Marked Genetic Divergence Research Articles

Haemonchus contortus, an obligatory haematophagus worm infection in small ruminants: Population genetics and genetic diversity

Haemonchus contortus, a stomach worm, is prevalent in ruminants worldwide. They particularly hamper profitable small ruminant production. Here, we estimate the genetic variation of H. contortus collected from slaughtered goats and sheep from various geographic zones of Bangladesh using multiple genes. To perform this, adult parasites were isolated from the abomasum of slaughtered animals (sheep and goats). Among them, 79 male H. contortus were identified by microscopy. Following the extraction of DNA, ITS-2 and cox1 genes were amplified and subsequently considered for sequencing. After alignment and editing, sequences were analyzed to find out sequence variation, diversity pattern of genes, and population genetics of isolates. Among the sequence data, the analyses identified 19 genotypes of ITS-2 and 77 haplotypes of cox1 genes. The diversity of nucleotides was 0.0103 for ITS-2 and 0.029 for cox1 gene. The dendogram constructed by the genotype and haplotype sequences of H. contortus revealed that two populations were circulating in Bangladesh without any demarcation of host and geographic regions. Analysis of population genetics demonstrated a high flow of genes (89.2 %) within the population of the worm in Bangladesh. The Fst value showed very little amount of genetic difference among the worm populations of Bangladesh but marked genetic variation between different continents. The findings are expected to help explain the risks of anthelmintic resistance and the transmission pattern of the parasite, and also provide a control strategy against H. contortus.

Interspecific transfer of genetic information through polyploid bridges

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

Genome-wide exploration reveals distinctive northern and southern variants of Clonorchis sinensis in the Far East.

Clonorchis sinensis is a carcinogenic liver fluke that causes clonorchiasis-a neglected tropical disease (NTD) affecting ~35 million people worldwide. No vaccine is available, and chemotherapy relies on one anthelmintic, praziquantel. This parasite has a complex life history and is known to infect a range of species of intermediate (freshwater snails and fish) and definitive (piscivorous) hosts. Despite this biological complexity and the impact of this biocarcinogenic pathogen, there has been no previous study of molecular variation in this parasite on a genome-wide scale. Here, we conducted the first extensive nuclear genomic exploration of C.sinensis individuals (n=152) representing five distinct populations from mainland China, and one from Far East Russia, and revealed marked genetic variation within this species between "northern" and "southern" geographical regions. The discovery of this variation indicates the existence of biologically distinct variants within C.sinensis, which may have distinct epidemiology, pathogenicity and/or chemotherapic responsiveness. The detection of high heterozygosity within C.sinensis specimens suggests that this parasite has developed mechanisms to readily adapt to changing environments and/or host species during its life history/evolution. From an applied perspective, the identification of invariable genes could assist in finding new intervention targets in this parasite, given the major clinical relevance of clonorchiasis. From a technical perspective, the genomic-informatic workflow established herein will be readily applicable to a wide range of other parasites that cause NTDs.

Delineating species boundary through DNA barcodes ofsome fishes inhabiting river Murti in the foothills of Darjeeling Himalayas

The aim of the present study was to establish a global bioidentification system in the form of a reference sequencelibrary where fish species inhabiting river Murti were delineated by a particular sequence denoted as genetic‘barcode’.40 species representing 27 genera, 16 families and 5 orders were collected along different altitudinal gradients if river Murti. Mitochondrial DNA was isolated from the samples followed by amplification of COI gene, alignment by CLUSTAL W and submission to GenBank. The average nucleotide frequencies were calculated whereall the fishes showed relatively higher GC content at second codon position. Haplotypes showed gradually decreasinggenetic distance within orders, families, genera with very low genetic distance within species indicating markedgenetic divergence beyond species boundaries. The average transitional pairs were found more frequent than averagetransversional pairs. The Neighbour Joining tree revealed distinct clusters formed by members of order Cypriniformes, Siluriformes, Perciformes, Synbranchiformes and Beloniformes, where the conspecific individualswere always found to cluster under the same node supported by high bootstrap value, while dissimilar species wereclustered under separate nodes, ensuring unambiguous identification of species. The research work suggests that COI barcoding can be taken up as a sensible approach to eliminate obscurity in the identification of the fish fauna withapplications in its management and conservation of the species inhabiting in specific microhabitats. Keywords: COI gene, DNA Barcode, sequence library, unambiguous identification, conservation.

Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny.

Italy hosts a large number of endemic freshwater fish species due to complex geological events which promoted genetic differentiation and allopatric speciation. Among them, the South European roach Sarmarutilus rubilio inhabits various freshwater environments in three different ichthyogeographic districts. We investigated the genetic diversity of S. rubilio using two different mitochondrial markers (COI and CR), aiming to define its relationship with other similar taxa from the Balkan area and, from a phylogeographic perspective, test the effects of past hydrogeological dynamics of Italian river basins on its genetic structure and demographic history. Our analysis highlighted a marked genetic divergence between S. rubilio and all other roach species and, among Italian samples, revealed the existence of three deeply divergent geographic haplogroups, named A, B and C. Haplogroup C likely corresponds to a new putative cryptic species and is located at the northern border of the South European roach range; haplogroup B is restricted to Southern Italy; and haplogroup A is widespread across the entire range and in some sites it is in co-occurrence with C or B. Their origin is probably related to the tectonic uplifting of the Apuan Alps in the north and of the Colli Albani Volcano in the south during the Pleistocene, which promoted isolation and vicariance followed by secondary contacts.

Genetic variation of macronutrient tolerance in Drosophila melanogaster

Carbohydrates, proteins and lipids are essential nutrients to all animals; however, closely related species, populations, and individuals can display dramatic variation in diet. Here we explore the variation in macronutrient tolerance in Drosophila melanogaster using the Drosophila genetic reference panel, a collection of ~200 strains derived from a single natural population. Our study demonstrates that D. melanogaster, often considered a “dietary generalist”, displays marked genetic variation in survival on different diets, notably on high-sugar diet. Our genetic analysis and functional validation identify several regulators of macronutrient tolerance, including CG10960/GLUT8, Pkn and Eip75B. We also demonstrate a role for the JNK pathway in sugar tolerance and de novo lipogenesis. Finally, we report a role for tailless, a conserved orphan nuclear hormone receptor, in regulating sugar metabolism via insulin-like peptide secretion and sugar-responsive CCHamide-2 expression. Our study provides support for the use of nutrigenomics in the development of personalized nutrition.

Genome sequencing of a novel variant of fowl adenovirus B reveals mosaicism in the pattern of homologous recombination events.

We determined the genomic sequence of a Ukrainian strain of fowl adenovirus B (FAdV-B). The isolate (D2453/1) shared 97.2% to 98.4% nucleotide sequence identity with other viruses belonging to the species Fowl aviadenovirus B. Marked genetic divergence was seen in the hexon, fiber, and ORF19 genes, and phylogenetic analysis suggested that recombination events had occurred in these regions. Our analysis revealed mosaicism in the recombination patterns, a finding that has also been described in the genomes of strains of FAdV-D and FAdV-E. The shared recombination breakpoints, affecting the same genomic regions in viruses belonging to different species, suggest that similar selection mechanisms are acting on the key neutralization antigens and epitopes in viruses of different FAdV species.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00705-021-04972-9.

Marked mitochondrial genetic variation in individuals and populations of the carcinogenic liver fluke Clonorchis sinensis.

Clonorchiasis is a neglected tropical disease caused by the Chinese liver fluke, Clonorchis sinensis, and is often associated with a malignant form of bile duct cancer (cholangiocarcinoma). Although some aspects of the epidemiology of clonorchiasis are understood, little is known about the genetics of C. sinensis populations. Here, we conducted a comprehensive genetic exploration of C. sinensis from endemic geographic regions using complete mitochondrial protein gene sets. Genomic DNA samples from C. sinensis individuals (n = 183) collected from cats and dogs in China (provinces of Guangdong, Guangxi, Hunan, Heilongjiang and Jilin) as well as from rats infected with metacercariae from cyprinid fish from the Russian Far East (Primorsky Krai region) were deep sequenced using the BGISEQ-500 platform. Informatic analyses of mitochondrial protein gene data sets revealed marked genetic variation within C. sinensis; significant variation was identified within and among individual worms from distinct geographical locations. No clear affiliation with a particular location or host species was evident, suggesting a high rate of dispersal of the parasite across endemic regions. The present work provides a foundation for future biological, epidemiological and ecological studies using mitochondrial protein gene data sets, which could aid in elucidating associations between particular C. sinensis genotypes/haplotypes and the pathogenesis or severity of clonorchiasis and its complications (including cholangiocarcinoma) in humans.

