459 research outputs found
Testing for dependence on tree structures
No full textTree structures, showing hierarchical relationships and the latent structures between samples, are ubiquitous in genomic and biomedical sciences. A common question in many studies is whether there is an association between a response variable measured on each sample and the latent group structure represented by some given tree. Currently, this is addressed on an ad hoc basis, usually requiring the user to decide on an appropriate number of clusters to prune out of the tree to be tested against the response variable. Here, we present a statistical method with statistical guarantees that tests for association between the response variable and a fixed tree structure across all levels of the tree hierarchy with high power while accounting for the overall false positive error rate. This enhances the robustness and reproducibility of such findings
Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a
No full textStudies have shown that hepatitis C virus subtype 3a (HCV-3a) is likely to have been circulating in South Asia before its global spread. However, the time and route of this dissemination remain unclear. For the first time, we generated host and virus genome-wide data for more than 500 patients infected with HCV-3a from the UK, North America, Australia, and New Zealand. We used the host genomic data to infer the ancestry of the patients and used this information to investigate the epidemic history of HCV-3a. We observed that viruses from hosts of South Asian ancestry clustered together near the root of the tree, irrespective of the sampling country, and that they were more diverse than viruses from other host ancestries. We hypothesized that South Asian hosts are more likely to have been infected in South Asia and used the inferred host ancestries to distinguish between the location where the infection was acquired and where the sample was taken. Next, we inferred that three independent transmission events resulted in the spread of the virus from South Asia to the UK, North America, and Oceania. This initial spread happened during or soon after the end of World War II. This was subsequently followed by many independent transmissions between the UK, North America, and Oceania. Using both host and virus genomic information can be highly informative in studying the virus epidemic history, especially in the context of chronic infections where migration histories need to be accounted for
Tagging of Biomedical Articles on CiteULike: A Comparison of User, Author and Professional Indexing
No full textThis paper examines the context of online indexing from the viewpoint of three different groups: users, authors, and professional indexers. User tags, author keywords and descriptors were collected from academic journal articles, which were both indexed in Pubmed and tagged on CiteULike, and analysed. Descriptive statistics, informetric measures, and thesaural term comparison shows that there are important differences in the use of keywords between the three groups in addition to similarities which can be used to enhance support for search and browse. While tags and author keywords were found that matched descriptors exactly, other terms which did not match but provided important expansion to the indexing lexicon were found. These additional terms could be used to enhance support for searching and browsing in article databases as well as to provide invaluable data for entry vocabulary and emergent terminology for regular updates to indexing systems. Additionally, the study suggests that tags support organisation by association to task, projects and subject while making important connections to traditional systems which classify into subject categories
Myrsidea simplex Ansari 1956
