Research Article |
Corresponding author: Bader H. Alhajeri ( bader.alhajeri@gmail.com ) Academic editor: Clara Stefen
© 2022 Zainab Dashti, Hasan Alhaddad, Bader H. Alhajeri.
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:
Dashti Z, Alhaddad H, Alhajeri BH (2022) Skull variation in populations of the Indian gerbil Tatera indica (Gerbillinae, Rodentia) sampled across its broad geographic range. Vertebrate Zoology 72: 1077-1098. https://doi.org/10.3897/vz.72.e90474
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Populations of broadly distributed species often exhibit geographic structuring, which is sometimes reflected in phenotype. The monotypic Indian gerbil (Tatera indica) is an example of a widely distributed species, with its range encompassing much of Asia. This study aims to determine if T. indica populations exhibit marked variation in skull morphology—this structure is particularly adaptable and thus could be amenable to show such variation. Furthermore, the potential drivers of skull variation are examined, including the role of climate and geography. To achieve these goals, 21 linear measurements were measured on the skulls of 509 specimens, coming from 111 different localities, across this species wide range. The specimens were then assigned into one of four broad geographic groups (≈ populations) based on their geographic proximity, and the overall and the pairwise differences in the 21 skull measurements among these groups were assessed. Specimens from Pakistan significantly differed from those belonging to the West Iran, East Iran, and India populations, which in turn did not significantly differ from each other. Pairwise bioclimatic and geographic distances between the localities explained a significant, yet small amount of variation in the measurements. Thus, while the Pakistani T. indica population was distinct in skull measurements, both climatic and non-climatic spatial factors seem not to account largely for its distinctiveness (from the other populations).
Adaptation, climate, geographic variation, morphometrics, populations, skull morphology
The Indian gerbil Tatera indica (Hardwicke, 1807) is a large rat-like rodent, with a heavily constructed body (
Indian gerbil populations are found throughout the Middle East and Central Asia (
Within a single species, geographically separated populations can show differences in morphology, including in the skull. When these conspecific populations occupy widely different habitats, then selective pressures could potentially direct this differentiation (i.e., adaptive), otherwise, morphological differentiation could be neutral (i.e., when spatially separated populations occupy similar habitats). The effect of spatial separation and climate on skull differentiation is a widely studied topic in rodents, both within populations (
While skull differentiation has been examined in T. indica, most studies so far have been geographically restricted to a single country such as Syria (e.g.,
The skulls of 509 T. indica specimens, sampled from a range extending from Kuwait to Nepal (Fig.
Map of specimen sampling localities. Sampling localities are divided into four geographic groups based on their proximity (see legend). The Y and X axis are the latitude and longitude, respectively. A geographic WGS84 projection is used. For more details, see the “Materials and methods” and Appendix
Photographs were captured with a Nikon D3200 DSLR camera using a Micro-Nikkor lens (Nikon, Tokyo, Japan) at a 6016×4000-pixel resolution. The dorsal, ventral, and lateral views of the crania were photographed, along with the occlusal and lateral views of the mandibles. A scale bar was included in all photographs to convert pixels to millimeters. The left side of each skull was photographed. In a few specimens, this side was severely broken, and as such the right side was photographed and the photograph was reflected before taking the measurements. A total of 21 linear measurements were extracted from each photograph (Fig.
Extracted linear measurements. The 21 measurements collected in this study, shown on the (a) ventral cranium, (b) lateral cranium, (c) dorsal cranium, (d) occlusal mandible, and (e) lateral mandible, of
Each measurement was taken twice in order to allow for the calculation of the repeatability of the measurements using the intraclass correlation coefficient (ICC) (
In instances where geographic coordinates were not available in museum databases, specimens were assigned this information based on the most precise locality information available from these databases and/or specimen vial labels. This was done by converting geographic information into coordinates using the distance-measuring tool in Google Maps (
Latitude and longitude values of the localities were obtained in decimal degrees to the nearest four decimal places (precision ~11 meters at the equator). A geographic coordinate system with the 1984 World Geodetic System (WGS84) datum (EPSG:4326) was assigned to the latitude and longitude values for subsequent analyses (
The resulting geographic coordinates were used in order to divide the 111 localities into four geographic groups based on their geographic proximity—this was mostly geographic breaks along longitude, which is more variable than the latitude in the geographic distribution of this species (Fig.
