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

Identification of non-volant small mammals of Sungai Rawog conservation area, Segaliud Lokan forest reserve, Sabah, Malaysia

Small mammals are varying in Malaysia, and they play important roles in various ecosystems as they help to maintain the forest environment and landscape health, and also important in local food chain as they involve in prey-predator interactions which can affect their distribution and diversity. This study focused on identifying and documenting the species of non-volant small mammals present at Sg Rawog Conservation Area (SRCA) through morphological characteristics and molecular analysis. Sample collections were conducted using 20 cage traps and 25 pitfalls for approximately one week of study period to capture the small mammals for species identification. The morphological characteristics for species identification were derived by looking at their fur characteristics and external body measurements by recording their body size measurements. Furthermore, molecular analysis was done by using BLAST software where the samples’ sequences were compared with those in the GenBank database using BLAST software to identify the small mammals’ species. A total of 11 individuals of non-volant small mammals captured throughout the sampling period which consists of Maxomys whiteheadi, M. surifer, Rattus sp., Callosciurus notatus, Tupaia tana and Crocidura sp. It is important to identify and document the species of non-volant small mammals in this conservation area as it will aid the plantation management which is KTS Plantation Sdn. Bhd. in improving their management strategies for this region, including the monitoring of species and the conservation of biodiversity

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

Functional data geometric morphometrics with machine learning for craniodental shape classification in shrews

Abstract This work proposes a functional data analysis approach for morphometrics in classifying three shrew species (S. murinus, C. monticola, and C. malayana) from Peninsular Malaysia. Functional data geometric morphometrics (FDGM) for 2D landmark data is introduced and its performance is compared with classical geometric morphometrics (GM). The FDGM approach converts 2D landmark data into continuous curves, which are then represented as linear combinations of basis functions. The landmark data was obtained from 89 crania of shrew specimens based on three craniodental views (dorsal, jaw, and lateral). Principal component analysis and linear discriminant analysis were applied to both GM and FDGM methods to classify the three shrew species. This study also compared four machine learning approaches (naïve Bayes, support vector machine, random forest, and generalised linear model) using predicted PC scores obtained from both methods (a combination of all three craniodental views and individual views). The analyses favoured FDGM and the dorsal view was the best view for distinguishing the three species

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