Publications by authors named "Matthew G King"

21 Publications

  • Page 1 of 1

The Validity, Reliability, and Responsiveness of the International Hip Outcome Tool-33 (iHOT-33) in Patients With Hip and Groin Pain Treated Without Surgery.

Am J Sports Med 2021 08 15;49(10):2677-2688. Epub 2021 Jul 15.

La Trobe Sport and Exercise Medicine Research Centre, School of Allied Health, Human Services and Sport, La Trobe University, Melbourne, Victoria, Australia.

Background: The International Hip Outcome Tool-33 (iHOT-33) was developed to evaluate patients seeking surgery for hip and/or groin (hip/groin) pain and may not be appropriate for those seeking nonsurgical treatment.

Purpose: To evaluate the psychometric properties of the iHOT-33 total (iHOT-Total) score and all subscale scores in adults with hip/groin pain who were not seeking surgery.

Study Design: Cohort study (diagnosis); Level of evidence, 3.

Methods: Patients with hip/groin pain who were not seeking surgery were recruited from 2 ongoing studies in Australia. Semistructured one-on-one interviews assessed content validity. Construct validity was assessed by testing hypothesized correlations between iHOT-33 and Copenhagen Hip and Groin Outcome Score (HAGOS) subscale scores. Test-retest reliability was assessed in patients not undertaking treatment and who reported "no change" in their Global Rating of Change (GROC) score at 6-month follow-up. Scores were reliable at group and individual levels if intraclass correlation coefficients (ICCs) were ≥0.80 and ≥0.90, respectively. Scores were responsive if Spearman rank correlations (ρ) between the change in the iHOT-33 score and the GROC score were ≥0.40.

Results: In total, 278 patients with hip/groin pain (93 women; mean age, 31 years) and 55 pain-free control participants (14 women; mean age, 29 years) were recruited. The iHOT-33 demonstrated acceptable content validity. Construct validity was acceptable, with all hypothesized strong positive correlations between iHOT-33 and HAGOS subscale scores confirmed ( range, 0.60-0.76; < .001), except for one correlation between the iHOT-Sport and HAGOS-Sport ( = .058; < .001). All scores were reliable at the group level, except for the iHOT-33 job subscale (iHOT-Job) (ICC range, 0.78-0.88 [95% CI, 0.60-0.93]). None of the subscales met the criteria for adequate reliability for use at the individual level (all ICCs <0.90). Minimal detectable change values (group level) ranged from 2.3 to 3.7 (95% CI, 1.7-5.0). All iHOT-33 subscale scores were responsive (ρ range, 0.40-0.58; ≤ .001), except for the iHOT-Job in patients not undertaking treatment (ρ = 0.27; = .001).

Conclusion: All iHOT-33 subscale scores were valid for use in patients with hip/groin pain who were not seeking surgery. Acceptable test-retest reliability was found for all subscale scores at the group level, except the iHOT-Job. All subscale scores, excluding the iHOT-Job, were responsive, regardless of undertaking physical therapist-led treatment or no treatment.
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http://dx.doi.org/10.1177/03635465211027180DOI Listing
August 2021

Physiotherapist-led treatment for femoroacetabular impingement syndrome (the PhysioFIRST study): a protocol for a participant and assessor-blinded randomised controlled trial.

BMJ Open 2021 04 7;11(4):e041742. Epub 2021 Apr 7.

La Trobe Sport and Exercise Medicine Research Centre, La Trobe University, Bundoora, Victoria, Australia.

Introduction: This double-blind, randomised controlled trial (RCT) aims to estimate the effect of a physiotherapist-led intervention with targeted strengthening compared with a physiotherapist-led intervention with standardised stretching, on hip-related quality of life (QOL) or perceived improvement at 6 months in people with femoroacetabular impingement (FAI) syndrome. We hypothesise that at 6 months, targeted strengthening physiotherapist-led treatment will be associated with greater improvements in hip-related QOL or greater patient-perceived global improvement when compared with standardised stretching physiotherapist-led treatment.