The sample includes 255 females, 247 males, and 7 specimens of unknown sex (Data S1). Most specimens come from Iran (233) and Pakistan (198); the rest of the countries were much less sampled: Afghanistan had 43 specimens, Sri Lanka had 15 specimens, India had 12, Kuwait had seven, and Nepal had one. (Data S1). The most sampled geographic group was “Pakistan” (235), followed by “West Iran” (126), “East Iran” (120), and India (28), respectively (Data S1). Out of the 111 localities, the most sampled was “Changa Manga Forest Park” (31), followed by “Andimeshk, 30 km S” (21), and “Kandahar International Airport” (21) (Data S1; Appendix
The first set of analyses were conducted to determine if T. indica populations (as represented by the four geographic groups; see above) show marked skull differentiation. Firstly, morphometric variation was summarized in the form of descriptive statistics (mean, standard deviation, minimum, maximum, and number of specimens) both overall and divided by geographic groups. Descriptive statistics were calculated using the stat.desc() function in the pastecs library (
Subsequently, all 21 measurements were natural log-transformed to reduce the effect of outliers and to linearize their relationships for subsequent statistical analyses. The effect of group membership, sex, and their interaction on overall morphology was then examined with a permutational MANOVA (PERMANOVA) (
While PERMANOVA is robust to unbalanced designs (
To determine which measurements differed the most between the geographic groups, univariate tests on individual logged measurements were conducted. Both parametric ANOVA assumptions were not satisfied for most measurements. Normality of model residuals was tested using the Shapiro-Wilk test as implemented in the shapiro.test() function in the R base package and homogeneity of variance across groups were tested using Levene’s test as implemented in the leveneTest() function in the in the car R package (
The affinities of the four geographic groups based on overall morphology were visualized using PCA scatterplots of the first three principal component axes, with specimens color-coded based on group membership. For these scatterplots, the PCA was applied to the 21 logged measurements using the pca() function in the pcaMethods R package (
The above analyses showed that the variation in the 21 skull measurements is geographically structured (see Results). Furthermore, similar results were found for most of the univariate tests of the 21 examined measurements, and their loadings onto the first principal component seem to suggest that the reason for this concordance is their potentially high correlation with each other, by virtue of being associated with overall size (see Results). The subsequent analyses test the possible influence of climatic and non-climatic spatial factors in driving this geographic skull variation. To achieve this goal, the morphometric data need to first be processed to be suitable for redundancy analysis (RDA) (as described in the section: Association between morphometric variation with climate and other spatial factors). This data preprocessing, along with its rationale is described in detail in Table S2. Briefly, the mice package (
To determine the effect of climatic spatial factors (i.e., climatic adaptation) in driving geographic skull variation, a proxy for overall climate need to be used for the RDA (see section: Association between morphometric variation with climate and other spatial factors). Climate was based on 19 bioclimatic variables downloaded as raster files from WorldClim (version 2) (
The climatic variables were standardized by transforming them to a mean of zero and unit variance using the scale() function in the R base package to account for different units. Preliminary analyses indicated high multicollinearity among the standardized climatic variables. Variance inflation factors (VIFs) were computed using the R function vif() from the usdm package (
To determine the effect of non-climatic spatial factors (i.e., geographic distance) in driving geographic skull variation, an index of geographic structure is needed for the RDA (see section: Association between morphometric variation with climate and other spatial factors). This was based on a set of geographic variables which were calculated as follows.
First, pairwise geographic distances were computed between the latitude and longitude values of the localities. Distance calculations between localities are inaccurate in unprojected data if the Euclidean distance formula is used, especially at increasingly large spatial scales. As an alternative to projecting the geographic coordinates to an equidistant projection, the rdist.earth() R function in the fields package (
The spatial relationships among the localities were then summarized using distance-based Moran’s Eigenvector Maps (dbMEMs;
The processed morphometric data (see section: Morphometric data preprocessing), along with the climatic (see section: Extraction of climate variables) and spatial variables (see section: Extraction of spatial variables) were used to quantify the influence of climatic and non-climatic spatial factors (i.e., geographic distance and/or climatic adaptation) in driving this geographic skull variation. This was done by variation partitioning (
Prior to running this analysis, the forward.sel() function in adespatial was used to perform a forward variable selection procedure to identify the most parsimonious combinations of explanatory variables in each of the climatic and spatial datasets (the variables that are the strongest predictors of the response variables) (and to prevent model overfitting) by permutation of residuals under the reduced model (1000 permutations) (
The reduced sets of climatic and spatial variables were then subjected to variation partitioning by means of partial RDA in order to determine the unique and combined effects of both the spatial and the climatic variables on skull morphology. The varpart() function in vegan was used to partition variation, with a model that uses a matrix of the logged skull measurements (including the imputed data) as the response variables and the climatic and the spatial variables as two separate sets of explanatory variables. As such, this function partitions the variation in the morphological measurements into components accounted for by either the spatial or the climatic variables, and their combination—this partitioning is based on partial RDA, with the R2adj from the RDA used to assess the partitions explained by each subset of variables and their combinations (
The exact same analyses, starting with forward selection, were then repeated on the size-corrected morphometric variables, to determine the effect of size in driving the pattern detected in the previous analyses.
