Divergence Times Research Articles

Complete Chloroplast Genome of Megacarpaea megalocarpa and Comparative Analysis with Related Species from Brassicaceae.

Megacarpaea megalocarpa, a perennial herbaceous species belonging to the Brassicaceae family, has potential medicinal value. We isolated and characterized the chloroplast (cp) genome of M. megalocarpa and compared it with closely related species. The chloroplast genome displayed a typical quadripartite structure, spanning 154,877 bp, with an overall guanine-cytosine (GC) content of 36.20%. Additionally, this genome contained 129 genes, 105 simple sequence repeats (SSRs), and 48 long repeat sequences. Significantly, the ycf1 gene exhibited a high degree of polymorphism at the small single copy (SSC) region and the inverted repeat a (IRa) boundary. Despite this polymorphism, relative synonymous codon usage (RSCU) values were found to be similar across species, and no large segment rearrangements or inversions were detected. The large single copy (LSC) and SSC regions showed higher sequence variations and nucleotide polymorphisms compared to the IR region. Thirteen distinct hotspot regions were identified as potential molecular markers. Our selection pressure analysis revealed that the protein-coding gene rpl20 is subjected to different selection pressures in various species. Phylogenetic analysis positioned M. megalocarpa within the expanded lineage II of the Brassicaceae family. The estimated divergence time suggests that M. megalocarpa diverged approximately 4.97 million years ago. In summary, this study provides crucial baseline information for the molecular identification, phylogenetic relationships, conservation efforts, and utilization of wild resources in Megacarpaea.

Molecular phylogenetics of the superfamily Stromboidea (Caenogastropoda): New insights from increased taxon sampling

AbstractThe superfamily Stromboidea is a clade of morphologically distinctive gastropods which include the iconic Strombidae, or ‘true conchs’. In this study, we present the most taxonomically extensive phylogeny of the superfamily to date, using fossil calibrations to produce a chronogram and extant geographical distributions to reconstruct ancestral ranges. From these results, we confirm the monophyly of all stromboidean families; however, six genera are not monophyletic using current generic assignments (Strombidae: Lentigo, Canarium, Dolomena, Doxander; Xenophoridae: Onustus, Xenophora). Within Strombidae, analyses resolve an Indo‐West Pacific (IWP) clade sister to an East Pacific/Atlantic clade, together sister to a second, larger IWP clade. Our results also indicate two pulses of strombid diversification within the Miocene, and a Tethyan/IWP origin for Strombidae—both supported by the fossil record. However, conflicts between divergence time estimates and the fossil record warrant further exploration. Species delimitation analyses using the COI barcoding gene support several taxonomic changes. We synonymise Euprotomus aurora with Euprotomus bulla, Strombus alatus with Strombus pugilis, Dolomena abbotti with Dolomena labiosa, and Dolomena operosa with Dolomena vittata. We identified cryptic species complexes within Terebellum terebellum, Lambis lambis, “Canarium” wilsonorum, Dolomena turturella and Maculastrombus mutabilis. We reinstate Rimellopsis laurenti as a species (previously synonymised with R. powisii) and recognise Harpago chiragra rugosus and Lambis truncata sowerbyi valid at the rank of species. Finally, we establish several new combinations to render Lentigo, Dolomena, and Canarium monophyletic: Lentigo thersites, Dolomena robusta, Dolomena epidromis, Dolomena turturella, Dolomena taeniata, Dolomena vanikorensis, D. vittata, “Canarium” wilsonorum, Hawaiistrombus scalariformis, Maculastrombus mutabilis, Maculastrombus microurceus.

Phylogenetic relationships and divergence time of Hydrangea sect. Macrophyllae (Hydrangeaceae) revealed by genome-wide SNPs

Hydrangea sect. Macrophyllae comprises deciduous shrubs including two species with seven infraspecific taxa distributed throughout the Japanese Archipelago and adjacent areas. In this study, we revealed a phylogeny of Hydrangea sect. Macrophyllae by using a larger dataset of genome-wide SNPs than those employed in a previous study and by adding more comprehensive taxa/populations, which cover the entire distribution of the section. We then revised the taxonomic treatment of sect. Macrophyllae based on the higher-resolution phylogenetic trees obtained in this study. The phylogenetic trees estimated in this study showed five major clades, suggesting that H. serrata var. minamitanii and var. yesoensis should be treated as independent species from other H. serrata, that H. serrata var. australis and var. yakushimensis could be subclassified under the major clades and that var. angustata could be a synonym of var. serrata. The divergence time of these major clades was estimated to be in the Pleistocene.

Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion.

The role of balancing selection is a long-standing evolutionary puzzle. Balancing selection is a crucial evolutionary process that maintains genetic variation (polymorphism) over extended periods of time; however, detecting it poses a significant challenge. Building upon the Polymorphism-aware phylogenetic Models (PoMos) framework rooted in the Moran model, we introduce a PoMoBalance model. This novel approach is designed to disentangle the interplay of mutation, genetic drift, and directional selection (GC-biased gene conversion), along with the previously unexplored balancing selection pressures on ultra-long timescales comparable with species divergence times by analyzing multi-individual genomic and phylogenetic divergence data. Implemented in the open-source RevBayes Bayesian framework, PoMoBalance offers a versatile tool for inferring phylogenetic trees as well as quantifying various selective pressures. The novel aspect of our approach in studying balancing selection lies in polymorphism-aware phylogenetic models' ability to account for ancestral polymorphisms and incorporate parameters that measure frequency-dependent selection, allowing us to determine the strength of the effect and exact frequencies under selection. We implemented validation tests and assessed the model on the data simulated with SLiM and a custom Moran model simulator. Real sequence analysis of Drosophila populations reveals insights into the evolutionary dynamics of regions subject to frequency-dependent balancing selection, particularly in the context of sex-limited color dimorphism in Drosophila erecta.

Mitochondrial phylogenomics supports a Carboniferous origin of Xenonomia

Polyneoptera includes some of the best-known insect species, such as grasshoppers and cockroaches. While the evolutionary history of many Polyneoptera orders has been thoroughly explored, others have been partially overlooked. This is the case with Xenonomia, a clade consisting of two species-poor insect orders with a relatively recent taxonomic history: Mantophasmatodea and Grylloblattodea. Here, we provide a temporal framework for their evolution, leveraging a mitochondrial phylogenomics approach encompassing all Polyneoptera orders. To strengthen the confidence in our divergence times estimation, we specifically focused on the possible impact of phylogenetic biases, such as long branch attraction, the influence of specific fossil priors, the use of nucleotide or amino acid alignments, and different clock models. Our results consistently support the origin of Xenonomia during the Carboniferous, and the divergence between the two orders is inferred to have happened before the Permian. While Grylloblattodea diversification is inferred to have occurred earlier than that of Mantophasmatodea, extant species of both orders most likely diversified after the Permian/Triassic and Triassic/Jurassic mass extinctions. Our molecular divergence time analyses complement the fossil record and support the ancient relict status of these two polyneopteran orders.

Characteristics of the chloroplast genome and genetic divergence of Tamarix hispida Willd. 1816 (Tamaricaceae)

Tamarix hispida Willd. 1816, a crucial native plant species in the arid desert region of northwestern China, plays a significant role in maintaining ecological stability. It is instrumental in addressing soil salinity–alkalinity and heavy metal pollution. This research aims to analyze the phylogenetic divergence pattern and evolutionary history of T. hispida by comparing chloroplast genome structures across different populations. Despite the minimal differences in chloroplast genome structure due to conserved genes and junction regions, sequencing was conducted using the Illumina NovaSeq platform to verify the historical evolutionary processes between different populations, followed by assembly and annotation. The results revealed that the T. hispida chloroplast genome is approximately 156,164–156,186 bp in length, with a quadripartite structure and 131 annotated genes. Phylogenetic analysis indicated two lineages within T. hispida, with a divergence time of 3.15 Ma. These findings emphasize the low genetic diversity in T. hispida and offer valuable insights into its evolutionary past. To effectively protect and manage this species, increased scientific research and monitoring of its genetic diversity are necessary. This study underscores the importance of comprehending the genetic mechanisms behind species divergence to develop informed conservation strategies.

