Allopatric Research Articles

BIOGEOGRAPHIC PATTERNS OF COLOMBIAN FROGS AND TOADS

Using the data provided in Ruiz-Carranza et al. (1996) the distributions of the 540 species of frogs and toads are partitioned among ten ecogeographic units of Colombia defined on the basis of precipitation and elevation. Sorne lowlands areas (Pacific lowlands, Amazonia) exhibit high diversity (85-94 species) but lowlands areas in general are impoverished (30-52 species), especially when contrasted with upland areas. The three Andean cordilleras harbor between 87 and 121 species of frogs and toads, demonstrating that the biodiversity of Colombia resides primarily in its montane components, not in its lowland rainforests. When biological endemicity is separated from political endemicity, five areas of high endemicity remain (the three Andean cordilleras, the Sierra Nevada de Santa Marta, and the Pacific lowlands). We endeavor to explain this description by recourse to cladistic analyses of several groups of leptodactylid frogs where we find that the general pattem of diversification is by meaos of horizontal diversification (allopatric speciation) with a minor contribution from vertical diversification.

Whole genome resequencing reveals the evolutionary history and geographic isolation of the eastern Asian Hickory (Carya)

Societal Impact StatementUnraveling the genetic intricacies and evolutionary history of Asian Hickories through advanced genome sequencing gives valuable insights into their ecological adaptations. Understanding the impact of historical dynamics, climate fluctuations, and geographical barriers on Asian hickories not only contributes to scientific knowledge but also empowers policymakers with evidence‐based decisions and guides conservationists in their efforts to protect vulnerable species. The identification of potential habitats, especially for the endangered Carya kweichowensis, offers a promising avenue for targeted conservation efforts, aligning with global initiatives to preserve Earth's precious biodiversity, but also ensures the conservation of a vital genetic reservoir for nut‐bearing economic tree species.SummaryBiogeographic characteristics of disjunct distribution play a vital role in plant geography and the endangered mechanism. The whole genome resequencing provides an opportunity to study the genetic relationship, population diffusion, and floristic evolution of disjunctive‐distribution flora. Based on the SNPs (single nucleotide polymorphisms) data generated by the whole genome deep resequencing of five EA (Eastern Asian) Carya species, we constructed the phylogenetic tree, genetic structure, and species distribution modeling to clarify the phylogenetic relationships and to predict the potential distribution area of EA Carya. Phylogenetic analysis of Carya revealed two distinct clades, separating EA Carya from NA (North America) Carya. C. kweichowensis, an endangered species, showed the lowest nucleotide diversity and the earliest divergence among studied EA Carya species. Species distribution modeling predicted suitable habitats for five EA Carya species, revealing the potential distribution of endangered C. kweichowensis. Importantly, minimal spatial overlap was observed among distribution regions of EA Carya species during different time periods. The uneven regional distribution of EA Carya is believed to be a consequence of Quaternary climate fluctuations, mountain barriers hindering species dispersal, and the limited cold tolerance of these trees. EA Carya highlights the significant role of climate and geological changes in their regional distribution and migration routes in Asia. Furthermore, the discovery of potential habitats offers a promising avenue for the conservation of C. kweichowensis.

Panmixia and local endemism: a revision of the Eubranchus rupium species complex with a description of new species.

Species of the genus Eubranchus Forbes, 1838 (Mollusca: Gastropoda: Nudibranchia) are common faunistic elements of boreal benthic ecosystems, associated with hydroid communities. Recent studies have suggested that the widely distributed trans-Arctic E. rupium (Møller, 1842) constitutes a complex of at least three candidate species, but the detailed taxonomy of the complex remains unresolved. The purpose of the present paper is to conduct an integrative taxonomic study including molecular genetic methods (a phylogenetic analysis using COI , 16S rRNA and histone H3 with application of species delimitation methods) and morphological study (light and scanning electron microscopy) of E. rupium and closely related species. The specific aims of this study were to establish the species boundaries, morphological variability, and the phylogeographic structure within this group. The phylogeographic analysis included a TCS -based network analysis, an analysis of molecular variance (AMOVA), divergence time estimations, and ancestral area reconstructions. We demonstrate that specimens initially identified as E. rupium included three distinctive species: the nominal E. rupium with an amphiboreal range, the new species Eubranchus novik sp. nov. from the Sea of Japan, for which a taxonomic description is provided in this paper, and Eubranchus sp. from the northern Kuril Islands, which requires the collection and study of additional material for formal description. Our results confirm the amphiboreal distribution of E. rupium , as no geographic structure was found across Pacific, Arctic and Atlantic populations, and the results of the AMOVA analysis showed no differences between groups of samples from different geographic regions. The divergence of the 'Eubrancus rupium species complex' is estimated from the late Miocene or the Miocene-Pliocene boundary to the late Pliocene. It is hypothesised that the most probable ancestral region for the Eubranchus rupium species complex is the north-western Pacific, and the subsequent speciation likely occurred due to dispersal followed by allopatric speciation. ZooBank: urn:lsid:zoobank.org:pub:228E0C46-0BF7-4DDD-9C00-67B50E298D65.