The two trials of the morphometric measurements were highly repeatable, all of which had an ICC score > 0.71. This is greater than the average repeatability of other morphological studies (ICC = 0.65;
Descriptive statistics of measurements (in mm). Measurements are presented as mean ± standard deviation, minimum–maximum, and number of specimens. Values are visualized in Figure
Measurement | Overall | West Iran | East Iran | Pakistan | India |
---|---|---|---|---|---|
IW | 3.85 ± 0.38 2.67–5.11, n = 503 | 3.93 ± 0.39 2.93–4.86, n = 124 | 4.00 ± 0.40 2.67–4.86, n = 119 | 3.72 ± 0.30 2.67–4.45, n = 232 | 3.94 ± 0.42 3.16–5.11, n = 28 |
ML | 7.16 ± 0.53 5.97–9.15, n = 500 | 7.42 ± 0.56 6.33–8.55, n = 122 | 7.36 ± 0.51 6.43–9.15, n = 117 | 6.89 ± 0.38 5.97–8.05, n = 233 | 7.51 ± 0.51 6.41–8.25, n = 28 |
MB | 2.74 ± 0.24 2.17–3.50, n = 499 | 2.89 ± 0.20 2.51–3.50, n = 122 | 2.86 ± 0.22 2.28–3.32, n = 117 | 2.59 ± 0.17 2.17–3.14, n = 232 | 2.82 ± 0.25 2.30–3.32, n = 28 |
BW | 2.10 ± 0.36 1.00–3.83, n = 466 | 2.07 ± 0.37 1.35–2.92, n = 103 | 2.22 ± 0.37 1.22–3.27, n = 105 | 2.01 ± 0.30 1.00–2.79, n = 231 | 2.43 ± 0.43 1.92–3.83, n = 27 |
BOL | 5.30 ± 0.59 3.34–6.94, n = 443 | 5.28 ± 0.78 3.34–6.69, n = 98 | 5.57 ± 0.61 4.00–6.94, n = 94 | 5.20 ± 0.46 3.52–6.26, n = 225 | 5.24 ± 0.35 4.38–5.96, n = 26 |
BL | 12.00 ± 0.88 9.43–15.28, n = 443 | 11.99 ± 0.97 10.02–14.18, n = 97 | 12.49 ± 1.03 10.03–15.28, n = 92 | 11.83 ± 0.68 9.43–13.35, n = 228 | 11.81 ± 0.84 9.96–13.33, n = 26 |
WOB | 7.65 ± 0.58 6.12–10.54, n = 441 | 7.86 ± 0.59 6.53–9.36, n = 96 | 7.87 ± 0.70 6.52–10.54, n = 92 | 7.54 ± 0.45 6.28–8.96, n = 227 | 7.15 ± 0.55 6.12–8.53, n = 26 |
CB | 8.56 ± 0.62 6.57–10.38, n = 418 | 8.92 ± 0.66 6.57– 10.32, n = 90 | 8.72 ± 0.69 7.36–10.26, n = 86 | 8.30 ± 0.42 6.86–9.76, n = 220 | 9.07 ± 0.54 8.14–10.38, n = 22 |
ID | 2.61 ± 0.31 1.55–3.59, n = 495 | 2.68 ± 0.38 1.74–3.59, n = 120 | 2.76 ± 0.27 2.12–3.37, n = 119 | 2.48 ± 0.24 1.55–3.29, n = 228 | 2.74 ± 0.27 2.08–3.50, n = 28 |
DR | 9.47 ± 0.97 6.66–12.98, n = 501 | 9.64 ± 1.08 7.36–11.76, n = 123 | 9.87 ± 1.04 7.57–12.69, n = 118 | 9.07 ± 0.63 6.66–10.86, n = 232 | 10.30 ± 1.02 8.29–12.98, n = 28 |
HB | 9.23 ± 0.80 5.83–11.49, n = 452 | 9.35 ± 0.94 6.74–11.49, n = 102 | 9.54 ± 0.92 5.83–11.15, n = 96 | 9.05 ± 0.61 6.70–10.58, n = 227 | 9.10 ± 0.82 6.83–11.24, n = 27 |
DL | 42.33 ± 3.50 30.26–52.23, n = 401 | 43.17 ± 4.06 34.95–50.92, n = 81 | 43.90 ± 3.51 34.40–50.20, n = 83 | 41.15 ± 2.67 30.26–47.26, n = 211 | 44.30 ± 4.12 34.91–52.23, n = 26 |
DW | 21.80 ± 1.88 15.90–28.53, n = 458 | 22.14 ± 2.16 17.57–26.63, n = 106 | 22.80 ± 1.96 18.00–27.38, n = 105 | 21.11 ± 1.40 15.90–24.11, n = 222 | 22.23 ± 1.75 19.96–28.53, n = 25 |
WOI | 7.14 ± 0.57 5.61–9.78, n = 501 | 7.28 ± 0.55 6.21–9.05, n = 123 | 7.36 ± 0.50 5.83–8.52, n = 116 | 6.87± 0.45 5.61–8.12, n = 234 | 7.79 ± 0.76 6.10–9.78, n = 28 |
WN | 4.38 ± 0.42 3.12–6.06, n = 501 | 4.48 ± 0.44 3.60–5.63, n = 121 | 4.51 ± 0.41 3.50–5.73, n = 119 | 4.22 ± 0.32 3.12–5.03, n = 233 | 4.78 ± 0.52 3.76–6.06, n = 28 |
LN | 16.38 ± 1.92 9.71–21.86, n = 465 | 17.02 ± 2.18 12.25–21.86, n = 103 | 16.93 ± 1.94 12.16–21.36, n = 116 | 15.65 ± 1.48 9.71–18.62, n = 218 | 17.34 ± 1.93 14.41–21.31, n = 28 |
WI | 1.01 ± 0.14 0.62–1.75, n = 503 | 1.03 ± 0.18 0.62–1.75, n = 125 | 1.07 ± 0.14 0.75–1.41, n = 119 | 0.97 ± 0.12 0.66–1.36, n = 232 | 0.99 ± 0.12 0.76–1.30, n = 27 |
MDL | 5.43 ± 0.59 2.47–7.60, n = 506 | 5.54 ± 0.62 4.27–7.13, n = 126 | 5.57 ± 0.59 4.16–7.60, n = 120 | 5.29 ± 0.54 2.47–6.64, n = 233 | 5.45 ± 0.58 4.36–7.06, n = 27 |
