Biodiversity Data Journal :
Single Taxon Treatment
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Corresponding author: Paolo Ramoni Perazzi (rpaolo1967@gmail.com)
Academic editor: Pavel Stoev
Received: 06 Nov 2017 | Accepted: 12 Dec 2017 | Published: 15 Dec 2017
© 2017 Paolo Ramoni Perazzi, Karl Schuchmann, Magdiel Ablan Bortone, Alejandra Soto Werschitz
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Ramoni Perazzi P, Schuchmann K, Ablan Bortone M, Soto Werschitz A (2017) On the absence of the Green-tailed Trainbearer Lesbia nuna (Trochilidae) from Venezuela: an analysis based on environmental niche modelling. Biodiversity Data Journal 5: e22092. https://doi.org/10.3897/BDJ.5.e22092
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Lesbia nuna, a hummingbird distributed in the tropical Andes, has been included in Venezuela's bird list on the basis of a specimen collected in 1873 at Sierra Nevada, Mérida and deposited in the Natural History Museum, London, with no further records for this country since then. This record, largely considered as valid by most authors, has been questioned by others, although without formal analyses.
The potential habitat range of the Green-Tailed Trainbearer, Lesbia nuna gouldii (Trochilidae), in the northern Andes from Ecuador to Venezuela was modelled, using maximum entropy niche modelling, environmental covariates and records from locations across the Colombian Andes. The predicted suitable habitat range corresponded well to the known range of the subspecies L. n. gouldii in Colombia and clearly excluded Sierra Nevada. Therefore, these analyses suggest that this species should be removed from the Venezuelan bird list.
Lesbia nuna gouldii, suitable habitat, model, distribution, Colombia, Venezuela
Lesbia nuna, a hummingbird inhabiting the tropical Andes between 1700 and 3800 m (
Habitat alteration often follows the assessment of newly explored areas, with the concomitant extinctions (
In such cases, ecological niche models (hereafter ENMs;
The goal of the present study was to develop ENMs for the L. n. gouldii hummingbird subspecies in the northern Andes, from Ecuador to Venezuela, in order to determine whether its range actually reaches the Sierra Nevada in the latter country.
The northern Andes from Ecuador to Venezuela (ca. 4°S to 11°N; sensu
In the northern Andes, climate is influenced by the Intertropical Convergence Zone, thus both slopes receive high annual precipitation rates (
The vegetation is distributed in longitudinal belts along slopes, imperfectly correlated with elevation. Upper slopes, below the snowline, are covered by "páramo", a herbaceous vegetation co-dominated by grasses and Espeletia (Compositae), while lower slopes are covered by forests, with a treeline of usually around 3200-3500 m associated with the 6°C isotherm of mean annual temperature (
During the late Tertiary and the Quaternary, orbital forcing promoted several alternating cold and warm stages with major consequences for biota composition and distribution, especially during the Last Glacial Maximum (hereafter LGM, ca. 20 kyr BP), through mechanisms that are still being debated (
Today, the biota is also laterally segmented in physiognomically similar but taxonomically differentiable ecoregions occupying contiguous areas of the slopes (
The correction of biases in geographic space is an important step in avoidingmodels “overfitting” in environmental space. This is effected by sub-sampling the occurrence database and reducing the autocorrelation, sacrificing statistical power in favour of increasing the statistical independence of sampling units (
The bioclimatic and elevation layers provided by Worldclim, version 1.4 (
The grids of variables used in this study were processed using the libraries “raster” version 2.3-12 (
To remove the effects of multi-collinearity, Pearson's correlations between continuous variables, polyserial correlations between continuous and categorical variables and polychoric correlations between the categorical variables for those pixels where L. nuna was present, were tested. The highly correlated variables (r ≥ 0.75, p ≥ 0.001) were excluded from further analysis.
Four variable combinations were evaluated: continuous variables alone (= climate and elevation; hereafter CON), continuous variables and geology (C+G), continuous variables and soil (C+S), and the combination of all (ALL). There are several ENM algorithms whose performances have been compared by several authors (e.g.
