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This revision is based on sampling efforts over the past three decades in the southern Appalachian Mountains which have provided Nesticus (Araneae, Nesticidae) collections of approximately 2100 adult specimens from more than 475 unique collecting events. Using a "morphology first" framework we examined recently collected specimens plus museum material to formulate morphology-based species hypotheses for putative new taxa (discovery phase). Using sequence capture of nuclear ultraconserved elements (UCEs) we analyzed 801 nuclear loci to validate new (and prior) morphology-based species hypotheses (validation phase) and reconstructed a robust backbone phylogeny including all described and new species. Sanger sequencing and UCE-bycatch were also used to gather mitochondrial data for more than 240 specimens. Based on our integrative taxonomic framework ten new Nesticus species are herein described, including N.binfordaesp. nov., N.bondisp. nov., N.caneisp. nov., N.cherokeensissp. nov., N.dellingerisp. nov., N.dykemanaesp. nov., N.jemisinaesp. nov., N.lowderisp. nov., N.roanensissp. nov., and N.templetonisp. nov. Previously unknown males are also described for N.bishopi Gertsch, 1984, N.crosbyi Gertsch, 1984, and N.silvanus Gertsch, 1984, as well as the previously unknown female for N.mimus Gertsch, 1984. Based on combined evidence N.cooperi Gertsch, 1984 is placed in synonymy with N.reclusus Gertsch, 1984. Overall, the montane radiation of Appalachian Nesticus reveals a general lack of species sympatry and compelling biogeographic patterns. Several regional Nesticus taxa are rare, microendemic habitat specialists that deserve conservation attention and detailed future monitoring as conservation sentinels.

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The process of phenotypic adaptation to the environments is widely recognized. However, comprehensive studies integrating phylogenetic, phenotypic, and ecological approaches to assess this process are scarce. Our study aims to assess whether local adaptation may explain intraspecific differentiation by quantifying multidimensional differences among populations in closely related lucanid species, Platycerus delicatulus and Platycerus kawadai, which are endemic saproxylic beetles in Japan. First, we determined intraspecific analysis units based on nuclear and mitochondrial gene analyses of Platycerus delicatulus and Platycerus kawadai under sympatric and allopatric conditions. Then, we compared differences in morphology and environmental niche between populations (analysis units) within species. We examined the relationship between morphology and environmental niche via geographic distance. P. kawadai was subdivided into the "No introgression" and "Introgression" populations based on mitochondrial COI gene - nuclear ITS region discordance. P. delicatulus was subdivided into "Allopatric" and "Sympatric" populations. Body length differed significantly among the populations of each species. For P. delicatulus, character displacement was suggested. For P. kawadai, the morphological difference was likely caused by geographic distance or genetic divergence rather than environmental differences. The finding showed that the observed mitochondrial-nuclear discordance is likely due to historical mitochondrial introgression following a range of expansion. Our results show that morphological variation among populations of P. delicatulus and P. kawadai reflects an ecological adaptation process based on interspecific interactions, geographic distance, or genetic divergence. Our results will deepen understanding of ecological specialization processes across the distribution and adaptation of species in natural systems.

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Abstract Background: Two biotypes of Aberdeen Angus cattle breed, known as Old Type and New Type, that differ in their origin and beef production are formally recognized. In Colombia, this breed has been commercialized for approximately 80 years. Studies on the origin, kinship and levels of genetic diversity of this breed in Colombian herds are scarce, yet important for planning crossing and management strategies. Objective: To measure the genetic diversity and structure of two Colombian herds of Old Type and New Type biotypes of Aberdeen Angus from Huila and Cundinamarca provinces and assess mitochondrial introgression with other breeds. Methods: A set of ten microsatellites and sequences of the Mitochondrial Control Region were characterized. Estimators of genetic diversity and population differentiation along with tests of population assignment were applied. Results: Nuclear loci were highly polymorphic as shown by the Polymorphic Information Content (0.599) and the Probability of Identity (1.896 10-08). Both populations were highly diverse and clearly differentiated into two groups corresponding to the Old Type and New Type phenotypes. In contrast, mitochondrial data failed to distinguish these two groups and showed extensive admixture. Conclusions: This study optimized a set of ten highly polymorphic nuclear markers that may be used for parentage and population genetic studies of Aberdeen Angus. Genetic differentiation in these loci agreed with phenotypic differences of the Old and New Types. However, mitochondrial data indicated ancestry of multiple European breeds in the origin of Colombian Aberdeen Angus.