De-novo assembly of a reference genome for a critically threatened Aotearoa New Zealand tree species, Syzygium maire (Myrtaceae)

Aotearoa New Zealand’s swamp forests have experienced significant habitat loss in fewer than two hundred years. Many of the country’s tree species are endemic with sparse to no genetic information available to underpin conservation strategies. Syzygium maire, Aotearoa’s only endemic Syzygium species, is a culturally and ecologically important component of swamp forest habitats. Unfortunately, populations of S. maire have been greatly reduced, heavily fragmented and are susceptible to the emergent pathogen Austropuccinia psidii (myrtle rust), posing eminent danger of a further decline of the species. We sought to develop genomic resources to inform conservation management of S. maire. To this end, we used long read, high accuracy sequencing technology to produce a highly complete reference quality genome for S. maire. The genome sequence was named ‘Ngā Hua o te Ia Whenua’ by the local Māori tribe where the tree used for genome sequencing grows. We assess whether genome-level divergence with other Myrtaceae may have followed geographic isolation of the species. We detect conservation of large scale synteny between three Syzygium species and Eucalyptus grandis, providing support for the stability of Syzygium genomes across evolutionary time. We annotate genes implicated in fungal pathogen defence, identifying several hundred putative NLR genes, including putative homologs of previously identified Austropuccinia psidii resistance genes. Finally, we evaluate the genetic relationships of individuals of a small, isolated population of trees. We find evidence of high levels of kinship and inbreeding within small and isolated S. maire populations, informing local-scale conservation strategies for the species. Our findings enable practical conservation actions and provide resources for larger scale studies of S. maire and other Syzygium species in the future.

Genetic polymorphisms of common sandflies in selected areas of Henan Province based on DNA barcoding

To characterize the species of common sandflies in Henan Province using DNA barcoding with cytochrome c oxidase subunit I (COI) gene as the molecular marker, and to analyze the genetic polymorphisms of sandflies, so as to provide insights into visceral leishmaniasis prevention and control in Henan Province. Sandfly specimens were sampled from 13 sandflies surveillance sites from 2021 to 2023 in Anyang City, Zhengzhou, Luoyang and Xuchang cities (Zhengzhou-Luoyang-Xuchang areas) where visceral leishmaniasis cases were reported and in Jiaozuo and Xinxiang cities (Jiaozuo-Xinxiang areas) without visceral leishmaniasis cases reported. Genomic DNA was extracted from a single sandfly, and COI gene was amplified. The amplification product was subjected to bidirectional sequencing. Following sequence assembly, the species of sandflies was characterized through sequence alignment using the BLAST tool. The intra-specific and inter-specific genetic distances of sandflies were estimated among different areas using the software Mega 11, and phylogenetic trees were created. The polymorphisms of nucleotide sequences in the sandflies COI gene were estimated using the software DnaSP. The fixation index (FST) of different geographical isolates of sandflies was calculated using the Arlequin software, and the gene flow value (Nm) was used to measure the gene flow in the sandflies populations. In addition, the population genetic structure of different geographical populations of Phlebotomus chinensis was analyzed using the STRUCTURE software. A total of 978 sandflies were collected from 13 sandflies surveillance sites in Zhengzhou-Luoyang-Xuchang areas, Jiaozuo-Xinxiang areas and Anyang City of Henan Province from 2021 to 2023, and 475 sandflies were randomly sampled for subsequent detections. A total of 304 Ph. chinensis, 162 Se. squamirostris and 9 Se. bailyi were identified based on molecular biological detection of the COI gene, and Se. bailyi was reported for the first time in Henan Province. The intraspecific genetic distances of sandflies were 0.000 to 0.040, and the inter-specific genetic distances ranged from 0.133 to 0.161. Phylogenetic analysis revealed that each of the three sandfly species was clustered into a clade. The genetic polymorphisms of Ph. chinensis populations varied among different areas, with the highest haplotype diversity (0.966 ± 0.007) and the greatest nucleotide diversity (0.011) in Zhengzhou-Luoyang-Xuchang areas, and the lowest haplotype diversity (0.720 ± 0.091) and nucleotide diversity (0.004) in Anyang City. The dominant haplotype of Ph. chinensis populations was Pch_Hap_2 in Anyang City and Jiaozuo-Xinxiang areas, with moderate genetic differentiation (0.05 < FST < 0.15) and frequent gene exchange (Nm value > 1) between Ph. chinensis populations sampled from Anyang City, and Jiaozuo-Xinxiang areas. Population genetic structure analysis showed that the dominant component of Ph. chinensis populations was K5 in Anyang City and Jiaozuo-Xinxiang areas. No obvious dominant haplotype was observed in Ph. chinensis populations sampled from Zhengzhou-Luoyang-Xuchang areas, which had very high genetic differentiation (FST > 0.25) and little gene exchange (Nm value < 1) with Ph. chinensis populations from Anyang City, and Jiaozuo-Xinxiang areas, with K3 as the dominant component. In addition, there was no significant difference in the genetic polymorphism level among Se. squamirostris populations from the three areas. There are Ph. chinensis, Se. squamirostris and Se. bailyi in Henan Province, and S. bailyi is recorded for the first time in Henan Province by molecular biological assays. There are different levels of genetic differentiation and gene exchange among P. chinensis populations in different areas of Henan Province.