To remove the uncertainty that arises from differing use of pseudo-absence points, model predictions were cross-validated, conducting 10 runs, splitting training and test data on a 90:10 ratio and 1000 maximum iterations. As it was assumed that the L. n. gouldii occurrence data is biased, a bias grid was built with the same dimensions, cell size and projection as the environmental variables with relative sampling probabilities of 1 for the elevation range from 700 m a.s.l (the alleged lowest elevation range of this hummingbird during LGM) and above and -9999 elsewhere. Projections were made for each run and the average projection, according to the corresponding standard deviation, were created. The significance of each variable was tested through jackknifing.
Binary maps of presence/absence were created to facilitate the visualisation of model predictions. Different threshold methods result in discrepancies in omission errors and unsuitable areas (
In each case, the mean logistic threshold value was used from the ten runs to determine the amount of false negatives (omissions) and the suitable area predicted for the control country (Ecuador), selecting those having the lower false negatives (omissions) and, at the same time, predicting the smaller area for the control country to determine the suitable area in Venezuela.
For ENMs, information was gathered on presence localities for L. nuna in Colombia which was considered as belonging to L. n. gouldii from three main sources. First, information relating to 21 collections from Canada, Colombia, The Netherlands, United Kingdom and United States, whose information is provided online in VertNet (vertnet.org), BioMap (www.biomap.net), or
The information provided by the citizen-science data was used, i.e. human observations (hereafter Appendix 2, available at http://cobra.ic.ufmt.br/web/guest/publications-data_sets) from the web-based repositories
The quality of georeferencing of these localities varied from GPS recordings to coordinates of the nearest towns listed on specimen labels. A variety of gazetteers and scientific publications to infer coordinates from the available locality information or to corroborate/correct this information when provided by the source consulted were used.
There is a specimen of L. nuna in the American Museum of Natural History (No. 38126) whose locality is simply “Pamplona” and this isprobably the reason why authors such as
Appendix 1. List of localities where L. nuna has been recorded in Colombia and included in the modelling process. Coordinates are presented in the decimal degree system. Acronyms: (AMNH) American Museum of Natural History; (ANS) Academy of Natural Sciences, Philadelphia; (DMNH) Delaware Natural History Museum; (FMNH) Field Museum of Natural History; (IAvH) Instituto Alexander von Humboldt; (ICN) Instituto de Ciencias Naturales; (INCIVA) Instituto Vallecaucano de Investigaciones; (IBC) Internet Bird Collection (http://ibc.lynxeds.com/photo/green-tailed-trainbearer-lesbia-nuna/male-feeding-blackberry-flower); (LACM) Natural History Museum of Los Angeles County; (MCBM) Museo Madre Caridad Brader Zahner; (MCZ) Museum of Comparative Zoology, Harvard University; (MHNCSJ) Museo de Historia Natural, Colegio San José; (MHN-UCC) Universidad del Cauca; (MLS) Universidad de la Salle; (MVZ) Museum of Vertebrate Zoology, University of California, Berkeley; (NHM) Natural History Museum, London; (RMNH) Nationaal Natuurhistorisch Museum; (RMNH) Naturalis Biodiversity Center; (ROM) Royal Ontario Museum; (UNIANDES) Universidad de los Andes; (USNM) National Museum of Natural History; (WFVZ) Western Foundation of Vertebrate Zoology; (XC) Xeno-Canto (www.xeno-canto.org); (YPM) Yale Peabody Museum.
The record catalogue number 1888.7.25.185 (Natural History Museum, London) was excluded given its obscure origin (
Map of northern Andes showing: (1) areas from 700 m to 1700 m a.s.l. (lighter grey); (2) areas from 1700 m to 3800 m a.s.l. (darker grey); (3) recording localities of L. n. gouldii used in the authors' ENMs analyses (solid circles); (4) "Pamplona" in Norte de Santander Department (solid diamond); (5) Bolívar Peak (= “El Picácho de la Colúna” according to
A correlation matrix (Table
Pearson's correlations between continuous environmental variables, polyserial correlations between continuous and categorical environmental variables and polychoric correlations between the categorical environmental variables for the record localities of Lesbia nuna in Colombia. Continuous variables: Elev, elevation; Bio01, annual mean temperature; Bio02, mean monthly temperature range; Bio03, isothermality; Bio04, temperature seasonality; Bio05, max temperature of the warmest month; Bio06, min temperature of the coldest month; Bio07, temperature annual range; Bio08, mean temperature of the wettest quarter; Bio09, mean temperature of the driest quarter; Bio10, mean temperature of the warmest quarter; Bio11, mean temperature of the coldest quarter; Bio12, annual precipitation; Bio13, precipitation of the wettest month; Bio14, precipitation of the driest month; Bio15, precipitation seasonality; Bio16, precipitation of the wettest quarter; Bio17, precipitation of the driest quarter; Bio18, precipitation of warmest quarter; Bio19, precipitation of the coldest quarter. Categorical variables: Soil and Geol, geology.