Resumen Antecedentes: Dentro de la raza Aberdeen Angus existen dos biotipos conocidos como Old Type y New Type, las cuales difieren en su origen y producción de carne. En Colombia, esta raza se ha venido comercializando desde hace aproximadamente 80 años. No obstante, aún no se han realizado estudios sobre su origen, parentesco y niveles de diversidad genética de esta raza en hatos colombianos, lo cual es importante para planear estrategias de cruce y manejo. Objetivo: Medir la diversidad y estructura genética de dos hatos colombianos de Aberdeen Angus Old Type y New Type de Huila y Cundinamarca y evaluar la introgresión mitocondrial con otras razas. Métodos: Se caracterizó un grupo de diez loci microsatélite y se secuenció la Región Control Mitocondrial. Se aplicaron estimadores de diversidad genética y diferenciación poblacional, junto con pruebas de asignación poblacional. Resultados: Los loci microsatélite fueron altamente polimórficos, tal como lo indicaron el Contenido de Información Polimórfica (0,599) y la Probabilidad de Identidad (1,896 10-08). Las poblaciones evaluadas de Aberdeen Angus en Colombia fueron altamente diversas y se diferenciaron claramente en dos grupos correspondientes a los fenotipos Old Type y New Type. En contraste, los datos mitocondriales no recobraron estos dos grupos y mostraron una amplia mezcla genética. Conclusiones: Este estudio optimizó un grupo de diez marcadores altamente polimórficos que pueden ser usados para estudios de parentesco y genética poblacional de Aberdeen Angus. La diferenciación genética en loci nucleares concordó con las diferencias fenotípicas entre Old y New Types, pero los datos mitocondriales indicaron ancestría de múltiples razas europeas en el origen del Aberdeen Angus colombiano.

Resumo Antecedentes: Dentro da raça Aberdeen Angus há dois biótipos conhecidos como Old Type e New Type, que diferem em sua origem e produção de carne. Na Colômbia, esta raça é comercializada há aproximadamente 80 anos. Entretanto, estudos sobre a origem, o parentesco e os níveis de diversidade genética desta raça em rebanhos colombianos ainda não foram realizados, o que é importante para o planejamento de cruzamentos e estratégias de manejo. Objetivo: Medir a diversidade genética e a estrutura de dois rebanhos colombianos de biótipos de Old Type e New Type de Aberdeen Angus de Huila e Cundinamarca e avaliar a introgressão mitocondrial com outras raças. Métodos: Um grupo de dez loci de microssatélites foi caracterizado e a Região de Controle Mitocondrial foi sequenciada. As estimativas de diversidade genética e diferenciação populacional foram aplicadas, juntamente com testes de designação populacional. Resultados: Os locus microssatélites foram altamente polimórficos, conforme indicado pelo Conteúdo de Infomação Polimórfica (0,599) e Probabilidade de Identidade (1,896 10-08). As populações avaliadas de Aberden Angus na Colômbia eram altamente diversificadas e claramente diferenciadas em dois grupos correspondentes aos fenótipos do Old Type e New Type. Em contraste, os dados mitocondriais não recuperaram esses dois grupos e mostraram um amplo mix genético. Conclusões: Este estudo otimizou um grupo de dez marcadores altamente polimórficos que podem ser usados para estudos genéticos de parentesco e população de Aberdeen Angus. A diferenciação genética nos loci nucleares concordou com as diferenças fenotípicas entre os Old e New Types, mas os dados mitocondriais indicam ancestralidade de várias raças européias na origem do Aberdeen Angus colombiano.

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The golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphisms (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results indicate deeper divergences between Z. atricapilla and Z. leucophrys than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.

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Researchers seeking to generate genomic data for non-model organisms are faced with a number of trade-offs when deciding which method to use. The selection of reduced representation approaches versus whole genome resequencing will ultimately affect the marker density, sequencing depth, and the number of individuals that can multiplexed. These factors can affect researchers' ability to accurately characterize certain genomic features, such as landscapes of divergence-how FST varies across the genomes. To provide insight into the effect of sequencing method on the estimation of divergence landscapes, we applied an identical bioinformatic pipeline to three generations of sequencing data (GBS, ddRAD, and WGS) produced for the same system, the yellow-rumped warbler species complex. We compare divergence landscapes generated using each method for the myrtle warbler (Setophaga coronata coronata) and the Audubon's warbler (S. c. auduboni), and for Audubon's warblers with deeply divergent mtDNA resulting from mitochondrial introgression. We found that most high-FST peaks were not detected in the ddRAD data set, and that while both GBS and WGS were able to identify the presence of large peaks, WGS was superior at a finer scale. Comparing Audubon's warblers with divergent mitochondrial haplotypes, only WGS allowed us to identify small (10-20 kb) regions of elevated differentiation, one of which contained the nuclear-encoded mitochondrial gene NDUFAF3. We calculated the cost per base pair for each method and found it was comparable between GBS and WGS, but significantly higher for ddRAD. These comparisons highlight the advantages of WGS over reduced representation methods when characterizing landscapes of divergence.