FH | 1.56 ± 0.23 0.92–2.48, n = 502 | 1.60 ± 0.26 0.92–2.33, n = 124 | 1.63 ± 0.24 1.18–2.48, n = 120 | 1.50 ± 0.20 0.93–2.13, n = 231 | 1.57 ± 0.24 1.21–2.47, n = 27 |
CLM | 20.49 ± 2.05 13.89–27.18, n = 481 | 21.08 ± 2.28 15.81–25.41, n = 114 | 21.36 ± 2.11 14.25–27.18, n = 112 | 19.66 ± 1.54 13.89–22.97, n = 228 | 21.32 ± 1.88 18.30–26.60, n = 27 |
ALM | 20.35 ± 2.21 14.23–26.96, n = 458 | 20.98 ± 2.50 15.26–26.59, n = 113 | 21.38 ± 2.25 14.51–26.41, n = 111 | 19.34 ± 1.50 14.23–22.84, n = 209 | 21.34 ± 2.07 17.50–26.96, n = 25 |
Notes: Measurement acronyms are described in Table S1. All values are untransformed. |
Boxplots of the 21 measurements, separated by geographic group. Inner box lines are medians (50% quantile), the lower and upper hinges are the 25th and 75th quantiles, the upper and lower points of the whiskers represent the minimum and maximum, and the outer points are outliers. Values appear in Table
According to the PERMANOVA, a significant effect on the ln-transformed skull measurements was found for the geographic group factor (p < 0.050), but not for the sex factor (p = 0.166), nor the interaction of geographic group with sex (p = 0.652; Table
Multifactorial PERMANOVA table. The effect of geographic group (“Group”), sex (“Sex”), and their interaction on the logged measurements is examined.
Terms | DF | SS | MS | F | R 2 | p |
Group | 3 | 7.25 | 2.41 | 11.93 | 0.1064 | < 0.001 |
Sex | 1 | 0.32 | 0.32 | 1.60 | 0.0047 | 0.166 |
Group × Sex | 3 | 0.43 | 0.14 | 0.71 | 0.0063 | 0.652 |
Residuals | 297 | 60.18 | 0.20 | 0.8835 | ||
Total | 304 | 68.11 | 1.0012 | |||
Notes: df = degrees of freedom; SS = Type-II sums of squares; MS = mean squares; F = pseudo-F statistic; R2 = amount of the total variation explained by each model term (term SS/total SS); p = p-value based on 1000 permutations. Type-II SS are non-additive, as such the “Total” SS is not exactly the sum of all the model term SS, and the R2 values for the terms do not add up to exactly one (as is the case for Type-I SS). Statistically significant factors (p < 0.05) are highlighted in bold. |
Pairwise PERMANOVA tables. The effect of the geographic group factor on the logged measurements is examined.
Group | SS | MS | F | R 2 | p | Holm-p |
EI vs. IN | 0.67 | 0.67 | 2.88 | 0.0343 | 0.058 | 0.176 |
EI vs. PK | 3.66 | 3.66 | 21.44 | 0.0870 | < 0.001 | 0.005 |
EI vs. WI | 0.28 | 0.28 | 1.05 | 0.0083 | 0.300 | 0.300 |
IN vs. PK | 2.62 | 2.62 | 17.10 | 0.0885 | < 0.001 | 0.005 |
IN vs. WI | 0.75 | 0.75 | 2.53 | 0.0323 | 0.095 | 0.191 |
PK vs. WI | 3.32 | 3.32 | 17.44 | 0.0734 | < 0.001 | 0.005 |
Notes: All column labels correspond to those in Table |
The PERMDISP analysis indicated homogeneous multivariate dispersions in the logged skull measurements for sex (p = 0.060) but not for the geographic group factor (p < 0.050). This indicated that for the geographic group factor, the significant PERMANOVA result detected earlier is not only explained by differences in medians of the geographic groups but is also driven by differences in group multivariate dispersions. However, the pairwise PERMANOVAs and the results of the PCA analyses seem to suggest substantial differences in the logged skull measurements between some of the geographic groups (and not just in their dispersions).
The Kruskal-Wallis tests found significant differences between the geographic groups in all the measurements (p < 0.050 for all measurements; Table
Univariate statistical analyses. The analyses are of the differences in each of the 21 measurements among the four geographic groups. Results of both the omnibus Kruskal-Wallis and the pairwise Scheffé tests are shown.