No full textMyrsidea simplex Ansari, 1956 Myrsidea simplex Ansari, 1956: Pak. J. Health, 5: 168, Fig. 5. Type host: Catharus fuscater mentalis Sclater & Salvin, 1876 —Slaty-backed Nightingale-Thrush Material studied. Two females, 3 males, ex Catharus fuscater, COSTA RICA: Tapanti National Park, Sector Tapanti (09° 46 ’N, 83 ° 47 ’W; 1200 m), 2–10 August 2009, Literak and Sychra leg. Deposited in INBio (O.Sychra CR 211–212) and MMBC (O.Sychra CR 213); 2 females and 2 males, ex Catharus aurantiirostris, COSTA RICA: Braulio Carrillo National Park, Sector Barva (10 ˚07’N, 84 ˚07’W; 2600 m), 2 August 2010, Sychra and Literak leg. Deposited in INBio (O.Sychra CR 214–215); 1 male and 1 female ex Catharus aurantiirostris, COSTA RICA: Zona Protectora Las Tablas, La Amistad Lodge (8 ° 54 ’N, 82 ° 47 ’W; 1300 m), 21 August 2010, Sychra and Literak leg. Deposited in MMBC (O.Sychra CR 216); 2 females, ex Catharus mexicanus, COSTA RICA: Rincon de la Vieja National Park, Sector Santa Maria, Sendero del Padre (10 ° 46 ’N, 85 ° 18 ’W; 800 m), 24 August 2009, Literak and Sychra leg. Deposited in INBio (O.Sychra CR 217). Remarks. This is the first record of chewing lice from Catharus aurantiirostris and the second species of Myrsidea from Catharus mexicanus. Our specimens differ from the redescription of M. simplex presented by Clay (1966) by setal counts and dimensions as follows [setal counts and dimensions mentioned by Clay (1966) are in parentheses]: Female (n = 7). Length of DHS 10, 0.040–0.045; DHS 11, 0.100– 0.110; ratio DHS 10 / 11, 0.36–0.45 (0.38–0.42). Metasternal plate with 6–7 setae. Postspiracular setae extremely long, 0.45–0.48, on II, IV and VIII; long, 0.30, on I, and short, 0.11–0.20, on III, V, VI and VII. Sternites III–VII without medioanterior setae. Anal fringe formed by 35–39 dorsal and 34–37 ventral setae. Male (n = 6). Length of DHS 10, 0.040–0.045; DHS 11, 0.090 –0.100; ratio DHS 10 / 11, 0.40–0.50. Metasternal plate with 5–7 setae. With median gap in each tergal setal row. Postspiracular setae as for female. Sternites III–VII without medioanterior setae. Comparisons of females from each host species: ex Catharus fuscater (Lafresnaye, 1845) —Slaty-backed Nightingale-Thrush (n = 2) As in Fig. 30. Metanotum with 12–14 (16–18) marginal setae. Tergal setae: VII, 9–12 (8–11). Sternal setae: II, 7–8 (5) anterior; III, 25–28 (13–15); IV, 35–37 (24–30); V, 33–35 (22–29); VI, 30–31 (20–27); VII, 25 (8–12); VIII–IX, 27–29 (23–27) including 15–16 (12–15) setae on vulval margin. Dimensions: TW, 0.47–0.48 (0.45–0.47); PW, 0.28–0.29 (0.26–0.28); MW, 0.48–0.49 (0.42); AW, 0.54–0.59 (0.53); ANW, 0.22–0.23; TL, 1.47–1.49 (1.50). ex Catharus aurantiirostris (Hartlaub, 1850) — Orange-billed Nightingale-Thrush (n = 3) Metanotum with 14–15 (16–18) marginal setae. Tergal setae: III, 19–22 (22–24); IV, 21–23 (23–27); V, 19–20 (22–27); VII, 10–12 (8–11). Sternal setae: II, 10 (5) anterior; III, 19–20 (13–15); V, 27–31 (22–29); VII, 18–20 (8–12); VIII–IX, 22–24 (23–27) including 12–14 setae on deeply serrated vulval margin. Dimensions: TW, 0.43–0.44 (0.45–0.47); HL, 0.27–0.29 (0.29–0.30); PW, 0.25 (0.26–0.28); MW, 0.42–0.43 (0.42); AW, 0.50–0.53 (0.53); ANW, 0.21–0.22; TL, 1.37–1.41 (1.50). ex Catharus mexicanus (Bonaparte, 1856) —Black-headed Nightingale-Thrush (n = 2) Tergal setae: III, 18–20 (22–24); IV, 20–22 (23–27); V, 19 (22–27). Sternal setae: II, 19–20 (14–16) marginal setae between asters, 9–11 (5) anterior; III, 21–22 (13–15); IV, 30–33 (24–30); V, 29–33 (22–29); VII, 16–18 (8–12). Dimensions: TW, 0.44–0.45 (0.45–0.47); PW, 0.27–0.29 (0.26–0.28); MW, 0.43–0.44 (0.42); AW, 0.51–0.52 (0.53); ANW, 0.20–0.21; TL, 1.37–1.38 (1.50). Comparisons of males from each host species: ex Catharus fuscater (n = 3) As in Fig. 34. Metanotum with 11 (12) marginal setae. Tergal setae: I, 10–11 (10); II, 12–13 (15); III, 14–15 (17–18); IV, 15–16 (14); V, 13 (15); VI, 14 (11); VII, 8 (9). Sternal setae: II, 14 (15) marginal setae between asters, 7 (9) anterior; III, 22 (17); IV, 29–30 (27); V, 29–33 (26); VI, 27–28 (25); VII, 17–22 (15); VIII, 8–11 (8). Dimensions: TW, 0.40–0.43 (0.42); HL, 0.28–0.29 (0.27); PW, 0.26–0.27 (0.25); MW, 0.36–0.37 (0.32); AW, 0.44–0.45 (0.42); TL, 