Methods And Analysis: We will recruit 164 participants with FAI syndrome who will be randomised into one of the two intervention groups, both receiving one-on-one treatment with the physiotherapist over 6 months. The targeted strengthening physiotherapist-led treatment group will receive a personalised exercise therapy and education programme. The standardised stretching physiotherapist-led treatment group will receive standardised stretching and personalised education programme. Primary outcomes are change in hip-related QOL using International Hip Outcome Tool-33 and patient-perceived global improvement. Secondary outcomes include cost-effectiveness, muscle strength, range of motion, functional task performance, biomechanics, hip cartilage structure and physical activity levels. Statistical analyses will make comparisons between both treatment groups by intention to treat, with all randomised participants included in analyses, regardless of protocol adherence. Linear mixed models (with baseline value as a covariate and treatment condition as a fixed factor) will be used to evaluate the treatment effect and 95% CI at primary end-point (6 months).

Ethics And Dissemination: The study protocol was approved (La Trobe University Human Ethics Committee (HEC17-080)) and prospectively registered with the Australian New Zealand Clinical Trials Registry. The findings of this RCT will be disseminated through peer reviewed scientific journals and conferences. Patients were involved in study development and will receive a short summary following the completion of the RCT.

Trial Registration Number: ACTRN12617001350314.
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http://dx.doi.org/10.1136/bmjopen-2020-041742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8031040PMC
April 2021

Lower-limb work during high- and low-impact activities in hip-related pain: Associations with sex and symptom severity.

Gait Posture 2021 01 29;83:1-8. Epub 2020 Sep 29.

La Trobe Sport and Exercise Medicine Research Centre, School of Allied Health, Human Services and Sport, La Trobe University, Bundoora, Victoria, Australia. Electronic address:

Background: Hip-related pain (HRP) is described as a movement-related disorder. However, little attention is given to the way people with HRP move, especially in populations still participating in sport. Thus, limiting our understanding of movementbased impairments in HRP and their potential relationships with pain/symptoms.

Research Question: (1) What are the differences in absolute and relative amounts of positive and negative lower-limb joint work during walking and the single-leg drop jump (SLDJ) in football players with and without HRP? (2) What are the relationships between lower-limb joint work and HRP burden?

Methods: 88 football players with HRP and 30 control football players were recruited. Positive and negative work done by the hip, knee, and ankle (and each joint's relative contribution to total work done) were calculated. The effect of sex on the relationship between HRP and work done, as well as the association between work done and International Hip Outcome Tool (iHOT33) scores, were assessed using linear and beta regressions models.

Results: Walking: No joint work variables were significantly different between groups, nor were any relationships with iHOT33 scores evident. SLDJ: The knee's relative contribution to total lower-limb negative work done was 37.7 % and 42.4 % for women with and without HRP, respectively (P = 0.04). The iHOT33 was significantly associated with positive (P = 0.03 to <0.01) and negative (P = 0.02 to <0.01) work done by the hip as well as negative work done by the ankle (P = 0.03 to 0.01), independent of sex.

Significance: Only one significant between-group comparison was revealed, involving the knee in female football players. In addition, football players with a greater selfreported burden of HRP tended to display lower hip joint work during the SLDJ. Rehabilitation programs could be targeted to address these impairments and normalize work done during high impact tasks in the management of HRP.
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http://dx.doi.org/10.1016/j.gaitpost.2020.09.025DOI Listing
January 2021

Limb symmetry index on a functional test battery improves between one and five years after anterior cruciate ligament reconstruction, primarily due to worsening contralateral limb function.

Phys Ther Sport 2020 Jul 8;44:67-74. Epub 2020 May 8.

La Trobe Sport and Exercise Medicine Research Centre, School of Allied Health, La Trobe University, Bundoora, Australia. Electronic address:

Objective: Evaluate change in functional performance from 1- to 5-years after anterior cruciate ligament reconstruction (ACLR).

Methods: 59 participants (38 men) aged 29 ± 16 years completed three hops and one-leg rise 1- and 5-years following ACLR. Linear mixed-effects models evaluated differences in change between the ACLR and contralateral limbs. Participants were classified with stable, improving or worsening function relative to previously published minimal detectable change thresholds. Healthy controls completed the three hops (n = 41) and one-leg rise (n = 31) as reference data.

