Wiley: Evolutionary Applications: Table of Contents

Whole Genome Analyses of the Endangered Northern Abalone (Haliotis kamtschatkana) Reveal Population Differentiation and a Genomic Signature of a Dramatic Population Decline

Thu, 04 Jun 2026 20:50:21 -0700

ABSTRACT

Despite widespread declines of many wildlife species, the effects of population decline on the genome and the recovery potential of affected species are still poorly understood, especially beyond a few charismatic species. The Northern abalone (or Pinto abalone; Haliotis kamtschatkana) is a marine gastropod mollusk of social, cultural and historical economic importance in the Pacific Northwest of North America that experienced a decline in population density due to commercial harvest, and is currently listed as endangered in Canada under the Species at Risk Act. Previous genetic investigations based on microsatellites and reduced-representation approaches concluded that Northern abalone is panmictic throughout its range, from Alaska to California, and identified high levels of genetic variation with no indication of population decline. Using whole genome resequencing data from Northern abalone sampled across the northern part of the species range, we instead identified both: (1) significant differentiation between two genetic groups, albeit concentrated in few genomic regions, and (2) a strong signature of a dramatic population decline, without genomic evidence of genetic inbreeding. Demographic reconstructions showed a modest signal of recent population expansion, supported by an increasing number of juveniles observed during dive surveys. We also found evidence of historical, rather than current, connectivity throughout the area investigated. These results are important for management decisions and highlight the utility of whole genome data in conservation, especially in species with historically large effective population sizes like the Northern abalone.

In Search of the Lost Brown Trout (Salmo trutta Complex) Using DNA of Ancient and Modern Samples From the Southern Italian Peninsula

Wed, 03 Jun 2026 22:11:55 -0700

ABSTRACT

The current diversity and distribution of species and populations have been shaped by the major climatic oscillations during the Quaternary. The brown trout (Salmo trutta) is a striking example of the strong effect of past climate changes on the evolutionary history of species, in fact, the alternation of glacial/interglacial cycles has led to continuous phenomena of expansion and contraction of its distribution and, consequently, to the evolution of different genetic lineages. This phenomenon was also directly observed by the genetic analysis of S. trutta bones recovered from the archaeological assemblage of a coastal cave named ‘Grotta del Santuario Della Madonna’ (Southern Italy). In this study, additional S. trutta remains were morphologically and genetically analysed, and the genetic results were compared with those of modern samples caught from streams close to the cave locality. The analysis of S. trutta bones confirms that changes in abundance, body size and genetic diversity observed in different stratigraphic sections were determined by environmental changes caused by the Younger Dryas-Holocene transition and by the ability of the species to perform anadromous migration, a behaviour that had disappeared at the end of the Pleistocene in the Mediterranean region. The comparison between ancient and modern samples highlights that extinctions and recolonizations due to past environmental changes affected also the current diversity and distribution of S. trutta in Southern Italian streams. Unfortunately, incorrect management policies related to sport fishing (i.e., stocking with alien brown trout strains) have been eroding millions of years of the trout evolution in just a few centuries.

Vulnerable Juniper Populations Show Adaptive Potential in the Face of a Highly Damaging Invasive Tree Pathogen

Wed, 03 Jun 2026 22:05:56 -0700

ABSTRACT

Invasive tree pathogens pose a significant and increasing threat to natural ecosystems. The outcome of these novel host-pathogen interactions depends largely on the presence and nature of resistance in host populations, which will govern the host's potential to respond through natural selection and adaptation to the new threat. This study assessed the adaptive potential of juniper (Juniperus communis) in the face of the invasive tree pathogen Phytophthora austrocedri through two inoculation experiments: an excised-shoot trial using six different P. austrocedri isolates and a progeny-provenance trial that inoculated whole trees with a single highly virulent isolate. We found evidence for both qualitative and quantitative resistance in juniper populations, with lesion length (quantitative resistance) showing moderate to high heritability and lesion development (qualitative resistance) showing very high heritability. There was a significant genotype-by-genotype interaction between pathogen isolate and host genotype, lowering the estimate of heritability to moderate values when calculated across six different isolates. Finally, we found evidence that P. austrocedri is imposing natural selection on juniper populations, with individuals originating from highly exposed populations having a lower predicted probability of developing a lesion. Based on the results of this study, we recommend that the most effective management strategy for vulnerable UK juniper populations is to promote natural regeneration within populations, making use of existing genetic diversity in resistance within natural populations without risking the introduction of new P. austrocedri genotypes through the planting of nursery-grown juniper.