Bio01 |
Bio02 |
Bio03 |
Bio04 |
Bio05 |
Bio06 |
Bio07 |
Bio08 |
Bio09 |
Bio10 |
Bio11 |
Bio12 |
Bio13 |
Bio14 |
Bio15 |
Bio16 |
Bio17 |
Bio18 |
Bio19 |
Soil |
Geol |
|
Elev |
-0.99 |
-0.41 |
-0.29 |
-0.07 |
-0.96 |
-0.97 |
-0.10 |
-0.98 |
-0.99 |
-0.98 |
-0.99 |
-0.34 |
-0.44 |
0.07 |
-0.47 |
-0.44 |
0.04 |
0.04 |
-0.54 |
-0.28 |
-0.18 |
Bio01 |
- |
0.40 |
0.22 |
0.14 |
0.98 |
0.97 |
0.14 |
1.00 |
1.00 |
1.00 |
1.00 |
0.26 |
0.36 |
-0.17 |
0.52 |
0.37 |
-0.15 |
-0.09 |
0.48 |
0.20 |
0.12 |
Bio02 |
- |
-0.23 |
0.03 |
0.54 |
0.21 |
0.83 |
0.42 |
0.40 |
0.40 |
0.41 |
-0.19 |
-0.04 |
-0.27 |
0.35 |
-0.06 |
-0.30 |
-0.55 |
0.03 |
-0.20 |
0.16 |
|
Bio03 |
- |
-0.44 |
0.09 |
0.40 |
-0.74 |
0.20 |
0.22 |
0.18 |
0.24 |
0.61 |
0.54 |
0.58 |
-0.12 |
0.54 |
0.59 |
0.60 |
0.27 |
0.58 |
0.62 |
||
Bio04 |
- |
0.22 |
0.11 |
0.27 |
0.12 |
0.18 |
0.20 |
0.08 |
-0.01 |
0.04 |
-0.18 |
0.24 |
0.06 |
-0.20 |
-0.25 |
0.20 |
-0.22 |
-0.40 |
|||
Bio05 |
- |
0.92 |
0.31 |
0.98 |
0.98 |
0.98 |
0.98 |
0.20 |
0.33 |
-0.24 |
0.57 |
0.33 |
-0.22 |
-0.22 |
0.47 |
0.11 |
0.07 |
||||
Bio06 |
- |
-0.10 |
0.96 |
0.97 |
0.96 |
0.96 |
0.42 |
0.50 |
-0.02 |
0.47 |
0.50 |
0.01 |
0.07 |
0.56 |
0.31 |
0.17 |
|||||
Bio07 |
- |
0.16 |
0.13 |
0.16 |
0.14 |
-0.50 |
-0.36 |
-0.53 |
0.29 |
-0.37 |
-0.56 |
-0.72 |
-0.16 |
-0.48 |
-0.24 |
||||||
Bio08 |
- |
0.99 |
0.99 |
1.00 |
0.22 |
0.32 |
-0.19 |
0.49 |
0.32 |
-0.17 |
-0.10 |
0.44 |
0.18 |
0.11 |
|||||||
Bio09 |
- |
1.00 |
0.99 |
0.29 |
0.39 |
-0.14 |
0.51 |
0.40 |
-0.12 |
-0.09 |
0.52 |
0.21 |
0.11 |
||||||||
Bio10 |
- |
0.99 |
0.24 |
0.35 |
-0.20 |
0.54 |
0.35 |
-0.18 |
-0.11 |
0.47 |
0.17 |
0.09 |
|||||||||
Bio11 |
- |
0.25 |
0.35 |
-0.17 |
0.52 |
0.36 |
-0.15 |
-0.09 |
0.46 |
0.20 |
0.14 |
||||||||||
Bio12 |
- |
0.95 |
0.72 |
-0.09 |
0.97 |
0.77 |
0.61 |
0.86 |
0.56 |
0.23 |
|||||||||||
Bio13 |
- |
0.58 |
0.16 |
0.99 |
0.63 |
0.42 |
0.89 |
0.49 |
0.23 |
||||||||||||
Bio14 |
- |
-0.60 |
0.57 |
0.98 |
0.67 |
0.44 |
0.43 |
0.17 |
|||||||||||||
Bio15 |
- |
0.12 |
-0.58 |
-0.49 |
0.12 |
-0.19 |
0.05 |
||||||||||||||
Bio16 |
- |
0.62 |
0.44 |
0.91 |
0.53 |
0.24 |
|||||||||||||||
Bio17 |
- |
0.73 |
0.49 |
0.44 |
0.16 |
||||||||||||||||
Bio18 |
- |
0.26 |
0.34 |
0.09 |
|||||||||||||||||
Bio19 |
- |
0.45 |
0.02 |
||||||||||||||||||
Soil |
- |
0.46 |
All variables showed some degree of spatial autocorrelation. Moran’s I coefficients ranged from 0.533 (Bio03) to 0.086 (elevation), averaging 0.290. After removing four localities, these values were substantially reduced to a range between 0.465 (Bio03) and 0.002 (elevation), averaging 0.207. The omission rate on test samples was higher than the predicted omission rate when incorporating soil information. A similar pattern is observed when comparing the areas under the curves amongst the different combination of variables (Fig.