1.21–1.26 (1.22); GW, 0.10–0.11; GSL, 0.08. ex Catharus aurantiirostris (n = 3) Metanotum with 8–10 (12) setae on posterior margin. Tergal setae: I, 12 (10); II, 14–15 (15); III, 15–17 (17–18); IV, 13–15 (14); V 13–14 (15); VI 11–13 (11); VII, 8–9 (9); VIII, 6 (8). Sternal setae: II, 14–15 (15) marginal setae between asters, 6–8 (9) anterior; III, 15–19 (17); IV, 23–31 (27); V, 26–27 (26); VI, 25–26 (25); VII, 16–19 (15). Dimensions: TW, 0.38–0.39 (0.42); HL, 0.26–0.27 (0.27); PW, 0.24–0.25 (0.25); MW, 0.31–0.33 (0.32); AW, 0.40–0.41 (0.42); TL, 1.12–1.17 (1.22); GW, 0.10; GSL, 0.08. Myrsidea tapanti Sychra and Kounek sp. nov. (Figs 23 –24, 28, 32) Type host: Catharus fuscater (Lafresnaye, 1845) – Slaty-backed Nightingale-Thrush Female (n = 4). As in Fig. 28. This species belongs to the thoracica species group sensu Clay (1966). Length of DHS 10, 0.035; DHS 11, 0.105–0.110; ratio DHS 10 / 11, 0.32–0.33. Gula 4–5 setae on each side. Metasternal plate with 6 setae, metanotum enlarged, with 18–23 marginal setae. Femur III with 14–17 setae in ventral setal brush. Abdomen with tergite I enlarged. Tergites I–IV with medioposterior convexity (Fig. 23); wide median gap in the rows of tergal setae presented on IV–VIII. Tergal setae: I, 25; II, 29–31; III, 31–33; IV, 31–33; V, 26–29; VI, 20; VII, 12; VIII, 8. Postspiracular setae extremely long (0.42–0.49) on II, IV and VIII; long (0.25–0.30) on I, III and VII; short (0.15) on V, and very short (0.08–0.10) on VI. Sternal setae: II, 4–5 in each aster, 19–20 marginal setae between asters, 4–5 anterior; III, 18–22; IV, 36; V, 33–35; VI, 27–31; VII, 25; VIII–IX, 26–28 including 14–16 setae on deeply serrated vulval margin; without medioanterior setae on sternites III–VII. Sternites V–VI strongly arched (Fig. 23). Anal fringe formed by 35–40 dorsal and 33–35 ventral setae. Dimensions: TW, 0.46–0.50; HL, 0.29; PW, 0.28–0.29; MW, 0.49–0.51; AW, 0.59–0.60; ANW, 0.21; TL, 1.47–1.49. Male (n = 4). As in Fig. 32. Length of DHS 10, 0.030–0.035; DHS 11, 0.100– 0.105; ratio DHS 10 / 11, 0.29–0.35. Gula with 5 setae on each side. Metasternal plate with 6–7 setae. Metanotum with 14–15 marginal setae. Tergal setae: I, 16–17; II, 20; III, 19–21; IV, 17–19; V, 17; VI, 13–15; VII, 10; VIII, 8. Postspiracular setae: extremely long (0.45) on II and IV; long (0.19–0.25) on I and VII; and somewhat shorter (0.10–0.12) on V. Sternal setae: II, 4 in each aster, 16 marginal setae between asters, 7–11 anterior; III, 21–26; IV, 31–39; V, 32–37; VI, 30–31; VII, 23–24; VIII, 9–13; with medioanterior setae on sternites III, 1; IV, 2; V, 1; VI, 2. Genital sac sclerite short, with a relatively large subapical projection on each side, a concave posterior margin, and without medioposterior line (Fig. 24). Dimensions: TW, 0.40–0.42; HL, 0.24–0.26; PW, 0.26; MW, 0.36; AW, 0.43–0.44; TL, 1.17–1.22; GW, 0.10–0.11; GSL, 0.07–0.08. Type material. Female holotype and paratype male (O.Sychra CR 218), ex Catharus fuscater, COSTA RICA: Tapanti National Park, Sector Tapanti (09° 46 ’N, 83 ° 47 ’W; 1200 m), 2–10 August 2009, Literak and Sychra leg. Paratypes: 3 females and 3 males with the same data as holotype. Deposited in INBio (O.Sychra CR 218–221). Remarks. This is the second species of Myrsidea from Catharus fuscater. The female of M. tapanti sp. nov. is clearly distinguished from those of other species belonging to the thoracica species group by the following characters: (1) enlarged metanotum, (2) unique shape of tergites I–II (Fig. 23), (3) continuous rows of tergal setae on I–III. The male of M. tapanti sp. nov. is well characterized by its genital sac sclerite (Fig. 24), which places this species close to three species from Turdidae: M. rohi Ansari, 1956, M. simplex Ansari, 1956 and M. varia Ansari, 1956. However, the male of M. tapanti sp. nov. can be distinguished from the aforementioned species by its larger number of setae on tergites II–III (19–21 vs. 11–18); and on tergites II–V, together with 73–77 setae vs. 48–65. Etymology. The