POSTDOC para estudiar la morfometría de los cráneos de bisonte europeo y su relación con la endogamia de la especie

 Oferta compartida por Cristina

Post-doc position at the Mammal Research Institute Polish Academy of Sciences, Białowieża for the project:


"Historical morphometrics of the European bison skulls and its association with species inbreeding increase”


The summary and objectives of the project:
European bison is a species of unique demographic history. It has been through an extremely
severe bottleneck in the 1920s. The whole contemporary population originates from a meager
group of founders. Just two of them turned out to be predominant, and their share in the
contemporary gene pool is above 80%. The effects are extremely low genetic variation (Wójcik
et al., 2009; Tokarska et al., 2009; Tokarska et al., 2011) and highly increased inbreeding level,
reaching 75% (Pertoldi et al., unpublished). Although increased inbreeding is regarded as an
important factor affecting the viability of a population, resulting in lowered genetic
differentiation and decreased fitness, its impact on the European bison seems milder than
might be expected. Long term fertility coefficients are stable and satisfactory (Krasińska i
Krasiński, 2017) and no indisputable inbreeding depression symptoms are observed (Tokarska
et al., 2011). The reported potential inbreeding depression symptoms are related to skeleton
conformation. Baranov et al. (1997) reported signs of developmental instability of skull
morphology in the European bison skulls and indicated developmental instability as essential
for characterizing the condition of the population. Analyses of fluctuating symmetry of the
European bison, associated with genetic diversity (Makowiecka, 1994) suggest that the
Białowieża line of the European bison had the lowest, unbeneficial, developmental instability
as the result of inbreeding. Until recently, the only method of estimating inbreeding level was
pedigree analysis – a rough and inaccurate method. The development of genomic techniques
enables precise calculation of inbreeding level using high density SNP (single nucleotide
polymorphism) set. This method has been successfully used in the European bison studies and
allowed for the first, accurate inbreeding calculations, using ROH (Runs of Homozygosity)
analyses (Iacolina et al., 2016, Pertoldi et al., unpublished).
This project enables the actual effect of extreme inbreeding on skull conformation in a
historical context to be estimated, by association of genomic and morphometric data in one
of the most inbred mammals known – the European bison.
We will use hundreds of 3D skull scans from European collections and museums and
juxtaposition them with their inbreeding level information based on SNP markers. The
objective of the project is to specify whether and in what extent inbreeding level shaped the
skull conformation of European bison individuals by answering three questions:
Has the morphometry of the skull fluctuated over time? Has the growing inbreeding of the
European bison influenced its skull morphometry? If yes, what morphometric skull features
have been affected by growing inbreeding?


The working environment


Mammal Research Institute, Polish Academy of Sciences
(MRIPAS) in Białowieża, funded in 1952, conducts research in
the field of ecology, ethology, morphology, population
genetics as well as population management and
conservation of mammals and other terrestrial vertebrates.
The mission of the Institute is to acquire, advance, and
disseminate knowledge of natural patterns and processes in
order to improve the scientific basis for effective nature
conservation activities and sustainable development. We
focus mainly on Białowieża Primeval Forest (UNESCO
Biosphere Reserve and World Heritage Site) as a study area,
but also on other regions of Poland and Europe. The Institute
employs 60 people, including researchers, PhD students, and
qualified technical and office staff.


We provide:
1. 4-years contract;
2. Work in a friendly research team, in a well-equipped and organized laboratory with
support and supervision of competent colleagues;
3. The possibility of effective scientific development through cooperation with the best
world research centres;
4. Participation in an interesting scientific project with travelling opportunities;
5. The possibility to apply for inexpensive accommodation in MRI PAS flats.
Post-doc tasks and duties within the project
1. Writing scientific papers and participating in relevant conferences and workshops.
2. Supervising PhD students.
3. Performing genome-wide association analysis based on the genomic data and
morphometrical measurements on European bison skulls, preferably using
GoldenHelix or Plink softwares.
4. Visualisation of the data, presenting results and preparing manuscripts.
Requirements:
1. PhD in bioinformatics or genomics.
2. Experience in bioinformatic research, experience in Plink or GoldenHelix applications.
3. Team cooperation skills.
4. Fluent spoken and written English.
5. Fun and excitement from performing science and presenting the results higly
welcome.
Required documents:
1. CV and motivation letter.
2. Copy of PhD diploma.
3. Full-text version (pdf/word file) of your PhD thesis.


