More Like this

1. Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids?

   Gaynor, Michelle L ; Ng, Julienne ; Laport, Robert G. ( April 2018 , Frontiers in ecology and evolution)

   Polyploidy is widely acknowledged to have played an important role in the evolution and diversification of vascular plants. However, the influence of genome duplication on population-level dynamics and its cascading effects at the community level remain unclear. In part, this is due to persistent uncertainties over the extent of polyploid phenotypic variation, and the interactions between polyploids and co-occurring species, and highlights the need to integrate polyploid research at the population and community level. Here, we investigate how community-level patterns of phylogenetic relatedness might influence escape from minority cytotype exclusion, a classic population genetics hypothesis about polyploid establishment, and population-level species interactions. Focusing on two plant families in which polyploidy has evolved multiple times, Brassicaceae and Rosaceae, we build upon the hypothesis that the greater allelic and phenotypic diversity of polyploids allow them to successfully inhabit a different geographic range compared to their diploid progenitor and close relatives. Using a phylogenetic framework, we specifically test (1) whether polyploid species are more distantly related to diploids within the same community than co-occurring diploids are to one another, and (2) if polyploid species tend to exhibit greater ecological success than diploids, using species abundance in communities as an indicator of successful establishment.more »Overall, our results suggest that the effects of genome duplication on community structure are not clear-cut. We find that polyploid species tend to be more distantly related to co-occurring diploids than diploids are to each other. However, we do not find a consistent pattern of polyploid species being more abundant than diploid species, suggesting polyploids are not uniformly more ecologically successful than diploids. While polyploidy appears to have some important influences on species co-occurrence in Brassicaceae and Rosaceae communities, our study highlights the paucity of available geographically explicit data on intraspecific ploidal variation. The increased use of high-throughput methods to identify ploidal variation, such as flow cytometry and whole genome sequencing, will greatly aid our understanding of how such a widespread, radical genomic mutation influences the evolution of species and those around them.« less
2. Biotic interactions are the dominant drivers of phylogenetic and functional structure in bird communities along a tropical elevational gradient

   https://doi.org/10.1093/auk/ukz054  

   Boyce, Andy J ; Shakya, Subir ; Sheldon, Frederick H ; Moyle, Robert G ; Martin, Thomas E ( October 2019 , The Auk)

   Abstract Understanding how biotic and abiotic interactions influence community assembly and composition is a fundamental goal in community ecology. Addressing this issue is particularly tractable along elevational gradients in tropical mountains that feature substantial abiotic gradients and rates of species turnover. We examined elevational patterns of avian community structure on 2 mountains in Malaysian Borneo to assess changes in the relative strength of biotic interactions and abiotic constraints. In particular, we used metrics based on (1) phylogenetic relatedness and (2) functional traits associated with both resource acquisition and tolerance of abiotic challenges to identify patterns and causes of elevational differences in community structure. High elevation communities were composed of more phylogenetically and functionally similar species than would be expected by chance. Resource acquisition traits, in particular, were clustered at high elevations, suggesting low resource and habitat diversity were important drivers of those communities. Traits typically associated with tolerance of cold temperatures and low atmospheric pressure showed no elevational patterns. All traits were neutral or overdispersed at low elevations suggesting an absence of strong abiotic filters or an increased influence of interspecific competition. However, relative bill size, which is important for thermoregulation, was larger in low elevation communities, suggesting abiotic factorsmore »were also influential there. Regardless of metric, clustered and neutral communities were more frequent than overdispersed communities overall, implying that interspecific competition among close relatives may not be a pervasive driver of elevational distribution and community structure of tropical birds. Overall, our analyses reveal that a diverse set of predominantly biotic factors underlie elevational variation in community structure on tropical mountains.« less
3. Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)

   https://doi.org/10.1093/sysbio/syac043  

   Owen, Christopher L. ; Marshall, David C. ; Wade, Elizabeth J. ; Meister, Russ ; Goemans, Geert ; Kunte, Krushnamegh ; Moulds, Max ; Hill, Kathy ; Villet, M. ; Pham, Thai-Hong ; et al ( June 2022 , Systematic Biology)

   Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the anchored hybrid enrichment markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, inmore »part probably due to short length. The cleaned data set, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after the removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution. [Auchenorrhyncha; base-composition bias; Cicadidae; Cicadoidea; Hemiptera; phylogenetic conflict.]

   « less
4. Monkeys in the Middle: Modeling ecological flexibility and niche construction in African cercopithecid primates

   Smail, Irene E. ( March 2020 , Program of the Annual Meeting of the American Association of Physical Anthropologists)

   Niche construction is broadly defined as an organism’s influence over its environment, ranging from the depletion of local resources to the intentional modification of landscapes and ecosystems. While modern humans excel at the latter, the exact timing and nature of our transition to being complex cultural niche constructors remains to be determined. Here I use methods taken from community ecology to develop a baseline model of minimal niche construction within a group of primate generalists. This serves as an important comparison for interpretations of the hominin fossil record and broader paleontological record to determine when and how our hominin ancestors began to diverge from this pattern. Dental metric data were used in principal components analysis to reconstruct the dietary ecomorphological niches of a sample African cercopithecid primates from the Plio-Pleistocene to today. Potential niche construction is identified through the displacement of co-occurring species indicating that the focal taxon has excluded potential competitors through resource depletion. Overall, fossil taxa are shown to occupy a more restricted niche than their extant relatives, but otherwise exhibit similar patterns of dispersion and overlap within and across communities. The lack of consistent trends within the Plio-Pleistocene sample — either through time or in response tomore »potential confamilial competition — supports the idea that these generalized primates are not exerting a significant influence over their local environments. I conclude with some suggestions on expanding these analyses to look for evidence of niche construction in other paleontological and paleoanthropological contexts.« less
5. Unexpectedly high levels of lineage diversity in Sundaland Puddle Frogs (Dicroglossidae: Occidozyga Kuhl and Van Hasselt, 1822).

   Flury, J. ( January 2021 , Molecular phylogenetics and evolution)

   One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world’s so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads tomore »the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace’s Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.« less