Comparison of the areas under the curves for both training (black) and test (grey) of the ENMs using the 42 localities where Lesbia nuna has been recorded in Colombia (excluding "Pamplona" and the four most highly autocorrelated localities) for each of the four environmental variable combinations: continuous variables alone (= climate and elevation, CON), continuous variables and geology (C+G), continuous variables and soil (C+S) and the combination of all (ALL). “W” and “p” are, respectively, the values of the statistics and the probability of Wilcoxon rank sum tests.
Summary statistics for variables used for ENMs are shown in Table
Summary statistics for explanatory variables used in ENMs for the 42 localities where Lesbia nuna has been recorded in Colombia and for the same elevational range in the Venezuelan Andes. In the categorical variables, “n” refers to the number of localities (Colombia) or the number of pixels (Venezuela). In Geology, codes correspond to those provided by layer GEO6EXP_ID.
Variable |
Colombia |
Venezuela |
||||
Continuous |
Median |
Min |
Max |
Median |
Min |
Max |
Elev |
2614.0 |
1654.0 |
3522.0 |
2263.0 |
1654.0 |
3522.0 |
Bio03 |
81.0 |
75.0 |
91.0 |
81.0 |
75.0 |
84.0 |
Bio04 |
303.5 |
185.0 |
640.0 |
428.0 |
339.0 |
608.0 |
Bio07 |
113.0 |
98.0 |
141.0 |
137.0 |
110.0 |
149.0 |
Bio12 |
991.5 |
772.0 |
2285.0 |
1021.0 |
706.0 |
1478.0 |
Bio14 |
35.0 |
20.0 |
123.0 |
22.0 |
8.0 |
38.0 |
Bio15 |
40.0 |
25.0 |
60.0 |
49.0 |
37.0 |
68.0 |
Bio18 |
290.5 |
153.0 |
685.0 |
310.0 |
198.0 |
503.0 |
Nominal |
Code |
n |
% |
Code |
n |
% |
Soil |
16039 |
17 |
40.5 |
27614 |
172 |
30.8 |
16047 |
10 |
23.8 |
27615 |
172 |
30.8 |
|
16017 |
4 |
9.5 |
27616 |
107 |
19.1 |
|
16015 |
4 |
9.5 |
27621 |
59 |
10.6 |
|
Others(04) |
7 |
16.7 |
Others (04) |
49 |
8.8 |
|
Geology |
219 |
15 |
35.7 |
0 |
138 |
24.7 |
434 |
6 |
14.3 |
230 |
115 |
20.6 |
|
542 |
5 |
11.9 |
219 |
36 |
6.4 |
|
Others (10) |
19 |
38.1 |
Others (33) |
270 |
48.3 |
Occurrence points in Colombia are found in four of the geologic provinces (sensu
In Colombia, soils were mostly Leptosols (40.5% of the points), followed by Acrisols (23.8%), various Cambisols (21.4%), various Phaeozems (11.9%) and Luvisols (2.4%) while, in Venezuela, various Cambisols predominated (61.7%), followed by Leptosols (19.0%), Luvisols (10.6%), Ferralsols (5.5%), Solonetz (2.5%) and Arenosols (0.5%)i.e., weakly developed soils whose development has been limited by landscape instability (
The relative contribution of each environmental variable to the different models is shown in Table
Average relative contribution of each environmental variable to the Lesbia nuna environmental niche model. C%: percent contribution values; PI: permutation importance; ALL = model combining all variables; CON = model based uniquely on continuous variables (bioclimatic and elevation); C+G = model combining continuous and geologic variables; C+S = models combining continuous and soil variables.