Hybridization in the Anthropocene - how pollution and climate change disrupt mate selection in freshwater fish.

Chemical pollutants and/or climate change have the potential to break down reproductive barriers between species and facilitate hybridization. Hybrid zones may arise in response to environmental gradients and secondary contact between formerly allopatric populations, or due to the introduction of non-native species. In freshwater ecosystems, field observations indicate that changes in water quality and chemistry, due to pollution and climate change, are correlated with an increased frequency of hybridization. Physical and chemical disturbances of water quality can alter the sensory environment, thereby affecting chemical and visual communication among fish. Moreover, multiple chemical compounds (e.g. pharmaceuticals, metals, pesticides, and industrial contaminants) may impair fish physiology, potentially affecting phenotypic traits relevant for mate selection (e.g. pheromone production, courtship, and coloration). Although warming waters have led to documented range shifts, and chemical pollution is ubiquitous in freshwater ecosystems, few studies have tested hypotheses about how these stressors may facilitate hybridization and what this means for biodiversity and species conservation. Through a systematic literature review across disciplines (i.e. ecotoxicology and evolutionary biology), we evaluate the biological interactions, toxic mechanisms, and roles of physical and chemical environmental stressors (i.e. chemical pollution and climate change) in disrupting mate preferences and inducing interspecific hybridization in freshwater fish. Our study indicates that climate change-driven changes in water quality and chemical pollution may impact visual and chemical communication crucial for mate choice and thus could facilitate hybridization among fishes in freshwater ecosystems. To inform future studies and conservation management, we emphasize the importance of further research to identify the chemical and physical stressors affecting mate choice, understand the mechanisms behind these interactions, determine the concentrations at which they occur, and assess their impact on individuals, populations, species, and biological diversity in the Anthropocene.

Phenotypic covariation predicts diversification in an adaptive radiation of pupfishes.

Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.

Vicariant speciation resulting from biogeographic barriers in the Australian tropics: The case of the red-cheeked dunnart (Sminthopsis virginiae).

