogenetic structure. This suggests that arthropod community assembly is driven, in part, by plant–arthropod interactions at the level of cottonwood tree type. We discuss potential hypotheses to explain the effect of plant genetic dissimilarity on arthropod phylogenetic community structure, including the role of competition and environmental filtering. Our findings suggest that cottonwood species and their hybrids function as evolutionarily significant units (ESUs) that affect the assembly and composition of associated arthropod communities and deserve high priority for conservation.

Evolutionary conservatism explains increasing relatedness of plant communities along a flooding gradient.

Abiotic filters have been found either to increase or reduce evolutionary relatedness in plant communities, making it difficult to generalize responses of this major feature of biodiversity to future environmental change. Here, we hypothesized that the responses of phylogenetic structure to environmental change ultimately depend on how species have evolved traits for tolerating the resulting abiotic changes. Working within ephemeral wetlands, we tested whether species were increasingly related as flooding duration intensified. We also identified the mechanisms underlying increased relatedness by measuring root aerenchyma volume (RAV), a trait which promotes waterlogging tolerance. We found that species-specific responses to flooding explained most of the variation in occurrence for 63 vascular plant species across 5170 plots. For a subset of 22 species, we attributed these responses to variation in RAV. Large RAV specifically increased occurrence when flooding lasted for longer time periods, because large RAV reduced above-ground biomass loss. As large RAV was evolutionarily conserved within obligate wetland species, communities were more phylogenetically related as flooding increased. Our study shows how reconstructing the evolutionary history of traits that influence the responses of species to environmental change can help to predict future patterns in phylogenetic structure.

No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses.

The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudoposterior distributions of phylogenetic trees that are complete at the species level, even in the absence of genetic data for many species. Many researchers have used these distributions of phylogenies for downstream evolutionary analyses that involve inferences on phenotypic evolution, geography, and community assembly. I demonstrate that the use of phylogenies constructed in this fashion is inappropriate for many questions involving traits. Because species are placed on trees at random with respect to trait values, the birth-death polytomy resolver breaks down natural patterns of trait phylogenetic structure. Inferences based on these trees are predictably and often drastically biased in a direction that depends on the underlying (true) pattern of phylogenetic structure in traits. I illustrate the severity of the phenomenon for both continuous and discrete traits using examples from a global bird phylogeny.

Contrasting lineage‐specific patterns conceal community phylogenetic structure in larger clades

AbstractQuestionCommunity phylogenetic approaches can provide information on the ecological forces structuring plant community composition. For example, assuming evolutionary conservatism of ecological traits, environmental filtering has been suggested to result in phylogenetic clustering, whereas competition has been suggested to lead to phylogenetic over‐dispersion. However, current approaches report aggregate community‐wide metrics and typically assume that all lineages respond similarly. Here, we question this assumption and evaluate evidence for lineage‐specific patterns of co‐occurrence.LocationEastern Canadian subarctic.MethodsWe use a novel individual‐based, neighbourhood approach to evaluate lineage‐specific co‐occurrence patterns among 35 focal species of Cyperaceae (sedges). Cyperaceae is a species‐rich clade, with many species sharing similar niche preferences and environmental tolerances, making this a model clade for evaluating interspecific interaction strengths.ResultsWe reveal striking differences in co‐occurrence patterns between clades. Within the Cyperaceae, the two species of the genus Trichophorum tended to cluster with each other, whereas species within Eriophorum co‐occurred more often with less closely related neighbours. These contrasting patterns repeated themselves within Carex, with species in the Core Carex clade more often co‐occurring with close relatives, while phylogenetic over‐dispersion was more prominent in the Vignea clade. As a consequence of these opposing lineage‐specific relationships, the overall phylogenetic structure of sedge communities appears random.ConclusionsWe show opposing lineage‐specific patterns in phylogenetic structure that are obscured when species are aggregated into larger clades. Our results reveal cryptic complexities in plant community assembly across taxonomic scales, and indicate that different plant lineages may vary in their response to community‐level processes. We suggest that the processes underlying community composition can be better understood by using alternative sampling and analytical approaches combined with thoughtfully‐created null models.

Phylogenetic gradient analysis: environmental drivers of phylogenetic variation across ecological communities

Differences in species composition across ecological communities are the result of multiple interacting mechanisms. Gradient analysis has been perhaps the most widely used statistical framework in describing how ecological communities vary in space, and aiding in determining the causes underlying these patterns. Direct gradient analysis allows the use of predictors such as environmental factors and spatial descriptors to directly estimate their contributions in explaining common and independent patterns of species distributions. In recent years, ecologists have started to explore how evolutionary history is associated with community patterns given the observation that species that share a common phylogenetic history tend also to have similar niches. Although ecological phylogenetics is among the fastest-growing fields in ecology, gradient analysis has not yet been fully integrated in this field. In this paper, we show and adapt the versatility of gradient analysis in describing and interpreting patterns of ecological communities based on their patterns of phylogenetic structure. Describing phylogenetic patterns across communities presents additional challenges regarding statistical inference in contrast to classic direct gradient analysis that are described and tackled here. We investigate the performance of our phylogenetic gradient analysis frameworks using simulations and provide a detailed example using a grassland community dataset.

Phylogenetic structure and phylogenetic diversity of angiosperm assemblages in forests along an elevational gradient in Changbaishan, China

Aims Understanding what drives the variation in species composition and diversity among local communities can provide insights into the mechanisms of community assembly. Because ecological traits are often thought to be phylogenetically conserved, there should be patterns in phylogenetic structure and phylogenetic diversity in local communities along ecological gradients. We investigate potential patterns in angiosperm assemblages along an elevational gradient with a steep ecological gradient in Changbaishan, China. Methods We used 13 angiosperm assemblages in forest plots (32 × 32 m) distributed along an elevational gradient from 720 to 1900 m above sea level. We used Faith’s phylogenetic diversity metric to quantify the phylogenetic alpha diversity of each forest plot, used the net relatedness index to quantify the degree of phylogenetic relatedness among angiosperm species within each forest plot and used a phylogenetic dissimilarity index to quantify phylogenetic beta diver sity among forest plots. We related the measures of phylogenetic structure and phylogenetic diversity to environmental (climatic and edaphic) factors. Important Findings Our study showed that angiosperm assemblages tended to be more phylogenetically clustered at higher elevations in Changbaishan. This finding is consistent with the prediction of the phylogenetic niche conservatism hypothesis, which highlights the role of niche constraints in governing the phylogenetic structure of assemblages. Our study also showed that woody assemblages differ from her baceous assemblages in several major aspects. First, phylogenetic clustering dominated in woody assemblages, whereas phylogenetic overdispersion dominated in herbaceous assemblages; second, patterns in phylogenetic relatedness along the elevational and temperature gradients of Changbaishan were stronger for woody assemblages than for herbaceous assemblages; third, environmental variables explained much more variations in phylogenetic relatedness, phylogenetic alpha diversity and phylogenetic beta diversity for woody assemblages than for herbaceous assemblages.