4. Information on the candidate’s scientific experience (specialization, research
techniques, and achievements (including list of publications and reports) (max. 500
words).
5. An opinion from the academic tutor or/and previous scientific employer.
6. Declaration of consent for processing of personal data, attached below (only first
signed page should be scanned and delivered through e-mail).
Conditions of employment
1. Post-doc salary of 6200.00 złotych netto / month = approx. 1300 Euro netto. This is the
highest allowed salary for PhD in the NCN project. As living in Poland is cheaper that in
Western Europe, this ensures quite satisfactory standard of living.
2. Project will last 4 years, starting summer 2023 and finish summer 2027. Position is full
time, but can be realized partly remote.
The recruitment rules will follow NCN regulations. The selection will be based on the
qualifications of the candidates including scientific achievements, experience, awards,
internships, skills and competences. An interview will be part of the selection of candidates.
Recruitment is a two-stage process and includes: 1) evaluation of candidates’ documentation
and 2) an interview with selected candidates (you will be asked to shortly present your PhD
thesis).
Applications should be sent directly to Małgorzata Tokarska by letter or electronically by 31st
August 2023. The selected candidates will be invited to an online or stationary interview and
the decision will be announced by 10th September 2023.
Contact:
Małgorzata Tokarska PhD – project leader
Mammal Research Institute Polish Academy of Sciences
ul. Stoczek 1, 17-230 Białowieża, Poland
e-mail: tokarska@ibs.bialowieza.pl; phone +48 85 682 77 61


Declaration of consent for processing of personal data within the framework
of the competition procedure for granting scientific scholarships in research
projects funded by the National Science Centre
I consent for my personal data to be processed by the Institute of Mammal Research Institute
Polish Academy of Sciences (hereinafter referred to as IBS PAN) for the purposes necessary
for the recruitment process on the award of scientific scholarships in research projects funded
by the National Science Centre (in accordance with the Regulation of the European Parliament
and of the Council (EU) 2016/679 of 27 April 2016, on the protection of natural persons with
regard to the processing of personal data and on the free movement of such data, and
repealing Directive 95/46/EC (General Regulation on Data Protection ) (J.L. EU. 2016, No. 119,
p. 1) - hereinafter referred to as RODO, and national data protection regulations issued on its
basis.


...................................................... ...........................................
Place, date Signature


I consent for my personal data to be processed by the Mammal Research Institute Polish
Academy of Sciences in Białowieża (hereinafter referred to as IBS PAN) for the purposes of the
recruitment process for the award of scientific scholarships in research projects funded by the
National Science Centre (required if the data provided include special categories of data
referred to in Article 9(1) of the RODO).


...................................................... ...........................................
Place, date Signature


General Regulation on Data Protection (RODO) information clause
(drawn up in connection with the implementation of the obligation indicated in Article 13 of
Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on
the protection of natural persons in connection with the processing of personal data and on
the free movement of such data and repealing Directive 95/46/EC. (Official Journal of the EU


L 119, p. 1).