Genetic variability of Corynespora cassiicola isolates from Amazonas, Brazil

ABSTRACT: Corynespora cassiicola is a cosmopolitan ascomycete widely known as phytopathogen in several crops, and more recently as an emerging pathogen in humans. In this study the genetic variability of 60 isolates of Corynespora cassiicola from different hosts and cities of Amazonas was evaluated, using AFLP molecular markers. Seven genetic groups were identified according to a dendrogram obtained by the Unweighted Pair Group Method using Arithmetical Averages, indicating significant variability among the isolates. Three isolates of different hosts (28, obtained from papaya; 55, obtained from cucumber; and 58, from tomato) remained as single individuals in distinct groups, suggesting marked genetic variation in comparison to the other isolates and possible specificity by the host.

Cryptic speciation in Southern Ocean Aequiyoldia eightsii (Jay, 1839): Mio-Pliocene trans-Drake Passage separation and diversification

The species of the genus Aequiyoldia Soot-Ryen, 1951, previously known as Yoldia, are common, soft-substratum, sareptid bivalves. In the Southern Ocean, Aequiyoldia eightsii (Jay, 1839) was originally described from the Antarctic Peninsula and has also been reported in southern South America. The species A. woodwardi (Hanley, 1960) was reported for the Falkland/Malvinas Islands and Tierra del Fuego, but this taxon has been recently synonymised within the broadly distributed A. eightsii. Aequiyoldia has received little attention across its distribution in the Southern Ocean, and although its taxonomy and systematics remain uncertain, all the species have been grouped under a single and broadly distributed unit: A. eightsii. Nevertheless, preliminary mtDNA comparisons demonstrated a marked genetic divergence (>7%) between A. eightsii populations from South America and Antarctic Peninsula. In order to further understand the diversity and biogeography of Aequiyoldia, we analyzed A. eightsii populations from different provinces of the Southern Ocean including South America (SA), the Falkland/Malvinas Islands (FI), the Antarctic Peninsula (AP), and Kerguelen Islands (KI). Individuals were characterized according to typical diagnostic morphological measurements and phylogenetic relationships were reconstructed based on mtDNA (cytochrome c oxidase subunit I). Patterns of genetic divergence of nucDNA intergenic transcribed spacers (ITS1, ITS2) were also estimated. The statistical analysis of external diagnostic characteristics revealed two morphotypes: (1) individuals with the morphology recorded for the nominal FI species, A. woodwardi, and (2) individuals from SA, AP, and KI, with the morphology recorded for A. eightsii. However, phylogenetic reconstructions based on mtDNA and nucDNA suggest the presence of at least five lineages within A. eightsii including: one lineage in Kerguelen Island, two lineages in the Antarctic Peninsula, one lineage in South America, and the last one restricted to the Falkland/Malvinas Islands. Such results are evidence that the Antarctic Polar Front represents an historical biogeographic barrier for this group and that after the separation of these lineages, they followed independent evolutionary pathways in different provinces of the Southern Ocean. Estimates of divergence time suggest that KI separated from other Aequiyoldia lineages close to the middle Miocene. Following this, the separation between the AP and SA lineages occurred at the end of the Miocene around 7.5 Ma. Finally, Aequiyoldia diversified during the Pliocene in Antarctic Peninsula (∼4.5 Ma) and South America (∼3.0 Ma). Individuals from FI exhibited morphological differences, and 4% of divergence from South American individuals, suggesting that A. woordwardi could be revalidated. Similarly, the marked molecular divergence between the KI and the rest of the recorded lineages also support the validity of A. kerguelensis (Thiele, 1931).

Characterization of spaC-type Erysipelothrix sp. isolates causing systemic disease in ornamental fish.