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BACKGROUND: In addition to their well characterized role in cellular energy production, new evidence has revealed the involvement of mitochondria in diverse signaling pathways that regulate a broad array of cellular functions. The mitochondrial genome (mtDNA) encodes essential components of the oxidative phosphorylation (OXPHOS) pathway whose expression must be coordinated with the components transcribed from the nuclear genome. Mitochondrial dysfunction is associated with disorders including cancer and neurodegenerative diseases, yet the role of the complex interactions between the mitochondrial and nuclear genomes are poorly understood. RESULTS: Using a Drosophila model in which alternative mtDNAs are present on a common nuclear background, we studied the effects of this altered mitonuclear communication on the transcriptomic response to altered nutrient status. Adult flies with the 'native' and 'disrupted' genotypes were re-fed following brief starvation, with or without exposure to rapamycin, the cognate inhibitor of the nutrient-sensing target of rapamycin (TOR). RNAseq showed that alternative mtDNA genotypes affect the temporal transcriptional response to nutrients in a rapamycin-dependent manner. Pathways most greatly affected were OXPHOS, protein metabolism and fatty acid metabolism. A distinct set of testis-specific genes was also differentially regulated in the experiment. CONCLUSIONS: Many of the differentially expressed genes between alternative mitonuclear genotypes have no direct interaction with mtDNA gene products, suggesting that the mtDNA genotype contributes to retrograde signaling from mitochondria to the nucleus. The interaction of mitochondrial genotype (mtDNA) with rapamycin treatment identifies new links between mitochondria and the nutrient-sensing mTORC1 (mechanistic target of rapamycin complex 1) signaling pathway.

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The Ethiopian highlands represent a remarkable biodiversity 'hot spot' with a very high number of endemic species, even among vertebrates. Ethiopian representatives of a species complex of speckled brush-furred rats (Lophuromys flavopunctatus sensu lato) inhabit highland habitats ranging from low-elevation forests to Afroalpine grasslands. These may serve as a suitable model for understanding evolutionary processes leading to high genetic and ecological diversity in montane biodiversity hot spots. Here, we analyse the most comprehensive genetic data set of this group, comprising 315 specimens (all nine putative Ethiopian Lophuromys taxa sampled across most of their distribution ranges) genotyped at one mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD sequencing. We performed phylogenetic analyses, delimited species and mapped their distribution and estimated divergence time between species (under the species-tree framework) and mitochondrial lineages. We found significant incongruence between mitochondrial and nuclear phylogenies, most probably caused by multiple interspecific introgression events. We discuss alternative scenarios of Ethiopian Lophuromys evolution, from retention of ancestral polymorphism to hybridization upon secondary contact of partially reproductively isolated lineages leading to reticulate evolution. Finally, we use the diversity of the speckled brush-furred rats for the description of the main biogeographic patterns in the fauna of the Ethiopian highlands.

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Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.

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Biogeography and genetic variation of freshwater organisms are influenced not only by current freshwater connections but also by past drainage networks. The Seto Inland Sea is a shallow enclosed sea in Japan, but geological evidence showed that a large freshwater drainage had intermittently appeared in this area between the late Pliocene and Pleistocene. Here, we demonstrated that this paleodrainage greatly affected the genetic variation of the East Asian freshwater snails, Semisulcospira spp. We found that the mtDNA haplotypes originated in the Lake Biwa endemic Semisulcospira species at the upstream side of the paleodrainage were frequently observed in the riverine Semisulcospira species at its downstream side. The genome-wide DNA and morphological analyses consistently showed that there was no clear evidence of nuclear introgression between the Lake Biwa endemics and riverine species. These results suggest that the large paleodrainage had facilitated mitochondrial introgression and had broadly spread the introgressed mtDNA haplotypes to its downstream region around the Seto Inland Sea. Our study highlights the role of paleodrainages in shaping the genetic variation of freshwater organisms.