1. The Administrator of your personal data is the Mammal Research Institute of the Polish
Academy of Sciences in Białowieża (hereinafter referred to as IBS PAN), represented by the
Director of IBS PAN 1 Stoczek St., 17-230 Białowieża, e-mail address:
mripas@ibs.bialowieza.pl, tel. 85 682 77 50.
2. Any questions regarding the manner and extent of the processing of your personal data and
your rights under the RODO, can be directed to the designated Data Protection Officer at email
address: iod@ibs.bialowieza.pl or by writing to the registered office address indicated above
with the reference "Data Protection Officer".
3. Your personal data will be processed for the purpose and in the scope necessary to carry
out the competition procedure for the scholarship, awarding scientific scholarships in research
projects funded by the National Centre for Science, and in the case of selection for the position
of a scholarship holder, in connection with the conclusion of a scholarship agreement for the
payment of a scientific scholarship and activities connected with the collection of the scientific
scholarship, your data will be processed on the basis of the Rules of Procedure for Awarding
Scientific Scholarships in Research Projects Funded by the National Centre for Science, the
Agreement for the Implementation and Financing of the Research Project (hereinafter
referred to as "Project") in the framework of which the competition for the position of a
scholarship holder is carried out (art. 6 1(b) RODO). Your personal data will also be processed
on the basis of your consent to the processing of data in order to carry out the competition
procedure - the basis for the processing of personal data will then be Article 6(1)(a) RODO and
Article 9(2)(a) RODO. The Administrator may also process personal data in order to protect its
legitimate interests (Article 6(1)(f) RODO) - in order to service, investigate and defend in the
event of the occurrence of mutual claims.
4. The recipients of your personal data will be: The National Science Centre in Cracow, the
appointed Scholarship Committee, entities assessing or controlling the proper
implementation of the Project, within the framework of which the agreement was concluded,
entities conducting control and evaluation and other entities entitled to obtain data on the
basis of legal regulations.
5. Your personal data will be stored until the end of the recruitment process from the date of
your application, unless, before the expiry of the period indicated above, you withdraw your
consent to the processing of your data or restrict it, subject to point 6. In the event, that the
basis for the processing of your personal data after the recruitment process has been
completed is the legitimate interest of the administrator (e.g. in case when the processing of
your personal data after the recruitment process is based on the legitimate interest of the
administrator (e.g. in connection with the proceedings before the administrative court
initiated by the candidate as a result of the refusal to grant the NCN research scholarship or
suspension of the NCN research scholarship payment in connection with the termination of
the scholarship agreement), your personal data will be processed only until the proceedings
based on the legitimate interest of the administrator is completed or until you make an
effective objection.


6. In the case of obtaining a NCN research scholarship (i.e. successful completion of the
recruitment process and conclusion of an agreement for a NCN research scholarship
payment), the processing of your personal data will take place for the entire period of the
agreement for the implementation and financing of the research project within the framework
of which the competition for the position of a scholarship holder was held, until the
completion of Project implementation and settlement of the agreement for Project
implementation and financing concluded with National Science Centre, and then until the
expiration of the period of limitation of any possible claims resulting from the contract in the
Project, and after that period the data will be kept for archiving purposes - for the period
provided for by the law.
7. You have the right to request access to your personal data (including making a copy of it)
and, under the conditions set out in the RODO, the right to rectify (amend), erase or restrict
processing, object to the processing of your data, transfer your data and the right to lodge a
complaint to the supervisory authority, which in Poland is the Inspector General for the Office
for Personal Data Protection, having its registered office at: Office for Personal Data
Protection, 2 Stawki St., 00-193 Warsaw.
8. You also have the right to withdraw your consent for the control to process your personal
data at any time. Withdrawal of consent does not affect the compliance of the processing of
your personal data which was performed on the basis of consent given before its withdrawal.
However, revoking your consent to data processing during the recruitment process may make
it impossible to grant an NCN research scholarship.
9. Providing your personal data is voluntary, but necessary to participate in the competition
procedure in the competition procedure, and in the case of a scholarship award it is a
condition for the conclusion and performance of the agreement for the payment of a NCN
research scholarship.
10. Your personal data obtained for recruitment purposes will not be transferred to a third
country or international organization.
11. Your personal data will not be subject to automated decision-making, including in the form
of profiling.

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PhD para estudiar la morfometría de los cráneos de bisonte europeo y su relación con la endogamia de la especie

Oferta compartida por Cristina

PhD position at the Mammal Research Institute, Polish Academy of Sciences, Białowieża for the project:


" Historical morphometrics of the European bison skulls and its association with species inbreeding increase”