Meas. | Kruskal-Wallis test | Scheffé test | |||||
WI–EI | WI–PK | WI–IN | EI–PK | EI–IN | PK–IN | ||
IW |
η
2 = 0.115, p < 0.050 |
g = 0.185, p = 0.526 |
g = 0.632, p < 0.050 |
g = 0.033, p = 0.999 |
g = 0.843, p < 0.050 |
g = 0.147, p = 0.899 |
g = 0.709, p < 0.050 |
ML |
η
2 = 0.212, p < 0.050 |
g = 0.106, p = 0.855 |
g = 1.161, p < 0.050 |
g = 0.162, p = 0.832 |
g = 1.084, p < 0.050 |
g = 0.287, p = 0.540 |
g = 1.550, p < 0.050 |
MB |
η
2 = 0.352, p < 0.050 |
g = 0.169, p = 0.555 |
g = 1.651, p < 0.050 |
g = 0.345, p = 0.344 |
g = 1.379, p < 0.050 |
g = 0.160, p = 0.833 |
g = 1.245, p < 0.050 |
BW |
η
2 = 0.062, p < 0.050 |
g = 0.391, p < 0.050 |
g = 0.176, p = 0.690 |
g = 0.922, p < 0.050 |
g = 0.622, p < 0.050 |
g = 0.549, p = 0.106 |
g = 1.293, p < 0.050 |
BOL |
η
2 = 0.041, p < 0.050 |
g = 0.405, p < 0.050 |
g = 0.136, p = 0.944 |
g = 0.051, p = 0.999 |
g = 0.707, p < 0.050 |
g = 0.563, p = 0.167 |
g = 0.096, p = 0.976 |
BL |
η
2 = 0.059, p < 0.050 |
g = 0.502, p < 0.050 |
g = 0.194, p = 0.616 |
g = 0.181, p = 0.853 |
g = 0.805, p < 0.050 |
g = 0.673, p < 0.050 |
g = 0.025, p = 0.998 |
WOB |
η
2 = 0.084, p < 0.050 |
g = 0.018, p = 0.999 |
g = 0.616, p < 0.050 |
g = 1.184, p < 0.050 |
g = 0.592, p < 0.050 |
g = 1.047, p < 0.050 |
g = 0.828, p < 0.050 |
CB |
η
2 = 0.164, p < 0.050 |
g = 0.298, p = 0.117 |
g = 1.184, p < 0.050 |
g = 0.222, p = 0.735 |
g = 0.778, p < 0.050 |
g = 0.519, p = 0.071 |
g = 1.747, p < 0.050 |
ID |
η
2 = 0.172, p < 0.050 |
g = 0.221, p = 0.180 |
g = 0.684, p < 0.050 |
g = 0.156, p = 0.744 |
g = 1.101, p < 0.050 |
g = 0.061, p = 0.995 |
g = 1.053, p < 0.050 |
DR |
η
2 = 0.157, p < 0.050 |
g = 0.209, p = 0.280 |
g = 0.699, p < 0.050 |
g = 0.614, p < 0.050 |
g = 0.996, p < 0.050 |
g = 0.417, p = 0.169 |
g = 1.800, p < 0.050 |
HB |
η
2 = 0.064, p < 0.050 |
g = 0.201, p = 0.460 |
g = 0.396, p < 0.050 |
g = 0.267, p = 0.604 |
g = 0.660, p < 0.050 |
g = 0.480, p = 0.125 |
g = 0.076, p = 0.997 |
DL |
η
2 = 0.095, p < 0.050 |
g = 0.192, p = 0.543 |
g = 0.623, p < 0.050 |
g = 0.277, p = 0.540 |
g = 0.918, p < 0.050 |
g = 0.109, p = 0.976 |
g = 1.098, p < 0.050 |
DW |
η
2 = 0.122, p < 0.050 |
g = 0.317, p = 0.064 |
g = 0.599, p < 0.050 |
g = 0.043, p = 0.989 |
g = 1.042, p < 0.050 |
g = 0.293, p = 0.622 |
g = 0.771, p < 0.050 |
WOI |
η
2 = 0.198, p < 0.050 |
g = 0.137, p = 0.732 |
g = 0.831, p < 0.050 |
g = 0.848, p < 0.050 |
g = 1.021, p < 0.050 |
g = 0.774, p < 0.050 |
g = 1.852, p < 0.050 |
WN |
η
2 = 0.126, p < 0.050 |
g = 0.057, p = 0.961 |
g = 0.702, p < 0.050 |
g = 0.634, p < 0.050 |
g = 0.797, p < 0.050 |
g = 0.611, p < 0.050 |
g = 1.563, p < 0.050 |
LN |
η
2 = 0.108, p < 0.050 |
g = 0.043, p = 0.996 |
g = 0.776, p < 0.050 |
g = 0.145, p = 0.864 |
g = 0.772, p < 0.050 |
g = 0.206, p = 0.789 |
g = 1.093, p < 0.050 |
WI |
η
2 = 0.078, p < 0.050 |
g = 0.215, p = 0.200 |
g = 0.400, p < 0.050 |
g = 0.238, p = 0.763 |
g = 0.721, p < 0.050 |
g = 0.534, p = 0.134 |
g = 0.137, p = 0.956 |
MDL |
η
2 = 0.034, p < 0.050 |
g = 0.050, p = 0.976 |
g = 0.426, p < 0.050 |
g = 0.141, p = 0.940 |
g = 0.492, p < 0.050 |
g = 0.199, p = 0.847 |
g = 0.287, p = 0.621 |
FH |
η
2 = 0.043, p < 0.050 |
g = 0.133, p = 0.671 |
g = 0.451, p < 0.050 |
g = 0.105, p = 0.979 |
g = 0.625, p < 0.050 |
g = 0.250, p = 0.706 |
g = 0.359, p = 0.478 |
CLM |
η
2 = 0.140, p < 0.050 |
g = 0.124, p = 0.750 |
g = 0.774, p < 0.050 |
g = 0.106, p = 0.931 |
g = 0.965, p < 0.050 |
g = 0.019, p = 1.000 |
g = 1.044, p < 0.050 |
ALM |
η
2 = 0.163, p < 0.050 |
g = 0.163, p = 0.520 |
g = 0.857, p < 0.050 |
g = 0.146, p = 0.849 |
g = 1.134, p < 0.050 |
g = 0.015, p = 1.000 |
g = 1.268, p < 0.050 |
Notes: p = raw p-value. For the Kruskal-Wallis tests, all p-values remained significant at p < 0.050 after correcting for multiple comparisons using |
For the PCA based on the 21 measurements, the first principal component (PC1) by far explained most of the variation (61.7%), while PC2 and PC3 explained only 6.7% and 4.2% of the variation, respectively (Fig.