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Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon.

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In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that generated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual "patterns" of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.

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Microsatellites are widely used as powerful markers in population genetics because of their ability to access recent genetic variation and to resolve subtle population genetic structures. However, their development, especially for non-model organisms with no available genome-wide sequence data has been difficult and time-consuming. Here, a commercial high-throughput sequencing approach (HTS) was used for the very first identification of microsatellite motifs in the genome of Xyela concava and the design of primer pairs flanking those motifs. Sixteen of those primer pairs were selected and implemented successfully to answer questions on the phylogeography and population genetics of X. concava. The markers were characterized in three geographically distinct populations of X. concava and tested for cross-species amplification in two additional Xyela and one Pleroneura species (Xyelidae). All markers showed substantial polymorphism as well as revealing subtle genetic structures among the three genotyped populations. We also analyzed a fragment of the nuclear gene region of sodium/potassium-transporting ATPase subunit alpha (NaK) and a partial mitochondrial gene region coding for cytochrome oxidase subunit I (COI) to demonstrate different genetic resolutions and sex-biased patterns of these markers, and their potential for combined use in future studies on the phylogeography and population genetics of X. concava. Although a limited number of populations was analyzed, we nevertheless obtained new insights on the latter two topics. The microsatellites revealed a generally high gene flow between the populations, but also suggested a deep historical segregation into two genetic lineages. This deep genetic segregation was confirmed by NaK. While the high gene flow was unexpected, because of assumed restricted dispersal ability of X. concava and the discontinuous distribution of the host trees between the populations, the segregation of two lineages is comprehensible and could be explained by different refuge areas of the hosts during glacial times. The COI results showed a discordant strong genetic structure between all populations, which might be explained by the smaller effective population size of the mitochondrial genome. However, given the frequent evidence of a similar nature in recent studies on sawflies, we also consider and discuss mitochondrial introgression on population level as an alternative explanation.

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Genomic introgression through interspecific hybridization has been observed in some species of the freshwater fish family Cobitidae. Within this family, a Cobitis hankugensis-Iksookimia longicorpa diploid-triploid hybrid species complex on the Korean peninsula is unique in displaying hybridogenesis, a unisexual reproduction mode that allows hybrids to mediate the transfer of mitochondrial DNA (but not nuclear DNA) between the two parent species. However, populations of the parental species in the wild have never been examined for the potential effect of introgression on their genomes. To address the genetic consequences of unisexual hybridization on the parental species, we examined genetic structure of the two parental species, C. hankugensis and I. longicorpa, in three independent natural habitats where they coexist with their hybrid complex using DNA sequence data of one mitochondrial gene and three nuclear genes. We found that mitochondrial introgression between the two species was extensive in all the examined localities, while there was no evidence of nuclear introgression across the species boundary. This result indicates that the hybridogenetic individuals mediate mitochondrial introgression from one species to the other, producing mito-nuclear mosaic genomes such as C. hankugensis nuclear genomes associated with I. longicorpa mitochondrial DNA and the reverse. The direction and degree of introgression varied among the three localities, but the underlying mechanisms for this observation proved elusive. Introgression might depend on which species serves as the predominant sperm or ovum donor or the environmental conditions of the localities. The present study suggests that introgressive hybridization between pure C. hankugensis and I. longicorpa species is highly likely where the two species co-occur with hybridogenetic individuals, but the consequence of introgression could be variable due to the history and environmental characteristics of particular populations across the parental species' ranges.

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In this work, we used mtDNA data as a tool to delimit species and we compared the resulting molecular operational taxonomic units (barcode index number, BIN) with morphology-based identifications in the Colombian species of Rhamma Johnson, 1992 exploring the usefulness of DNA barcodes for taxonomy, species identification and delimitation. We obtained cytochrome oxidase I (COI) sequences for 134 morphologically identified specimens, representing 12 species of Rhamma from Colombia. Ten of these species have not been previously barcoded. DNA barcodes suggested the potential for eight additional cryptic species in Colombia but we were readily able to morphologically diagnose just one of these linages as a new species which recently was described in a separate paper as Rhamma dawkinsi Prieto & Lorenc-Brudecka, 2017. The morphological species were separated into three categories: species showing a perfect match between morphological species and BINs (33%, four species); species sharing a BIN completely or partly (single specimens) with another morphological species (42%, five species placed in three BINs); and morphological species splitting up into more than one BIN (25%, three species placed in 10 BINs). The high percentages of incongruence between morphology-based identification and species delineation through BINs, could be explained as a consequence of high rates of introgressive hybridization. However, DNA barcodes can be considered diagnostic even in cases where specimens of a species were assigned to two or more distinct BINs and in species showing a low but constant divergence causing their assignment to a single BIN, which is often the case in young, allopatric species. We retain 10 of the 12 species (83%) to be diagnostic in molecular identification.