species epithet derives from the name of the type locality of this new species: Tapanti National Park. Myrsidea tapetapersi Sychra and Kounek sp. nov. (Figs 25 –26, 29, 33) Type host: Turdus nigrescens (Cabanis, 1861) — Sooty Thrush. Female (n = 2). As in Fig. 29. This species belongs to the thoracica species group sensu Clay (1966). Length of DHS 10, 0.075–0.085; DHS 11, 0.110–0.120; ratio DHS 10 / 11, 0.63–0.77. Gula with 5 setae on each side. Metasternal plate with 7 setae, metanotum not enlarged, with 13 marginal setae. Femur III with 18–22 setae in ventral setal brush. Abdomen with tergite I not enlarged, with slightly convex posterior margin. Tergite II enlarged, with strongly convex and pointed posterior margin, tergites III and IV with concave lateral margins and straight medioposterior margins, tergite V only slightly convex (Fig. 25). Tergal setae, with median gap in each row except in tergite I: I, 24; II, 23; III, 19; IV, 17; V, 20; VI, 21; VII, 16; VIII, 8. Postspiracular setae extremely long (0.50–0.56) on II, IV, VII and VIII; very long (0.38) on I; long (0.28) on III; and somewhat shorter (0.19–0.21) on V and VI. Sternal setae: II, 4 in each aster, 17 marginal setae between asters, 10 anterior; III, 23; IV, 31; V, 40; VI, 33; VII, 13; VIII–IX, 26 including 15–16 setae on deeply serrated vulval margin; without medioanterior setae on sternites III–VII. Sternite VI arched (Fig. 25). Anal fringe formed by 48 dorsal and 38 ventral setae. Dimensions: TW, 0.53; HL, 0.33–0.34; PW, 0.31; MW, 0.49; AW, 0.59–0.63; ANW, 0.21–0.25; TL, 1.58–1.65. Male (n = 4). As in Fig. 33. Length of DHS 10, 0.070–0.075; DHS 11, 0.105–0.115; ratio DHS 10 / 11, 0.61–0.71. Gula with 4–5 setae on each side. Metasternal plate with 8 setae, metanotum with 11–12 marginal setae. Tergal setae, with median gap in each row: I, 18; II, 17–18; III, 15–17; IV, 16–18; V, 17; VI, 15; VII, 11–12; VIII, 7–8. Postspiracular setae extremely long (0.50–0.52) on II, IV and VIII; very long (0.40) on VII; long (0.30) on I and III; and somewhat shorter (0.16–0.25) on V and VI. Sternal setae: II, 4 in each aster, 15 marginal setae between asters, 7–8 anterior; III, 18–21; IV, 27–28; V, 30–33; VI, 29; VII, 15–18; VIII, 7; without medioanterior setae. Genital sac sclerite with a large subapical projection on each side, a straight or slightly convex posterior margin and with short, dark medioposterior line (Fig. 26). Dimensions: TW, 0.48–0.49; HL, 0.31–0.32; PW, 0.28–0.29; MW, 0.39–0.41; AW, 0.50; TL, 1.39–1.42; GW, 0.11–0.12; GSL, 0.08. Type material. Holotype female and paratype male (O.Sychra CR 222), 1 female and 3 males paratypes (O.Sychra CR 223–224) ex Turdus nigrescens COSTA RICA: Tapanti National Park, Sector Cerro de la Muerte (9 ° 33 ’N, 83 ° 43 ’W; 3100 m), 12–14 August 2010, Sychra and Literak leg. Deposited in INBio (O.Sychra CR 222–223) and MMBC (O.Sychra CR 224). Remarks. This is the first record of a chewing louse from Turdus nigrescens. The female of M. tapetapersi sp. nov. is clearly distinguished from those of other species belonging to the thoracica species group by the unique shape of its tergites (Fig. 25). The male of M. tapetapersi sp. nov. is characterized by the following features: (1) genital sac sclerite, (2) tergal chaetotaxy, and (3) sternites III–VII without anterior setae and quite large dimensions. These characters place M. tapetapersi sp. nov. close to M. keniensis Clay, 1966 from Turdus abyssinicus Gmelin, 1789 from Kenya. However, the male of M. tapetapersi sp. nov. can be distinguished by its larger number of setae on tergite I (18 vs. 12–13) and sternites IV–V (35–37 vs. 27–33). Etymology. This species is named in honor of Oldrich Sychra Sr, father of the corresponding author, who is also known by his nickname TapeTapers.Published as part of Kounek, Filip, Sychra, Oldrich, Capek, Miroslav & Literak, Ivan, 2013, Chewing lice of genus Myrsidea (Phthiraptera: Menoponidae) from Turdidae (Passeriformes) of Costa Rica, with descriptions of seven new species, pp. 201-222 in Zootaxa 3620 (2) on pages 214-220, DOI: 10.11646/zootaxa.3620.2.1, http://zenodo.org/record/22074