PCA loadings. Loadings describe how much each of the 21 logged measurements contributes to each PC axis.
Measurement | PC1 | PC2 | PC3 |
IW | –0.196 | 0.126 | 0.184 |
ML | –0.218 | 0.352 | –0.135 |
MB | –0.156 | 0.586 | –0.256 |
BW | –0.215 | 0.047 | 0.167 |
BOL | –0.204 | –0.268 | –0.163 |
BL | –0.207 | –0.282 | –0.371 |
WOB | –0.158 | –0.335 | –0.424 |
CB | –0.159 | 0.313 | –0.339 |
ID | –0.243 | 0.003 | 0.033 |
DR | –0.268 | 0.037 | 0.050 |
HB | –0.202 | –0.268 | –0.218 |
DL | –0.227 | –0.059 | –0.096 |
DW | –0.253 | –0.059 | –0.005 |
WOI | –0.230 | 0.179 | –0.100 |
WN | –0.243 | 0.070 | 0.113 |
LN | –0.240 | –0.051 | 0.142 |
WI | –0.209 | –0.124 | 0.291 |
MDL | –0.223 | –0.094 | 0.242 |
FH | –0.191 | –0.020 | 0.343 |
CLM | –0.254 | –0.040 | 0.099 |
ALM | –0.231 | 0.022 | 0.128 |
Notes: Measurement acronyms are described in Table S1. To improve interpretation, measurments with PC loadings above an arbitrarily large cut-off value of ≥ |0.3| are highlighted in bold. Only PC1–3 are shown. |
The similar results that were found for most of the 21 examined measurements for the Kruskal-Wallis and the Scheffé tests (Table
The most parsimonious combination of variables chosen by the forward selection procedure (for the variation partitioning RDA analysis) for the climatic dataset were (in order of inclusion in the model): BIO9 (Mean Temperature of Driest Quarter), BIO3 (Isothermality), BIO5 (Max Temperature of Warmest Month), BIO15 (Precipitation Seasonality), BIO8 (Mean Temperature of Wettest Quarter), and BIO2 (Mean Diurnal Range); and for the spatial dataset were: MEM1, MEM6, MEM5, MEM19, MEM7, MEM3, MEM4, MEM9, MEM15, MEM17, and MEM2 (Table S4). The vegan function vif.cca() confirmed that all remaining explanatory variables in both datasets had VIFs ≤ 10, indicating an acceptable level of multicollinearity has been reached. For the size-corrected variables, the forward selection procedure led to the retention of the following sets of variables (in order of inclusion in the model): BIO8 (Mean Temperature of Wettest Quarter), BIO3 (Isothermality), BIO9 (Mean Temperature of Driest Quarter), BIO5 (Max Temperature of Warmest Month), BIO13 (Precipitation of Wettest Month), BIO18 (Precipitation of Warmest Quarter), BIO2 (Mean Diurnal Range), and BIO15 (Precipitation Seasonality) for the climatic dataset, and MEM1, MEM5, MEM4, MEM3, MEM11, MEM2, MEM19, MEM12, MEM8, MEM10, MEM7, MEM13, MEM16, MEM18, MEM15, and MEM17 (Table S4) for the spatial dataset, all of which had VIFs ≤ 12.
The variation partitioning by RDA analysis indicated that all fractions were significant at p < 0.05 for both the non-sheared and the sheared data (Table
Variation partitioning by RDA analysis. Summary of variation partitioning by (partial) RDA partitions explained by each subset of variables and their combinations. In all instances the response variables are the 21 morphometric measurements (logged, including imputed missing data; top = not sheared, bottom = sheared). The different combinations of spatial and climatic variables (explanatory variables) are indicated in each row.
