Introgression Research Articles

Phylogenomics, introgression, and demographic history of South American true toads (Rhinella).

The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multilocus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mitonuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.

Identification of Natural Hybrids between Ahlbergia frivaldszkyi (Lederer, 1853) and Callophrys rubi (Linnaeus, 1758) (Lepidoptera, Lycaenidae) Using Mitochondrial and Nuclear Markers.

Simple SummaryButterfly specimens with unusual morphological characters (e.g., unusual wing coloration) have contradictory interpretations in the literature and have been considered by different authors either as previously undescribed taxa, putative hybrids, or aberrations of well-known species. Such individuals clearly represent a taxonomic problem that needs to be addressed by scientists. The application of molecular techniques could shed light on the origin of morphological uncertainty. Here we use a combination of mitochondrial and nuclear DNA markers to analyze three lycaenid butterflies with unusual wing pattern, which are thought to represent naturally occurring hybrids due to their intermediate phenotype. We confirm their hybrid origin and indicate that the specimens are wild-caught hybrids between females of Callophrys rubi and males of Ahlbergia frivaldszkyi. Our data indicate that gene flow across species boundaries in these butterflies can occur long after speciation.Natural hybridization is rather widespread and common in animals and can have important evolutionary consequences. In terms of taxonomy, exploring hybridization and introgression is crucial in defining species boundaries and testing taxonomic hypotheses. In the present paper, we report on natural hybrid specimens between Ahlbergia frivaldszkyi (Lederer, 1853) and Callophrys rubi (Linnaeus, 1758). To test the hypothesis of their hybrid origin, we employed the molecular mitochondrial (COI gene) and nuclear (wingless, RPS5, and Ca-ATPase genes) markers commonly used in phylogenetic studies and explored the morphology of the specimens. Our analysis revealed that hybrids bear mitochondrial haplotypes of C. rubi, while nuclear fragments are heterozygous, sharing a combination of A. frivaldszkyi and C. rubi lineages. The hybrid specimens combine morphological characters of both genera. Our results for the first time empirically demonstrate the possibility of genetic introgression between these species and between the genera Callophrys and Ahlbergia on the whole.

Molecular Structure and Hybridization Patterns of Abramis brama × Rutilus rutilus Hybrids from Modrac Reservoir, Bosnia and Herzegovina

Abstract Interspecific hybridization in the Cyprinidae family has been recorded worldwide, with Abramis brama (bream) and Rutilus rutilus (roach) as one of the often-reported hybridizing pairs. The only account of such an event in Bosnia and Herzegovina has been in Modrac Reservoir. Using morphological and molecular markers, the presence of hybrids was surveyed, the hybridization direction was determined and the hybrid group structure in this ecosystem was evaluated. Our findings confirmed unhindered natural hybridization between roach and bream in Modrac Reservoir. Over 50% of the hybrid specimens were classified as F2 hybrids by the NewHybrids software, while the rest were categorized as pure parental form, making it the first such finding in Europe. The analysis of mitochondrial cytochrome b showed that 90% of hybrid individuals were of bream maternal origin. The hybrid group expressed higher mean values of observed heterozygosity and gene diversity than both parental species. Signs of introgressive hybridization between parental species were detected. The hybrid zone of Modrac Reservoir appears to follow the intermediate or “flat” hybrid model based on the balanced distribution of parental and hybrid genotypes. Further investigation is needed to elucidate the factors that enable the survival and mating success of post-F1 individuals.

Genetic Diversity and Population Structure of Wild Beets (Beta spp.) from the Western Iberian Peninsula and the Azores and Madeira Islands

