RFE-based feature selection to improve classification accuracy for morphometric analysis of craniodental characters of house rats

In conventional morphometrics, researchers often collect and analyze data using large numbers of morphometric features to study the shape variation among biological organisms. Feature selection is a fundamental tool in machine learning which is used to remove irrelevant and redundant features. Recursive feature elimination (RFE) is a popular feature selection technique that reduces data dimensionality and helps in selecting the subset of attributes based on predictor importance ranking. In this study, we perform RFE on the craniodental measurements of the Rattus rattus data to select the best feature subset for both males and females. We also performed a comparative study based on three machine learning algorithms such as Naïve Bayes, Random Forest, and Artificial Neural Network by using all features and the RFE-selected features to classify the R. rattus sample based on the age groups. Artificial Neural Network has shown to provide the best accuracy among these three predictive classification models

Phylogenetic relationships and morphological variation of gymnures (Galericidae: Hylomys) from Genting Highlands, Pahang, Malaysia

Gymnures from the genus Hylomys are widely distributed across Sundaland and the Indochinese region. However, the relationships among its members in Peninsular Malaysia especially from Genting Highlands are still lacking. This study aims to examine the morphology and genetically analyse of the Hylomys specimens collected from the new isolated population of Genting Highlands, Pahang, Malaysia. Morphometric analyses showed that morphological variation exists among the Hylomys lineage. The external morphology and the skull measurements of the taxa studied coincide with those of Hylomys maxi from Peninsular Malaysia and Sumatra based on descriptive statistics and principal component analysis (PCA). The differences within the Hylomys taxa are also evident in the phylogenetic tree and K2P genetic distances analyses inferred from cyt b. Hylomys samples from Genting Highlands formed a clade with H. maxi from Cameron Highlands and Fraser’s Hill, Peninsular Malaysia and Sumatra. However, they were separated from Hylomys parvus (Sumatra), Hylomys suillus (Java) and Hylomys dorsalis (Borneo). Relatively, low genetic distances were detected among the studied taxa with other H. maxi (<6% K2P distance) while high genetic distances were observed when compared to other Hylomys taxa (>18.0% K2P distance). Based on these facts, we confirm that the gymnures from Genting Highlands belong to a valid species, Hylomys maxi along with other Peninsular Malaysia samples based on genetics and morphological data which probably originated from Sumatra a long time ago

Molecular phylogeny of long-tailed giant rats (Muridae: genus leopoldamys) based on mitochondrial cytochrome B sequences

Two species of Leopoldamys long-tailed giant rats are found in Peninsular Malaysia. They are currently referred to as Leopoldamys ciliatus which inhabits montane habitat, and Leopoldamys vociferans which usually inhabits the lowland forest. To date, there is no report on the phylogenetic relationship of L. ciliatus with the other Leopoldamys taxa. The present study was carried out to determine its relationship, based on the mitochondrial cytochrome b (cyt b) gene sequence, with L. vociferans of Peninsular Malaysia and other congeners. Phylogenetic analysis shows that L. ciliatus is a sister-species to the lineage L1 of L. herberti and L. revertens, and is distantly related to L. edwardsi. L. vociferans, and L. sabanus form a distinct clade (lineage L5) from the other Leopoldamys taxa from Indochina. The Sumatra taxon currently known as L. sabanus is genetically distinct to L. vociferans with K2P distances between 0.065 and 0.069. Contrary to previous opinions, L. herberti, L. revertens, and L. neilli of Indochina are valid species based on more than 2.5% threshold genetic distance. Both the L. edwardsi and L. neilli species complexes are represented by several sibling species. A more extensive taxon sampling from various regions (particularly Sumatra and other regions of Indonesia) as well as the use of morphological and molecular (mitogenomes or multiple genes) data sets are needed to provide a robust phylogeny and systematics

Toxicity of Malaysian Medicinal Plant Extracts Against Sitophilus oryzae and Rhyzopertha dominica

The insecticidal activities of extracts from 22 Malaysian medicinal plant extracts from 8 botanical families were tested against rice weevil: Sitophilus oryzae (L.) and lesser grain borer: Rhyzopertha dominica (F.). The extracts were obtained using hexane, methanol, and dichloromethane to extract potential biopesticides from dried leaves. The toxicity levels were examined periodically based on antifeedant activity and contact toxicity assays using treated grain assay. Hexane extracts of Alpinia conchigera, Alpinia scabra, Curcuma mangga, Curcuma purpurascens, Goniothalamus tapisoides, Piper sarmentosum , and methanol extracts of Curcuma aeruginosa, C. mangga , and Mitragyna speciosa were the most potent extracts against S. oryzae and R. dominica with lethal concentration (LC50) values of ≤ 0.42 mg/mL and ≤ 0.49 mg/mL, respectively. The contact toxicity test results showed that methanol extracts of C. aeruginosa and C. mangga , dichloromethane extracts of Cryptocarya nigra , and hexane extracts of C. mangga, and C. purpurascens resulted in 100% mortality of both pests within 28 days exposure of 5 mg/cm2 concentration

