Dental Shape Variation and Phylogenetic Signal in the Rattini Tribe Species of Mainland Southeast Asia

Abstract

The Rattini tribe comprises some of the most specious genera in the mammalian kingdom. Many of these species are also highly morphologically conserved. As a result, identifying Rattini tribe animals, particularly those of the Rattus genus, to species level is extremely difficult. Problems with identification of conservative morphologies, particularly of the skeleton, have led to difficulties in understanding the fossil remains and as a result the systematics of this group. Here, we apply geometric morphometrics to the first lower molar of 14 species of the Rattini tribe. We find that the morphological data present a strong phylogenetic signal. However, within Rattus, this signal is rather complex and possibly hints at rapid evolutionary shape and size changes. In modern species, it is possible to identify specimens to species level with a good degree of confidence. We find that using both size and shape together affords further confidence with identification. However, we caution against the over-reliance on size in environments with unknown species composition and climate, particularly in archaeological contexts. This approach should prove to be a useful tool for identifying fossil and sub-fossil remains, particularly where biomolecular markers are absent in circumstances of poor preservation.

Exploring Rattus praetor (Rodentia, Muridae) as a possible species complex using geometric morphometrics on dental morphology

“…Landmarks and semi-landmarks were recorded from the photographs using tpsDig 2.12 ( Rohlf, 2004 ) for geometric morphometric analyses. Five fixed Type 2 landmarks (according to the Bookstein, 1991 categorisation) were recorded and 19 sliding semi-landmarks were used to describe the outline of the teeth (adapted from Hulme-Beaman et al, 2018 , see SI 1). The outline landmarks were recorded in five curves consisting of: 3, 5, 3, 3 and 5 sliding semilandmarks respectively ( Fig.…”

“…2 ). An artificial straight line was taken on the posterior part of the tooth from the maximum posterior point of the hypoconid to the maximum posterior point of the entoconid to remove variation introduced from the second molar because in fossil and sub-fossil material the second molar may not be present (following Hulme-Beaman et al, 2018 ).

Fig.

…”

Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies

“…Archaeological R. rattus mandible (image: Ewan Chipping), showing examples of further morphological and molecular analyses: a) taxonomic identification of post‐medieval Dutch rats via ZooMS collagen fingerprinting; [ 47 ] b) geometric morphometric (GMM) analysis of functional variation in mandibular shape (image: Phil Cox); c) GMM analysis of first molar shape for phylogenetic signal (image: Ardern Hulme–Beaman c) Reproduced under the terms and conditions of the Creative Commons Attribution 4.0 International License. [ 61a ] Copyright 2018, the Authors. ); d) calibrated radiocarbon date on R. rattus bone from Roman Portugal (made with rcarbon [ 82 ] ); e) dietary isotopic analysis of R. norvegicus bones from nineteenth century Ontario.…”

“…Where remains are more‐or‐less intact, Geometric Morphometric Methods (GMM) permit quantification of fine‐scale shape variation. GMM has been applied to murine molar teeth to identify (sub)species [ 61 ] and to detect finer‐scale structuring, either alongside aDNA or alone as a phylogenetic proxy. [ 62 ] By contrast, mandibular shape is highly plastic with regard to dietary and environmental factors, [ 63 ] potentially showing adaptive signals even over short timescales.…”

Deep learning for species identification of modern and fossil rodent molars

“…Furthermore, in the fossil record, morphological criteria are often the only data available for the description of the past biodiversity. In an archaeological framework, documenting the anthropogenic impact on vertebrate evolution since the Late Glacial period fostered the development of methods of numerical taxonomy to reach reliable identifications at the specific and intraspecific levels (Thomas Cucchi et al 2014;Thomas Cucchi et al 2017;Thomas Cucchi et al 2020;Thomas Cucchi et al 2019;Hulme-Beaman et al 2018; F. James Rohlf and Marcus 1993;Stoetzel et al 2017). Recent studies also explore morphological markers of behavioral change in order to document early steps of the domestication process (Harbers et al 2020;Owen et al 2014;Seetah et al 2014) that has driven the evolutionary trajectory at the root of modern societies (Vigne 2015).…”