Phylogenetics and the evolution of terrestriality in mudskippers (Gobiidae: Oxudercinae).

The initial vertebrate conquest of land by stegocephalians (Sarcopterygia) allowed access to new resources and exploitation of untapped niches precipitating a major phylogenetic diversification. However, a paucity of fossils has left considerable uncertainties about phylogenetic relationships and the eco-morphological stages in this key transition in Earth history. Among extant actinopterygians, three genera of mudskippers (Gobiidae: Oxudercinae), Boleophthalmus, Periophthalmus and Periophthalmodon are the most terrestrialized, with vertebral, appendicular, locomotory, respiratory, and epithelial specializations enabling overland excursions up to 14 h. Unlike early stegocephalians, the ecologies and morphologies of the 45 species of oxudercines are well known, making them viable analogs for the initial vertebrate conquest of land. Nevertheless, they have received little phylogenetic attention. We compiled the largest molecular dataset to date, with 29 oxudercine species, and 5 nuclear and mitochondrial loci. Phylogenetic and comparative analyses revealed strong support for two independent terrestrial transitions, and a complex suit of ecomorphological forms in estuarine environments. Furthermore, neither Oxudercinae nor their presumed sister-group the eel gobies (Amblyopinae, a group of elongated gobies) were monophyletic with respect to each other, requiring a merging of these two subfamilies and revealing an expansion of phenotypic variation within the "mudskipper" clade. We did not find support for the expected linear model of ecomorphological and locomotory transition from fully aquatic, to mudswimming, to pectoral-aided mudswimming, to lobe-finned terrestrial locomotion proposed by earlier morphological studies. This high degree of convergent or parallel transitions to terrestriality, and apparent divergent directions of estuarine adaptation, promises even greater potential for this clade to illuminate the conquest of land. Future work should focus on these less-studied species with "transitional" and other mud-habitat specializations to fully resolve the dynamics of this diversification.

Genetic Diversity and Population Structure of Dromedary Camel-Types.

The dromedary camel is a unique livestock for its adaptations to arid-hot environments and its ability to provide goods under extreme conditions. There are no registries or breed standards for camels. Thus, named camel populations (i.e., camel-types) were examined for genetic uniqueness and breed status. Camel populations are generally named based on shared phenotype, country or region of origin, tribal ownership, or the ecology of their habitat. A dataset of 10 Short-Tandem Repeat markers genotyped for 701 individual camels from 27 camel-types was used to quantify genetic diversity within camel-types, compare genetic diversity across camel-types, determine the population genetic structure of camel-types, and identify camel-types that may represent true breeds. Summary statistics (genotyping call rate, heterozygosity, inbreeding coefficient FIS, and allelic frequencies) were calculated and population-specific analyses (pairwise FST, neighbor-joining tree, relatedness, Nei's genetic distance, principal coordinate analysis [PCoA], and STRUCTURE) were performed. The most notable findings were 1) little variation in genetic diversity was found across the camel-types, 2) the highest genetic diversity measure was detected in Targui and the lowest was in Awarik, 3) camel-types from Asia (especially the Arabian Peninsula) exhibited higher genetic diversity than their counterparts in Africa, 4) the highest DeltaK value of population structure separated camel-types based on geography (Asia vs. Africa), 5) the most distinct camel-types were the Omani, Awarik, and the Gabbra, 6) camel-types originating from the same country did not necessarily share high genetic similarity (e.g., camel-types from Oman), and 7) camel-type names were not consistently indicative of breed status.

Cranial variation in species and subspecies of kangaroo rats (Dipodomys, Dipodomyinae, Rodentia) according to geometric morphometrics.

Traditional Dipodomys (sub)species identification uses geography, phenotype, and external/skull measurements. Such measurements are correlated with size and thus redundant. I assessed the value of scaled cranial shape, based on two-dimensional landmarks (analyzed using geometric morphometric methods) in distinguishing Dipodomys taxa, and in summarizing their variation. My dataset includes 601 adult specimens from 20 species (49 operational taxonomic units - OTUs) across 190 localities. Cranial shape was highly useful in classifying Dipodomys taxa without considering geography. The auditory bulla was the most variable region-taxa differed in its hypertrophy, accompanied by different degrees of nearby structure crowding. Cranial shape was weakly allometric, with no significant sexual dimorphism. Weak size dimorphism was detected. (Sub)specific taxonomy is not reflective of shape variation, as the number of subspecies per species is not associated with disparity. Shape had significant phylogenetic signal, but subspecies did not always cluster with conspecifics and species did not always cluster according to phylogenetic relationship/taxonomy. Shape variation was correlated with climate, and species differed in morphological disparity and degree of specialization, which may contribute to divergence in shape variation patterns from phylogeny. D. deserti was the most specialized species, diverging greatly from the genus mean; D. heermanni was the least specialized. This study provides new insights into morphological variation of North American keystone species, several of conservation interest, for example, D. heermanni berkeleyensis, D. h. dixoni, D. nitratoides brevinasus, and D. n. nitratoides.