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Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island-a habitat that is diminishing and becoming increasingly modified. Although management of this species is increasing, little has been published on their movements and demographics. In this study, both mitochondrial DNA (mtDNA) control region domain I and nuclear single nucleotide polymorphisms (SNPs) were examined to help understand the connectivity and population structure of black-billed gulls across the country and to help inform management decisions. Mitochondrial DNA showed no population structure, with high haplotype and low nucleotide diversity, and analyses highlighted mitochondrial introgression with the closely related red-billed gulls (Larus novaehollandiae scopulinus). Nuclear DNA analyses, however, identified two groups, with Rotorua birds in the North Island being distinct from the rest of New Zealand, and isolation-by-distance evident across the South Island populations. Gene flow primarily occurs between nearby colonies with a stepwise movement across the landscape. The importance from a genetic perspective of the more isolated North Island birds (1.6% of total population) needs to be further evaluated. From our results, we infer that the South Island black-billed gull management should focus on maintaining several populations within each region rather than focusing on single specific colonies or river catchments. Future study is needed to investigate the genetic structure of populations at the northern limit of the species' range, and identify the mechanisms behind, and extent of, the hybridisation between red-billed and black-billed gulls.

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The maternally inherited obligate bacteria Wolbachia is known for infecting the reproductive tissues of a wide range of arthropods and can contribute to phylogenetically discordant patterns between mtDNA and nDNA. In this study, we tested for an association between mito-nuclear discordance in Polytremis and Wolbachia infection. Six of the 17 species of Polytremis were found to be infected with Wolbachia. Overall, 34% (70/204) of Polytremis specimens were Wolbachia positive and three strains of Wolbachia identified using a wsp marker were further characterized as six strains based on MLST markers. Wolbachia acquisition in Polytremis appears to occur mainly through horizontal transmission rather than codivergence based on comparison of the divergence times of Wolbachia and Polytremis species. At the intraspecific level, one of the Wolbachia infections (wNas1) is associated with reduced mtDNA polymorphism in the infected Polytremis population. At the interspecific level, there is one case of mito-nuclear discordance likely caused by introgression of P. fukia mtDNA into P. nascens driven by another Wolbachia strain (wNas3). Based on an absence of infected males, we suspect that one Wolbachia strain (wNas2) affects sex ratio, but the phenotypic effects of the other strains are unclear. These data reveal a dynamic interaction between Polytremis and Wolbachia endosymbionts affecting patterns of mtDNA variation.

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Instantaneous mitochondrial introgression events allow the disentangling of the effects of hybridization from those of allospecific mtDNA. Such process frequently occurred in the fish Chrosomus eos, resulting in cybrid individuals composed of a C. eos nuclear genome but with a C. neogaeus mtDNA. This provides a valuable model to address the fundamental question: How well do introgressed individuals perform in their native environment? We infer where de novo production of cybrids occurred to discriminate native environments from those colonized by cybrids in 25 sites from two regions (West-Qc and East-Qc) in Quebec (Canada). We then compared the relative abundance of wild types and cybrids as a measure integrating both fitness and de novo production of cybrids. According to mtDNA variation, 12 introgression events are required to explain the diversity of cybrids. Five cybrid lineages could not be associated with in situ introgression events. This includes one haplotype carried by 93% of the cybrids expected to have colonized West-Qc. These cybrids also displayed a nearly complete allopatric distribution with wild types. We still inferred de novo production of cybrids at seven sites, that accounted for 70% of the cybrids in East-Qc. Wild-type and cybrid individuals coexist in all East-Qc sites while cybrids were less abundant. Allopatry of cybrids restricted to the postglacial expansion suggests the existence of higher fitness for cybrids in specific conditions, allowing for the colonization of different environments and expanding the species' range. However, allospecific mtDNA does not provide a higher fitness to cybrids in their native environment compared to wild types, making the success of an introgressed lineage uncertain.