Systematics and biogeography of shrews (soricomorpha: soricidae) in peninsular Malaysia / Hasmahzaiti Omar

total of 122 samples were examined in this study were trapped by using pitfall traps, except for Suncus murinus species, which was caught with a rat trap. The 14 skull characters of seven species measured from the past and present studies were subjected to principal component analysis. Although Crocidura negligens was never trapped in this study, earlier studies indicated that this species was distinct from other Crocidura species. Currently, Crocidura monticola are commonly found in Peninsular Malaysia and widely distributed in Sundaland. Previous studies indicated that Crocidura fuliginosa was dominant species in this region. Meanwhile, the smallest shrew Suncus malayanus formerly known as Suncus etruscus proved distinct morphologically from C. monticola. Finally, in this study I provide identification keys for shrew species, morphological measurements and skull drawings that may help in identification of Malay peninsula shrews for future studies. Small crocidurinae shrews (weight < 8g) from Southeast Asia have been poorly studied to date, mainly because of the difficulty to catch them and the concomitant paucity of reference specimens available in museums. Hence their systematics is still debated, and most small Crocidura shrews from Sundaland are assigned to the monticola species complex. Morphometric analyses based on 14 skull measurements showed that these shrews tend to be larger with increasing altitude, but showed otherwise no consistent variation. When compared to museum specimens of the monticola species complex sampled in the Sundaland (total: 77 specimens), the Malay shrews tend also to be larger than those living on Kalimantan and Sumatra. All are, however, morphologically distinct from the other species, C. maxi, found in eastern Java and on the Lesser Sundas. Molecular analyses of a subset of these small shrews based iv on a mitochondrial (cytochrome b) and a nuclear gene (Apolipoprotein B) suggest that samples from the central region of Peninsular Malaysia (Bukit Rengit and Ulu Gombak) differ genetically from other Malaysian populations (by about 7% K2P distance at the cyt b gene) and are more closely related to some samples from Sumatra and Borneo. These differences did not correlate with the altitudinal variation evidenced from the morphological analysis. Reference sequences from the terra typica of monticola and maxi (both species were originally described from Java) are however needed to determine if these unexpected genetic differences warrant additional taxonomic subdivision within the Sundaland. A portion of the mitochondrial cytochrome b gene was used to investigate the phylogenetic relationships of Suncus pygmy shrews and to help clarify the taxonomic status of the Malayan Pygmy Shrew (S. malayanus) and the Malagasy Pygmy Shrew (S. madagascariensis). Phylogenetic reconstructions were performed using neighbourjoining and Bayesian analysis methods and revealed that S. malayanus is related to, but distinct from S. etruscus. The K2P-corrected genetic distance among the Malaysian taxon and other pygmy shrews for the cytochrome b gene was between 6.1 and 8.5%, supporting recognition that S. malayanus represents a distinct species from the geographically widespread S. etruscus species complex. A close (1.5% K2P distance) sister-group relationship was revealed between S. etruscus from Sri Lanka and S. madagascariensis from Madagascar, which has been considered an island endemic, and suggests that these animals are not specifically distinct. The Malagasy population of this shrew most probably was translocated to the island by human intervention, with the lineage originating from Southeast Asia or the Indian subcontinent

Fig. 1 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences

Fig. 1. Male Malayan pygmy shrew (Suncus malayanus) captured in the Cameron Highlands, Pahang, Peninsular Malaysia, in a pitfall trap set on the forest floor. Notice the characteristic large ears and dark fine pelage.Published as part of &lt;i&gt;Omar, Hasmahzaiti, Adamson, Eleanor A. S., Bhassu, Subha, Goodman, Steven M. &amp; Soarimalala, Voahangy, 2011, Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences, pp. 237-243 in Raffles Bulletin of Zoology 59 (2)&lt;/i&gt; on page 238, DOI: &lt;a href="http://zenodo.org/record/10107452"&gt;10.5281/zenodo.10107452&lt;/a&gt

Morphometric Analysis of Craniodental Characters of the House Rat, Rattus rattus (Rodentia: Muridae) in Peninsular Malaysia

Rattus rattus which is believed to be native to India is easily found in all continents of the world. With the absence of R. rattus from lineage I and the presence of lineage IV in Southeast Asia, little is known about how rodent morphology varies biogeographically. We evaluate the skull morphometrics in the population of R. rattus in Peninsular Malaysia and examine the intraspecific variation of the skull by assessing 20 craniodental characters of 130 R. rattus specimens. After observing the correlation matrix, highly correlated characters were removed and the remaining 14 craniodental characters were analysed using the conventional morphometrics method via univariate and multivariate statistics. We assessed the impact of age, sex and geographical factors (latitude, longitude and precipitation) on craniodental size. Male and female specimens were analysed separately since statistically significant sexual dimorphism was present. Males showed greater craniodental measurements compared to females. Three distinct age groups (C2, C3 and C4) were visible in the principal component analysis (PCA) and canonical variate analysis (CVA) plots for male and female specimens. Ages C2 and C3 shared similarities in craniodental measurements while C4 showed variability compared to C2 and C3. None of the geographical factors studied showed statistical significance for both male and female R. rattus. The results obtained from this study could potentially be a yardstick to observe if similar variations in craniodental traits are present in R. rattus from other countries in the Southeast Asian region. © 2019 Penerbit Universiti Kebangsaan Malaysia. All rights reserved

Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences

Omar, Hasmahzaiti, Adamson, Eleanor A. S., Bhassu, Subha, Goodman, Steven M., Soarimalala, Voahangy (2011): Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences. Raffles Bulletin of Zoology 59 (2): 237-243, DOI: http://doi.org/10.5281/zenodo.1010745