Contributors: Haenel, Gregory J.
... Introgression of mtDNA appears common in animals but the implications of acquiring a novel mitochondrial genome are not well known. This study investigates mito-genome introgression between the lizard species Urosaurus graciosus, a thermal specialist, and U. ornatus, a species that occupies a wider range of thermal environments. As ectotherms, their metabolic rate is strongly influenced by the thermal environment; with mitochondria being linked to metabolic rates, overall energy budgets could be impacted by introgression. I use mitochondrial gene trees, inferred from Bayesian analyses of Cyt-B and ND1 gene sequences, along with morphology and microsatellites from nineteen populations of these two species to address if the direction and location of mito-nuclear discordance match predictions of introgression resulting from past population expansions. MtDNA is expected to move from resident species into expanding or invading species. Second, does having a heterospecific form of mitochondria impact body size, a trait strongly associated with fitness? Multiple independent introgression events of historic origin were detected. All introgression was unidirectional with U. ornatus-type mtDNA found in U. graciosus parental type individuals. This result was consistent with population expansions detected in U. graciosus but not U. ornatus. Females with heterospecific mtDNA were significantly smaller than homospecific forms and heterospecific males had a different relationship of body mass to body length than those with homospecific mtDNA. These changes indicate a potential selective disadvantage for individuals with heterospecific mitochondria and are consistent with the theoretical expectation that deleterious alleles are more likely to persist in expanding populations.
Data from: Construction of a species-level tree of life for the insects and utility in taxonomic profiling
Contributors: Chesters, Douglas
... Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications.
Data from: The diverse fossil chelonians from Milia (Late Pliocene, Grevena, Greece) with a new species of Testudo Linnaeus, 1758 (Testudines: Testudinidae)
Contributors: Vlachos, Evangelos, Tsoukala, Evangelia
... The late Pliocene (early Villafranchian, MN 16a) locality of Milia (Grevena, Greece) has yielded numerous remains of mammals, such as zygodons, mastodons, rhinocerotids, hipparions, bovids, cervids, suids, carnivorans and tapirs. Several specimens of chelonians have also been discovered and comprise a small testudinid, a geoemydid and a giant tortoise. The presence of a giant tortoise and the presence of a geoemydid with large dimensions are further examples of the trend towards gigantism evidenced by the diverse fauna of Milia. In terms of taxonomic abundance of extinct turtles, this is the richest locality in Greece. The small testudinid is of particular importance because it preserves a posteriorly flared carapace, as in the extant Testudo marginata, but the posterior carapace is much taller and anteroposteriorly shorter. These characters allow us to erect a new species, Testudo brevitesta sp. nov., and to discuss the presence of the marginated tortoise and closely related forms in Greece. The new taxon is analysed in a phylogenetic context within other extant and extinct testudinids, providing new information on the clade Testudona.
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Data from: Oceanographic currents and local ecological knowledge indicate, and genetics does not refute, a contemporary pattern of larval dispersal for the ornate spiny lobster, Panulirus ornatus in the South-East Asian archipelago
Contributors: Dao, Hoc Tan, Smith-Keune, Carolyn, Wolanski, Eric, Jones, Clive M., Jerry, Dean R.
... Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.
Data from: A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis
Contributors: Mimee, Benjamin, Duceppe, Marc-Olivier, Véronneau, Pierre-Yves, Lafond-Lapalme, Joël, Jean, Martine, Belzile, François, Bélair, Guy
... Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species.
Data from: A rich fossil record yields calibrated phylogeny for Acanthaceae (Lamiales) and evidence for marked biases in timing and directionality of intercontinental disjunctions
Contributors: Tripp, Erin A., McDade, Lucinda A.
... More than a decade of phylogenetic research has yielded a well-sampled, strongly supported hypothesis of relationships within the large (> 4,000 species) plant family Acanthaceae. This hypothesis points to intriguing biogeographic patterns and asymmetries in sister clade diversity but, absent a time-calibrated estimate for this evolutionary history, these patterns have remained unexplored. Here, we reconstruct divergence times within Acanthaceae using fossils as calibration points, experimenting both with fossil selection and effects of invoking a maximum age prior related to the origin of Eudicots. Contrary to earlier reports of a paucity of fossils of Lamiales (an order of ~23,000 species that includes Acanthaceae) and to the expectation that a largely herbaceous to soft-wooded and tropical lineages would have few fossils, we recovered 51 reports of fossil Acanthaceae. Rigorous evaluation of these for accurate identification, quality of age assessment, and utility in dating yielded eight fossils judged to merit inclusion in analyses. With nearly 10 kilobases of DNA sequence data, we used two sets of fossils as constraints to reconstruct divergence times. We demonstrate differences in age estimates depending on fossil selection and that enforcement of maximum age priors substantially alters estimated clade ages, especially in analyses that utilize a smaller rather than larger set of fossils. Our results suggest that long-distance dispersal events better explain present-day distributions than do Gondwanan or northern land bridge hypotheses. This biogeographical conclusion is for the most part robust to alternative calibration schemes. Our data support a minimum of 13 Old World to New World dispersal events but, intriguingly, only one in the reverse direction. Eleven of these 13 were among Acanthaceae s.s., which comprises > 90% of species diversity in the family. Remarkably, if minimum age estimates approximate true history, these 11 events occurred within the last ~20 million years even though Acanthaceae s.s is over three times as old. A simulation study confirmed that these dispersal events were significantly skewed towards the present and not simply a chance occurrence. Finally, we review reports of fossils that have been assigned to Acanthaceae that are substantially older than the lower Cretaceous estimate for Angiosperms as a whole (i.e., the general consensus that has resulted from several recent dating and fossil-based studies in plants). This is the first study to reconstruct divergence times among clades of Acanthaceae and sets the stage for comparative evolutionary research in this and related families that have until now been thought to have extremely poor fossil resources.