Global biodiversity loss continues unabated, and in Australia, the rate of recent mammal extinctions is among the worst in the world. Meanwhile, the diversity among and within many endemic mammal species remains undescribed. This information is crucial to delineate species boundaries and thus inform decision-making for conservation. Sminthopsis virginiae (the red-cheeked dunnart) is a small, dasyurid marsupial found in four disjunct populations around the northern coast of Australia and New Guinea. There are three currently recognized subspecies, each occupying a distinct geographic location. Sminthopsis v. virginiae occurs in Queensland, S. v. rufigenis is distributed across New Guinea and the Aru Islands, and S. v. nitela has populations in the Top End of the Northern Territory and the Kimberley region of Western Australia. Previous molecular work has suggested the current subspecies definitions are not aligned with DNA sequence data, though the sampling was limited. We undertook a comprehensive genetic and morphological review of S. virginiae to clarify relationships within the species. This included mitochondrial (CR, 12S, and cytb) and nuclear (omega-globin, IRBP, and bfib7) loci, and morphometric analysis of skulls and whole wet-preserved specimens held in museums. Maximum Likelihood and Bayesian phylogenetic analyses resolved samples into two distinct clades, demarcated by the Gulf of Carpentaria in Australia's north. Sminthopsis. v. nitela was consistently separated from S. v. virginiae and S. v. rufigenis, based on the overall body and skull size and craniodental features, while S. v. virginiae and S. v. rufigenis were more difficult to distinguish from each other. Thus, we redescribed S. virginiae, recognizing two species, S. nitela (raised from subspecies) and S. virginiae (now comprising the subspecies S. v. virginiae and S. v. rufigenis). This study highlights the importance of recognizing cryptic mammal fauna to help address the gap in our knowledge about diagnosing diversity during a time of conservation crisis.

Contemporary interventions tackling complex issues: Exploring pathways from online mental health forums to personal resilience

This paper identifies and examines pathways in which online mental health forums assist in building personal resilience and address the mental ill-health of rural residents. We use a resilience theory to develop a Theoretical Resilience Framework and apply it to empirical qualitative data deriving from three of Australia's online mental health forums as well as interviews with forum users. Using thematic analysis and an abductive approach to generating new knowledge, we develop a logic model illustrating links between factors influencing personal resilience, factors acting upon resilience, and intermediate and long-term outcomes that online mental health forums have on their users. Our study demonstrates that online forums can provide ongoing and timely services to those in need, and they support the adaptive capacity of individuals to cope with stressors and a variety of challenges they face. Embedded in a rural setting, the paper adds understanding to the role of technology and online forums in addressing geographical isolation. Ultimately, our work helps to develop new sources of knowledge about rural resilience and supporting mental health service provision in rural places.

Recent secondary contact, genome-wide admixture, and asymmetric introgression of neo-sex chromosomes between two Pacific island bird species.

Secondary contact between closely related taxa represents a "moment of truth" for speciation-an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family-Myzomela cardinalis and Myzomela tristrami-carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome.

Mitochondrial Genomes of Streptopelia decaocto: Insights into Columbidae Phylogeny.

In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management.

Geographical and ecological allopatry effects on niche change in two sister species pairs of hummingbirds in western North America

Here, we explored how variations in the allopatric speciation scenario, specifically ecological vs. vicariant allopatry, relate to climatic niche change in sister species. We selected two sister species pairs of North American hummingbirds (Calypte anna, C. costae, Basilinna leucotis, B. xantusii) that diverged 2.5 and 3.6 million years ago, under ecological (arid climate tendency during Pliocene) and vicariant (Baja California peninsula separation) allopatric processes, respectively. We constructed the climatic niche of each species using occurrence records and estimated the distance, similarity, and unique fraction of climatic niche between sister species. Calypte species showed moderate niche divergence (Euclidean distance between centroids = 1.94, Sørensen index of similarity = 0.080, unique fraction of hypervolume in C. costae = 0.57, and C. anna = 0.95). However, contrary to expectations, Basilinna species, which diverged under a vicariant scenario, displayed clear niche divergence (Euclidean distance between centroids = 3.78, Sørensen index of similarity = 0.0001, and unique fraction of hypervolume in B. xantusii = 0.98, and B. leucotis = 0.99). We explained dissimilarity in climatic niches between Basilinna species by the ecological divergence between habitats of disjunct populations, which would have also been associated with increased aridity during the Pliocene.