Results: The contralateral limb had a significantly greater decrease in functional performance between 1- and 5-years for the three hops, compared to the ACLR limb. Worsening was more common in the contralateral limb than the ACLR limb; resulting in significant improvements in the LSI for the single hop (mean 87% at 1-year to 95% at 5-years), side hop (77%to 86%) and one-leg rise (76% to85%). Performance of both ACLR and contralateral limbs and the LSI remained below the healthy controls.

Conclusion: Functional performance changes differ between limbs between 1- and 5-years post-ACLR. The LSI should not be used in isolation to evaluate functional performance changes after ACLR, as it may overestimate functional improvement, due to worsening contralateral limb function.
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http://dx.doi.org/10.1016/j.ptsp.2020.04.031DOI Listing
July 2020

Let's take the dog for a gait….

Gait Posture 2020 06 8;79:1-2. Epub 2020 Apr 8.

La Trobe Sport and Exercise Medicine Research Centre, School of Allied Health, Human Services and Sport, La Trobe University, Melbourne, Australia. Electronic address:

Background: In 1872, Eadweard Muybridge was hired to research unsupported transit in horses, i.e. the trot and the gallop. This research was the first instance of the use of photography to analyse movement and was the ultimate precursor to motion capture for biomechanical assessment of movement utilised today. With the expansion of the field continuing, the term "gait" has become synonymous with walking and is often used interchangeably. In this editorial, we discuss the term "gait" and its' origin in the context of scientific research and aim to address the heterogeneous taxonomy associated with the ambiguous use of the term "gait".

Research Question: What is the ambiguous use of the term gait?

Methods: A non-systematic review was conducted of the original research and short communications in the 2019 issues of Gait and Posture RESULTS: A total of 219 titles were characterised as directly addressing locomotion. Of these, a total of 108 titles quantified the form of locomotion (e.g. walk/ing, run/ing) and 111 titles utilised the word "gait" to describe the task. However, 104 of these clarified the form of locomotion either within the abstract or the main text of the manuscript.

Significance: "Gait" is not mutually exclusive to humans nor walking. The ambiguity associated with the use of this term demonstrates the importance of quantifying the type of locomotion being studied. Ultimately, such efforts will allow the streamlining search strategies for appropriate research for academics, clinicians, and scientists alike.
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http://dx.doi.org/10.1016/j.gaitpost.2020.03.018DOI Listing
June 2020

Lower-Limb Biomechanics in Football Players with and without Hip-related Pain.

Med Sci Sports Exerc 2020 08;52(8):1776-1784

La Trobe Sport and Exercise Medicine Research Centre, School of Allied Health, Human Services and Sport, La Trobe University, Bundoora, Victoria, AUSTRALIA.

Purpose: This study aimed to evaluate the differences in lower-limb biomechanics between adult subelite competitive football players with and without hip-related pain during two contrasting tasks-walking and single-leg drop jump (SLDJ)-and to determine whether potential differences, if present, are sex dependent.

Methods: Eighty-eight football players with hip-related pain (23 women, 65 men) and 30 asymptomatic control football players (13 women, 17 men) who were currently participating in competitive sport were recruited. Biomechanical data were collected for the stance phase of walking and SLDJ. Pelvis, hip, knee, and ankle angles, as well as the impulse of the external joint moments, were calculated. Differences between groups and sex-specific effects were calculated using linear regression models.

Results: Compared with their asymptomatic counterparts, football players with hip-related pain displayed a lower average pelvic drop angle during walking (P = 0.03) and a greater average pelvic hike angle during SLDJ (P < 0.05). Men with hip-related pain displayed a smaller total range of motion (excursion) for the transverse plane pelvis angle (P = 0.03) and a smaller impulse of the hip external rotation moment (P < 0.01) during walking compared with asymptomatic men. Women with hip-related pain displayed a greater total range of motion (excursion) for the sagittal plane knee angle (P = 0.01) during walking compared with asymptomatic women.

