Marginal likelihoods in phylogenetics: a review of methods and applications

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation (ABC) to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.Comment: 33 pages, 3 figure

How was it for you? Experiences of participatory design in the UK health service

Improving co-design methods implies that we need to understand those methods, paying attention to not only the effect of method choices on design outcomes, but also how methods affect the people involved in co-design. In this article, we explore participants' experiences from a year-long participatory health service design project to develop ‘Better Outpatient Services for Older People’. The project followed a defined method called experience-based design (EBD), which represented the state of the art in participatory service design within the UK National Health Service. A sample of participants in the project took part in semi-structured interviews reflecting on their involvement in and their feelings about the project. Our findings suggest that the EBD method that we employed was successful in establishing positive working relationships among the different groups of stakeholders (staff, patients, carers, advocates and design researchers), although conflicts remained throughout the project. Participants' experiences highlighted issues of wider relevance in such participatory design: cost versus benefit, sense of project momentum, locus of control, and assumptions about how change takes place in a complex environment. We propose tactics for dealing with these issues that inform the future development of techniques in user-centred healthcare design

Simulating the midlatitude atmospheric circulation: what might we gain from high-resolution modeling of air-sea interactions?

Purpose of Review. To provide a snapshot of the current research on the oceanic forcing of the atmospheric circulation in midlatitudes and a concise update on previous review papers. Recent findings. Atmospheric models used for seasonal and longer timescales predictions are starting to resolve motions so far only studied in conjunction with weather forecasts. These phenomena have horizontal scales of ~ 10–100 km which coincide with energetic scales in the ocean circulation. Evidence has been presented that, as a result of this matching of scale, oceanic forcing of the atmosphere was enhanced in models with 10–100 km grid size, especially at upper tropospheric levels. The robustness of these results and their underlying mechanisms are however unclear. Summary. Despite indications that higher resolution atmospheric models respond more strongly to sea surface temperature anomalies, their responses are still generally weaker than those estimated empirically from observations. Coarse atmospheric models (grid size greater than 100 km) will miss important signals arising from future changes in ocean circulation unless new parameterizations are developed

The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands

We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion

Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro- and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here, we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole

Boophis schuboeae

<i>Boophis schuboeae</i> <p> Madagascar: <i>Fianarantsoa province</i>: Ranomafana National Park, Ambatolahy (21°14'38"S, 47°25'34.3"E; 919 m, a.s.l.), UADBA-Uncatalogued (CRH 818) and UADBA-Uncatalogued (CRH 846).</p> <p> <b>APPENDIX II</b>. GenBank accession numbers of newly determined DNA sequences for taxa used in this study. All localities are within Madagascar.</p> <p> Museum or Species Locality GenBank Accession ID collection ID 16S DNAH-3 <b>APPENDIX III</b>. Previously available GenBank accession numbers used in this study for the mitochondrial marker 16S. GenBank Accession ID’s with an asterisk are those used in the phylogenetic analyses while all sequences listed were used for genetic distances.</p> <p> Museum or Collection ID Species Genbank Accession ID ZCMV 4946 <i>Boophis albipunctatus</i> GU974374</p> <p> ZCMV 4942 <i>Boophis albipunctatus</i> GU974373</p> <p> MRSN A6371 <i>Boophis albipunctatus</i> HM364574 MRSN A6219 <i>Boophis albipunctatus</i> HM364573 MRSN A6197 <i>Boophis albipunctatus</i> HM364572 FGZC 291 <i>Boophis albipunctatus</i> AY848446 * ZCMV 10348 <i>Boophis ankaratra</i> KF609605 * ZCMV 5989 <i>Boophis ankaratra</i> GU974475 * ZCMV 4917 <i>Boophis ankaratra</i> GU974476 * FGMV 2001/480 <i>Boophis ankaratra</i> AF411612</p> <p> FGMV 2002/1699 <i>Boophis ankaratra</i> DQ068398</p> <p> FGMV 2002/1697 <i>Boophis ankaratra</i> DQ068396 * FAZC 13998 <i>Boophis ankaratra</i> JF903873</p> <p> ZCMV 0 9739 <i>Boophis boppa</i> KF609604 * ZSM 1164/2007 <i>Boophis boppa</i> GU974477 * FAZC 11480 <i>Boophis boppa</i> AY848438 * FAZC 11462 <i>Boophis boppa</i> AY848437 * FAZC 11454 <i>Boophis boppa</i> AY848436 * FGZC 239 <i>Boophis haingana</i> AY848463 * FGZC 232 <i>Boophis haingana</i> AY848462 * FGZC 220 <i>Boophis haingana</i> AY848461 * FGZC 219 <i>Boophis haingana</i> AY848460 * FGZC 218 <i>Boophis haingana</i> AY848459 * FGZC 2390 <i>Boophis haingana</i> FJ559142 *</p> <p> ZCMV 687 <i>Boophis luciae</i> AY848443</p> <p> ZCMV 10501 <i>Boophis luciae</i> KF609714</p> <p> ZCMV 10100 <i>Boophis luciae</i> KF609745</p> <p> ZCMV 0 9106 <i>Boophis luciae</i> KF609730 * ZCMV 4564 <i>Boophis luciae</i> GU975078</p> <p> ZCMV 4202 <i>Boophis luciae</i> GU975079</p> <p> ZCMV 0 9744 <i>Boophis luciae</i> KF610983</p> <p> ZCMV 0 9740 <i>Boophis luciae</i> KF610982</p> <p> ZCMV 0 9731 <i>Boophis luciae</i> KF610981</p> <p> ZCMV 0 9192 <i>Boophis luciae</i> KF610980 * ZCMV 0 9513 <i>Boophis luciae</i> KF610971</p> <p> ZCMV 0 9628 <i>Boophis luciae</i> KF610968</p> <p> ZCMV 0 9626 <i>Boophis luciae</i> KF610967</p> <p> FGZC 2389 <i>Boophis miadana</i> FJ559141 *</p> <p> ZCMV 0 9349 <i>Boophis schuboeae</i> KF610486 * ZCMV 5090 <i>Boophis schuboeae</i> GU974829 * ZCMV 5080 <i>Boophis schuboeae</i> GU974830 *</p> <p> <i>......continued on the next page</i> <b>APPENDIX III.</b> (Continued)</p> <p> Museum or Collection ID Species Genbank Accession ID FGMV 2002/1804 <i>Boophis schuboeae</i> DQ068395 * FGMV 2002/1800 <i>Boophis schuboeae</i> DQ068394 * FGMV 2002/1790 <i>Boophis schuboeae</i> DQ068393 * ZSM 39/2002 <i>Boophis sibilans</i> AY341672 * LR 269 <i>Boophis sibilans</i> DQ792492</p>Published as part of <i>Hutter, Carl R., Lambert, Shea M., Cobb, Kerry A., Andriampenomanana, Zo Faniry & Vences, Miguel, 2015, A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex, pp. 531-555 in Zootaxa 4034 (3)</i> on pages 553-555, DOI: 10.11646/zootaxa.4034.3.6, <a href="http://zenodo.org/record/238090">http://zenodo.org/record/238090</a&gt