Discusiones sobre la teología de al-Bāqillānī en el Magreb: el Tasdīd fī šarḥ al-Tamhīd de ‘Abd al-Ŷalīl b. Abī Bakr al-Dībāŷī al-raba‘ī
No full text[EN] This paper presents a unique manuscript copy of a fifth/eleventh-century Maghribī commentary on al-Bāqillānī’s Kitāb al-Tamhīd. The work, entitled al-Tasdīd fī sharḥ al-Tamhīd, was written by ‘Abd al-Jalīl b. Abī Bakr alDībājī —also known as Ibn al-Ṣābūnī— who had studied the Kitāb al-Tamhīd with al-Bāqillānī’s disciples in Qayrawān. The present study first reviews the transmission of alBāqillānī’s work to the Islamic west. It then continues to present the author of the commentary, to reconstruct the work’s genesis and to describe its content. The final section focuses on a sample chapter and argues that alDībājī follows al-Bāqillānī’s later position on a specific theory —the so-called theory of aḥwāl— of which the Tamhīd strongly disapproved. The Tasdīd is one of the oldest texts of Maghribī Ash‘arism that has come down to us and provides valuable new insights into the school’s early history in the Islamic west[ES] En este artículo presentamos un manuscrito único de un comentario magrebí del Kitāb alTamhīd de al-Bāqillānī datado en elsiglo V/XI. La obra se titula al-Tasdīd fīšarḥ al-Tamhīd escrita por ‘Abd al-Ŷalīl b. Abī Bakr al-Dībāŷī —también conocido como Ibn al-Ṣābūnī—quien estudió el Tamhīd con otros discípulos de al-Bāqillānī en Qayrawān. El presente estudio revisa el proceso de transmisión de la obra de al-Bāqillānī en el Occidente Islámico. Después continúa presentando al autor del comentario, reconstruyendo la génesis del texto y describiendo su contenido. La sección final escoge un capítulo del texto que se ha seleccionado para demostrar cómo al-Dībāŷī sigue la posición tardía de al-Bāqillānī con respecto a la llamada teoría de los aḥwāl- duramente criticada en el Tamhīd. El Tasdīd constituye uno de los textos más antiguos del aš‘arismo magrebí que ha llegado hasta nosotros, ofreciéndonos nuevas y valiosas perspectivas sobre la historia de esta escuela teológica en el Occidente islámicoThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no 624808 and the Spanish government’s Ramón y Cajal programme (RYC-2015-18346) awarded to Jan Thiele. Hassan Ansari wishes to thank the Institute for Advanced Study, Princeton for granting him a Long-Term Membership during the preparation of this paper.Peer reviewe
Inference of the properties of the recombination process from whole bacterial genomes
No full textPatterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. Here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. The underlying model is sequentially Markovian so that data can be simulated very efficiently, and we use approximate Bayesian computation techniques to infer parameters. As this does not require us to calculate the likelihood function, the model can be easily extended to investigate less probed aspects of recombination. In particular, we extend our model to account for the bias in the recombination process whereby closely related bacteria recombine more often with one another. We show that this model provides a good fit to a data set of Bacillus cereus genomes and estimate several recombination properties, including the rate of bias in recombination. All the methods described in this article are implemented in a software package that is freely available for download at http://code.google.com/p/clonalorigin/
Inference of recombination properties in bacteria from whole genomes
No full textThe concept of species in bacteria is a matter of contention. The current definition is based on DNA-DNA hybridisation and does not account for evolutionary forces that are important in demarcating species. In this thesis we investigate two evolutionary forces that are important in speciation in bacteria, propose novel statistical models for them and infer parameters of interest.