Predictions From Evolutionary Theory for Urban Environments

Mon, 01 Jun 2026 22:47:30 -0700

ABSTRACT

Urbanization drives rapid and extreme environmental change, profoundly shaping the ecology and evolution of populations. In this Perspective, we call for the integration and development of evolutionary theory and empirical research through collaboration between theoretical and experimental biologists to provide new insights into urban evolutionary ecology. We argue that mathematical models derived from ecological and evolutionary theory can be tailored to provide a powerful framework for generating predictions that can guide empirical research in urban ecology and evolution. At the same time, empirical results can motivate and inform the development and analysis of new theoretical models specific to urban systems. We illustrate how existing evolutionary theory can be harnessed to generate specific predictions of how urbanization can influence evolution. These predictions span the range of urban impacts on all main evolutionary processes, including mutation, gene flow, genetic drift, non-random mating, and selection. We provide a summary of evidence supporting each prediction and outline empirical approaches available to test them. Importantly, these predictions require distinct modeling approaches that can be applied more broadly to better utilize theory for research on urban environments. To facilitate this, we provide an overview of these existing modeling approaches ranging from the application and syntheses of classic model results to the development of novel probabilistic predictions. We advocate for increased integration of theoretical and empirical research through the development of novel models using parameterization specific to urban systems, empirical tests grounded in theoretical models, model-based empirical tests, and model-based data analysis and inference to advance our understanding of evolution in urban environments.

Correction to “Environment and Pollen Diversity Differentially Affect the Gut Microbiomes of Introduced Honeybees and Bumblebees”

Mon, 01 Jun 2026 22:45:03 -0700

Evolutionary Applications, Volume 19, Issue 6, June 2026.

Integrative Genomics Identifies Candidate Genes Underlying Trypanotolerance in Hybrid African Cattle

Sun, 31 May 2026 21:59:33 -0700

ABSTRACT

Integrative genomics combines data from different omics sources to link genotypes and phenotypes with the aim of unravelling biological networks and pathways that undergird complex traits, particularly with respect to disease. In this respect, integrative genomics, leveraging population and functional genomic data, can be employed to understand the evolutionary processes that have shaped adaptation to infectious diseases in domestic cattle. This approach can be particularly informative for African cattle, which exhibit a complex mosaic of genomic ancestry from Bos taurus (taurine) and Bos indicus (indicine) populations. Some African taurine populations have an important evolutionary adaptation known as trypanotolerance, a genetically determined tolerance to infection by trypanosome parasites (Trypanosoma spp.) that cause African animal trypanosomiasis (AAT). AAT is one of the largest constraints to livestock production in sub-Saharan Africa and causes a financial burden of approximately $4.5 billion annually. In this study, we identified putative candidate genes underlying trypanotolerance by integrating local ancestry inference (LAI) from genome-wide SNP data across multiple trypanotolerant and trypanosusceptible hybrid cattle populations with RNA-seq and expression microarray transcriptomic data from multiple tissues collected across time course trypanosome infection experiments. These candidate genes included AGO2, CBL, CNOT1, EDN1, IL1B, NFKB1, RIPK1 and TRAF2. Functional analysis of the gene set outputs from this work highlighted GO terms associated with the immune system (including the major histocompatibility complex—MHC) and cell signalling processes. These results signpost future work to elucidate the cellular networks and pathways that drive trypanotolerance.

Farmed Escapees Threaten MHC Diversity in Wild Atlantic Salmon

Fri, 29 May 2026 22:06:31 -0700

ABSTRACT

Wild Atlantic salmon populations in Norway and elsewhere are experiencing long-term declines driven by reduced marine survival, climate change, impacts from aquaculture, introduction of alien species, and environmental degradation. Understanding how immune diversity is affected by these declines, and thus the ability of Atlantic salmon to combat current and future invading pathogens, is essential for the success of conservation programs such as gene banks. Major histocompatibility complex (MHC) genes, some of the most polymorphic genes known to date, are essential in the host immune defense against invading pathogens. Here we investigate MHC class I and class II diversity in escaped farmed salmon and in eight wild Atlantic salmon populations defined as being at risk. The study demonstrates that rare alleles can be found in single closely related wild populations within a fjord, and collectively, the populations hold a large immune diversity. Moreover, our study found that a broad spatial and temporal collection of escaped farmed salmon had an MHC-diversity at the same level as individual wild salmon populations, while escaped farmed salmon from single escape events had lower diversity. Overall, the wild salmon had considerably higher MHC diversity than escaped farmed salmon. Accumulated genetic introgression of escaped farmed salmon is therefore a major threat as it can compromise the MHC diversity within and among the wild populations. Conservation of MHC diversity in the ongoing gene bank program for Norwegian Atlantic salmon is important, and our observation emphasizes that a large number of founders to the gene bank are needed to conserve the many rare MHC alleles and that genotyping of potential founders may be useful in broodfish selection.