Static output feedback LFC for semi‐Markov type interconnected multi‐area power systems: A non‐fragile PI strategy

AbstractThis article addresses the static output feedback load frequency control (LFC) problem for semi‐Markov type interconnected multi‐area power systems (IMAPSs) through non‐fragile proportional‐integral (PI) strategy. Primarily, by roundly exploiting the dynamical properties and considering random mutations of the IMAPSs, the semi‐Markov jump process (MJP) is elaborately scheduled for establishing the dynamical model with precision. Subsequently, on account of the characteristic of geographical isolation, a memory‐like sampled‐data LFC mechanism considering time‐varying transmission delay for the semi‐Markov jump IMPASs is formulated accordingly. Additionally, the non‐fragile issue is explored for the PI controller gain fluctuations to meet the actual operation scenario. After that, a mode‐dependent two‐side polynomial‐type looped Lyapunov functional is constructed for enhancing flexibility. Then, in virtue of the stochastic analysis technique, some relaxed conditions guaranteeing stochastic stability with prescribed performance are thereby derived in the shape of linear matrix inequalities (LMIs). Ultimately, a numerical example is carried out to validate the efficacy of the developed control methodology.

Effects of isolation on invertebrate biodiversity among the bladderwrack Fucus vesiculosus

Geographic isolation is a factor that is known to affect species composition and diversity in marine systems. In this study, we tested the effects of geographic isolation on invertebrate fauna living among the belt-forming foundation species Fucus vesiculosus in the northern Baltic Sea. Sampling was carried out on reefs with varying levels of isolation (0.5, 1 and 2 km) in July 2021 in the Åland islands (between 59.96°N 20.24°E and 59.75°N 20.84°E). The total number of taxa, abundance, Shannon-Wiener index, Pielou’s evenness and biomass were calculated and the effects of isolation were tested using generalised linear models. Multivariate methods were used to analyse differences in the invertebrate community composition. Although the number of taxa and Shannon´s diversity index did not vary along the isolation gradient, the total abundance of fauna decreased with increasing isolation. In addition, some taxa-specific patterns were observed, e.g. the abundance of insect larvae decreased with isolation while isopods were more numerous in the most isolated locations. As diversity and the number of taxa were similar regardless of isolation, shallow Fucus vesiculosus belts likely act as important biodiversity refuges and potential stepping-stones for invertebrates in remote outer archipelago areas. In a changing climate, these kinds of refuges aiding species dispersal are likely to be even more important, and should be considered in conservation planning.

Asian Mus musculus: subspecies divergence, genetic diversity, and historical biogeography

Abstract The House Mouse, Mus musculus, is a model organism that has greatly contributed to evolutionary research. Despite its significance, there remain gaps in our understanding of its phylogeography and population genetic structure in Asian regions. This comprehensive study aims to elucidate the evolutionary history, genetic diversity, and distribution patterns of M. musculus. A diverse data set of 281 M. musculus samples was collected from across Asia, covering 101 localities in 19 countries. Phylogenetic analysis using Cytochrome b and D-Loop region unveiled well-supported lineages. These lineages correspond to: M. m. musculus, M. m. domesticus, M. m. castaneus, and M. m. bactrianus. Also, validity of M. m. bactrianus was questioned. The analysis suggests a monophyletic origin of these subspecies approximately 0.59 million years ago (Mya), followed by 2 main lineages—one consisting of M. m. domesticus (~0.59 Mya) and the other comprising M. m. castaneus, M. m. bactrianus, and M. m. musculus (~0.56 Mya). Genetic diversity varied among subspecies, with M. m. domesticus exhibiting the highest diversity due to its extensive global distribution and M. m. bactrianus exhibiting the lowest diversity due to restriction in southwest Asia. Pairwise genetic distances and Fst values confirmed significant genetic differentiation among the subspecies, underlining their historical isolation. Additionally, a Mantel test indicated that geographical distance played a pivotal role in shaping genetic differentiation. Demographic analysis revealed evidence of population expansions in M. m. domesticus, M. m. musculus, and M. m. castaneus, while M. m. bactrianus showed characteristics of neutral selection and genetic drift. Species distribution modeling, assessing both Current Conditions and the Last Glacial Maximum, indicated habitat shifts and losses during glacial periods, particularly in the eastern and northern regions of Asia. However, each subspecies displayed unique responses to climatic changes, reflecting their distinct ecological adaptations. Historical biogeography analysis pointed to complex origins and a network of dispersal and vicariance events that led to the contemporary distribution of subspecies. Deserts and xeric shrublands emerged as critical areas for diversification and speciation. This study contributes to our understanding of the phylogeography and population genetics of M. musculus in Asia, highlighting the significance of geographical factors and climatic fluctuations in shaping its evolutionary history and genetic diversity.