Conclusion: Overall, few differences were observed in lower-limb biomechanics between football players with and without hip-related pain, irrespective of the task. This outcome suggests that, despite the presence of symptoms, impairments in lower-limb biomechanics during function do not appear to be a prominent feature of people with hip-related pain who are still participating in sport.
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http://dx.doi.org/10.1249/MSS.0000000000002297DOI Listing
August 2020

Consensus recommendations on the classification, definition and diagnostic criteria of hip-related pain in young and middle-aged active adults from the International Hip-related Pain Research Network, Zurich 2018.

Br J Sports Med 2020 Jun 20;54(11):631-641. Epub 2020 Jan 20.

La Trobe Sport and Exercise Medicine Research Centre, La Trobe University, Melbourne, Victoria, Australia.

There is no agreement on how to classify, define or diagnose hip-related pain-a common cause of hip and groin pain in young and middle-aged active adults. This complicates the work of clinicians and researchers. The International Hip-related Pain Research Network consensus group met in November 2018 in Zurich aiming to make recommendations on how to classify, define and diagnose hip disease in young and middle-aged active adults with hip-related pain as the main symptom. Prior to the meeting we performed a scoping review of electronic databases in June 2018 to determine the definition, epidemiology and diagnosis of hip conditions in young and middle-aged active adults presenting with hip-related pain. We developed and presented evidence-based statements for these to a panel of 37 experts for discussion and consensus agreement. Both non-musculoskeletal and serious hip pathological conditions (eg, tumours, infections, stress fractures, slipped capital femoral epiphysis), as well as competing musculoskeletal conditions (eg, lumbar spine) should be excluded when diagnosing hip-related pain in young and middle-aged active adults. The most common hip conditions in young and middle-aged active adults presenting with hip-related pain are: (1) femoroacetabular impingement (FAI) syndrome, (2) acetabular dysplasia and/or hip instability and (3) other conditions without a distinct osseous morphology (labral, chondral and/or ligamentum teres conditions), and that these terms are used in research and clinical practice. Clinical examination and diagnostic imaging have limited diagnostic utility; a comprehensive approach is therefore essential. A negative flexion-adduction-internal rotation test helps rule out hip-related pain although its clinical utility is limited. Anteroposterior pelvis and lateral femoral head-neck radiographs are the initial diagnostic imaging of choice-advanced imaging should be performed only when requiring additional detail of bony or soft-tissue morphology (eg, for definitive diagnosis, research setting or when planning surgery). We recommend clear, detailed and consistent methodology of bony morphology outcome measures (definition, measurement and statistical reporting) in research. Future research on conditions with hip-related pain as the main symptom should include high-quality prospective studies on aetiology and prognosis. The most common hip conditions in active adults presenting with hip-related pain are: (1) FAI syndrome, (2) acetabular dysplasia and/or hip instability and (3) other conditions without distinct osseous morphology including labral, chondral and/or ligamentum teres conditions. The last category should not be confused with the incidental imaging findings of labral, chondral and/or ligamentum teres pathology in asymptomatic people. Future research should refine our current recommendations by determining the clinical utility of clinical examination and diagnostic imaging in prospective studies.
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http://dx.doi.org/10.1136/bjsports-2019-101453DOI Listing
June 2020

Physiotherapist-led treatment for young to middle-aged active adults with hip-related pain: consensus recommendations from the International Hip-related Pain Research Network, Zurich 2018.

Br J Sports Med 2020 May 15;54(9):504-511. Epub 2019 Nov 15.

Musculoskeletal Radiology, Corades, LLC, Brookline, Massachusetts, USA.

