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Biodiversity is under increasing pressure from environmental change, although the scope and severity of these impacts remain incompletely understood. For many species, a lack of information about population‐specific responses to future environmental change hinders the development of effective conservation strategies. Here, we use an East African reed frog species complex as a model to explore spatial variation in vulnerability to future environmental changes. Our sampling across two threatened biodiversity hotspots spans the entire geographic range of H. mitchelli and H. rubrovermiculatus in Kenya, Tanzania, and Malawi. Using genome‐wide (ddRAD‐seq) data, we evaluate levels of neutral genetic diversity and local adaptations across sampling localities. We then integrate spatial approaches (genomic offset, modeled dispersal barriers, and Species Distribution Models) to predict how populations may respond differently to future environmental changes, such as climate warming and predicted land use changes. Based on our analyses, we characterize population structure and identify region‐specific management needs that reflect genetic variation among populations and the uneven impacts of predicted change across the landscape. Peripheral populations are most vulnerable to future environmental changes due to (i) low levels of neutral genetic diversity (Malawi and Pare mountains in Tanzania), (ii) putative signals of local adaptation to wetter conditions with predicted disruptions to genotype–environment associations (i.e., high genomic offset, Kenya and Northern Tanzania), and (iii) the projected contraction of suitable habitat, which is a pervasive threat to the species complex in general. Populations in Northern, Central, and Southern Tanzania show the lowest vulnerability to environmental change and may serve as important reservoirs of genetic diversity for potential future genetic rescue initiatives. Our study highlights how populations across different parts of species ranges may be unevenly affected by future global changes and provides a framework to predict which conservation actions may help mitigate these effects.

Background There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.1), type 2 EBNA2 shares only ~ 50% amino acid identity with type 1 and thus may have distinct binding partners, human genome binding locations, and functions. Results In this study, we examined genome-wide EBNA2 binding in EBV-1 and EBV-2 transformed human B cells to identify shared and unique EBNA2 interactions with the human genome, revealing thousands of type-specific EBNA2 ChIP-seq peaks. Computational predictions based on hTF motifs and subsequent ChIP-seq experiments revealed that both type 1 and 2 EBNA2 co-occupy the genome with SPI1 and AP-1 (BATF and JUNB) hTFs. However, type 1 EBNA2 showed preferential co-occupancy with EBF1, and type 2 EBNA2 preferred RBPJ. These differences in hTF co-occupancy revealed possible mechanisms underlying type-specific gene expression of known EBNA2 human target genes: MYC (shared), CXCR7 (type 1 specific), and CD21 (type 2 specific). Both type 1 and 2 EBNA2 binding events were enriched at systemic lupus erythematosus (SLE) and multiple sclerosis (MS) risk loci, while primary biliary cholangitis (PBC) risk loci were specifically enriched for type 2 peaks. Conclusions This study reveals extensive type-specific EBNA2 interactions with the human genome, possible differences in EBNA2 interaction partners, and a possible new role for type 2 EBNA2 in autoimmune disorders. Our results highlight the importance of considering EBV type in the control of human gene expression and disease-related investigations.

Background Peripatric speciation and peripheral isolation have uncertain importance in species accumulation, and are largely overshadowed by assumed dominance of allopatric modes of speciation. Understanding the role of different speciation mechanisms within biodiversity hotspots is central to understanding the generation of biological diversity. Here, we use a phylogeographic analysis of the spiny-throated reed frogs and examine sister pairings with unbalanced current distributional ranges for characteristics of peripatric speciation. We further investigate whether forest/grassland mosaic adapted species are more likely created through peripatric speciation due to instability of this habitat type. Results We reconstructed a multi-locus molecular phylogeny of spiny-throated reed frogs which we then combined with comparative morphologic data to delimit species and analyze historical demographic change; identifying three new species. Three potential peripatric speciation events were identified along with one case of allopatric speciation. Peripatric speciation is supported through uneven potential and realized distributions and uneven population size estimates based on field collections. An associated climate shift was observed in most potentially peripatric splits. Morphological variation was highest in sexually dimorphic traits such as body size and gular shape, but this variation was not limited to peripatric species pairs as hypothesized. The potentially allopatric species pair showed no niche shifts and equivalent effective population sizes, ruling out peripatry in that speciation event. Two major ecological niche shifts were recovered within this radiation, possibly as adaptations to occupy areas of grassland that became more prevalent in the last 5 million years. Restricted and fluctuating grassland mosaics within forests might promote peripatric speciation in the Eastern Arc Biodiversity Hotspot (EABH). Conclusions In our case study, peripatric speciation appears to be an important driver of diversity within the EABH biodiversity hotspot, implying it could be a significant speciation mechanism in highly fragmented ecosystems. Extensive peripatric speciation in this montane archipelago may explain the abundance of discrete lineages within the limited area of the EABH, as inferred in remote island archipelagos. Future phylogenetic studies incorporating demographic and spatial analyses will clarify the role of peripatric speciation in creating biodiversity hotspots.