Phylogenetic and phylogeographic evidence for the colonization success of the diplochorous Astydamia latifolia across the Canary Islands.

Astydamia latifolia is the only species of the genus Astydamia, which forms an early-diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to the Canary Islands and one of the most representative species of the coastal environments of this archipelago. Astydamia displays diplochory, that is, diaspores with two long-distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemochorous and thalassochorous fruit traits (corky and winged mericarps). Although we expect this species to have a high dispersal capacity, there is no genetic study addressing it. The divergence time of this species from its sister taxon is also unknown. In this study, we aimed (i) to unveil the phylogenetic relationships and divergence times of A. latifolia; (ii) to reconstruct its phylogeographic structure across the Canary Islands; and (iii) to estimate the number of inter-island colonization events. To these ends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia, reconstructed the phylogenetic relationships of Astydamia and Apiaceae relatives and estimated divergence times. Then, two plastid DNA regions (psaI-aacD and psbK-trnS) were sequenced for 158 individuals (from 36 Canarian population and one NW African population) to reconstruct a haplotype network. The recently developed method Phylogeographic Analysis of Island Colonization Events (PAICE) was used to estimate the number of inter-island colonization events. Results show that A. latifolia is a phylogenetically isolated lineage that diverged from the most closely related genus (Molopospermum) in the Eocene-Miocene. It displays a low plastid DNA diversity (only four haplotypes detected), which is accompanied by a high degree of haplotype sharing between islands and highly linear rarefaction curves of colonization obtained in PAICE. These findings suggest a high colonization ability for this species, most likely related to the availability of two LDD syndromes.

Phylogeny and diversification analyses of extant planthopper families (Hemiptera: Fulgoromorpha) based on a mitochondrial dataset reveal ancient lineages originating during the Jurassic and originally feeding on gymnosperms

Abstract Phylogenetic analyses of planthoppers were conducted using a mitogenome dataset to examine the evolutionary relationships of current families based on both maximum likelihood (ML) and Bayesian inference methods. Delphacoidea, including Cixiidae and Delphacidae, and Fulgoroidea, including all other families, were consistently identified as monophyletic groups. However, Nogodinidae displayed a polyphyletic pattern, with various lineages emerging sister to several issidoid families. Variations were observed across different analyses in the positioning of (Dictyopharidae + Fulgoridae) and the relationships of Ricaniidae sister either to Issidae or to (Flatidae + Acanaloniidae). Several statistical tests indicate that the ML topology has the highest level of statistical confidence. The (Dictyopharidae + Fulgoridae) clade is best positioned as sister to (Derbidae + (Achilidae + (Tropiduchidae + other “higher” planthoppers families))) and the Ricaniidae as sister to (Flatidae + Acanaloniidae). With 13 fossil calibration points, origin times for Delphacoidea and Fulgoroidea were dated back to the Late Permian, approximately 257.46 million years ago. Delphacidae and Cixiidae split during the Late Triassic, while Fulgoroidea diversified earlier during the Middle Triassic. Divergence and diversification times are also provided for all other extant planthopper families. These results suggest that Delphacoidea and Fulgoroidea likely diverged from the older planthopper fossil families prior to the emergence of angiosperms and may have initially fed on gymnosperms and ancient ferns. The diversification of extant planthopper families occurred during the Jurassic and Cretaceous periods, influenced by evolving climatic conditions, the decline in gymnosperms, and the increasing diversity of angiosperm plants.

Time of sample collection is critical for the replicability of microbiome analyses.

As the microbiome field moves from descriptive and associative research to mechanistic and interventional studies, being able to account for all confounding variables in the experimental design, which includes the maternal effect1, cage effect2, facility differences3, as well as laboratory and sample handling protocols4, is critical for interpretability of results. Despite significant procedural and bioinformatic improvements, unexplained variability and lack of replicability still occur. One underexplored factor is that the microbiome is dynamic and exhibits diurnal oscillations that can change microbiome composition5-7. In this retrospective analysis of 16S amplicon sequencing studies in male mice, we show that sample collection time affects the conclusions drawn from microbiome studies and its effect size is larger than those of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups is unique to each experiment. Sample collection times as short as only 4 hours apart can lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. The impact of diurnal rhythms on the outcomes and study design of other fields is unknown but likely significant.