In this work, using simple sequence repeat (SSR) markers, we present new insights into the genetic diversity, differentiation, and structure of Beta vulgaris subsp. maritima of western Iberia and the Azores and Madeira islands and of B. macrocarpa from southern Portugal. B. macrocarpa occurs only in southern Portugal and frequently in sympatry with B. vulgaris subsp. maritima, showing genetic introgression. B. macrocarpa has a better-defined structure than B. vulgaris subsp. maritima, which has a high degree of admixture. A great differentiation (FST ranging from 0.277 to 0.184) was observed among the northern populations of B. vulgaris subsp. maritima. In contrast, only a small differentiation (FST ranging from 0.000 to 0.026) was detected among the southern B. vulgaris subsp. maritima populations. The inland B. vulgaris subsp. maritima populations (“RIO” and “VMT”) are distinct from each other, which also occurs with the two islands’ populations (“MAD” and “AZO”). The existence of two distinct Atlantic Sea currents can explain the fact that Madeira is related to the southern populations, while the Azores is related to the northern populations. We consider that understanding the relationships existing within Beta spp. is key to future genetic studies and for the establishment of conservation measures. Our results show that the southern coastal areas of Portugal should be considered as a potential site for in situ conservation of the beet wild relatives. Special attention is needed in what concerns B. macrocarpa because this is a rare species that also occurs in a sympatric relationship with B. vulgaris subsp. maritima.

Molecular analyses revealed three morphologically similar species of non‐native apple snails and their patterns of distribution in freshwater wetlands of Hong Kong

AbstractAimEffective control of invasive species and conservation of native biodiversity requires accurate species identification. Several species of apple snails (Ampullariidae: Pomacea) from South America have become widespread pests in Asia since their introduction in the early 1980s, but their taxonomic uncertainty has hindered our understanding of the invasive processes. We aim to determine the identity and distribution of Pomacea species in Hong Kong, which has been known as a stepping stone of species invasion.LocationHong Kong.MethodsWe collected 162 apple snails from five freshwater wetlands of Hong Kong, sequenced the mitochondrial COI, genotyped the nuclear EF1α and built a COI dataset of 1378 sequences of apple snails from mainland China, Malaysia, Argentina and Brazil. We identified the species, determine the introgression pattern and analysed their population structures.ResultsWe found the co‐occurrence of P. canaliculata, P. maculata and P. occulta in Hong Kong for the first time. Pomacea canaliculata represented the dominant species (85% of collected specimens). The three Pomacea species from Hong Kong had low genetic diversity. High genetic similarity existed between P. canaliculata populations of Hong Kong and Malaysia, P. occulta populations of Hong Kong and mainland China and P. maculata populations of mainland China and Malaysia. Our samples contained a high proportion of hybrids.Main conclusionsApple snails may have been introduced into Hong Kong multiple times: both P. canaliculata and P. occulta likely came from Argentina; P. maculata came from both Argentina and Brazil. Genetic drift largely explains the differentiation of Pomacea spp. among regions. Introgressive hybridization may have contributed to population fitness by increasing genetic variation to neutralize the founder effect. The knowledge on species identity, distribution and genetic diversity of apple snails from this study will contribute to better understanding their invasive mechanisms and prevention of their continued spread in Asia.

Genome and systems biology of Melilotus albus provides insights into coumarins biosynthesis.

SummaryMelilotus species are used as green manure and rotation crops worldwide and contain abundant pharmacologically active coumarins. However, there is a paucity of information on its genome and coumarin production and function. Here, we reported a chromosome‐scale assembly of Melilotus albus genome with 1.04 Gb in eight chromosomes, containing 71.42% repetitive elements. Long terminal repeat retrotransposon bursts coincided with declining of population sizes during the Quaternary glaciation. Resequencing of 94 accessions enabled insights into genetic diversity, population structure, and introgression. Melilotus officinalis had relatively larger genetic diversity than that of M. albus. The introgression existed between M. officinalis group and M. albus group, and gene flows was from M. albus to M. officinalis. Selection sweep analysis identified candidate genes associated with flower colour and coumarin biosynthesis. Combining genomics, BSA, transcriptomics, metabolomics, and biochemistry, we identified a β‐glucosidase (BGLU) gene cluster contributing to coumarin biosynthesis. MaBGLU1 function was verified by overexpression in M. albus, heterologous expression in Escherichia coli, and substrate feeding, revealing its role in scopoletin (coumarin derivative) production and showing that nonsynonymous variation drives BGLU enzyme activity divergence in Melilotus. Our work will accelerate the understanding of biologically active coumarins and their biosynthetic pathways, and contribute to genomics‐enabled Melilotus breeding.