The summary and objectives of the project:
European bison is a species of unique demographic history. It has been through an extremely
severe bottleneck in the 1920s. The whole contemporary population originates from a
meager group of founders. Just two of them turned out to be predominant, and their share
in the contemporary gene pool is above 80%. The effects are extremely low genetic variation
(Wójcik et al., 2009; Tokarska et al., 2009; Tokarska et al., 2011) and highly increased
inbreeding level, reaching 75% (Pertoldi et al., unpublished). Although increased inbreeding
is regarded as an important factor affecting the viability of a population, resulting in lowered
genetic differentiation and decreased fitness, its impact on the European bison seems milder
than might be expected. Long term fertility coefficients are stable and satisfactory (Krasińska
i Krasiński, 2017) and no indisputable inbreeding depression symptoms are observed
(Tokarska et al., 2011). The reported potential inbreeding depression symptoms are related
to skeleton conformation. Baranov et al. (1997) reported signs of developmental instability
of skull morphology in the European bison skulls and indicated developmental instability as
essential for characterizing the condition of the population. Analyses of fluctuating
symmetry of the European bison, associated with genetic diversity (Makowiecka, 1994)
suggest that the Białowieża line of the European bison had the lowest, unbeneficial,
developmental instability as the result of inbreeding. Until recently, the only method of
estimating inbreeding level was pedigree analysis – a rough and inaccurate method. The
development of genomic techniques enables precise calculation of inbreeding level using
high density SNP (single nucleotide polymorphism) set. This method has been successfully
used in the European bison studies and allowed for the first, accurate inbreeding
calculations, using ROH (Runs of Homozygosity) analyses (Iacolina et al., 2016, Pertoldi et al., unpublished) This project enables the actual effect of extreme inbreeding on skull conformation in a historical context to be estimated, by association of genomic and morphometric data in one of the most inbred mammals known – the European bison. We will use hundreds of 3D skull scans from European collections and museums and juxtaposition them with their inbreeding level information based on SNP markers. The objective of the project is to specify whether and in what extent inbreeding level shaped the skull conformation of European bison individuals by answering three questions: Has the morphometry of the skull fluctuated over time? Has the growing inbreeding of the European bison influenced its skull morphometry? If yes, what morphometric skull features have been affected by growing inbreeding?


The working environment


Mammal Research Institute, Polish Academy of Sciences (MRIPAS) in Białowieża, funded in 1952, conducts research in the field of ecology, ethology, morphology, population genetics as well as population management and conservation of mammals and other terrestrial vertebrates. The mission of the Institute is to acquire, advance, and disseminate knowledge of natural patterns and processes in order to improve the scientific basis for effective nature conservation activities and sustainable development. We focus mainly on Białowieża Primeval Forest (UNESCO Biosphere Reserve and World Heritage Site) as a study area, but also on other regions of Poland and Europe. The Institute employs 60 people, including researchers, PhD students, and qualified technical and office staff.


We provide:
1. Work in a friendly research team, in a well-equipped and organized laboratory with
support and supervision of competent colleagues;
2. The possibility of effective scientific development through cooperation with the best
world research centres;
3. Participation in an interesting scientific project with travelling opportunities;
4. The possibility to apply for inexpensive accommodation in MRI PAS flats.
PhD student tasks and duties within the project
1. Performing morphometrical measurements on modern and historical European bison
skulls.
2. Performing morphometrical analyzes.
3. Presenting results and preparing drafts of scientific articles.
Requirements:
1. MSc degree in biology,
2. Experience in morphometric research, knowledge of Landmark, Checkpoint or other
programs,
3. Team cooperation skills,
4. Fluent spoken and written English,
5. Fun and excitement from performing science and presenting the results heartly
welcome.


Required documents:
Recruitment process of the BioPlanet Doctoral School is joined with the recruitment of doctoral
applicants to a project funded by external institutions (National Science Centre, The National
Centre for Research and Development, Foundation for Polish Science, etc.), the beneficiary of
which is one of the institutes forming the Doctoral School.
1. Application for admission to the BIOPLANET Doctoral School along with consent for
the personal data to be processed for the purpose of recruitment, and declaration of
acceptance of the terms and conditions of admission (application form).
2. Certified copy of diploma or certificate of completion of studies. If the applicant does
not have proof of the qualifications, s/he is obliged to provide them before the
Doctoral School program begins.
3. CV including education, employment and research experience with a list of
publications and a short description of scientific achievements, particularly
information on participation in scientific conferences, workshops, training and
internships, participation in research projects, involvement in learned societies and
students’ scientific associations, and awarded distinctions and scholarships.
4. Certificates or other documents confirming knowledge of English, if the applicant has
them at his/her disposal.
5. An opinion on the applicant and their past scientific activity from an academic staff
member or a university teacher with at least a doctoral degree. Instead of providing
such a document, a person who is an academic staff member or a university teacher
and holds at least a doctoral degree can be designated from whom the Recruitment
Committee can obtain their opinion on the applicant independently.
6. Declaration of consent for processing of personal data, attached below (only first
signed page should be scanned and delivered through e-mail).