Integrative studies of Microtus hartingi and Microtus guentheri (Cricetidae, Arvicolinae) and taxonomic problem of Microtus elbeyli

In this study, Taxonomic differences between Microtus guentheri and Microtus hartingi, which are similar in terms of external morphological features, were determined using linear morphometric, geometric morphometric, karyological and molecular analyses methods. Through classical morphometric (mean values) and geometric morphometric analyses of craniodental and mandible characters, influenced by various genetic, developmental, and functional processes, it was found that M. hartingi and M. guentheri exhibited notable differences in both mean linear measurements and shape. The Jackknife in classical morphometric analyses of samples, which underwent molecular and karyological species diagnoses, was higher than 88 % for each character. In geometric morphometric analyses, the Procrustes distance for shape follows the order Ventral < Dorsal < Mandible < M3<M2<M1. Based on cross-validation, the accurate classification rate is between 73 and 100 %. In both mean linear measurements and centroid size, M. hartingi specimens exhibited significantly larger mandibles and craniodentals compared to individuals of M. guentheri. According to PLS results, there was a significant relationship between the shape of M1, M2 and M3 and environmental variables, while the relationship between their size and environmental variables was not significant. However, neither the shape nor the size of the other parts had an sufficient relationship with environmental variables. Both species exhibited karyological similarity with a chromosome number of 2n = 54, but display polymorphism in chromosome arm number. There were differences in the C-banding of autosomal chromosomes and X chromosome. The classification of species in classical and geometric morphometric analyses, diverges from the outcomes of karyological and molecular assessments. In both species, the intraspecific genetic distance remained below 1.35 %. The cyt-b exhibits significant differentiation between the two species (K2P = 6.55 %). The divergence time for M. guentheri from the clade containing M. hartingi + M. qazvinensis + Microtus dogramacii was estimated to be 0.73 million years ago. Since no sample of Microtus elbeyli with karyological and cyt-b characteristics was found in the samples taken from the type locality, the taxonomic status of M. elbeyli remains unclear.

Exploring the mitogenomes of Batracomorphus (Hemiptera: Cicadellidae: Iassinae): new insights from structural diversity and phylogenomic analyses

Abstract Comparisons of mitogenomes are widely used for species identification and to explore the phylogenetic relationship among insect taxa. Batracomorphus is the third most diverse and widely distributed genus in the Cicadellidae (Hemiptera). However, there have been no analyses of genome structure and phylogenetic relationships within the genus. To compensate for the paucity of genomic information in this genus, we sequenced novel complete mitochondrial genomes of 11 Batracomorphus species and combined these with 23 previously sequenced mitochondrial genomes to perform structural comparisons and phylogenomic studies. Our results reveal generally conserved mitogenome organization, with one case of tRNA gene rearrangement, with trnI-trnQ reversed to trnQ-trnI when compared with the ancestral arrangement. Analysis of the ratio of nonsynonymous (Ka) to synonymous substitutions (Ks) showed ATP8 is the fastest and COI is the slowest evolving gene. ND2 and ND6 have highly variable nucleotide diversity, whereas COI and ND1 exhibit the lowest diversity. Phylogenetic analysis of nucleotide sequences grouped Batracomorphus species into a clade within the subfamily Iassinae. Within Batracomorphus, 3 clades were reconstructed consistent with the observed gene rearrangement, indicating that such rearrangements can serve as reliable molecular markers supporting phylogenetic hypotheses. These clades also correspond to clusters of species recovered by morphometric analysis of aedeagal shape, suggesting that characters of the male genitalia traditionally used for species delimitation are phylogenetically informative. Molecular divergence time estimates indicate that most speciation events within Batracomorphus occurred between the Paleogene and Neogene. This study provides insight into the population genetics, molecular biology, phylogeny, and morphological evolution of the leafhopper subfamily Iassinae and its largest genus, Batracomorphus.

Does Urbanization Exacerbate Asymmetrical Changes in Precipitation at Divergent Time Scales in China?