The 1st International Hip-related Pain Research Network meeting discussed four prioritised themes concerning hip-related pain in young to middle-aged adults: (1) diagnosis and classification of hip-related pain; (2) patient-reported outcome measures for hip-related pain; (3) measurement of physical capacity for hip-related pain; (4) physiotherapist-led treatment for hip-related pain. Thirty-eight expert researchers and clinicians working in the field of hip-related pain attended the meeting. This manuscript relates to the theme of physiotherapist-led treatments for hip-related pain. A systematic review on the efficacy of physiotherapist-led interventions for hip-related pain (published separately) was conducted and found that strong evidence for physiotherapist-led treatments was lacking. Prior to the meeting, draft consensus recommendations for consideration in the meeting were also developed based on the systematic review. The draft consensus recommendations were presented to all of the meeting participants via email, at least 1 week prior to the meeting. At the meeting, these recommendations were discussed, revised and voted on. Six recommendations for clinical practice and five recommendations for research were included and all gained consensus. Recommendations for clinical practice were that (i) Exercise-based treatments are recommended for people with hip-related pain. (ii) Exercise-based treatment should be at least 3 months duration. (iii) Physiotherapist-led rehabilitation after hip surgery should be undertaken. (iv) Patient-reported outcome measures, measures of physical impairment and measures of psychosocial factors should be used to monitor response to treatment. (v) Physical activity (that may include sport) is recommended for people with hip-related pain. (vi) Clinicians should discuss patient expectations, use shared-decision making and provide education. Recommendations for research were (i) Reporting of exercise programmes: Exercise descriptors such as load magnitude, number of repetitions and sets, duration of whole programme, duration of contractile element of exercise, duration of one repetition, time under tension, rest between repetitions, range of motion through which the exercise is performed, and rest between exercise sessions should be reported. (ii) Research should investigate the optimal frequency, intensity, time, type, volume and progression of exercise therapy. (iii) Research should examine the effect of patient education in people with hip-related pain. (iv) Research should investigate the effect of other treatments used in people with hip-related pain (for example: manual therapy, medications, injections). (v) Research should examine the impact of comorbidities and social determinants on treatment effectiveness in people with hip-related pain. Clinicians and researchers working with young to middle-aged active adults with hip-related pain may use these consensus recommendations to guide, develop, test and implement individualised, evidence-based physiotherapist-led rehabilitation programmes.
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http://dx.doi.org/10.1136/bjsports-2019-101458DOI Listing
May 2020

Lower limb biomechanics during low- and high-impact functional tasks differ between men and women with hip-related groin pain.

Clin Biomech (Bristol, Avon) 2019 08 3;68:96-103. Epub 2019 Jun 3.

La Trobe Sport and Exercise Medicine Research Centre, La Trobe University, Bundoora, Victoria, Australia. Electronic address:

Background: The effect of pain on lower limb biomechanics during walking has been found to be sex specific for certain joint diseases. However, it is not known if sex is an effect-modifier in people with hip pain. Therefore, the aim of the study was to determine the differences in lower limb biomechanics between men and women with hip-related groin pain during functional tasks.

Methods: 65 male and 23 female football players with hip-related groin pain were recruited. Biomechanical data were recorded during walking and the single-leg drop jump. Hip, knee and ankle joint kinematics and kinetics were calculated. Differences between men and women were assessed using statistical parametric mapping.

Findings: Walking: Men with hip-related groin pain walked with lower hip flexion and internal rotation angles during stance compared to women. During different sections of stance, men also displayed a lower hip adduction angle and 'external' adduction moment, a lower knee flexion angle and 'external' flexion moment, as well as greater 'external' dorsi-flexion moment and impulse. Single-leg drop jump: Men with hip-related groin pain displayed a lower hip flexion angle during early stance, and greater 'external' knee flexion and ankle dorsi-flexion moments. The impulse of the 'external' dorsi-flexion moment was also greater for men compared to women.

Interpretation: Men and women with hip-related groin pain display differing lower limb biomechanics in both low and high impact tasks. Sex may therefore be a potential effect modifier in people with hip-related groin pain. Future research in this area should incorporate sex-specific analyses.

Trial Registration Number: NA.
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http://dx.doi.org/10.1016/j.clinbiomech.2019.06.001DOI Listing
August 2019

Sub-elite Football Players With Hip-Related Groin Pain and a Positive Flexion, Adduction, and Internal Rotation Test Exhibit Distinct Biomechanical Differences Compared With the Asymptomatic Side.

J Orthop Sports Phys Ther 2018 07 8;48(7):584-593. Epub 2018 May 8.