Terms | DF | F | p | R 2 adj |
Before size correction | ||||
Spatial | 11 | 9.94 | < 0.050 | 0.162 |
Climate | 6 | 17.63 | < 0.050 | 0.164 |
Spatial | climate | 11 | 6.19 | < 0.050 | 0.085 |
Climate | spatial | 6 | 10.64 | < 0.050 | 0.087 |
Spatial + climate | 17 | 10.94 | < 0.050 | 0.250 |
Joint effect [b] | 0.077 | |||
After size-correction | ||||
Spatial | 16 | 5.31 | < 0.050 | 0.119 |
Climate | 8 | 6.83 | < 0.050 | 0.084 |
Spatial | climate | 16 | 3.39 | < 0.050 | 0.065 |
Climate | spatial | 8 | 3.14 | < 0.050 | 0.030 |
Spatial + climate | 24 | 4.71 | < 0.050 | 0.149 |
Joint effect [b] | 0.055 | |||
Notes: “Spatial” = fraction explained by spatial variables (RDA model that only includes spatial explanatory variables); “Climate” = fraction explained by climate variables (RDA model that only includes climatic explanatory variables); “Spatial | climate” = fraction explained by spatial variables after partialing out the effects of climatic variables (partial RDA model that includes spatial explanatory variables and climatic conditioning variables); “Climate | spatial” = fraction explained by climatic variables after partialing out the effects of spatial variables (partial RDA model that includes climatic explanatory variables and spatial conditioning variables); “Spatial + climate” = total explained by both spatial and climatic variables (RDA model that includes both spatial and climatic explanatory variables); and “Joint effect [b]” = joint effect (common fraction) of spatial and climate variables (non-testable component calculated as the difference “Climate” minus “Climate | spatial” or “Spatial” minus “Spatial | climate”; this fraction arises because explanatory variables in different sets are correlated). Geographic variables were extracted from dbMEM analysis (positive MEM variables), while the climatic variables are standardized (to a mean of zero and unit variance) and based on WorldClim (version 2). F = pseudo-F based of permutation tests, R2adj = adjusted coefficient of multiple determination. All p-values are significant. For the un-sheared dataset, spatial variables are based on (in order of inclusion in the model): MEM1, MEM6, MEM5, MEM19, MEM7, MEM3, MEM4, MEM9, MEM15, MEM17, and MEM2, while the climatic variables are based on: BIO9, BIO3, BIO5, BIO15, BIO8, and BIO2. For the sheared dataset, spatial variables are based on (in order of inclusion in the model): MEM1, MEM5, MEM4, MEM3, MEM11, MEM2, MEM19, MEM12, MEM8, MEM10, MEM7, MEM13, while the climatic variables are based on BIO8, BIO3, BIO9, BIO5, BIO13, BIO18, BIO2, and BIO15. Statistical significance was based on 1000 permutations. |
The RDA plots of the climate variables after removing the effect of the spatial variables (showing the response of the morphometric variation to climate variables) show no clear separation of the geographic groups on the first two RDA axes both for the non-sheared data (Fig. S3a) and for the sheared data (Fig. S3c). The amount of variation accounted for by the first two RDA axes and their significance are indicated in the Fig. S3 legend. When not considering the geographic groups, and examining the specimens as a whole, the strongest separation among the specimens (main axes of variation for climate, represented by the longest vectors) seems to be based on BIO5 (Max Temperature of Warmest Month), followed by BIO9 (Mean Temperature of Driest Quarter), and BIO8 (Mean Temperature of Wettest Quarter), respectively, for the non-sheared data (Fig. S3b), while for the sheared data, the separation seems to be greatest for BIO5 (Max Temperature of Warmest Month) followed by BIO18 (Precipitation of Warmest Quarter) (Fig. S3d). For the most part, the directions of this climatic variation seem to be neither strongly correlated nor opposed (Fig. S3b, d). However, among the variables, specimens with increasing BIO9 (Mean Temperature of Driest Quarter) have decreasing BIO8 (Mean Temperature of Wettest Quarter) (for the non-sheared data; Fig. S3b), while specimens with increasing BIO5 (Max Temperature of Warmest Month) have decreasing BIO18 (Precipitation of Warmest Quarter) (for the sheared data; Fig. S3d). BIO5 (Max Temperature of Warmest Month) seems to be the strongest contributor to RDA axis 1 for the non-sheared data (Fig. S3b), while BIO8 (Mean Temperature of Wettest Quarter) seems to be the strongest contributor to RDA axis 1 for the sheared data (Fig. S3d). The other climatic variables seem to more strongly contribute to RDA axis 2 (Fig. S3b, d).
The results of each of the omnibus and the pairwise PERMANOVAs, along with the omnibus Kruskal-Wallis and the pairwise Scheffé tests, in addition to the PCA, all support the idea that the considered geographic groups differ from each other in skull morphology. The Pakistan group was the most distinct among the geographic groups (Figs
The distinctiveness of the Pakistani T. indica population found here could not be detected in the earlier T. indica morphometric studies because of their more restrictive geographic scale. For example,
The distinctiveness of the Pakistani T. indica skulls detected in this study was mostly a result of differences in their dentition, as captured by M1 breadth and the molar row length (Table
While minor, this study found that non-climatic spatial factors did explain some of the skull variation (Table
Similarly, this study also found a significant, but minor, influence of climatic spatial factors on geographic skull variation, potentially explained by climatic adaptation (Table
T. indica specimens from Pakistan significantly differed in skull morphology from those belonging to the West Iran, East Iran, and India populations, which in turn did not significantly differ from each other. This differentiation was found to be driven to a similar (but small) degree by both climatic and non-climatic spatial factors. Thus, the distinctiveness of the Pakistani T. indica population could be driven by unexamined factors. Potential factors that could be examined in future studies include environmental heterogeneity and dispersal barriers. The taxonomic implications of the results of the present study are that T. indica could hide cryptic diversity, if only at the subspecific level. This could be explored further and in more detail with a larger dataset that incorporates more specimens from, or from near the Pakistan group of localities, as well as by including other localities that are unexamined in the present study. Characters other than the cranial measurments examined herein, and other phenotypic characters can also be explored to further elucidate the aforementioned patterns.