AbstractUrbanization alters the thermal and dynamic environment of the local climate system, resulting in significant impacts on precipitation in both urban and adjacent areas. Nevertheless, there remains a significant gap in our understanding of urbanization‐induced effects on asymmetrical, symmetrical, and other precipitation patterns in urban agglomerations (UAs) with divergent background climates and geographic regions at different timescales. Specifically, this asymmetrical change pattern is characterized by an increase in heavy (or light) rainfall and a decrease in light (or heavy) rainfall. Here, we assessed the effects of urbanization on precipitation patterns across 18 UAs situated in diverse background climates and geographical areas in China at different timescales. The results demonstrate that urbanization predominantly alters precipitation patterns in UAs located in the humid region. Specifically, urbanization amplified asymmetrical changes in Yangtze River Delta, Pearl River Delta, Beibu Gulf, Middle Yangtze River, and Guanzhong, but exacerbated symmetrical changes in precipitation in some regions such as Chengdu‐Chongqing. Notably, the urbanization effect demonstrates greater significance at the hourly scale, as exemplified in the Yangtze River Delta, Pearl River Delta, and Middle Yangtze River, where the urban impact is nearly twice as pronounced when compared to the daily scale. Moreover, urbanization had either no effect or has a negative impact on precipitation patterns in UAs located within continental and arid regions. This is related to the intensity of urbanization, background climate and complex topography. This finding implies that urban managers should consider the impact of urbanization on precipitation patterns in different contexts to provide scientific guidance for urban planning.

Diversification over deep and shallow temporal scales in the Holarctic genus Perpolita (Gastropoda: Gastrodontidae)

Abstract The Holarctic land snail genus Perpolita was used to explore the influence of past and current biogeography on diversification. The number of empirically-supported species was determined using a consensus between mtDNA sequence, nDNA sequence, conchology, and geographic and ecological range with five valid temperate-boreal species (Perpolita binneyana, Perpolita electrina, Perpolita hammonis, Perpolita petronella, and Perpolita radiatella) being recognized. Only P. petronella was unchanged in both nomenclature and diagnostic characteristics with the remainder requiring alterations. Perhaps the most important of these was elevation of P. radiatella to a valid species, with its populations having been previously lumped either under European P. hammonis or North American P. electrina. Divergence times of 18.7–10.0 Mya were suggested through genome-wide SNPs in combination with the fossil record, indicating a pre-Pleistocene origin for all Perpolita species. Using genetically-confirmed diagnostic shell characters, we accumulated &amp;gt; 2000 valid occurrences and used these to estimate appropriate modern and Last Glacial Maximum climate extents for all species. These models suggest that modern intra-specific gene pool diversity may generally reflect Pleistocene palaeoclimatology.

Populations of the stygobiotic amphipod Palearcticarellus pusillus (Martynov, 1930) maintain genetic connectivity between the mountain springs and the deep bottom habitats of Lake Teletskoye (Altai Mountains, Russia)

The diversity of underground fauna is often associated with the presence of karst areas, which have extensive underground cavities and connecting channels. Non-karst areas, however, make up a larger portion of the planet’ surface, and our understanding of the distribution and dispersal abilities of underground fauna in these areas currently remains limited. During a recent study of the diversity of stygobiotic crustaceans in the mountain streams of the Kurai Mountain Range (Altai, Russia), a small-sized species of crangonyctid amphipod, Palearcticarellus pusillus (Crustacea, Amphipoda, Crangonyctidae) was found in high-altitude springs. This species has been previously known only from deep-water habitats in Lake Teletskoye, and molecular genetic analysis revealed that these amphipods maintain genetic connections between the springs and bottom lake habitats. We assume that individuals of this certainly stygobiotic species fall to the bottom of the lake as a result of leaching from tectonic faults connecting these habitats and are not permanent inhabitants of the lake bottom. This hypothesis also suggests that the very small body size of these animals may be related to the narrow crevices and pores of the tectonic faults, rather than neoteny, as it has been previously suggested. The estimated divergence time calculation has also revealed that P. pusillus obviously diverged from its sister species, Palearcticarellus mikhaili from valley springs in Kurai Steppe, ~5 Ma, at the beginning of the Pliocene, possibly due to the uplifting of the Kurai Mountain Range. Subsequent speciation occurred as a result of secondary tectonic activity and changes in groundwater flow, likely during the Pleistocene, approximately 2.7–0.7 Ma. Populations that were isolated for a long time continue to live near mountain springs in the study area.