Genetic and morphological data demonstrate hybridization and backcrossing in a pair of salamanders at the far end of the speciation continuum.

Deeply diverged yet hybridizing species provide a system to investigate the final stages of the speciation process. We study a hybridizing pair of salamander species—the morphologically and genetically drastically different newts Triturus cristatus and T. marmoratus—with a panel of 32 nuclear and mitochondrial genetic markers. Morphologically identified hybrids are mostly of the F1 generation and mothered by T. cristatus. The sex ratio of the F1 hybrid class is reciprocally skewed, with a preponderance of females in T. cristatus‐mothered hybrids and males in T. marmoratus‐mothered hybrids. This amounts to the Haldane effect operating in one direction of the cross. Deeper generation hybrids are occasionally produced, possibly including F1 hybrid × backcross hybrid offspring. Interspecific gene flow is low, yet skewed toward T. cristatus. This asymmetry may be caused by hybrid zone movement, with the superseding species being predisposed to introgression. The persisting gene flow between deeply differentiated species supports the notion that full genetic isolation may be selected against. Conversely, published morphological data suggest that introgressive hybridization is detrimental, with digital malformations occurring more frequently in the area of sympatry. Finally, to assist field identification, both within the area of natural range overlap and concerning anthropogenic introductions elsewhere, we document the phenotypical variation of two generations of hybrids compared with both parental species. We suggest that fluctuating range boundaries, ecological segregation, cytonuclear incompatibilities and hybrid breakdown through Bateson–Dobzhansky–Muller incompatibilities all contribute to species integrity, despite incomplete isolation during secondary contact.

Distribution of tiger salamanders in northern Sonora, Mexico: comparison of sampling methods and possible implications for an endangered subspecies

Abstract Many aquatic species in the arid USA-Mexico borderlands region are imperiled, but limited information on distributions and threats often hinders management. To provide information on the distribution of the Western Tiger Salamander (Ambystoma mavortium), including the USA-federally endangered Sonoran Tiger Salamander (Ambystoma mavortium stebbinsi), we used traditional (seines, dip-nets) and modern (environmental DNA [eDNA]) methods to sample 91 waterbodies in northern Sonora, Mexico, during 2015-2018. The endemic Sonoran Tiger Salamander is threatened by introgressive hybridization and potential replacement by another sub-species of the Western Tiger Salamander, the non-native Barred Tiger Salamander (A. m. mavortium). Based on occupancy models that accounted for imperfect detection, eDNA sampling provided a similar detection probability (0.82 [95% CI: 0.56-0.94]) as seining (0.83 [0.46-0.96]) and much higher detection than dip-netting (0.09 [0.02-0.23]). Volume of water filtered had little effect on detection, possibly because turbid sites had greater densities of salamanders. Salamanders were estimated to occur at 51 sites in 3 river drainages in Sonora. These results indicate tiger salamanders are much more widespread in northern Sonora than previously documented, perhaps aided by changes in land and water management practices. However, because the two subspecies of salamanders cannot be reliably distinguished based on morphology or eDNA methods that are based on mitochondrial DNA, we are uncertain if we detected only native genotypes or if we documented recent invasion of the area by the non-native sub-species. Thus, there is an urgent need for methods to reliably distinguish the subspecies so managers can identify appropriate interventions.

Introgressive hybridization between two phylogenetic lineages of charrs ( Salvelinus : Salmonidae) in northeastern Asia

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Genetic analysis of hybridization between white-handed (Hylobates lar) and pileated (Hylobates pileatus) gibbons in a contact zone in Khao Yai National Park, Thailand.

Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.

Hybridization and genetic population structure of Alosa population in the United Kingdom.

Human-mediated habitat fragmentation has been proposed as the main factor driving hybridization between the sympatric migratory European shads Alosa alosa and Alosa fallax, which has co-occurred with substantial population declines in A. alosa. In river systems across Great Britain, shad are negatively affected by navigation weirs constructed in the last 150 years that impede their spawning migrations. Consequently, the aim here was to assess the impact of human disturbances on the genetic introgression and population structure of shad in Great Britain through genotyping 119 Alosa spp. using 24 microsatellite loci.