Since 2012, low-to-moderate mortality associated with an Erysipelothrix sp. bacterium has been reported in ornamental fish. Histological findings have included facial cellulitis, necrotizing dermatitis and myositis, and disseminated coelomitis with abundant intralesional Gram-positive bacterial colonies. Sixteen Erysipelothrix sp. isolates identified phenotypically as E.rhusiopathiae were recovered from diseased cyprinid and characid fish. Similar clinical and histological changes were also observed in zebrafish, Danio rerio, challenged by intracoelomic injection. The Erysipelothrix sp. isolates from ornamental fish were compared phenotypically and genetically to E.rhusiopathiae and E.tonsillarum isolates recovered from aquatic and terrestrial animals from multiple facilities. Results demonstrated that isolates from diseased fish were largely clonal and divergent from E.rhusiopathiae and E.tonsillarum isolates from normal fish skin, marine mammals and terrestrial animals. All ornamental fish isolates were PCR positive for spaC, with marked genetic divergence (<92% similarity at gyrB, <60% similarity by rep-PCR) between the ornamental fish isolates and other Erysipelothrix spp. isolates. This study supports previous work citing the genetic variability of Erysipelothrix spp. spa types and suggests isolates from diseased ornamental fish may represent a genetically distinct species.

Multilocus Sequencing of Corynebacterium pseudotuberculosis Biotype Ovis Strains.

Thirteen Corynebacterium pseudotuberculosis biotype ovis strains isolated from clinical cases of caseous lymphadenitis in Hungary were characterised using multilocus sequencing and their phylogenetic comparison was carried out on the basis of four housekeeping genes (groEL1, infB, dnaK, and leuA). The in silico analysis of the 16 frequently studied housekeeping genes showed that C. pseudotuberculosis strains could be readily distinguished from C. diphtheriae and C. ulcerans strains; however, sequences of the same genes in the two biotypes of the C. pseudotuberculosis were highly similar; the heterogeneity values were low. Genes dnaK, infB, groEL1, and leuA showed marked genetic variation within C. pseudotuberculosis, and strains of the two biotypes of C. pseudotuberculosis could be differentiated. Analysis of the individual genes showed a fairly conservative nature of C. pseudotuberculosis biotype ovis strains. The greatest genetic differentiation was seen in the dnaK and infB genes and concatenations of these two genes were very useful in the genetic separation of the studied strains.

Examining the evolutionary relationships amongst three species of West African freshwater crabs Liberonautes Bott, 1955 (Brachyura: Potamonautidae) using mtDNA sequence data

Evolutionary relationships amongst three species of freshwater crabs, Liberonautes latidactylus (De Man, 1903), L. nimba Cumberlidge, 1999, and L. rubigimanus Cumberlidge and Sachs, 1989, were examined using DNA sequence data of the mitochondrial cytochrome oxidase subunit I (COI) locus. The latter three species are listed in the IUCN Red List for 2008 as least concerned, vulnerable, and endangered, respectively. Specimens of the three species were collected in Liberia and neighbouring Guinea, West Africa. Phylogenetic results derived from maximum parsimony, maximum likelihood, and Bayesian inference revealed the monophyly of all three species. Moderate genetic variation was observed within L. latidactylus . Within the narrow endemic, montane species, L. nimba shallow divergence was observed, whereas marked genetic divergence was observed within L. rubigimanus . Three statistically well-supported clades were observed within the latter taxon, two of these clades were sympatric at Simandou, Liberia (clades A and B), and characterised by a 10% uncorrected sequence divergence for the COI locus, whereas the divergence between the latter two clades and the larger L. rubigimanus clade was 8%. Haplotype networks corroborate the absence of maternal gene flow amongst the three L. rubigimanus clades suggesting possible reproductive isolation and the presence of two novel species. Our results suggest that Liberonautes harbours undescribed, narrowly distributed species. The results are discussed in a conservation framework for the three Liberonautes species.

A new species of the Craugastor podiciferus species group (Anura: Craugastoridae) from the premontane forest of southwestern Costa Rica.

In this report, we describe a new species of the Craugastor podiciferus species group from the premontane forest of the Pacific versant along the Costa Rican-Panamanian border. Mitochondrial DNA and karyotype analyses previously showed a marked genetic divergence between populations of the premontane forest of the Fila Costeña and the lowlands South Pacific Costa Rica near Panama. Analyses of the mitochondrial DNA sequences and the morphological variation revealed significant differences between the populations of the premontane forest relative to the other populations of C. stejnegerianus, including the type locality. We recognize these premontane populations as a new species and show that they differ from the typical C. stejnegerianus in the coloration of the venter, the head and the body proportions, and mtDNA divergence. With the addition of this new species, the C. podiciferus species group now contains nine species.

