Population Divergence Research Articles

Genetic diversity of noble crayfish in Finland based on ITS1 microsatellite-like repeat variation: implications to the conservation and management

During the last two centuries, native noble crayfish (Astacus astacus) has been introduced and re-introduced into many waters in Finland, to widen the area of distribution, and to re-establish the collapsed populations. Recent studies have revealed narrowed genetic diversity in A. astacus populations, especially in North Europe, due to crayfish plagues and due to the past translocation policies with numerous introductions also with small number of individuals. However, preliminary data based on the microsatellite like-repeat variation in ITS1 (Internal Transcribed Spacer 1) have indicated also genetic heterogeneity among Swedish and Finnish populations. In this study, the genetic diversity of 38 Finnish A. astacus populations was analysed based on variation in ITS1 region. Stocking histories of populations were obtained from official records and from local fishermen. Eighth out of 38 populations showed divergence in paired comparison with other analysed populations (Population Divergence Test, p < 0.05) indicating either possibility of autochthonous origin or donor. Potential autochthonous populations, as well as refugee areas within original distribution range and within designated protection area, should be further distinguished and monitored to maintain the remaining genetic diversity of the populations.

The Population Divergence and Genetic Basis of Local Adaptation of Wild Soybean (Glycine soja) in China.

Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource.

Morphological and functional trait divergence in endemic fish populations along the small-scale karstic stream

BackgroundOrganisms with broad distribution ranges, such as fish, often exhibit local ecological specializations based on their utilization of food and habitat. Populations of species that live in different habitat types (lotic vs. lentic) show morphological variations. However, the phenotypic differences of endemic fish populations in a small karst river basin under anthropogenic pressure are still not fully understood. In this study, the functional traits and morphological variations of the populations of endemic Pseudophoxinus antalyae Bogutskaya, 1992, in the Düden Stream basin, which is subjected to various anthropogenic disturbances and habitat types in southwestern Anatolia of Türkiye, were examined using linear measurements and geometric morphometric analysis.ResultsDifferences have been identified in functional traits, particularly those related to food acquisition between populations. Results of both univariate and multivariate analyses revealed significant differences in body shape and size among populations living at sites along the stream with different habitat and environmental characteristics.ConclusionsThe reason for these differences determined in the morphology and traits of the populations may depend on habitat types, ecological, or environmental, and obstruction of gene flow. More detailed studies are needed to explain the mechanisms (genetic and ecological) that cause these differences.

ABO gene may be salient to the out of Africa migrations to the Americas

The source populations of Native Americans lived in Asia and Eurasia some 35,000 to 40,000 years ago. Consensus is that they migrated to Beringia some 25,000 to 30,000 years ago, when the low sea levels from the Last Glacial Maximum period allowed a land bridge to form to Beringia. Subsequently, the Native American ancestors migrated south to North and South America, whereas the remaining Beringia population, Eskimos, migrated into Canada and Greenland. Genetic evidence along with anthropological research adds much to the understanding of the course of their migrations and population growth. Because present-day Native Americans are essentially all of ABO O blood type, and the other Beringia populations, the Eskimos, were polymorphic for the ABO blood groups given the extensive research revealing pleiotropy of ABO blood group alleles, this unusual population frequency distribution of ABO blood groups offers an opportunity to understand how a population with no diversity of ABO blood groups differs from one that is similar in other genes but polymorphic in ABO blood groups. ABO blood groups in migrating populations provide supporting evidence for the timelines, destinations, and cultures of those populations leaving Africa. Other genes add to the power of ABO blood groups to provide this evidence. One of those genes, in the case of Native American and Eskimo migrations, is the gene for a dental trait called shovel shaped incisors, ectodysplasin A receptor (EDAR), which is prevalent in northeast Asian populations and is fixed in Native American populations. Because of the known climatic conditions in Africa at the time of the major out-of-Africa migration periods and malaria-related climatic aspects of the selection of the ABO A2 vs ABO A1 gene, it appears that the population ratio of ABO A2 to ABO A1 and EDAR associated shovel shaped incisor frequencies is associated with the timelines of the population leaving Africa as well as their further migrations. Because Native Americans have a very high shovel shaped incisor frequency and no ABO A2, their timeline of migrating from northeast Asia and Eurasia, observed using this approach and agreeing with other lines of evidence, is supported to be 25,000–30,000 years ago. Furthermore, separation of the Beringia population into a monomorphic ABO O group, the Native Americans, and an ABO polymorphic group, the Eskimos, in light of research supporting pleiotropy of ABO alleles enhances our understanding of their respective divergent migration paths, cultures, and population growth.

Gene expression and alternative splicing contribute to adaptive divergence of ecotypes.

Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here, we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, even when grown in a common environment, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for both cis and trans-regulation. Together, our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at short evolutionary time scales.

Approximate Bayesian computation and ecological niche models elucidate the demographic history and current fragmented population distribution of a Korean endemic shrub.