Conditions of employment:
PhD student scholarship of 4180.00 PLN / month netto. This is the highest allowed salary for
PhD in the NCN project. As living in Poland is cheaper that in Western Europe, this ensures
quite satisfactory standard of living.
Project will last 4 years, starting summer 2023 and finish summer 2027. The PhD studies
start in October thus the candidate is optimally supposed to be in Białowieża at that time.
The recruitment rules will follow NCN regulations. The selection will be based on the
qualifications of the candidates including scientific achievements, experience, awards,
internships, skills and competences. An interview will be part of the selection of candidates.
Recruitment is a two-stage process and includes: 1) evaluation of candidates’ documentation
and 2) an interview with selected candidates.


Applications should be sent directly to Małgorzata Tokarska by letter or electronically by
16th August 2023. The selected candidates will be invited to an online or stationary
interview and the decision will be announced by 18th September 2023.


Contact:
Małgorzata Tokarska PhD – project leader
Mammal Research Institute Polish Academy of Sciences
ul. Stoczek 1,
17-230 Białowieża, Poland
e-mail: tokarska@ibs.bialowieza.pl; phone +48 85 682-77-61

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Un postdoc de lo más interesante estudiando la evolución de las suturas craneales en mamíferos

Oferta compartida por Nuria

This post is funded by a Leverhulme Trust research grant focused on the evolution of cranial sutures through the synapsid to mammal transition. The mammal skull performs numerous critical functions, from prey capture and feeding to protecting the brain to fighting. These functions impose enormous pressures which are buffered by the skull's shock absorbers: cranial sutures. These highly variable joints between skull bones are intimately linked with ecology and development, but their complex 3D anatomy makes them tricky to capture using traditional methods. As a result, we know almost nothing about their evolution. Bridging imaging, machine learning, cranial function and evolution, this project will reconstruct suture evolution and its role in one of the most important events in the history of life: the rise of mammals. This post will be based in the Goswami Lab within the Science Group at the Natural History Museum in London, with project collaborators based at London South Bank University, the University of Liverpool, the Field Museum of Natural History, and North Carolina Museum of Natural Sciences.

The successful applicant for this post will be responsible for developing and analysing a 3D dataset of suture morphology spanning extant mammals and their extinct relatives back to the earliest synapsids. Working with another project PDRA who is developing machine learning and computer vision tools for the automated extraction of cranial suture morphology from 3D meshes, the successful applicant will lead delivery of the biological and evolutionary aspects of this project, including expanding an existing 3D scan dataset spanning hundreds of living and extinct synapsid (including mammal) species, continuing development of a training dataset for the AI pipeline by annotating sutures on 3D scans, and conducting phylogenetic comparative and macroevolutionary analyses of suture evolution through time, as it relates to key innovations in mammal evolution and diversification.

The successful applicant will be expected to travel to international collections to build the 3D dataset, work closely with all project team members and collaborators, including organising project meetings, and lead on scientific publications and conference presentations describing the evolutionary analyses, as well as promoting the project at various outreach events at the NHM and outside the museum as the opportunity arises. There will be opportunities for supervising students and for developing independent collaborations, as part of supporting career development of the successful candidate. We provide a friendly, flexible, and collaborative environment to accommodate and support diverse circumstances, backgrounds, and needs.

About you

The successful candidate will have a PhD in Evolutionary Biology or related subject, either completed or submitted by the time of starting this position. You should have familiarity with mammal evolution and cranial anatomy and experience with 3D data and models, morphometrics, and phylogenetic comparative analysis in R. You should be willing to travel to work with collaborators and collect data in international institutions. You should have a track record of presenting research at conferences and publishing in peer-reviewed journals, demonstrating strong communication skills. You will have the ability to work independently, but also as part of a team, including contributing to wider lab activities and discussions. You must demonstrate ability to complete a research project and be eager to lead research in new areas and with new methods. International applicants welcome, and funds are available to support visa costs and NHS surcharge.

How to apply

If that sounds like you, please apply online on the Natural History Museum's careers portal, at https://careers.nhm.ac.uk/ . Please include a full curriculum vitae and cover letter detailing your interest
and relevant experience.

Closing date: 9am, March 3
Interviews expected w/c March 13

For further information and any queries, please contact: Prof. Anjali Goswami, The Natural History Museum, Cromwell Road, London SW7 5BD UK; a.goswami@nhm.ac.uk; goswamilab.com

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Postdoc en morfología y evolución de artrópodos

Oferta compartida por Nuria

Postdoc position, 100% TV-L E13LMU Munich, Faculty of Biology, Zoology
Starting date: 01 April 2023
End of application: 15 January 2023

Postdoc position (m/f/d) – Morphological diversity of arthropod larvae

We are seeking a highly motivated Postdoc (m/f/d) to take part in the investigation of diversity of arthropod larvae, including extant and fossil representatives. The project is funded by the Volkswagen Foundation.