ALL |
CON |
C+G |
C+S |
|||||
Variables |
C% |
PI |
C% |
PI |
C% |
PI |
C% |
PI |
Bio03 |
0.6 |
2.5 |
15.5 |
13.5 |
3.1 |
4.7 |
1.0 |
1.1 |
Bio04 |
0.2 |
1.3 |
11.3 |
14.5 |
2.2 |
12.0 |
0.5 |
2.3 |
Bio07 |
0.1 |
0.0 |
0.5 |
0.8 |
0.7 |
1.3 |
0.2 |
0.1 |
Bio12 |
3.2 |
3.3 |
9.3 |
1.7 |
4.4 |
0.8 |
2.6 |
8.2 |
Bio14 |
2.1 |
4.1 |
9.5 |
2.9 |
5.0 |
4.5 |
2.4 |
0.5 |
Bio15 |
1.6 |
3.2 |
5.3 |
8.3 |
1.8 |
6.0 |
1.8 |
1.5 |
Bio18 |
1.6 |
7.6 |
4.4 |
11.5 |
1.6 |
10.2 |
2.4 |
13.0 |
Elevation |
19.6 |
22.1 |
44.2 |
46.8 |
29.4 |
37.0 |
20.9 |
27.9 |
Geology |
14.1 |
9.3 |
- |
- |
51.8 |
23.5 |
- |
- |
Soil |
57 |
46.5 |
- |
- |
- |
- |
68.1 |
45.3 |
All combinations of variables, especially CONs, predicted suitable areas in Ecuador, false negatives in Colombia and suitable areas in Venezuela, when using given thresholds. Two combinations of variables and thresholds performed differentially better (Fig.
Number of Lesbia nuna test localities omitted in Colombia, contrasted against the number of pixels predicted for Ecuador. ● ALL models, ▲C+S , ○ CON, □ C+G, combined with seven thresholds. A5 refers to ALL model + Equal training sensitivity and specificity logistic threshold and D6 refers to C+S + Maximum training sensitivity plus specificity logistic threshold.
These combinations only predicted three false negatives in the case of Colombia (Fig.
Habitat suitability ranges of Lesbia nun gouldii
Similar results were achieved when including Pamplona in the ENMs with three main differences: (1) only one combination performed differentially better (C+S + X10 percentile training presence logistic threshold), (2) fewer, small and scattered patches of suitable areas predicted in Norte de Santander and (3) the same, but smaller, two patches of suitable areas predicted for Ecuador. This model also predicted some suitable areas for Venezuela similar to, but smaller than those described in the previous paragraph, excluding again “Sierra Nevada, Merida”.
Habitat suitability for L. n. gouldii under current conditions was predicted using bioclimatic variables, elevation, information on geology and soil, as well as data available on the distribution of this hummingbird. However, the highest omission rate on test samples compared to the predicted omission rate and the statistically significant differences between the AUCTrain and AUCTest strongly indicated that models including soil information should be preferred in this case. Moreover, the combination of few omissions of test localities in Colombia and the small area predicted for Ecuador, highlight the convenience of applying the Equal training sensitivity and specificity logistic threshold, as well as the Maximum training sensitivity plus specificity logistic thresholds. The authors' conclusions are based on these modelling conditions.