Background Hip-related groin pain is common in sub-elite football players and may be associated with altered hip biomechanics. Objectives To compare the hip biomechanics, bony hip morphology associated with femoroacetabular impingement (FAI) syndrome, and hip strength and range of motion (ROM) between the symptomatic and asymptomatic limbs of sub-elite football players with unilateral hip-related groin pain and a positive flexion, adduction, and internal rotation (FADIR) test. Methods Fifteen sub-elite football (soccer) players with unilateral hip-related groin pain and a positive FADIR test were recruited for this observational cross-sectional study. Three-dimensional motion analysis and ground reaction force data were recorded for walking and a single-leg drop-jump (SLDJ) task. Participants also underwent a standard anterior-posterior hip radiograph and hip strength and ROM assessment. Between-limb differences were assessed using paired t tests or Wilcoxon signed-rank tests. Results The symptomatic limb displayed a smaller peak hip extension angle (P = .01) and a lower peak hip adduction moment (P = .03) compared with the asymptomatic limb during the stance phase of walking. Additionally, during the SLDJ, the symptomatic limb demonstrated less total sagittal plane ROM (P = .04). The symptomatic limb also demonstrated less external rotation ROM (P = .03). However, no differences were found between limbs for bony hip morphology associated with FAI syndrome or hip strength. Conclusion This study found between-limb asymmetries in low- and high-impact functional tasks, such as walking and an SLDJ, in football players with unilateral hip-related groin pain. Despite unilateral pain, bony morphology associated with FAI syndrome did not differ between limbs. J Orthop Sports Phys Ther 2018;48(7):584-593. Epub 8 May 2018. doi:10.2519/jospt.2018.7910.
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http://dx.doi.org/10.2519/jospt.2018.7910DOI Listing
July 2018

Lower limb biomechanics in femoroacetabular impingement syndrome: a systematic review and meta-analysis.

Br J Sports Med 2018 May 13;52(9):566-580. Epub 2018 Feb 13.

La Trobe Sport and Exercise Medicine Research Centre, School of Allied Health, College of Science, Health and Engineering, La Trobe University, Bundoora, Victoria, Australia.

Objective: (1) Identify differences in hip and pelvic biomechanics in patients with femoroacetabular impingement syndrome (FAIS) compared with controls during everyday activities (eg, walking, squatting); and (2) evaluate the effects of interventions on hip and pelvic biomechanics during everyday activities.

Design: Systematic review.

Data Sources: Medline, CINAHL, EMBASE, Scopus and SPORTDiscus until February 2017.

Methods: Primary aim: studies that investigated hip or pelvic kinematics and/or joint torques of everyday activities in patients with FAIS compared with the asymptomatic contralateral limb or a control group. Secondary aim: studies that evaluated effects of conservative or surgical interventions on patients with FAIS using pre-post or controlled clinical trial designs. Biomechanical data must have been collected using three-dimensional motion capture devices. Reporting quality was assessed using the Epidemiological Appraisal Instrument and data were pooled (standardised mean difference (SMD), 95% CI) where populations and primary outcomes were similar.

Results: Fourteen studies were included (11 cross-sectional and three pre/post intervention), varying between low and moderate reporting quality. Patients with FAIS walked with a lower: peak hip extension angle (SMD -0.40, 95% CI -0.71 to -0.09), peak internal rotation angle (-0.67, 95% CI -1.19 to -0.16) and external rotation joint torque (-0.71, 95% CI -1.07 to -0.35), and squatted to a lesser depth with no difference in hip flexion range. Pre/post intervention data were limited in number and quality, and to surgical cohorts.

Conclusion: This review suggests that patients with FAIS may demonstrate hip biomechanical impairments during walking and squatting, with minimal literature available to comment on other tasks.

Clinical Relevance: The information presented in the review provides insight into the biomechanical differences associated with FAIS; however, the between-group differences were small to moderate. This information may aid in the development of management strategies for people with the condition.

Prosperoregistration Number: CRD42016038677.
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http://dx.doi.org/10.1136/bjsports-2017-097839DOI Listing
May 2018

Femoroacetabular impingement and hip OsteoaRthritis Cohort (FORCe): protocol for a prospective study.

J Physiother 2018 01 27;64(1):55. Epub 2017 Dec 27.

La Trobe Sport and Exercise Medicine Research Centre, College of Science, Health and Engineering, La Trobe University; Department of Mechanical Engineering, University of Melbourne, Melbourne.

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http://dx.doi.org/10.1016/j.jphys.2017.10.004DOI Listing
January 2018

Genomic resources notes accepted 1 February 2013-31 March 2013.