Differential contribution of genomic regions to marked genetic variation and prediction of quantitative traits in broiler chickens.

BackgroundGenome-wide association studies in humans have found enrichment of trait-associated single nucleotide polymorphisms (SNPs) in coding regions of the genome and depletion of these in intergenic regions. However, a recent release of the ENCyclopedia of DNA elements showed that ~80 % of the human genome has a biochemical function. Similar studies on the chicken genome are lacking, thus assessing the relative contribution of its genic and non-genic regions to variation is relevant for biological studies and genetic improvement of chicken populations.MethodsA dataset including 1351 birds that were genotyped with the 600K Affymetrix platform was used. We partitioned SNPs according to genome annotation data into six classes to characterize the relative contribution of genic and non-genic regions to genetic variation as well as their predictive power using all available quality-filtered SNPs. Target traits were body weight, ultrasound measurement of breast muscle and hen house egg production in broiler chickens. Six genomic regions were considered: intergenic regions, introns, missense, synonymous, 5′ and 3′ untranslated regions, and regions that are located 5 kb upstream and downstream of coding genes. Genomic relationship matrices were constructed for each genomic region and fitted in the models, separately or simultaneously. Kernel-based ridge regression was used to estimate variance components and assess predictive ability. Contribution of each class of genomic regions to dominance variance was also considered.ResultsVariance component estimates indicated that all genomic regions contributed to marked additive genetic variation and that the class of synonymous regions tended to have the greatest contribution. The marked dominance genetic variation explained by each class of genomic regions was similar and negligible (~0.05). In terms of prediction mean-square error, the whole-genome approach showed the best predictive ability.ConclusionsAll genic and non-genic regions contributed to phenotypic variation for the three traits studied. Overall, the contribution of additive genetic variance to the total genetic variance was much greater than that of dominance variance. Our results show that all genomic regions are important for the prediction of the targeted traits, and the whole-genome approach was reaffirmed as the best tool for genome-enabled prediction of quantitative traits.

English

Istrian dairy sheep is a local breed essential for the identity and development of the NorthernAdriatic karstic region through high-quality products, primarily the hard sheep artisanal cheese. Border changes fragmented the initial Istrian dairy sheep population in three genetically isolated subpopulations in Italy (1000 animals), Slovenia (1150 animals) and Croatia (2500 animals). Due to the drastic reduction of their population sizes and fragmentation, the populations in Croatia and Slovenia are included in governmentally supported conservation programs. The initial subpopulation in Italy was restored after near extinction with stock from Slovenia, and is used today in meat production. The aim of this study was to provide an initial understanding of the current genetic structure and distribution of the genetic variability that exists in Istrian sheep by analysing individuals sampled in two regional groups of Istrian sheep from Croatia and Slovenia. Cres island sheep and Lika pramenka sheep were used as out-groups for comparison. Genetic differentiation was analysed using factorial correspondence analysis and structure clustering over 26 microsatellite loci for a total of 104 sheep belonging to three breeds from Croatia and Slovenia. Factorial correspondence analysis and clustering-based structure analysis both showed three distinct populations: Lika pramenka sheep, Cres island sheep and Istrian sheep. We did not find a marked genetic divergence of the regional groups of Istrian sheep. Istrian sheep regional group from Slovenia showed lower genetic variability compared to the one from Croatia. Variability and structure information obtained in this study considered alongside with socio-cultural-contexts and economic goals for the Istrian sheep reared in Croatia and Slovenia indicate that the cross-border exchange of genetic material of animals carrying private alleles among populations would maintain these alleles at low frequencies and minimize the inbreeding rate.

Divergence history of the Rufous-tailed Tailorbird (Orthotomus sericeus) of Sundaland: Implications for the biogeography of Palawan and the taxonomy of island species in general

ABSTRACT The Rufous-tailed Tailorbird (Orthotomus sericeus)—a Sunda endemic—is divided into 3 morphologically based subspecies: one in western Sundaland (Malay Peninsula, Sumatra, and associated islands), one from the Natuna Islands in the South China Sea, and one on Borneo, Palawan, and smaller islands of the Sunda continental shelf east of Borneo. Previous study, however, suggested that these subspecies do not conform to molecular genetic subdivisions of the species. We reexamined the morphology and performed molecular phylogeographic and multi-locus coalescent analysis of two subspecies of Rufous-tailed Tailorbird comprising populations on the Malay Peninsula, Sumatra, Borneo, and Palawan. We found (1) little morphological difference among the two subspecies, (2) no substantial genetic differences between the Borneo and western Sunda populations, but (3) marked genetic divergence between the Palawan and other populations. We conclude that the Bornean and western Sunda populations interbred extensively ...