These predictions fitted almost exactly to the range reported by the independent datasets consulted (Fig.
Climate variability characterised the Holocene (11,500 BP to the present), with several periods of significant rapid climate change of polar cooling, tropical variation of moisture and major atmospheric circulation changes (
Conversely, soil and geology are more stable features and were the most important in L. n. gouldii than any other variable when included in the modelling processes. Bedrock geochemistry (
In South American lowlands, where the effect of physical barriers is expected to be low, a broad range of evidence from plants (
Moreover, most of the articles cited in the previous paragraph and (up to a point) one of the currently accepted ecoregional divisions of South America (
Adaptation to local environmental conditions is a primary driver for morphological evolution and speciation (
The lack of further L. n. gouldii records for Venezuela can be analysed through three postulates. First, trochilids include long-distance and elevational migrants, acknowledged for their ability to travel long distances. Furthermore, most Andean hummingbird species have patchy distribution patterns including prominent cases such as Eriocnemis luciani, whose population in Ecuador and the extreme southwestern Colombia is separated by a gap of ca. 1100 km in Eastern Cordillera from a population in the Venezuelan Andes (
Second, L. n. gouldii could have occurred in the Venezuelan Andes until historical times but the dynamics of habitat transformation on both sides of the Colombian-Venezuelan border led to its extinction in the latter country. However, similar considerations should be made in this case as in the previous paragraph. Moreover, (1) the “Venezuelan” locality is a well-preserved area minimally impacted by human activities and (2) in Colombia, this hummingbird has been considered “fairly common” (
Third, this hummingbird was never established in the Venezuelan Andes, as indicated by these analyses. Available data indicate a substantial variation in precipitation and temperature patterns with latitude along the tropical Andes since the LGM and thus regions sharing synchronous changes during one period could be asynchronous during another
Moreover, the information in Fig.
The possibility of an "accidental" status of the "Venezuelan" specimen is also possible, but a clue in this respect can be obtained directly from the alleged collector: Christian Anton Goering. According to
However, the journey depicted in the previous paragraph contrasts with many of the details narrated by Herr Goering himself in his book published in Leipzig in 1893, translated into Spanish by M. L. de Blay and published by Universidad de Los Andes, Mérida, Venezuela, in 1958, thisbeing the version consulted by the authors. According to
Moreover, the book of
Therefore, it is striking that a spectacular species like L. nuna (Fig.
All this suggests that the “Venezuelan” specimen was simply a case of mislabelling, "perhaps from the large collections of these birds [hummingbirds] that are constantly being forwarded from the vicinity of Bogotá" (
In conclusion, it is very unlikely that the range of L. nuna extended to Venezuela or that it even occurred in the country as an accidental visitor. In consequence, this species should be removed from the Venezuelan bird list.
We are grateful to Mark Adams for providing us with photos of the “Venezuelan” specimen, relevant literature and information on the specimens deposited at The Natural History Museum (NHM), London, UK. We thank the following individuals and institutions for providing data on the specimens used in this study: Paul R Sweet, American Museum of Natural History (AMNH); Claudia Medina and Claudia Munera Roldan, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH); José Joaquín Celeita Bernal, Museo De La Salle Bogota (MLS); Janet Hinshaw, Museum of Zoology of the University of Michigan (UMMZ); Kimball L. Garrett, Natural History Museum of Los Angeles County (NHM); Steven van der Mije, Naturalis Biodiversity Center (RMNH); Helen James and Christopher Milensky, Smithsonian Institution (NMHN); René Corado, Western Foundation of Vertebrate Zoology (WFVZ). Luis Fernando Chaves and Carlos Rengifo provided us with valuable literature. Miguel Lentino and an anonymous reviewer provided valuable comments on our manuscript. The authors thank Dr. Luis Mazariegos, Cali, Colombia, for the photos of Lesbia nuna he provided. The authors declare that they have no conflict of interests.
All authors included made substantial contributions to conception and design, acquisition of data and/or analysis and interpretation of data: PRP conceived the study; PRP and IASW collected and depurated the occurrence data set; PRP and MAB developed and analysed the ENMs models; PRP and KLS analysed the ENMs outputs from a biological point of view. All four authors participated in drafting the article and revising it critically for important intellectual content and all four authors gave final approval of the version submitted.