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INTRODUCTION: Phylogenetic relationships between different lineages of Trypanosoma cruzi, the agent of Chagas disease, have been controversial for several years. However, recent phylogenetic and phylogenomic analyses clarified the nuclear relationships among such lineages. However, incongruence between nuclear and kinetoplast DNA phylogenies has emerged as a new challenge. This incongruence implies several events of mitochondrial introgression at evolutionary level. However, the mechanism that gave origin to introgressed lineages is unknown. Here, I will review and discuss how maxicircles of the kinetoplast were horizontally and vertically transferred between different lineages of T. cruzi. CONCLUSION: Finally, I will discuss what we know - and what we don't - about the kDNA transference and inheritance in the context of sexual reproduction in this parasite.

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The Ethiopian highlands are the most extensive complex of mountainous habitats in Africa. The presence of the Great Rift Valley (GRV) and the striking elevational ecological gradients inhabited by recently radiated Ethiopian endemics, provide a wide spectrum of model situations for evolutionary studies. The extant species of endemic rodents, often markedly phenotypically differentiated, are expected to possess complex genetic features which evolved asa consequence of the interplay between geomorphology and past climatic changes. In this study, we used the largest available multi-locus genetic dataset of the murid genus Stenocephalemys (347 specimens from ca 40 localities across the known distributional area of all taxa) to investigate the relative importance of disruptive selection, temporary geographic isolation and introgression in their adaptive radiations in the Pleistocene. We confirmed the four main highly supported mitochondrial (mtDNA) clades that were proposed as four species in a previous pilot study: S. albipes is a sister species of S. griseicauda (both lineages are present on both sides of the GRV), while the second clade is formed by two Afro-alpine species, S. albocaudata (east of GRV) and the undescribed Stenocephalemys sp. A (west of GRV). There is a clear elevational gradient in the distribution of the Stenocephalemys taxa with two to three species present at different elevations of the same mountain range. Surprisingly, the nuclear species tree corresponded only a little to the mtDNA tree. Multispecies coalescent models based on six nuclear markers revealed the presence of six separate gene pools (i.e. candidate species), with different topology. Phylogenetic analysis, together with the geographic distribution of the genetic groups, suggests a complex reticulate evolution. We propose a scenario that involves (besides classical allopatric speciation) two cases of disruptive selection along the elevational ecological gradient, multiple crosses of GRV in dry and cold periods of the Pleistocene, followed by hybridization and mtDNA introgression on imperfect reproductive barriers. Spatial expansion of the currently most widespread "albipes" mtDNA clade was followed by population fragmentation, lineage sorting and again by hybridization and mtDNA introgression. Comparison of this genetic structure to other Ethiopian endemic taxa highlight the geographical areas of special conservation concern, where more detailed biodiversity studies should be carried out to prevent many endemic taxa from going extinct even before they are recognized.

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The spatial subdivision of species often plays a pivotal role in speciation. Across their entire range, species are rarely panmictic and crucial consequences of spatial subdivision are (1) random genetic drift including historical factors, (2) uniform selection, and (3) divergent selection. Each of these consequences may result in geographic variation and eventually reproductive isolation, but their relative importance in speciation is still unclear. In this study, we used a combination of genetic, morphological, and climatic data to obtain a comprehensive picture of differentiation among three closely related, parapatrically distributed taxa of the land snail genus Theba occurring along the Atlantic coasts of South Morocco and Western Sahara. We conducted Mantel and partial Mantel tests to relate phenotypic and genotypic variation of these species to geography and/or climate. As null hypothesis for an evolutionary scenario, we assumed nonadaptive speciation and expected a pattern of isolation by distance among taxa. Rejection of the null hypothesis would indicate isolation by environment due to adaptation. Generally, genetic drift plays an important role but is rarely considered as sole driver of speciation. It is the combination of drift and selection that predominantly drives speciation. This study, however, provides a potential example, in which nonadaptive speciation, that is, genetic drift, is apparently the main driver of shaping the diversity of Theba in NW Africa. Restriction of gene flow between populations caused by geographic isolation probably has played an important role. Climate oscillations during the Plio- and Pleistocene may have led to repeated ecological changes in NW Africa and disruptions of habitats promoting differentiation by geographic isolation. The inferred evolutionary scenario, however, did not fully explain the incongruence between the AFLP- and mtDNA-tree topologies. This incongruence might indicate past hybridization among the studied Theba forms.