Towards phenotyping adaptive traits in camels: A study of the influence of hypotonic saline solutions on blood cell area.

Single-humped camels are livestock of physical, physiological, and biochemical adaptations to hot desert environments and to water scarcity. The tolerance of camels to water deprivation and their exceptional capacity for rapid rehydration requires blood cells with membranes of specialized organization and chemical composition. The objectives of this study are to examine the changes in the area (a proxy for volume) of camel blood cells in solutions with decreasing concentrations of NaCl and consequently identify the conditions under which blood cells can be phenotyped in a large population. Whole-blood samples from three healthy adult female camels were treated with four different concentrations of NaCl and examined at six incubation-periods. Observationally, red blood cells in all treatments remained intact and maintained their elliptical shape while white blood cells experienced some damage, lysing at concentrations below 0.90%. Average basal (in 0.90% NaCl) RBC area was ~15 µm² and swelled in the various treatments, in some cases reaching twice its original size. Excluding the damaged cells, the average area of combined WBCs, ~32.7 µm², expanded approximately three times its original size. We find that camel WBCs, like their RBCs, are adapted to hypotonic environments, and are capable of expanding while maintaining their structural integrity.

Cranial differences in three-toed jerboas (Dipodinae, Dipodidae, Rodentia) according to recent taxonomic revisions.

Recent phylogenetic studies amended the taxonomy of three-toed jerboas (subfamily Dipodinae), including raising subspecies to full species. Here, we use geometric morphometrics to compare scaled-shape differences in dipodine crania while considering their revised taxonomy. We sampled Dipus deasyi, D. sagitta halli, D. s. sowerbyi, Jaculus blanfordi blanfordi, J. hirtipes, J. jaculus, J. loftusi, J. orientalis gerboa, J. o. mauritanicus, and Stylodipus andrewsi. Crania were not sexually dimorphic. Common allometry explained some of the shape variation, for example, reduced braincases in larger specimens. Most operational taxonomic unit pairs differed in both size and shape. Dipus and Stylodipus clustered together based on their cranial shape. Jaculus differed from the aforementioned genera by its larger tympanic bulla, broader braincase, larger infraorbital foramen, along with reduced molars and rostra. Jaculus orientalis differed from other Jaculus by its broader face versus reduced cranial vault. Jaculus blanfordi (subgenus Haltomys) resembles members of the subgenus Jaculus more than its consubgener (J. orientalis). Jaculus loftusi, previously considered a synonym of J. jaculus, clearly differed from the latter by its shorter rostrum, smaller infraorbital foramen, and more caudolaterally expanded tympanic bulla. Jaculus hirtipes, another recent synonym of J. jaculus, resembled J. blanfordi more in scaled cranial shape than it did J. jaculus. Dipus sagitta halli and D. s. sowerbyi were indistinguishable, but they clearly differed from D. deasyi (recently raised to full species) with the latter having a larger molar row, more inflated tympanic bulla, and shorter, slenderer rostrum. Ecological explanations for detected cranial shape differences are considered, including diet and habitat (particularly substrate).

Cranial variation in allactagine jerboas (Allactaginae, Dipodidae, Rodentia): a geometric morphometric study.

Allactaginae is a subfamily of dipodids consisting of four- and five-toed jerboas ( Allactaga, Allactodipus, Orientallactaga, Pygeretmus, Scarturus) found in open habitats of Asia and North Africa. Recent molecular phylogenies have upended our understanding of this group's systematics across taxonomic scales. Here, I used cranial geometric morphometrics to examine variation across 219 specimens of 14 allactagine species ( Allactaga major, A. severtzovi, Orientallactaga balikunica, O. bullata, O. sibirica, Pygeretmus platyurus, P. pumilio, P. shitkovi, Scarturus aralychensis, S. euphraticus, S. hotsoni, S. indicus, S. tetradactylus, S. williamsi) in light of their revised taxonomy. Results showed no significant sexual size or shape dimorphism. Species significantly differed in cranial size and shape both overall and as species pairs. Species identity had a strong effect on both cranial size and shape. Only a small part of cranial shape variation was allometric, with no evidence of unique species allometries, and most specimens fit closely to the common allometric regression vector. Allactaga was the largest, followed by Orientallactaga, Scarturus, and finally Pygeretmus. Principal component 1 (PC1) separated O. bullata+ O. balikunica+ S. hotsoni (with inflated bullae along with reduced zygomatic arches and rostra) from A. major+ A. severtzovi+ O. sibirica (with converse patterns), while PC2 differentiated Orientallactaga (with enlarged cranial bases and rostra along with reduced zygomatic arches and foramina magna) from Scarturus+ Pygeretmus (with the opposite patterns). Clustering based on the unweighted pair group method with arithmetic mean (UPGMA) contained the four genera, but S. hotsoni clustered with O. bullata+ O. balikunica and O. sibirica clustered with A. major+ A. severtzovi, likely due to convergence and allometry, respectively.

Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types.

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders' governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula "Mezayen" camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

Habitat productivity is a poor predictor of body size in rodents.

The "resource availability hypothesis" predicts occurrence of larger rodents in more productive habitats. This prediction was tested in a dataset of 1,301 rodent species. We used adult body mass as a measure of body size and normalized difference vegetation index (NDVI) as a measure of habitat productivity. We utilized a cross-species approach to investigate the association between these variables. This was done at both the order level (Rodentia) and at narrower taxonomic scales. We applied phylogenetic generalized least squares (PGLS) to correct for phylogenetic relationships. The relationship between body mas and NDVI was also investigated across rodent assemblages. We controlled for spatial autocorrelation using generalized least squares (GLS) analysis. The cross-species approach found extremely low support for the resource availability hypothesis. This was reflected by a weak positive association between body mass and NDVI at the order level. We find a positive association in only a minority of rodent subtaxa. The best fit GLS model detected no significant association between body mass and NDVI across assemblages. Thus, our results do not support the view that resource availability plays a major role in explaining geographic variation in rodent body size.

Cdrom Archive: A Gateway to Study Camel Phenotypes.

Camels are livestock that exhibit unique morphological, biochemical, and behavioral traits, which arose by natural and artificial selection. Investigating the molecular basis of camel traits has been limited by: (1) the absence of a comprehensive record of morphological trait variation (e.g., diseases) and the associated mode of inheritance, (2) the lack of extended pedigrees of specific trait(s), and (3) the long reproductive cycle of the camel, which makes the cost of establishing and maintaining a breeding colony (i.e., monitoring crosses) prohibitively high. Overcoming these challenges requires (1) detailed documentation of phenotypes/genetic diseases and their likely mode of inheritance (and collection of related DNA samples), (2) conducting association studies to identify phenotypes/genetic diseases causing genetic variants (instead of classical linkage analysis, which requires extended pedigrees), and (3) validating likely causative variants by screening a large number of camel samples from different populations. We attempt to address these issues by establishing a systematic way of collecting camel DNA samples, and associated phenotypic information, which we call the "Cdrom Archive." Here, we outline the process of building this archive to introduce it to other camel researchers (as an example). Additionally, we discuss the use of this archive to study the phenotypic traits of Arabian Peninsula camel breeds (the "Mezayen" camels). Using the Cdrom Archive, we report variable phenotypic traits related to the coat (color, length, and texture), ear and tail lengths, along with other morphological measurements.

Quality and quantity of dromedary camel DNA sampled from whole-blood, saliva, and tail-hair.

Camels are livestock with unique adaptations to hot-arid regions. To effectively study camel traits, a biobank of camel DNA specimens with associated biological information is needed. We examined whole-blood, saliva (buccal swabs), and tail-hair follicle samples to determine which is the best source for establishing a DNA biobank. We inspected five amounts of each of whole-blood, buccal swabs, and tail-hair follicles in nine camels, both qualitatively via gel electrophoresis and quantitatively using a NanoDrop spectrophotometer. We also tested the effects of long term-storage on the quality and quantity of DNA, and measured the rate of degradation, by analyzing three buccal swab samples and 30 tail-hair follicles over a period of nine months. Good quality DNA, in the form of visible large size DNA bands, was extracted from all three sources, for all five amounts. The five volumes of whole-blood samples (20-100µl) provided ~0.4-3.6 µg, the five quantities of buccal swabs (1-5) produced ~0.1-12 µg, while the five amounts of tail-hair follicles (10-50) resulted in ~0.7-25 µg. No differences in the rate of degradation of buccal swab and tail-hair follicle DNA were detected, but there was clearly greater deterioration in the quality of DNA extracted from buccal swabs when compared to tail-hair follicles. We recommend using tail-hair samples for camel DNA biobanking, because it resulted in both an adequate quality and quantity of DNA, along with its ease of collection, transportation, and storage. Compared to its success in studies of other domesticated animals, we anticipate that using ~50 tail-hair follicles will provide sufficient DNA for sequencing or SNP genotyping.

SamplEase: a simple application for collection and organization of biological specimen data in the field.

Careful collection and organization of biological specimens and their associated data are at the core of field research (e.g., ecology, genetics). Fieldwork data are often collected by handwriting or unsystematically via an electronic device (e.g., laptop), a process that is time-intensive, disorganized, and may lead to transcription errors, as data are copied to a more permanent repository. SamplEase is an iOS and Android application that is designed to ease the process of collecting biological specimen data in the field (data associated with biological samples, such as location, age, and sex). In addition to biological specimen data, SamplEase allows for the assignment of photographs to each collected sample, which provides visual records of each specimen in its environment. SamplEase outputs biological specimen data in a tabular format, facilitating subsequent analyses and dissemination. Despite the simplicity of SamplEase, no similar data management application is readily available for researchers.