Comparative phylogeography study reveals introgression and incomplete lineage sorting during rapid diversification of Rhodiola.

Many plant taxa in the Qinghai-Tibetan Plateau (QTP) and the Hengduan Mountains (HM) radiated rapidly during the Quaternary but with frequent secondary contact between diverging populations. Incomplete lineage sorting and introgressive hybridization might be involved during the rapid radiation, but their effects on phylogeography have not been fully determined. We investigated the chloroplast DNA (cpDNA)/internal transcribed spacer (ITS) sequence variations of 611 samples of Rhodiola bupleuroides, R. discolor, R. fastigiata and R. chrysanthemifolia from the QTP and HM to compare the phylogeographic patterns between the four species with different evolutionary histories, geographic ranges and reproductive modes. The divergence times of these species were consistent with the last peak of in situ speciation in the HM. While closely related species exhibited different phylogeographic patterns, they shared several ribotypes and haplotypes in sympatric populations, suggesting introgressive hybridization. A significant phylogenetic discordance between ribotypes and haplotypes was detected in three species, implying incomplete lineage sorting. Rhodiola discolor houses an extraordinary richness of cpDNA haplotypes, and this finding may be attributed to adaptive radiation. In addition to geographic isolation and climate oscillations during the Quaternary, both introgressive hybridization and incomplete lineage sorting play important roles in species that experienced rapid diversification in the QTP and HM.

A multispecies BCO2 beak color polymorphism in the Darwin’s finch radiation

Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles,1 but generally little is known about the factors affecting their maintenance in populations.2 We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive.3 Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.

Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression.

The intriguing recent discovery of Campylobacter coli strains, especially of clade 1, that (i) possess mosaic C. coli / C. jejuni alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined ‘despeciation’. In an MLST-based neighbour-joining tree of a number of C. coli and C. jejuni isolates of different clades, three prominent Campylobacter isolates formed a seemingly separate cluster besides the previously described C. coli and C. jejuni clades. In the light of the suspected, ongoing genetic introgression between the C. coli and C. jejuni species, this cluster of Campylobacter isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative C. coli / C. jejuni hybrid strains were explored, their genomic mosaic structure caused by C. jejuni introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid Campylobacter strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid Campylobacter strains are clade 1 C . coli strains, which have acquired between 8.1 and 9.1 % of their genome from C. jejuni . The C. jejuni genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from C. jejuni are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from C. jejuni has contributed 8.1–9.1% to the genome of three C. coli isolates and initiated the despeciation between C. jejuni and C. coli . Based on their functional annotation, the genes originating from C. jejuni enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the C. jejuni genetic material with C. coli genomes.

Genetic diversity analysis of the invasive gall pest Leptocybe invasa (Hymenoptera: Apodemidae) from China.