Boophis luciae

<i>Boophis luciae</i> <p> Madagascar: <i>Fianarantsoa province</i>: Ranomafana National Park, Maharira (21°20'06.3"S, 47°24'28.31"E; 1233 m, a.s.l.), KU 336854. Ranomafana National Park, Valohoaka (21°17'51.3"S, 47°26'20.1"E; 1064 m, a.s.l.), KU 336855 and UADBA- Uncatalogued (CRH 002).</p>Published as part of <i>Hutter, Carl R., Lambert, Shea M., Cobb, Kerry A., Andriampenomanana, Zo Faniry & Vences, Miguel, 2015, A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex, pp. 531-555 in Zootaxa 4034 (3)</i> on page 553, DOI: 10.11646/zootaxa.4034.3.6, <a href="http://zenodo.org/record/238090">http://zenodo.org/record/238090</a&gt

A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex

Hutter, Carl R., Lambert, Shea M., Cobb, Kerry A., Andriampenomanana, Zo Faniry, Vences, Miguel (2015): A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex. Zootaxa 4034 (3): 531-555, DOI: http://dx.doi.org/10.11646/zootaxa.4034.3.

Boophis ankaratra

<i>Boophis ankaratra</i> <p> Madagascar: <i>Fianarantsoa province</i>: Ranomafana National Park, Maharira (21°20'06.3"S, 47°24'28.31"E; 1233 m, a.s.l.), KU 336830 and UADBA-Uncatalogued (CRH-177).</p> <p>Boophis boppa</p> <p> Madagascar: <i>Fianarantsoa province</i>: Ranomafana National Park, Maharira (21°20'06.3"S, 47°24'28.31"E; 1233 m, a.s.l.), KU 336824 (holotype), KU 336825–336829, UADBA-Uncatalogued (CRH 080), UADBA-Uncatalogued (CRH 168), and UADBA-Uncatalogued (CRH 178). Ranomafana National Park, Andemaka (21°07'43.4"S, 47°30'19.4"E, 1237 m, a.s.l.), Uncatalogued (CRH 775).</p>Published as part of <i>Hutter, Carl R., Lambert, Shea M., Cobb, Kerry A., Andriampenomanana, Zo Faniry & Vences, Miguel, 2015, A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex, pp. 531-555 in Zootaxa 4034 (3)</i> on page 553, DOI: 10.11646/zootaxa.4034.3.6, <a href="http://zenodo.org/record/238090">http://zenodo.org/record/238090</a&gt