The project is based on an interdisciplinary approach, in which morphological data of extant and fossil larvae are incorporated into an evolutionary framework. The major data base is provided by morphological investigations of extant and fossil specimens with modern imaging methods. Data are interpreted in a strict phylogenetic framework. We use quantitative methods to compare changes of morphological diversity, especially between different geological time slices.

Focus groups of research are malacostracan crustaceans and insects. Both groups exhibit a large diversity of morphology and developmental patterns and have a rich fossil record. Specimens will be provided via scientific collections, fieldwork is not considered.

The prospective Postdoc should have experience in some of the following fields (and is expected to gain experience in the other fields):
identification by DNA-barcoding, approaches to handle Big Data, data-banking, statistics in general, programming in R (or equivalent), geometric morphometrics (documentation, image processing, digital
measurements, landmarks, Fourier-analysis), preparation of figure plates (Adobe Photoshop), digital drawings with a vector graphics program. 

Ideally, the candidate has expertise in an ingroup of malacostracan crustaceans or insects that is not yet represented in the workgroup.

The results of the project are expected to be presented regularly at national and international conferences by the prospective Postdoc as well as published in peer-reviewed journals. The Postdoc is expected to develop project ideas for continuing own research after the end of the funding period. The successful candidate will be based in the work group of Zoomorphology at the campus Martinsried south-west of Munich, in close proximity to Munich. Child care facilities as well as schools are nearby.

The position is limited to a duration of 18 months. Starting date is 01 April 2023.

We offer: Postdoc position for 18 months; salary according to wage agreement (TV-L); interdisciplinary research project and working environment; modern imaging equipment (macro- and microscopic)

We expect: PhD in biology or a closely related field; solid knowledge in general ecology and evolution; very good English communication skills (oral and written); ability to efficiently work in teams; high motivation; keen interest in zoological evolutionary questions

Applications of women are strongly encouraged. Severely challenged persons will be given preference in case of otherwise equal qualifications.

Please send your application to jhaug@bio.lmu.de until January 15, 2023. The application should include CV, letter of motivation, and the names and contact details of potential referees.

Contact for further information:
Prof. Dr. Joachim T. Haug, LMU Munich, Faculty of Biology, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany, jhaug@bio.lmu.de, Phone: +49-89-2180-74132; https://www.en.zoomorphologie.bio.lmu.de/index.html, https://www.palaeo-evo-devo.info/

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Course: Geometric Morphometrics in R - January 20th-24th, 2020, Barcelona (Spain)

GEOMETRIC MORPHOMETRICS IN R

January 20th-24th, 2020, Barcelona (Spain)

Course Overview
Concepts in geometric morphometrics will be taught using a series of original data sets and working in R for solving a series of tasks. The course will start with an introduction to R and will rapidly go into shape analysis with measurements, landmark data and outlines. The participants are welcome to bring their own data and problems so that we may find R solutions.

This is not an introductory course to Geometric Morphometrics, therefore basic knowledge of Multivariate Statistics, R and Geometric Morphometric is recommended in order to take this course.

Requirements

Graduate or postgraduate degree in any Life Sciences discipline.

Knowledge of Multivariate Statistics, R and Geometric Morphometrics. Participants with that are not familiar with R environment are strongly recommended to read the book ‘R for beginners‘ and practice before the course. Participants who are not familiar with Geometric Morphometrics are recommended to take first the course Introduction to Geometric Morphometrics.

All participants must bring their own personal laptop (Windows, Macintosh, Linux).

Register here (mention Bioblogia to get a discount)

Program

Monday, January 20th, 2020.

1. An Introduction to R / Image Processing / Organizing Morphometric Data.

1.1. Some Basics in R.

1.1.1. The R Environment.

1.1.2. R objects, Assigning, Indexing.

1.1.3. Generating Data in R.

1.1.4. 2D and 3D Plots in R; Interacting with the Graphs.