Phylogenetic relationships, genetic divergence, historical biogeography and conservation of an endangered gecko, Goniurosaurus kuroiwae (Squamata: Eublepharidae), from the Central Ryukyus, Japan.

The Kuroiwa's eyelid gecko Goniurosaurus kuroiwae is an endangered species in a state of relict endemism in the Central Ryukyus, Japan, and is divided into five subspecies. We analyzed variations in sequence data for approximately 1900 base positions of mitochondrial 12S and 16S rRNA, and cytochrome b genes from samples representing all recognized subspecies of G. kuroiwae together with those from congeneric species in order to test the relevant previous phylogenetic hypotheses and discuss biogeographical implications in the degree and pattern of genetic divergence within G. kuroiwae. Our results, while confirming a previous molecular phylogenetic hypothesis proposed on the basis of much smaller data set, negate the relationships hypothesized on morphological grounds by explicitly supporting: 1) the primary dichotomy, with substantial genetic divergence, between G. k. splendens from the Amami Island Group and the remaining subspecies all from the Okinawa Island Group; and 2) the presence of at least six independent lineages within the latter, indicating non-monophyly for two of the subspecies, G. k. kuroiwae and G. k. orientalis, in the current taxonomic definitions. The marked genetic divergence between populations of the two island groups seems to have initiated in the middle Miocene, i.e., prior to formation of straits that have consistently been separating these two island groups since the early Pleistocene. All populations of G. kuroiwae are regarded as endangered from the viewpoint of conservation genetics.

Revalidation and redescription of Potamon elbursi Pretzmann, 1976 (Brachyura, Potamidae) from Iran, based on morphology and genetics

Abstract In the current study, we redescribe and revalidate a freshwater crab species of the genus Potamon Savigny, 1816, from northern Iran. Potamon elbursi Pretzmann, 1962, differs from the species it has been synonymised with, Potamon persicum Pretzmann, 1962, mainly by the shape of the first gonopods in males. Consistent and marked genetic divergence was also recognised in the mitochondrial 16S rRNA and cytochrome oxidase subunit I genes. This study elevates P. elbursi to species rank and therefore increases the number of valid species of the genus Potamon to a total of twenty-two.

Quaternary donaciine beetles (Coleoptera, Chrysomelidae) in Japan: Colonization and divergence patterns inferred from fossil and molecular data

We review the current knowledge of the distribution, ecology, fossils, and molecular phylogeny of donaciine beetles in Japan and its adjacent regions, and discuss historical faunal change on the Japanese islands during the Quaternary. The present Japanese fauna consists of 23 species within the genera Donacia, Plateumaris, and Macroplea, nine of which are endemic to Japan. Five fossil species have been found in strata from the Late Miocene to the Middle Pleistocene; the fossil species became extinct by the Middle Pleistocene. The oldest fossils of the extant species are of two endemic species Plateumaris akiensis and P. constricticollis from the Pliocene. P. akiensis is currently confined to a single locality, whereas P. constricticollis occurs over a wide geographic range and shows marked morphological and genetic divergence. Early Pleistocene fossils of the endemic species Donacia japana and D. ozensis, and the non-endemic Donacia vulgaris have been found. Middle Pleistocene fossils of non-endemic species such as Plateumaris sericea and D. splendens have been found, suggesting their colonization of Japan during this period. Mitochondrial COI gene sequences indicate that the haplotype coalescence times date back to the Middle–Late Pleistocene in most extant species, suggesting the occurrence of colonization and/or bottleneck events during this period. Exceptionally, P. constricticollis shows a Pliocene coalescence coincident with fossil records. In addition, P. sericea likely colonized Hokkaido and Honshu/Kyushu separately during the Middle Pleistocene following the divergence of two different haplotype lineages during the Early Pleistocene.