A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history.

The genera Cephalotrichum and Microascus contain ecologically, morphologically and lifestyle diverse fungi in Microascaceae (Microascales, Sordariomycetes) with a world-wide distribution. Despite previous studies having elucidated that Cephalotrichum and Microascus are highly polyphyletic, the DNA phylogeny of many traditionally morphology-defined species is still poorly resolved, and a comprehensive taxonomic overview of the two genera is lacking. To resolve this issue, we integrate broad taxon sampling strategies and the most comprehensive multi-gene (ITS, LSU, tef1 and tub2) datasets to date, with fossil calibrations to address the phylogenetic relationships and divergence times among major lineages of Microascaceae. Two previously recognised main clades, Cephalotrichum (24 species) and Microascus (49 species), were re-affirmed based on our phylogenetic analyses, as well as the phylogenetic position of 15 genera within Microascaceae. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of species belonging to Cephalotrichum and Microascus, as well as detailed descriptions and illustrations of 21 species of which eight are newly described. Furthermore, the divergence time estimates indicate that the crown age of Microascaceae was around 210.37 Mya (95 % HPD: 177.18-246.96 Mya) in the Late Triassic, and that Cephalotrichum and Microascus began to diversify approximately 27.07 Mya (95 % HPD: 20.47-34.37 Mya) and 70.46 Mya (95 % HPD: 56.96-86.24 Mya), respectively. Our results also demonstrate that multigene sequence data coupled with broad taxon sampling can help elucidate previously unresolved clade relationships. Citation: Wei TP, Wu YM, Zhang X, et al. 2024. A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history. Persoonia 52: 119-160. https://doi.org/10.3767/persoonia.2024.52.05 .

Characterization of the organellar genomes of Mazzaella laminarioides and Mazzaella membranacea (Gigartinaceae, Rhodophyta).

Mazzaella, a genus with no genomic resources available, has extensive distribution in the cold waters of the Pacific, where they represent ecologically and economically important species. In this study, we aimed to sequence, assemble, and annotate the complete mitochondrial and chloroplast genomes from two Mazzaella spp. and characterize the intraspecific variation among them. We report for the first time seven whole organellar genomes (mitochondria: OR915856, OR947465, OR947466, OR947467, OR947468, OR947469, OR947470; chloroplast: OR881974, OR909680, OR909681, OR909682, OR909683, OR909684, OR909685) obtained through high-throughput sequencing for six M. laminarioides sampled from three Chilean regions and one M. membranacea. Sequenced Mazzaella mitogenomes have identical gene number, gene order, and genome structure. The same results were observed for assembled plastomes. A total of 52 genes were identified in mitogenomes, and a total of 235 genes were identified in plastomes. Although the M. membranacea plastome included a full-length pbsA gene, in all M. laminarioides samples, the pbsA gene was split in three open reading frames (ORFs). Within M. laminarioides, we observed important plastome lineage-specific variations, such as the pseudogenization of the two hypothetical protein-coding genes, ycf23 and ycf45. Nonsense mutations in the ycf23 and ycf45 genes were only detected in the northern lineage. These results are consistent with phylogenetic reconstructions and divergence time estimation using concatenated coding sequences that not only support the monophyly of M. laminarioides but also underscore that the three M. laminarioides lineages are in an advanced stage of divergence. These new results open the question of the existence of still undisclosed species in M. laminarioides.