We present the first attempt at inferring the bias in the recombination process from whole bacterial genomes. Despite empirical evidence that recombination is biased and theoretical results that this bias is important in speciation, it is usually ignored. We propose a coalescent based model that accounts for the bias in the recombination process. We use approximate Bayesian computation for inference and describe an efficient method for simulating from the model. We show that our method performs well on simulated datasets and is robust to slight misspecification of the history of the samples. Application of our method to a Bacillus cereus dataset shows that it contain evidence that the recombination process depends on the evolutionary distance between donors and recipients. We demonstrate that the rate of bias in the recombination process for this dataset is far lower than what theoretical studies require for the spontaneous generation of populations that can be called species under neutral model.
Next we propose a model for occurrence of adaptive events on a phylogenetic tree. We use the model to infer the boundaries of clusters on a phylogenetic tree that correspond to ecologically distinct lineages. we characterise our method using simulated datasets and show that it is conservative in estimating the number of adaptive events. Finally we apply our method to two bacterial datasets of Salmonella enterica and Vibrionaceae. We show that there is decisive evidence that isolates in these datasets partition into numerous ecologically distinct lineages and use our method to delineate the boundaries of these lineages.</p
Inference of recombination properties in bacteria from whole genomes
No full textThe concept of species in bacteria is a matter of contention. The current definition is based on DNA-DNA hybridisation and does not account for evolutionary forces that are important in demarcating species. In this thesis we investigate two evolutionary forces that are important in speciation in bacteria, propose novel statistical models for them and infer parameters of interest. We present the first attempt at inferring the bias in the recombination process from whole bacterial genomes. Despite empirical evidence that recombination is biased and theoretical results that this bias is important in speciation, it is usually ignored. We propose a coalescent based model that accounts for the bias in the recombination process. We use approximate Bayesian computation for inference and describe an efficient method for simulating from the model. We show that our method performs well on simulated datasets and is robust to slight misspecification of the history of the samples. Application of our method to a Bacillus cereus dataset shows that it contain evidence that the recombination process depends on the evolutionary distance between donors and recipients. We demonstrate that the rate of bias in the recombination process for this dataset is far lower than what theoretical studies require for the spontaneous generation of populations that can be called species under neutral model. Next we propose a model for occurrence of adaptive events on a phylogenetic tree. We use the model to infer the boundaries of clusters on a phylogenetic tree that correspond to ecologically distinct lineages. we characterise our method using simulated datasets and show that it is conservative in estimating the number of adaptive events. Finally we apply our method to two bacterial datasets of Salmonella enterica and Vibrionaceae. We show that there is decisive evidence that isolates in these datasets partition into numerous ecologically distinct lineages and use our method to delineate the boundaries of these lineages
Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
No full textThe distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realisation from the phenotype distribution of that individual. If all individuals in a phylogeny had the same phenotype distribution, measured phenotypes would be randomly distributed on the tree leaves. This is however often not the case, implying that the phenotype distribution evolves over time. Here we propose a new model based on this principle of evolving phenotype distribution on the branches of a phylogeny, which is different from ancestral state reconstruction where the phenotype itself is assumed to evolve. We develop an efficient Bayesian inference method to estimate the parameters of our model and to test the evidence for changes in the phenotype distribution. We use multiple simulated datasets to show that our algorithm has good sensitivity and specificity properties. Since our method identifies branches on the tree on which the phenotype distribution has changed, it is able to break down a tree into components for which this distribution is unique and constant. We present two applications of our method, one investigating the association between HIV genetic variation and human leukocyte antigen, and the other studying host range distribution in a lineage of Salmonella enterica, and we discuss many other potential applications. All the methods described in this paper are implemented in a software package called TreeBreaker which is freely available for download at https://github.com/ansariazim/TreeBreaker
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