Rhynchocyon udzungwensis is a recently described and poorly understood sengi (giant elephant-shrew) endemic to two small montane forests in Southern Tanzania, and surrounded in lower forests by R. cirnei reichardi. In this study, we investigate the molecular genetic relationship between R. udzungwensis and R. c. reichardi, and the possible role that shifting species distributions in response to climate fluctuations may have played in shaping their evolutionary history. Rhynchocyon udzungwensis and R. c. reichardi individuals were sampled from five localities for genetic analyses. Three mitochondrial and two nuclear loci were used to construct species trees for delimitation and to determine whether introgression was detectable either from ancient or ongoing hybridization. All species-tree results show R. udzungwensis and R. c. reichardi as distinct lineages, though mtDNA shows evidence of introgression in some populations. Nuclear loci of each species were monophyletic, implying introgression is exclusively historical. Because we found evidence of introgression, we used distribution data and species distribution modelling for present, glacial, and interglacial climate cycles to predict how shifting species distributions may have facilitated hybridization in some populations. Though interpretations are affected by the limited range of these species, a likely scenario is that the mtDNA introgression found in eastern mid-elevation populations was facilitated by low numbers of R. udzungwensis that expanded into lowland heavily occupied R. c. reichardi areas during interglacial climate cycles. These results imply that relationships within the genus Rhynchocyon may be confounded by porous species boundaries and introgression, even if species are not currently sympatric.

The sub-montane East African Reed Frog, Hyperolius substriatus Ahl, 1931 (Spotted Reed Frog) has a fragmented highland distribution throughout East Africa. Previous studies show extensive mitochondrial divergence between four lineages of African Spotted Reed Frogs that roughly correspond to previously-recognized subspecies. These may have conservation implications if formally described. However, as mitochondrial-based population models only track maternal patterns, further genomic datasets are necessary to assess the distinctness of these lineages in relation to historically recognized morphological subspecies. In this study, we expanded sampling to newly discovered localities and assessed mitochondrial and genomic data to better understand phylogeography and landscape genomics of this species. We found that genomic clades (biparentally inherited) confirm some of the mitochondrial structure (female inherited), but also revealed multiple cases of mitonuclear discordance particularly within the Udzungwa Mountain block, which may have two separate founding events based on peripatric mitochondrial lineages and panmictic genomic signals. Taken together, the three clades within the geographical range of H. substriatus through Tanzania, Malawi, and Mozambique correspond to three previously-identified subspecies and lineages, and have both spatially cohesive and population-specific patterns of geneflow and isolation with neighboring highland locations.

The spiny-throated reed frog species group is a small radiation of Hyperolius frogs from East Africa. Unlike many members of the genus which have relatively wide distributions, these species tend to be small-range endemics found in montane and submontane forests. Recent discovery of a golden-hued frog with the clade-specific traits of spines on their gular discs prompted a morphological and genetic exploration of the distinctness of this new lineage and relationships to other members of the clade. Genetic (mitochondrial and nuclear loci) results resolved many sister-relationships, but deeper nodes in the phylogeny were poorly resolved. A reduced-representation genome-wide Single Nucleotide Polymorphism (SNP) dataset was able to fully resolve the phylogenetic relationships within this clade, placing this new lineage, here named after the mountain range in which is it found– H . ukaguruensis sp. nov., as an early diverging lineage within the group. This new species is distinct from all other spiny-throated reed frogs, necessitating further understanding as a single-mountain endemics vulnerable to habitat loss and potential decline. Morphometric analyses identify clear morphological characteristics that are distinct for the herein described species, most noticeably in that the eyes are significantly smaller than other members of the genus for which we have samples.

