Phylogeographic differentiation in Sorex araneus: morphology in relation to geography and karyotype

Morphological Species Delimitation in The Western Pond Turtle (Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification?

As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.

Chromosomal Radiation: A model to explain karyotypic diversity in cryptic species

We present a concept that explains the pattern of occurrence of widely distributed organisms with large chromosomal diversity, large or small molecular divergence, and the insufficiency or absence of morphological identity. Our model is based on cytogenetic studies associated with molecular and biological data and can be applied to any lineage of sister species, chronospecies, or cryptic species. Through the evaluation of the karyotypic macrostructure, as the physical location of genes e satellites DNAs, in addition to phylogenetic reconstructions from mitochondrial and nuclear genes, per example, we have observed morphologically indistinguishable individuals presenting different locally fixed karyomorphs with phylogeographic discontinuity. The biological process behind this pattern is seen in many groups of cryptic species, in which variation lies mainly in the organization of their genomes but not necessarily in the ecosystems they inhabit or in their external morphology. It's similar to the processes behind other events observed in the distribution of lineages. In this work, we explore the hypothesis of a process analogous to ecological-evolutionary radiation, which we called Chromosomal Radiation. Chromosomal Radiation can be adaptive or non-adaptive and applied to different groups of organisms.

Molecular phylogenetic and taxonomic status of the large-eared desert shrew Notiosorex evotis (Eulipotyphla: Soricidae)

Notiosorex is the only genus of shrews in North America with particular adaptations for arid habitats such as deserts. Five species currently are recognized in the genus, one of which, Notiosorex evotis, lives in deciduous rain forest from northern Sinaloa to the state of Jalisco in México. Notiosorex evotis originally was described as a subspecies of N. crawfordi; however, it was recently proposed as a valid species based on a discriminant function analysis of craniodental characters. Morphological differentiation between N. evotis populations and sympatric occurrences with N. crawfordi in northern Sinaloa have been recognized. Here, we used a phylogenetic analysis of a mitochondrial gene (Cytb; 1,140 bp) and the nuclear beta fibrinogen intron 7 (β-fib I7; 385 bp), as well as cranial geometric morphometrics, to assess the taxonomic status of N. evotis. We found sequences of N. evotis forming two main subclades: one that includes the populations of the state of Sinaloa, the other including populations of Nayarit and Jalisco. The boundaries between the two groups seem to be related to the ecotonal cline between the Pacific Lowlands province and the Trans-Mexican Volcanic Belt province, which acts as a geographical barrier. The discriminant function analysis revealed clear differences in skull shape between the three species of Notiosorex to the northwest of its distribution. Considering these multiple lines of evidence from our data set, we confirm that N. evotis is a monotypic species. Our results suggest that geometric morphometrics can be used successfully to identify sibling species by shape, especially in groups where determination by craniodental measurements is not possible.

Microevolutionary variation in molar morphology of Onychomys leucogaster decoupled from genetic structure

In neutral models of quantitative trait evolution, both genetic and phenotypic divergence scale as random walks, producing a correlation between the two measures. However, complexity in the genotype-phenotype map may alter the correlation between genotypic and phenotypic divergence, even when both are evolving neutrally or nearly so. Understanding this correlation between phenotypic and genetic variation is critical for accurately interpreting the fossil record. This study compares the geographic structure and scaling of morphological variation of the shape of the first lower molar of 77 individuals of the northern grasshopper mouse Onychomys leucogaster to genome-wide SNP variation in the same sample. We found strong genetic structure but weak or absent morphological structure indicating that the scaling of each type of variation is decoupled from one another. Low P_ST values relative to F_ST values are consistent with a lack of morphological divergence in contrast to genetic divergence between groups. This lack of phenotypic structure and the presence of notable within-sample phenotypic variance are consistent with uniform selection or constraints on molar shape across a wide geographic and environmental range. Over time, this kind of decoupling may result in patterns of phenotypic stasis masking underlying genetic patterns.

Dental polymorphisms in Crocidura (Soricomorpha: Soricidae) and evolutionary diversification of crocidurine shrew dentition

The upper dentition of Crocidura exhibits polymorphic characters that were revealed for the first time in this study via high-resolution X-ray computed microtomography. Our analyses of 11 Crocidura species and selected Diplomesodon, Suncus and Sylvisorex species from different geographical regions and size groups revealed the most complex character states of upper dentition in the Ethiopian endemic species Crocidura yaldeni. A three-dimensionally based geometric morphometric analysis revealed the dependence of variation in skull muzzle shape on alterations in general upper dentition, such as a reduction in the number of antemolars. Principal components analysis revealed highly significant shape alterations and morphological trajectories in C. yaldeni (and more moderate ones in Suncus murinus) toward the Sorex-like morphotype in the outgroup, and less significant shape alterations in Crocidura obscurior, Crocidura phanluongi and Crocidura sapaensis with double-rooted third antemolar. Cladistic analysis based on a new data matrix for 20 species and 46 characters allowed us to determine the directions of the morphological trajectories: the apomorphic state of the most complex antemolars of C. yaldeni is associated with deviating skull muzzle shape changes, which we determined to be attributable to neomorphosis, and the less significant alterations in the shape of other Crocidura with complex antemolars are attributable to regional adaptation.