Mol Ecol Resour 2013 Jul 23;13(4):759. Epub 2013 May 23.

DuPont Pioneer, Johnston, IA 50131-0184, USA.

This article documents the public availability of three transcriptome sequences. These genomic resources were developed for the following species: Helianthus anomalus, Helianthus deserticola and Helianthus paradoxus.
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http://dx.doi.org/10.1111/1755-0998.12123DOI Listing
July 2013

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.

Evol Bioinform Online 2010 Oct 20;6:143-9. Epub 2010 Oct 20.

The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems.
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http://dx.doi.org/10.4137/EBO.S5861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978936PMC
October 2010

Range persistence during the last glacial maximum: Carex macrocephala was not restricted to glacial refugia.

Mol Ecol 2009 Oct 15;18(20):4256-69. Epub 2009 Sep 15.

Department of Botany, University of British Columbia, Vancouver, BC, Canada.

The distribution of many species inhabiting northwestern North America has been heavily influenced by the climatic changes during the late Pleistocene. Several studies have suggested that species were restricted to glacial refugia north and/or south of the continental ice sheet front. It is also hypothesized that the coast of northwestern North America could have been a prime location for glacial refugia because of the lowering of the eustatic sea level and the concomitant rise of the continental shelf because of tectonic rebound. Alternatively, some coastal species distributions and demographics may have been unaffected in the long-term by the last glacial maximum (LGM). We tested the glacial refugium hypothesis on an obligate coastal plant species, Carex macrocephala by sampling 600 individuals from 41 populations with 11 nuclear microsatellite loci and the rpL16 plastid intragenic spacer region. The microsatellite data sets suggest a low level of population differentiation with a standardized G'(ST) = 0.032 and inbreeding was high with an F = 0.969. The homogenization of the populations along the coast was supported by a principal coordinate analysis, amovas and samova analyses. Analyses using the rpL16 data set support the results of the microsatellite analyses, with a low F(ST) of 0.042. Coalescent and mismatch analyses using rpL16 suggest that C. macrocephala has not gone through a significant bottleneck within the past 100,000 years, although a much earlier population expansion was indicated by the mismatch analysis. Carex macrocephala exhibits the characteristics of metapopulation dynamics and on the basis of these results, we concluded that it was not restricted to glacial refugia during the LGM, but that it existed as a large metapopulation.
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http://dx.doi.org/10.1111/j.1365-294X.2009.04280.xDOI Listing
October 2009

Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent helianthus species.

Evolution 2009 Aug 9;63(8):2061-75. Epub 2009 May 9.

Department of Biology, Indiana University, Bloomington, Indiana, USA.

While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct.
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http://dx.doi.org/10.1111/j.1558-5646.2009.00703.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731706PMC
August 2009

Using parentage analysis to examine gene flow and spatial genetic structure.

Mol Ecol 2009 Apr 20;18(8):1551-2. Epub 2009 Feb 20.

Department of Botany, University of British Columbia, Vancouver, BC, Canada.

Numerous approaches have been developed to examine recent and historical gene flow between populations, but few studies have used empirical data sets to compare different approaches. Some methods are expected to perform better under particular scenarios, such as high or low gene flow, but this, too, has rarely been tested. In this issue of Molecular Ecology, Saenz-Agudelo et al. (2009) apply assignment tests and parentage analysis to microsatellite data from five geographically proximal (2-6 km) and one much more distant (1500 km) panda clownfish populations, showing that parentage analysis performed better in situations of high gene flow, while their assignment tests did better with low gene flow. This unusually complete data set is comprised of multiple exhaustively sampled populations, including nearly all adults and large numbers of juveniles, enabling the authors to ask questions that in many systems would be impossible to answer. Their results emphasize the importance of selecting the right analysis to use, based on the underlying model and how well its assumptions are met by the populations to be analysed.
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http://dx.doi.org/10.1111/j.1365-294X.2009.04110.xDOI Listing
April 2009

Discordance between phylogenetics and coalescent-based divergence modelling: exploring phylogeographic patterns of speciation in the Carex macrocephala species complex.