Comparative analyses of complete mitochondrial genomes of four sillaginids fish (Perciformes: Sillaginidae) and phylogenetic implications

Sillago muktijoddhai, S. mengjialensis, S. sihama and Sillaginops macrolepis (Perciformes, Sillaginidae) are common coastal sand borers. The first three species are found in the Northeastern Indian Ocean, and the fourth one is located in the Western Central Pacific Ocean only. Molecular data applying in the prior investigations on systematics and phylogenetic relationships were not only incomplete but also uncertain for these fishes. This study sequenced their complete mitochondrial genomes using Sanger Dideoxy DNA sequencing for the first time. Their complete mitochondrial genome was a circular molecule of 17,022, 16,624, 16,825 and 16,502bp in length for S. muktijoddhai, S. mengjialensis, S. sihama and Sillaginops macrolepis, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA or TAG codon and the incomplete termination codon T/TA could be detected in the four species. The majority of AT-skew and GC-skew values of the entire mitogenomes among the four species were negative. The Ka/Ks ratio analyses indicated 13 PCGs were suffering strong purifying selection. In the phylogenetic analysis, S. muktijoddhai, S. mengjialensis, and S. sihama were placed with relative species of the genus Sillago supporting morphological phylogeny. However, S. macrolepis was situated in the clade of genus Sillago that contrasted to morphological phylogeny. Divergence time analysis showed that Sillaginidae species diverged around 61 million years ago. Bangladesh J. Sci. Ind. Res. 59(2), 87-104, 2024

Morphological observation, molecular identification and evolutionary analysis of Hydatigera kamiyai found in Neodon fuscus from the Qinghai-Tibetan plateau

Hydatigera kamiyai (H. kamiyai) is a new species within Hydatigera that has recently been resurrected. Voles and cats are hosts of H. kamiyai and have a certain impact on its health and economy. Moreover, the Qinghai-Tibetan plateau (QTP) is a research hotspot representing Earth's biodiversity, as its unique geographical environment and climatic conditions support the growth of a variety of mammals and provide favorable conditions for various parasites to complete their life history. The aim of this study was to reveal the phylogenetic relationships and divergence times of H. kamiyai strains isolated from Neodon fuscus on the QTP using morphological and molecular methods. In this study, we morphologically observed H. kamiyai and sequenced the whole mitochondrial genome. Then, we constructed phylogenetic trees with the maximum likelihood (ML) and Bayesian inference (BI) methods. The GTR alternative model was selected for divergence time analysis. These data demonstrated that the results were consistent with the general morphological characteristics of Hydatigera. The whole genome of H. kamiyai was 13,822 bp in size, and the A + T content (73%) was greater than the G + C content (27%). The Ka/Ks values were all <1, indicating that all 13 protein-coding genes (13 PCGs) underwent purifying selection during the process of evolution. The phylogenetic tree generated based on the 13 PCGs, cytochrom oxidase subunit I (COI), 18S rRNA and 28S rRNA revealed close phylogenetic relationships between H. kamiyai and Hydatigera, with high node support for the relationship. The divergence time based on 13 PCGs indicated that H. kamiyai diverged approximately 11.3 million years ago (Mya) in the Miocene. Interestingly, it diverged later than the period of rapid uplift in the QTP. We also speculated that H. kamiyai differentiation was caused by host differentiation due to the favorable living conditions brought about by the uplift of the QTP. As there have been relatively few investigations on the mitochondrial genome of H. kamiyai, our study could provide factual support for further studies of H. kamiyai on the QTP. We also emphasized the importance of further studies of its hosts, Neodon fuscus and cats, which will be important for further understanding the life cycle of H. kamiyai.

Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae).

Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species' mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26-27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20-68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae.

TSPM-Net: A probabilistic spatio-temporal approach for scanpath prediction

Predicting the path followed by the viewer’s eyes when observing an image (a scanpath) is a challenging problem, particularly due to the inter- and intra-observer variability and the spatio-temporal dependencies of the visual attention process. Most existing approaches have focused on progressively optimizing the prediction of a gaze point given the previous ones. In this work we propose instead a probabilistic approach, which we call tSPM-Net. We build our method to account for observers’ variability by resorting to Bayesian deep learning and a probabilistic approach. Besides, we optimize our model to jointly consider both spatial and temporal dimensions of scanpaths using a novel spatio-temporal loss function based on a combination of Kullback–Leibler divergence and dynamic time warping. Our tSPM-Net yields results that outperform those of current state-of-the-art approaches, and are closer to the human baseline, suggesting that our model is able to generate scanpaths whose behavior closely resembles those of the real ones.