Quantifying the link between craniodental morphology and diet in the Soricidae using geometric morphometrics

Dietary adaptations have often been associated with heightened taxonomic diversity. Yet, one of the most species-rich mammalian families, the Soricidae, is often considered to be ecologically and morphologically relatively homogenous. Here, we use geometric morphometrics to capture skull and dentary morphology in a broad sample of shrew species and test the hypothesis that morphological variation among shrew species reflects adaptations to food hardness. Our analyses demonstrate that morphology is associated with dietary ecology. Species that consume hard food items are larger and have specific morphological adaptions including an anteroposteriorly expanded parietal, an anteroposteriorly short and dorsoventrally tall rostrum, a mediolaterally wide palate, buccolingually wide cheek teeth, a large coronoid process and a dorsoventrally short jaw joint. The masseter muscle does not appear to play an important role in the strong bite force of shrews and the dentary is a better indicator of ecology than the skull. Our phylogenetic flexible discriminant function analysis suggests that the evolutionary history of shrews has shaped their morphology, canalizing dietary adaptations and enabling functional equivalence whereby different morphologies achieve similar dietary performances. Our work makes possible future studies of niche partitioning among sympatric species as well as the investigation of the diet of extinct soricids.

Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews)

Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.

The relative efficacy of the cranium and os coxa for taxonomic assessment in macaques

OBJECTIVES

The cranium is generally considered more reliable than the postcranium for assessing primate taxonomy, although recent research suggests that pelvic shape may be equally reliable. However, little research has focused on intrageneric taxonomic discrimination. Here, we test the relative taxonomic efficacy of the cranium and os coxa for differentiating two macaque species, with and without considering sexual dimorphism.

MATERIALS AND METHODS

Geometric morphometric analyses were performed on cranial and os coxa landmarks for 119 adult Macaca fascicularis, M. mulatta, and Chlorocebus pygerythrus. Among-group shape variation was examined using canonical variates analyses. Cross-validated discriminant function analysis provided rates of correct group classification. Additionally, average morphological distances were compared with neutral genetic distances.

RESULTS

Macaque species were clearly differentiated, both cranially and pelvically, when sex was not considered. Males were more often correctly classified based on the os coxa, while female classification rates were high for both morphologies. Female crania and male os coxa were differentiated approximately the same as genetic distance, while male crania were more similar (convergent), and female os coxa were more divergent than expected based on genetic distance.

DISCUSSION

The hypothesis that cranial and os coxal shape can be used to discriminate among macaque species was supported. The cranium was better at differentiating females, while the os coxa was better at differentiating male macaques. Hence, there is no a priori reason for preferring the cranium when assessing intragenetic taxonomic relationships, but the effects of high levels of sexual dimorphism must be corrected for to accurately assess taxonomic signatures.

Gene networks, occlusal clocks, and functional patches: new understanding of pattern and process in the evolution of the dentition

Our understanding of the evolution of the dentition has been transformed by advances in the developmental biology, genetics, and functional morphology of teeth, as well as the methods available for studying tooth form and function. The hierarchical complexity of dental developmental genetics combined with dynamic effects of cells and tissues during development allow for substantial, rapid, and potentially non-linear evolutionary changes. Studies of selection on tooth function in the wild and evolutionary functional comparisons both suggest that tooth function and adaptation to diets are the most important factors guiding the evolution of teeth, yet selection against random changes that produce malocclusions (selectional drift) may be an equally important factor in groups with tribosphenic dentitions. These advances are critically reviewed here.

Phenotypic variation across chromosomal hybrid zones of the common shrew (Sorex araneus) indicates reduced gene flow

Sorex araneus, the Common shrew, is a species with more than 70 karyotypic races, many of which form parapatric hybrid zones, making it a model for studying chromosomal speciation. Hybrids between races have reduced fitness, but microsatellite markers have demonstrated considerable gene flow between them, calling into question whether the chromosomal barriers actually do contribute to genetic divergence. We studied phenotypic clines across two hybrid zones with especially complex heterozygotes. Hybrids between the Novosibirsk and Tomsk races produce chains of nine and three chromosomes at meiosis, and hybrids between the Moscow and Seliger races produce chains of eleven. Our goal was to determine whether phenotypes show evidence of reduced gene flow at hybrid zones. We used maximum likelihood to fit tanh cline models to geometric shape data and found that phenotypic clines in skulls and mandibles across these zones had similar centers and widths as chromosomal clines. The amount of phenotypic differentiation across the zones is greater than expected if it were dissipating due to unrestricted gene flow given the amount of time since contact, but it is less than expected to have accumulated from drift during allopatric separation in glacial refugia. Only if heritability is very low, Ne very high, and the time spent in allopatry very short, will the differences we observe be large enough to match the expectation of drift. Our results therefore suggest that phenotypic differentiation has been lost through gene flow since post-glacial secondary contact, but not as quickly as would be expected if there was free gene flow across the hybrid zones. The chromosomal tension zones are confirmed to be partial barriers that prevent differentiated races from becoming phenotypically homogenous.