The Great Rift Valley is a more pronounced biogeographic barrier than the Blue Nile Valley for six Ethiopian Highland passerines in the eastern Afromontane biodiversity hotspot

ABSTRACT The Ethiopian Highlands are divided by lowland biogeographic barriers, including the Blue Nile Valley (BNV) and Great Rift Valley (GRV). We show that the GRV is a more pronounced phylogeographic break than the BNV for 6 focal passerines. Previous research suggests that the BNV greatly shaped phylogeographic patterns in relatively sedentary montane taxa such as frogs and rodents, whereas the GRV shaped phylogeographic patterns in volant taxa such as birds. However, no previous research simultaneously compares the impact of each valley on phylogeographic patterns in birds, and as these barriers vary in geographic extent and topography, the relative extent of their effects on gene flow is unclear. Using whole-genome resequencing, we quantified genetic variation in 6 montane forest passerines in the Ethiopian Highlands and found that their phylogeographic patterns varied, with general trends distinct from those of taxa that were previously studied across the same barriers. Genetic variation was assessed by estimating genome-wide genetic diversity (HO), demographic history, phylogeographic structure, and phylogeographic concordance among taxa. Population pairs flanking the GRV showed higher FST and more distinct population clusters in principal component analysis than those separated by the BNV. HO was broadly consistent across populations, excluding noticeable reductions in 2 populations (1 population each in 2 separate species). The overall phylogenetic signature and concordance across study taxa supported populations separated by the BNV as sister and populations southeast of the GRV as most distinct.

Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates

Plasmodium vivax, traditionally overlooked has experienced a notable increase in cases in East Africa. This study investigated the geographical origin and genetic diversity of P. vivax in Sudan using 14 microsatellite markers. A total of 113 clinical P. vivax samples were collected from two different ecogeographical zones, New Halfa and Khartoum, in Sudan. Additionally, 841 geographical samples from the database were incorporated for a global genetic analysis to discern genetic relationships among P. vivax isolates on regional and worldwide scales. On the regional scale, our findings revealed 91 unique and 8 shared haplotypes among the Sudan samples, showcasing a remarkable genetic diversity compared to other geographical isolates and supporting the hypothesis that P. vivax originated from Africa. On a global scale, distinct genetic clustering of P. vivax isolates from Africa, South America, and Asia (including Papua New Guinea and Solomon Island) was observed, with limited admixture among the three clusters. Principal component analysis emphasized the substantial contribution of African isolates to the observed global genetic variation. The Sudanese populations displayed extensive genetic diversity, marked by significant multi-locus linkage disequilibrium, suggesting an ancestral source of P. vivax variation globally and frequent recombination among the isolates. Notably, the East African P. vivax exhibited similarity with some Asian isolates, indicating potential recent introductions. Overall, our results underscore the effectiveness of utilizing microsatellite markers for implementing robust control measures, given their ability to capture extensive genetic diversity and linkage disequilibrium patterns.

The Social and Spatial Mismatch of Women Returning From Jail Contexts: An Intersectional Mixed-Methods Analysis

Seminal work on spatial mismatch has shown that geographic isolation from job-rich areas resulted in unemployment for low-income women of color. Though social capital is a critical component of the job search for justice-involved individuals, justice-involved women of color may have unique barriers to accessing social capital related to spatial mismatch. This concurrent mixed-methods study addresses the interconnections of race, economic opportunity, social capital, and employment for a sample of 56 women returning from jail contexts. Results reveal racialized differences in the mobilization of social capital to address the spatial mismatch problem, identifying a source of inequity for women of color leaving carceral settings.

Genome analysis reveals three distinct lineages of the cosmopolitan white shark

The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans,1,2 is classified as Vulnerable globally3-with global abundance having dropped to 63% of 1970s estimates,4-and as Critically Endangered in Europe.5 Identification of evolutionary significant units and their management are crucial for conservation,6 especially as the white shark is facing various but often region-specific anthropogenic threats.7,8,9,10,11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers.12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites,13,14,15,16,17,18,19 which can be plagued by various genotyping artefacts and thus require cautious interpretation.20 Sequencing and computational advances are finally allowing genomes21,22,23 to be leveraged into population studies,24,25,26,27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC)28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range,12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic.

Waves of Colonization and Gene Flow in a Great Speciator.

Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones-where reproductive isolation can further develop via reinforcement or phenotypic displacement-or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr's foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.