Shifting distributions and speciation: species divergence during rapid climate change

Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200 000 and 300 000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species distributions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75592/1/j.1365-294X.2006.03167.x.pd

Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats

Coalescent model–based methods for phylogeny estimation force systematists to confront issues related to the identification of species boundaries. Unlike conventional phylogenetic analysis, where species membership can be assessed qualitatively after the phylogeny is estimated, the phylogenies that are estimated under a coalescent model treat aggregates of individuals as the operational taxonomic units and thus require a priori definition of these sets because the models assume that the alleles in a given lineage are sampled from a single panmictic population. Fortunately, the use of coalescent model–based approaches allows systematists to conduct probabilistic tests of species limits by calculating the probability of competing models of lineage composition. Here, we conduct the first exploration of the issues related to applying such tests to a complex empirical system. Sequence data from multiple loci were used to assess species limits and phylogeny in a clade of North American Myotis bats. After estimating gene trees at each locus, the likelihood of models representing all hierarchical permutations of lineage composition was calculated and Akaike information criterion scores were computed. Metrics borrowed from information theory suggest that there is strong support for several models that include multiple evolutionary lineages within the currently described species Myotis lucifugus and M. evotis. Although these results are preliminary, they illustrate the practical importance of coupled species delimitation and phylogeny estimation

Navigating the unknown: model selection in phylogeography

Despite the widespread use and obvious strengths of model-based methods for phylogeographic study, a persistent concern for such analyses is related to the definition of the model itself. The study by Peter et al. (2010) in this issue of Molecular Ecology demonstrates an approach for overcoming such hurdles. The authors were motivated by a deceptively simple goal; they sought to infer whether a population has remained at a low and stable size or has undergone a decline, and certainly there is no shortage of software packages for such a task (e.g., see list of programs in Excoffier & Heckel 2006 ). However, each of these software packages makes basic assumptions about the underling population (e.g., is the population subdivided or panmictic); these assumptions are explicit to any model-based approach but can bias parameter estimates and produce misleading inferences if the model does not approximate the actual demographic history in a reasonable manner. Rather than guessing which model might be best for analyzing the data (microsatellite data from samples of chimpanzees), Peter et al. (2010) quantify the relative fit of competing models for estimating the population genetic parameters of interest. Complemented by a revealing simulation study, the authors highlight the peril inherent to model-based inferences that lack a statistical evaluation of the fit of a model to the data, while also demonstrating an approach for model selection with broad applicability to phylogeographic analysis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79081/1/j.1365-294X.2010.04851.x.pd

INTEGRATING COALESCENT AND ECOLOGICAL NICHE MODELING IN COMPARATIVE PHYLOGEOGRAPHY

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73659/1/Appendix+S1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/73659/2/j.1558-5646.2007.00117.x.pd

Pemasaran Hijau Yang Semakin Menjadi Kebutuhan Dalam Dunia Bisnis

Green marketing is a type of marketing where a company sells a product that is envi-ronmentally friendly. In the concept of green marketing, a company has done greenmarketing since the beginning of the production process which transform raw materi-als into environmentally friendly finished product, called green product. The growingglobal warming make the green marketing is a major issue in today\u27s business world.Green marketing has become a necessity for both producers and consumers for thecreation of a healthy environment. A company can do green marketing that matchesto the company\u27s business. Implementation of green marketing can cover many ac-tivities depending on what the company wants to do. Automotive manufacturers arean example of a company that must implement a comprehensive green marketingbecause its products could potentially damage the environment due to pollution fromvehicle fumes

X Chromosome Inactivation and Xist Evolution in a Rodent Lacking LINE-1 Activity

Dosage compensation in eutherian mammals occurs by inactivation of one X chromosome in females. Silencing of that X chromosome is initiated by Xist, a large non-coding RNA, whose coating of the chromosome extends in cis from the X inactivation center. LINE-1 (L1) retrotransposons have been implicated as possible players for propagation of the Xist signal, but it has remained unclear whether they are essential components. We previously identified a group of South American rodents in which L1 retrotransposition ceased over 8 million years ago and have now determined that at least one species of these rodents, Oryzomys palustris, still retains X inactivation. We have also isolated and analyzed the majority of the Xist RNA from O. palustris and a sister species retaining L1 activity, Sigmodon hispidus, to determine if evolution in these sequences has left signatures that might suggest a critical role for L1 elements in Xist function. Comparison of rates of Xist evolution in the two species fails to support L1 involvement, although other explanations are possible. Similarly, comparison of known repeats and potential RNA secondary structures reveals no major differences with the exception of a new repeat in O. palustris that has potential to form new secondary structures