1.2. Organizing Data for Morphometrics.

1.2.1. Data-frame, Array and List.

1.2.2. Converting and Coercing Objects.

1.2.3. Read and Write Morphometric Data in R.

1.3. Image Processing in R.

1.3.1. Reading Various Image Files.

1.3.2. Obtaining Image Properties.

1.3.3. Modifying Image Properties: Contrast, Channels, Saturation Directly from R or by Interfacing R with Imagemagick.

1.4. Simple Tests, Simple Linear Modelling, Alternatives to Linear Modelling, an example using traditional morphometrics.

1.4.1. Defining size and shape using PCA and log-shape ratio approaches.

1.4.2. Getting stats and test outputs.

1.4.3. Testing assumptions of linear modelling.

1.4.4. Testing for allometry and isometry.

1.4.5. Solutions when assumptions of linear modelling are not met.


Tuesday, January 21st, 2020.

2. Landmark data.

2.1. Acquiring Landmark Data in R.

2.2. Plotting Landmark Configurations in 2 and in 3D.

2.2.1. Using Different Symbols and Setting the Graphical Parameters.

2.2.2. Labeling Landmarks.

2.3. Geometric Transformation with Landmark Configurations.

2.3.1. Translation.

2.3.2. Scaling using Baseline or Centroid Size.

2.3.3. Rotation.

2.4. Superimposing and Comparing Two Shapes.

2.4.1. Baseline Superimposition.

2.4.2. Ordinary Least Squares Superimposition.

2.4.3. Resistant Fit.

2.5. Representing Shape Differences.

2.5.1. Plotting Superimposed Shape with Wireframe.

2.5.2. Lollipop Diagrams and Vector Fields.

2.5.3. Thin Plate Splines and Warped Shapes.

2.6. Superimposing More Than Two Shapes.

2.6.1. Baseline Registration.

2.6.2. Full Generalized Procrustes Analysis.

2.6.3. Partial Generalized Procrustes Analysis.

2.6.4. Dimensionality of Superimposed Coordinates.



Wednesday, January 22nd, 2020.

2.7. Exploring Shape Variation and Testing Hypotheses.

2.7.1. PCA.

2.7.2. Multivariate Linear Modelling (Multivariate Regression and MANOVA).

2.7.3. Allometry free approaches (Burnaby correction).

2.7.4. Linear discriminant and Canonical Analysis.

3. Outlines.

3.1. Acquiring outline Data in R.

3.2. Fourier Analysis.

3.2.1. Principles.

3.2.2. Fourier Analysis of the Tangent Angle.

3.2.3. Radius Fourier Analysis.

3.2.4. Elliptic Fourier Analysis.

3.2.5. Reduction of Shape Variables.

3.2.6. Statistical Analysis of Shape Variation with Fourier Analysis.

3.2.6.1. Exploring Shape Variation and Testing Hypotheses.

3.2.6.2. PCA.

3.2.6.3. Multivariate Linear Modelling (Multivariate Regression and MANOVA).

3.2.6.4. Canonical Analysis.

Thursday, January 23rd, 2020.

3.3. Combining Landmarks and Curves.



3.3.1. Hybrid Methods between Fourier and Procrustes Analysis.

3.3.2. Sliding Semi Landmarks.

3.4. Solutions for Open Curves.

4. Specific Applications.

4.1. Testing Measurement Error.

4.2. Partitional Clustering.

4.2.1. K-means, Partition Around Medoids.

4.2.2. Mclust.

4.2.3. Combining Genetic, Geographic and Morphometric Data.

Friday, January 24th, 2020.

4.3. Modularity / Integration Studies.

4.3.1. Two-block Partial Least Squares.

4.3.2. Testing Among Various Sets of Modules.

4.4.Fluctuating Asymmetry and Directional Asymmetry.

4.4.1. Inter-Individual and Intra-Individual Variation.

4.4.2. Object and Matching Symmetry.

4.5.Bending Energy, Uniform and Non-uniform Shape Variation.



Literature

“Morphometrics with R“, Julien Claude. R. Gentleman, K. Hornik and G. Parmigiani, eds.

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Curso de Morfometría Geométrica en 3D, 23-27 de Mayo (Barcelona, Spain)

"3D Geometric Morphometrics – 6th ed."

Fechas: 23 – 27 de mayo, 2016.

Profesora: Dra. Melissa Tallman (Grand Valley State University, USA).

Lugar: Centro de Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (España).

Programa y más información: http://www.transmittingscience.org/courses/gm/3d-gm/

Póster del curso: http://www.transmittingscience.org/wp-content/uploads/Poster-3D-GM.pdf

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