Issue Information

Thu, 28 May 2026 20:57:33 -0700

Evolutionary Applications, Volume 19, Issue 6, June 2026.

Genome‐Wide Population Structure of Lake Whitefish (Coregonus clupeaformis) in a Subarctic Great Lake

Thu, 28 May 2026 20:55:28 -0700

ABSTRACT

Advances in genomics have facilitated the delineation of fisheries management units, which can be challenging in systems such as large lakes, in which high gene flow tends to limit genetic structure. In Great Slave Lake, Lake Whitefish populations have supported an important commercial fishery since the mid-1940s. The genetic structure of Lake Whitefish, however, has never been assessed, preventing the implementation of population-specific monitoring. Using low-coverage whole-genome resequencing of 305 samples from 10 sampling locations, we identified eight genetically differentiated populations of Lake Whitefish in Great Slave Lake and its main tributary, the Slave River. In the lake, we observed elevated levels of genetic differentiation among putative spawning locations in environmentally heterogeneous sections of the Main Basin despite small geographic distances among sites. In contrast, we observed weak genetic structure between populations in the comparatively homogeneous East Arm despite large geographic distances. Our observations suggest that mechanisms such as spawning site fidelity, adfluvial migratory behaviour, or local adaptation might shape population structure in this system. Using genome-wide scans, we found multiple genomic regions of elevated differentiation, with some displaying patterns coherent with chromosomal inversions. These results highlight the potential role of chromosomal rearrangements in maintaining local adaptation in the face of gene flow in environmentally heterogeneous lakes. Overall, our study provides novel insights into the genetic structure of fish populations in vast, recently deglaciated lakes. Furthermore, our results highlight the power of genomic data for population delineation in systems with high gene flow. Lastly, our precise assessment of genetic structure will provide a baseline for the genetic monitoring of culturally and socio-economically important Lake Whitefish commercial fisheries in this subarctic Great Lake.

Blood Relatives: Linking Evolutionary History and Conservation of Medicinal Leeches (Hirudo spp.)

Thu, 28 May 2026 20:54:19 -0700

ABSTRACT

Medicinal leeches of the genus Hirudo are both historically important in medicine and increasingly studied as models in ecology and biomedicine. However, the taxonomy, population structure and evolutionary history of this genus remain partially unresolved. Here, we present the most comprehensive phylogenetic analysis of the Hirudo complex to date, incorporating 350 COX1 sequences (103 newly generated) and 247 complete mitogenomes from across the distribution range. In Hirudo verbana, three major clades corresponding to Iberian (A), Western (B) and Eastern (C) haplogroups were found, with sub-haplogroups reflecting glacial refugia and Pleistocene expansions. Diversity was highest in Eastern populations, consistent with Anatolia and the Black Sea basin acting as long-term refugia. Bayesian divergence dating indicates that the genus originated in the mid-Miocene (~15 Mya), with an early split of H. nipponia in East Asia. Subsequent radiations shaped the Western Eurasian clade, with H. sulukii diverging ~9.9 Mya, H. orientalis splitting from European lineages ~6.4 Mya and differentiating ~440 kya, and recent radiations of H. verbana, H. medicinalis and H. troctina occurring during the late Pleistocene. Notably, nucleotide diversity within H. nipponia (~8.8%) and deep divergence among its haplogroups suggest the presence of multiple cryptic species, with H. tianjinensis clustering within these lineages. We also molecularly identified several Italian specimens as Haemopis sanguisuga or a potential new Dina species. These findings emphasise the importance of taxonomic clarity and genetic monitoring to guide conservation and prevent overexploitation of Hirudo leeches, ensuring the long-term sustainability and biomedical utility of these ecologically significant annelids.