Mol Ecol 2009 Feb;18(3):468-82

University of British Columbia, Department of Botany, Vancouver, BC, Canada.

We fit a molecular data set, consisting of the rpL16 cpDNA marker and eight microsatellite loci, to the isolation-with-migration model as implemented in IMa to test a well-supported phylogenetic hypothesis of relationships within the Carex macrocephala species complex (Cyperaceae). The phylogenetic hypothesis suggests C. macrocephala from North America is reciprocally monophyletic and is sister to a reciprocally monophyletic clade of C. kobomugi. The North American C. macrocephala and C. kobomugi clade form a sister clade with a lineage of Asian C. macrocephala, thereby forming a paraphyletic C. macrocephala species. Not only does the phylogenetic hypothesis suggest C. macrocephala is paraphyletic, but it also suggests that the two lineages which share a partially overlapping distribution, Asian C. macrocephala and C. kobomugi, are not the most closely related. To test these relationships, we used coalescent-based population genetic models to infer divergence time for each lineage pair within the species complex. The coalescent-based models account for the stochastic forces which drive population divergence, and can account for the lineage sorting that occurs prior to lineage divergence. A drawback to phylogenetic-based phylogeographical analyses is that they do not account for stochastic lineage sorting that occurs between gene divergence and lineage divergence. By comparing the relative divergence time of the three main lineages within this group, Asian C. macrocephala, North American C. macrocephala, and C. kobomugi, we concluded that the phylogenetic hypothesis is incorrect, and the divergence between these lineages occurred during the Late Pleistocene epoch.
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http://dx.doi.org/10.1111/j.1365-294X.2008.04033.xDOI Listing
February 2009

A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages.

Syst Biol 2008 Oct;57(5):693-707

School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, Washington, USA.

Island systems have long been useful models for understanding lineage diversification in a geographic context, especially pertaining to the importance of dispersal in the origin of new clades. Here we use a well-resolved phylogeny of the flowering plant genus Cyrtandra (Gesneriaceae) from the Pacific Islands to compare four methods of inferring ancestral geographic ranges in islands: two developed for character-state reconstruction that allow only single-island ranges and do not explicitly associate speciation with range evolution (Fitch parsimony [FP; parsimony-based] and stochastic mapping [SM; likelihood-based]) and two methods developed specifically for ancestral range reconstruction, in which widespread ranges (spanning islands) are integral to inferences about speciation scenarios (dispersal-vicariance analysis [DIVA; parsimony-based] and dispersal-extinction-cladogenesis [DEC; likelihood-based]). The methods yield conflicting results, which we interpret in light of their respective assumptions. FP exhibits the least power to unequivocally reconstruct ranges, likely due to a combination of having flat (uninformative) transition costs and not using branch length information. SM reconstructions generally agree with a prior hypothesis about dispersal-driven speciation across the Pacific, despite the conceptual mismatch between its character-based model and this mode of range evolution. In contrast with narrow extant ranges for species of Cyrtandra, DIVA reconstructs broad ancestral ranges at many nodes. DIVA results also conflict with geological information on island ages; we attribute these conflicts to the parsimony criterion not considering branch lengths or time, as well as vicariance being the sole means of divergence for widespread ancestors. DEC analyses incorporated geological information on island ages and allowed prior hypotheses about range size and dispersal rates to be evaluated in a likelihood framework and gave more nuanced inferences about range evolution and the geography of speciation than other methods tested. However, ancestral ranges at several nodes could not be conclusively resolved, due possibly to uncertainty in the phylogeny or the relative complexity of the underlying model. Of the methods tested, SM and DEC both converge on plausible hypotheses for area range histories in Cyrtandra, due in part to the consideration of branch lengths and/or timing of events. We suggest that DEC model-based methods for ancestral range inference could be improved by adopting a Bayesian SM approach, in which stochastic sampling of complete geographic histories could be integrated over alternative phylogenetic topologies. Likelihood-based estimates of ancestral ranges for Cyrtandra suggest a major dispersal route into the Pacific through the islands of Fiji and Samoa, motivating future biogeographic investigation of this poorly known region.
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http://dx.doi.org/10.1080/10635150802426473DOI Listing
October 2008
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