Leptocybe invasa Fisher et LaSalle is a global invasive pest that seriously damages Eucalyptus plants. Studying the genetic diversity, genetic structure and introgression hybridization of L. invasa in China is of great significance for clarifying the breeding strategy, future invasion and diffusion trends of L. invasa in China and developing scientific prevention and control measures. Genetic diversity and phylogenetic analyses of 320 L. invasa female adults from 14 geographic populations in China were conducted using 10 polymorphic microsatellite loci (SSRs) and mitochondrial DNA cytochrome oxidase I gene sequences (COIs). (1) The Bayesian phylogenetic tree and haplotype network diagram showed that only haplotype Hap3 existed in L. invasa lineage B in China, while haplotypes Hap1 and Hap2 existed in lineage A, among which haplotype Hap2 was found for the first time. The nucleotide and haplotype diversities of lineage A were higher than those of lineage B. (2) The SSR genetic diversity of the Wuzhou Guangxi, Ganzhou Jiangxi and Panzhihua Sichuan populations was higher than that of the other 11 populations, and the SSR genetic diversity of lineage A was higher than that of lineage B. (3) The AMOVA analysis of mitochondrial COI data showed that 75.55% of the variation was among populations, and 99.86% of the variation was between lineages, while the AMOVA analysis of nuclear SSR data showed that 35.26% of the variation was among populations, and 47.04% of the variation was between lineages. There were obvious differences in the sources of variation between the COI and SSR data. (4) The optimal K value of COI and SSR data in structure analysis was 2, and PCoA analysis also divided the dataset into two obvious categories. The UPMGA phylogenetic tree based on SSR data clustered 14 geographic species into two groups. The results of genetic structure analysis supported the existence of two lineages, A and B, in China. (5) Structural analysis showed that there was obvious introgressive hybridization in Wuzhou Guangxi, Ganzhou Jiangxi, Panzhihua Sichuan and other populations. These results suggest that lineage introgressive hybridization has occurred in the L. invasa population in China. The introgressive hybridization degree and genetic diversity of lineage A are obviously higher than those of lineage B. Lineage introgressive hybridization may be the driving force for further L. invasa invasion and diffusion in China in the future.

Evidence for introgressive hybridization of wild black‐necked pheasant with the exotic ring‐necked pheasant during the past 50 years in the Hyrcanian zone, an integrative molecular and morphological approach

Hybridization with non-native-related taxa, especially with introgression, is a major conservation problem, as it may disturb local adaptations, resulting in population decline and biodiversity loss. It is important to identify hybrid individuals, which can be difficult to break up morphologically. Using morphometric and genetic approaches [multivariate analysis, microsatellites, and amplified fragment length polymorphism (AFLP)], this research attempts to classify the interaction and the prevalence of introgressive hybridization in four native pheasant subspecies of Phasianus colchicus with non-native P. c. torquatus. According to principal component analysis and canonical discriminant function results, hybrid individuals are placed between these two major groups of native and exotic birds. Also, we assessed the population structure, genetic variation, and gene flow between native subspecies and exotic pheasants using 16 microsatellite loci in 129 samples. Our findings revealed that hybridization occurred between two native subspecies, P. c. talischensis and P. c. persicus, and exotic subspecies (P. c. torquatus). Observation of hybrids in P. c. persicus were almost three times higher than P. c. talischensis. The levels of the genetic variation within and among the natural populations were investigated using the AFLP markers method to identify hybrids. A total of 202 distinct bands were amplified using four primer combinations, with 179 of them being polymorphic. AMOVA analysis revealed a low degree of genetic differentiation among the populations. The hybrid samples were closely related to the P. c. talischensis and P. c. persicus populations, according to the UPGMA clusters and discriminant analysis of principal components. It appears that disruption of gene flow between pheasant populations in the Hyrcanian zone is a serious issue. The data from molecular markers prompted us to raise a concern about the genetic integrity in some native subspecies in the Iranian plateau. As a result, a clear cut-level can now be used to differentiate the hybrids, which is also supported by morphological evidence. A direct relationship was found between farmed pheasants and hybrid frequency. Farmed individuals should be closely monitored, and non-native taxa should not be released into the wild.

Space use in free-ranging canids: are gonadal hormones required for territory maintenance?

Fertility control among carnivores has been used to reduce depredations on livestock and wild neonates, population control, modify behavior, inhibit genetic introgression, and reduce human–wildlife conflicts. Although there is considerable knowledge on techniques to sterilize carnivores, there is little information concerning how the absence of gonadal hormones influences behavior, space use, and survival of wild canids. We examined territorial fidelity, home-range size and overlap, and survival of 179 surgically sterilized free-ranging canids (124 coyotes (Canis latrans Say, 1823), 55 coyote – red wolf (Canis rufus Audubon and Bachman, 1851) hybrids) with gonadal hormones present (tubal-ligated females (n = 70), vasectomized males (n = 73)) versus absent (spayed females (n = 22), neutered males (n = 14)). The absence of gonadal hormones did not influence annual home-range size and home-range overlap, territory fidelity, and annual survival rates. Additionally, no differences were detected across sexes and hormonal treatments in annual home-range size, percent home-range overlap, annual home-range residency rates, and annual survival rates. Methods of fertility control that do not keep gonadal organs intact may prove useful for management without concern for changes in behavior, mainly territoriality, space use, and survival.