Pengaruh Macam Bahan Organik Dan Inokulum Rhizobium Terhadap Pertumbuhan Dan Hasil Tanaman Kedelai (Glycine Max (L.) Merril)

Kedelai (Glycine max (L.) Merril) merupakan tanaman pangan yang penting di Indonesia. Sebagai tanaman golongan Leguminoceae, tanaman kedelai mampu mengadakan simbiosis dengan bakteri tertentu sehingga dapat langsung memfiksasi nitrogen dari udara. Tujuan penelitian ini ialah mempelajari pengaruh interaksi macam bahan organik dan dosis legin terhadap peningkatan pertumbuhan dan hasil tanaman kedelai (Glycine max (L.) Merril). Hipotesis yang diajukan ialah macam bahan organik dapat mempengaruhi kebutuhan dosis legin untuk meningkatkan pertumbuhan dan hasil tanaman kedelai (Glycine max (L.) Merril). Penelitian dilaksanakan di Kebun Percobaan Fakultas Pertanian desa Jatikerto, kecamatan Kromengan, kabupaten Malang. Penelitian dilaksanakan pada bulan Juni 2014 sampai bulan September 2014. Alat yang digunakan pada penelitian ialah Leaf Area Meter (LAM), timbangan analitik, meteran dan oven. Bahan yang digunakan adalah benih kedelai varietas Grobogan. Perlakuan yang diberikan yaitu faktor satu adalah pemberian bahan organik yang terdiri dari: B1=tanpa aplikasi bahan organik, B2=residu biochar dan B3= kompos 10 ton ha-1. Faktor kedua adalah penggunaan legin yang terdiri dari: L1 = tanpa legin, L2 = dosis legin 8 g kg-1 dan L3 = dosis legin 12 g kg-1. Hasil penelitian menunjukkan penambahan bahan organik kompos 10 ton ha-1 dan residu biochar tidak mempengaruhi kebutuhan dosis legin. Kompos 10 ton ha-1 nyata untuk meningkatkan jumlah polong per tanaman kedelai (Glycine max (L.) Merril) sebesar 71,21 %. Dosis legin tidak nyata terhadap hasil panen tanaman kedelai (Glycine max (L.) Merril)

Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater)

Brown-headed Cowbirds (Molothrus ater) are the most widespread avian brood parasite in North America, laying their eggs in the nests of approximately 250 host species that raise the cowbird nestlings as their own. It is currently unknown how these heterospecific hosts influence the cowbird gut microbiota relative to other factors, such as the local environment and genetics. We test a Nature Hypothesis (positing the importance of cowbird genetics) and a Nurture Hypothesis (where the host parents are most influential to cowbird gut microbiota) using the V6 region of 16S rRNA as a microbial fingerprint of the gut from 32 cowbird samples and 16 potential hosts from nine species. We test additional hypotheses regarding the influence of the local environment and age of the birds.We found no evidence for the Nature Hypothesis and little support for the Nurture Hypothesis. Cowbird gut microbiota did not forma clade, but neither did members of the host species. Rather, the physical location, diet and age of the bird, whether cowbird or host, were the most significant categorical variables. Thus, passerine gut microbiota may be most strongly influenced by environmental factors. To put this variation in a broader context, we compared the bird data to a fecal microbiota dataset of 38 mammal species and 22 insect species. Insects were always the most variable; on some axes, we found more variation within cowbirds than across all mammals. Taken together, passerine gut microbiota may be more variable and environmentally determined than other taxonomic groups examined to date. © 2014 Hird et al

Poor fit to the multispecies coalescent is widely detectable in empirical data

Model checking is a critical part of Bayesian data analysis, yet it remains largely unused in systematic studies. Phylogeny estimation has recently moved into an era of increasingly complex models that simultaneously account for multiple evolutionary processes, the statistical fit of these models to the data has rarely been tested. Here we develop a posterior predictive simulation-based model check for a commonly used multispecies coalescent model, implemented in *BEAST, and apply it to 25 published data sets. We show that poor model fit is detectable in the majority of data sets; that this poor fit can mislead phylogenetic estimation; and that in some cases it stems from processes of inherent interest to systematists. We suggest that as systematists scale up to phylogenomic data sets, which will be subject to a heterogeneous array of evolutionary processes, critically evaluating the fit of models to data is an analytical step that can no longer be ignored. [Gene duplication and extinction; gene tree; hybridization; model fit; multispecies coalescent; next-generation sequencing; posterior predictive simulation; species delimitation; species tree.] © The Author(s) 2013