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales.

The spiny-throated reed frog species group is a small radiation of Hyperolius frogs from East Africa. Unlike many members of the genus which have relatively wide distributions, these species tend to be small-range endemics found in montane and submontane forests. Recent discovery of a golden-hued frog with the clade-specific traits of spines on their gular discs prompted a morphological and genetic exploration of the distinctness of this new lineage and relationships to other members of the clade. Genetic (mitochondrial and nuclear loci) results resolved many sister-relationships, but deeper nodes in the phylogeny were poorly resolved. A reduced-representation genome-wide Single Nucleotide Polymorphism (SNP) dataset was able to fully resolve the phylogenetic relationships within this clade, placing this new lineage, here named after the mountain range in which is it found-H. ukaguruensis sp. nov., as an early diverging lineage within the group. This new species is distinct from all other spiny-throated reed frogs, necessitating further understanding as a single-mountain endemics vulnerable to habitat loss and potential decline. Morphometric analyses identify clear morphological characteristics that are distinct for the herein described species, most noticeably in that the eyes are significantly smaller than other members of the genus for which we have samples.

Many classic examples of adaptive radiations take place within fragmented systems such as islands or mountains, but the roles of mosaic landscapes and variable gene flow in facilitating species diversification is poorly understood. Here we combine phylogenetic and landscape genetic approaches to understand diversification in Darwin's finches, a model adaptive radiation. We combined sequence data from 14 nuclear introns, mitochondrial markers, and microsatellite variation from 51 populations of all 15 recognized species. Phylogenetic species-trees recovered seven major finch clades: ground, tree, vegetarian, Cocos Island, grey and green warbler finches, and a distinct clade of sharp-beaked ground finches (Geospiza cf. difficilis) basal to all ground and tree finches. The ground and tree finch clades lack species-level phylogenetic structure. Interisland gene flow and interspecies introgression vary geographically in predictable ways. First, several species exhibit concordant patterns of population divergence across the channel separating the Galápagos platform islands from the separate volcanic province of northern islands. Second, peripheral islands have more admixed populations while central islands maintain more distinct species boundaries. This landscape perspective highlights a likely role for isolation of peripheral populations in initial divergence, and demonstrates that peripheral populations may maintain genetic diversity through outbreeding during the initial stages of speciation.

Darwin's finches represent a dynamic radiation of birds within the Galápagos Archipelago. Unlike classic island radiations dominated by island endemics and intuitive ‘conveyer belt’ colonization with little subsequent dispersal, species of Darwin's finches have populations distributed across many islands and each island contains complex metacommunities of closely related birds. Understanding the role of metacommunity and structured population dynamics in speciation within this heterogeneous island system would provide insights into the roles of fragmentation and dispersal in evolution. In this study, a large multi‐species dataset and a comparative ground finch dataset (two co‐distributed lineages) were used to show how landscape features influence patterns of gene flow across the archipelago. Factors expected to regulate migration including distance and movement from large, central islands to small, peripheral islands were rejected in the multi‐species dataset. Instead, the harsh northeast islands contributed individuals to the larger central islands. Successful immigration relies on three factors: arriving, surviving and reproducing, thus the dispersal towards the central islands may be either be due to more migrants orienting towards these land masses due to their large size and high elevation, or may reflect a higher likelihood of survival and successful reproduction due to the larger diversity of habitats and more environmentally stable ecosystems that these islands possess. Further, the overall directionality of migration was south‐southwest against the dominant winds and currents. In comparing dispersal between the common cactus finch and medium ground finch, both species had similar migration rates but the cactus finch had approximately half the numbers of migrants due to lower effective populations sizes. Significant population structure in the cactus finch indicates potential for further speciation, while the medium ground finch maintains cohesive gene flow across islands. These patterns shed light on the macroevolutionary patterns that drive diversification and speciation within a radiation of highly‐volant taxa.