Species divergence and repeated ancient hybridization in a Sulawesian lake system.

An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes; of these, one lake is inhabited by two species. Morphological and population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that these two sympatric species are phylogenetically sister to but substantially reproductively isolated from each other. Analyses of admixture and comparison of demographic models revealed that the two sympatric species experienced several substantial introgressions from outgroup populations that probably occurred soon after they had secondary contact with each other in the lake. However, the ratio of migrants from the outgroups was estimated to be different between the two species, which is consistent with the hypothesis that these introgressions aided their divergence or prevented them from forming a hybrid swarm. Repeated lake fragmentations and fusions may have promoted diversification of this freshwater fish species complex that is endemic to this ancient lake system.

Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs

Pudong White (PDW) pigs, historically originating from Shanghai, are the only Chinese indigenous pigs characterised by their completely white coats, with the exception of Rongchang pigs. However, there is limited information concerning their overall genetic structure or relationship with other breeds, especially the East Chinese (ECN) and European pigs. To uncover the genetic structure, selection signatures, and potential exotic introgression in PDW pigs, we sampled 15 PDW pigs using whole-genome sequencing (~20×). We then conducted in-depth population genetic analyses in 320 pigs from 27 global pig groups, namely, European wild boars, Chinese wild boars, and outgroup. Neighbour-joining tree and principal component analysis confirmed that PDW pigs belonged to the ecotype of ECN pigs. Both f3, D-statistics, and structure analysis showed that PDW pigs shared apparent alleles with Large White (LW) pigs. Three statistics, rIBD, a haplotype heat map and copy number variation, further indicated that PDW pigs shared apparent alleles with LW pigs at the KIT Proto-Oncogene, Receptor Tyrosine Kinase (KIT) and PARG-MARCHF8 loci, suggesting that the lineage of European pigs in PDW originated from LW pigs. After further detecting the KIT mutations in different pig breeds, PDW was confirmed to have the same duplication region 1, duplication region 2, and the splicing mutation on intron 17 of KIT as LW pigs that determine the white coat colour phenotype in European white pigs. We hypothesised that LW pigs were imported to China ∼110–160 years ago according to the admixture time estimate and then crossed with ECN pigs, resulting in the introgression of the KIT alleles that produce the white coat colour phenotype in the PDW pig breed. To our knowledge, this study presents the first thorough description of the genetic structure of PDW pigs via whole-genome resequencing data; moreover, the results provide a basis for the national project for the conservation of this unique Chinese local population.

Failure of Phenotypic Markers to Accurately Identify Black Bass Species and Associated Hybrids in the Mobile River Basin, Alabama

AbstractHybridization among the black basses Micropterus spp. occurs due to weak postzygotic reproductive barriers and anthropogenic factors, such as habitat alteration. Introduction of previously allopatric species can also result in hybrid swarms and, in some cases, extirpation of native species. Introgressive hybridization is a major conservation concern for the more range‐restricted black basses, which underscores the need for accurate identification of hybrids that often have cryptic phenotypes. To that end, we collected 1,723 fish from four river systems in the Mobile River basin, Alabama, to compare phenotypic identification in the field based on morphology with genotype determined from single‐nucleotide polymorphism analysis using diagnostic markers for black basses. Results indicated that phenotypic identification among these cryptic hybrids was only 11% accurate. Only 4% of the fish collected were identified as hybrids in the field, whereas genotype analysis classified 22% of the fish as hybrids. The majority of those misidentified in the field were hybrids between Alabama Bass M. henshalli and Redeye Bass M. coosae or between those species and another black bass species. Hybrid individuals composed 5–38% of the total number of fish collected from the four river systems, but 28–68% were misidentified in each river system. These results underscore the need for genetic tools to augment classic field surveys of the black basses, as cryptic hybridization may lead to errant management decisions based on inaccurate species distribution assessments.