All data generated in this study are deposited in the supporting information (see supplementary file 1: Data S1).
BHA conceived and designed the study. ZD and BHA photographed the specimens. ZD collected and analyzed the data. ZD, BHA, and HA wrote the manuscript. All authors read and approved the final version of the manuscript.
The authors declare no conflict of interest.
The authors are grateful to the following museum curators, collection managers, and staff for permitting access to their collections and general assistance:
Geographic localities of the 509 T. indica specimens sampled in this study. The voucher number of each specimen is indicated. In instances where museum databases and/or vial labels had spelling mistakes or outdated locality information (i.e., the name of a county changed), locality information was unified, with the original spelling or locality information between square brackets.
Afghanistan
Kandahar, Herat Highway [Herat-Kandahar Rd], 5 mi S (
India
Delhi (
Iran
Bam, 55 km E (
Kuwait
Kuwait City [Al Kuwait] (
Nepal
Tikapur (
Pakistan
Amandara (
Sri Lanka
Sri Lanka centroid (
Figure S1
Data type: .jpg
Explanation note: The full range of Tatera indica according to the International Union for Conservation of Nature (IUCN) Red List (
Figure S2
Data type: .pdf
Explanation note: Scatterplot of PC2 and PC3 of the PCA conducted on the 21 logged measurements. Specimens are divided into the four geographic groups (see legend). The amount of explained variance by each PC axis is indicated in parentheses. The plot was generated using ggplot2.
Figure S3
Data type: .pdf
Explanation note: RDA plots. The plots of the specimens and the measurements on the plane defined by the first two RDA axes shown for the partial RDA model that includes climatic explanatory variables and spatial conditioning variables (“climate | spatial”) and non-sheared (a, b) and sheared (c, d) morphometric measurements as the response variables. The amount of variation explained by each RDA axis as proportion of the total variation explained by each RDA model (proportion explained of accumulated constrained eigenvalues) is as follows. For the non-sheared morphometric variables, RDA axis 1 accounts for 87.7% of the variation while axis 2 accounts for 7.7% of the variation. For the sheared morphometric variables, RDA axis 1 accounts for 44.1% of the variation while axis 2 accounts for 17.3% of the variation. The significance of each RDA axis was tested using forward tests for axes with 1000 permutations (non-sheared axis 1: F = 56.00, p < 0.050; non-sheared axis 2: p = 0.183; sheared axis 1: F = 11.08, p < 0.050; sheared axis 2: F = 4.35, p < 0.050; sheared axis 3: p = 0.088). For all four plots, RDA axis 1 is on the x-axis, while RDA axis 2 is on the y-axis, and specimen scores are weighted sums of measurements. In (a) and (c) the specimens are color coded based on their geographic group membership, while crosses (+) in each plot correspond to the 21 measurements. In (b) and (d) the arrows are the explanatory climatic variables after removing the effect of the spatial covariables, shown on the same plane as plots (a) and (c). See the main text for more information about the bioclimatic variables. Plots were generated using ggord library (
Table S1
Data type: .docx
Explanation note: Descriptions of the morphometric measurements used in this study. The acronyms match those in Figure
Table S2
Data type: .docx
Explanation note: Supplemental methods.
Table S3
Data type: .docx
Explanation note: Bioclimatic variables used as an index of climate in this study. These variables are based on monthly temperature and precipitation values, and show annual trends, seasonality, and extremes. The descriptions are from: https://www.worldclim.org.
Table S4
Data type: .docx
Explanation note: Summary of forward stepwise variable selection. The most parsimonious combinations of explanatory variables in each of the climatic and the spatial dataset are indicated in their order of entry into the model. Variable selection stopped either when the significance alpha level of 0.05 was reached or when the adjusted coefficient of multiple determination (R2adj) value of the reduced model reached that of the global model.
Data S1
Data type: .cvs
Explanation note: Data matrix used for all the analyses in this study. For each specimen, the catalog number is indicated in the first column, followed by its sex (F = female, M = male, blank = unknown), the country to which it belongs, the most precise collection locality available for the specimen (i.e. specific locality, county, state, province, etc.), the basis for the geographic coordinates (see “Materials and methods”), the latitude and longitude of the locality, and the geographic group of each locality based on proximity, mostly along the longitude (see “Materials and methods”). The locality information matches Appendix
Data S2
Data type: .docx
Explanation note: Pairwise Pearson's correlation coefficients (r) among the 21 logged measurements. Measurement acronyms are described in Table S1.