Climatic fluctuations and geological events since the LGM are believed to have significantly impacted the population size, distribution, and mobility of many species that we observe today. In this paper, we determined the processes driving the phylogeographic structure of the Korean endemic white forsythia by combining the use of genome-wide SNPs and predicting paleoclimatic habitats during the LGM (21 kya), Early Holocene (10 kya), Mid-Holocene (6 kya), and Late Holocene (3 kya). Using a maximum of 1897 SNPs retrieved from 124 samples across nine wild populations, five environmental predictors, and the species' natural occurrence records, we aimed to infer the species' demographic history and reconstruct its possible paleodistributions with the use of approximate Bayesian computation and ecological niche models, respectively. Under this integrated framework, we found strong evidence for patterns of range shift and expansion, and population divergence events from the onset of the Holocene, resulting in the formation of its five distinct genetic units. The most highly supported model inferred that after the split of an ancestral population into the southern group and a larger central metapopulation lineage, the latter gave rise to the eastern and northern clusters, before finally dividing into two sub-central groups. While the use of molecular data allowed us to identify and refine the (phylo)genetic relationships of the species' lineages and populations, the use of ecological data helped us infer a past LGM refugium and the directions of post-glacial range dynamics. The time frames of these demographic events were shown to be congruent with climatic and geological events that affected the central Korean Peninsula during these periods. These findings gave us a better understanding of the consequences of past spatiotemporal factors that may have resulted in the current fragmented population distribution of this endangered plant.

Inferring phylogenetic structure, taxa hybridization, and divergence times within rock voles of subgenus Aschizomys (Cricetidae: Alticola) using quaddRAD sequencing and a cytb dataset.

The subgenus Aschizomys belongs to the genus Alticola (Central Asian mountain vole) and consists of two species: Alticola macrotis and Alticola lemminus. Phylogenetic relationships within the subgenus Aschizomys remain obscure due to limited sampling, an insufficient number of molecular markers used in phylogenetic studies, and paraphyly observed on mitochondrial trees. In this work, to infer reliable phylogenetic relationships and evaluate putative scenarios of ancient hybridization within the subgenus, we applied double-digest restriction site-associated DNA paired-end (quaddRAD) sequencing to 20 DNA samples (20 individuals), including five species of the genus Alticola, and dated the divergence of cytochrome b (cytb) lineages within Aschizomys using a "second calibration" approach. We showed monophyly of the two species on the basis of thousands of nuclear loci and demonstrated traces of introgression also in the nuclear genome. Observed paraphyly in cytb could be explained by an introgression event rather than incomplete lineage sorting. This explanation was confirmed by an analysis of the cytb divergence time. Overall, our results support the hypothesis of extensive migration of the Aschizomys species during the Late Pleistocene, with this migration leading to population divergence and introgression. We expect our article to become a starting point for a series of rigorous studies on the population history of the genus Alticola as a whole.

Disproportionate role of nuclear-encoded proteins in organismal and mitochondrial thermal performance in a copepod.

Determining the mechanisms by which organisms evolve thermal tolerance is crucial to predicting how populations may respond to changes in local temperature regimes. Although evidence of relationships between mitochondrial background and thermal adaptation have been found, the presence of both nuclear-encoded and mitochondrial DNA (mtDNA)-encoded proteins warrants experiments aimed at parsing out the relative role of each genome in thermal adaptation. We investigated the relative role of mtDNA-encoded products in thermal tolerance between two divergent populations of Tigriopus californicus using first-generation (F1) hybrids that vary in maternally inherited mtDNA but are heterozygous for population-specific alleles across nuclear loci. We tested two measures of thermal tolerance, (1) survivorship to acute thermal stress and (2) thermal stability of mitochondrial performance in Complex I-fueled ATP synthesis, both across a range of increasing temperatures. We found that the southern population (San Diego, CA, USA) outperformed the northern population (Strawberry Hill, OR, USA) in survivorship, and that both reciprocal F1 hybrid crosses had intermediate survival. Mitochondria from the San Diego population displayed greater stability in ATP synthesis with increasing temperatures compared with those from Strawberry Hill. Interestingly, hybrids from both cross directions had synthesis profiles that were very similar to that of Strawberry Hill. Taken together, these results suggest that the relative role of the mtDNA in these phenotypes is negligible compared with that of elements encoded by nuclear DNA in this system.

Genetic and morphological differentiation within Euphorbia japygica (Euphorbiaceae) suggests divergence of populations from the south-eastern Apennine Peninsula

Abstract The Mediterranean Basin is a hotspot of animal and plant diversity. Contrary to the Balkan and Iberian Peninsulas that were subject of many phylogeographic studies in past decades, the Apennine Peninsula and, in particular, the diversification of its flora has been neglected in contemporary phylogenetic studies. The few available studies showed a complex pattern of north–south differentiation of genetic diversity in Italy, both among the Alps, the Apuan Alps, and the Apennines, as well as within the Apennines. Here, we explore phylogeographic patterns within recently described Euphorbia adriatica, distributed in the central and northern Apennine Peninsula, the southern margin of the Eastern Alps and the north-western Balkan Peninsula, and its relationship to the southern Italian E. japygica. Our integrative approach using nuclear ITS sequences, amplified fragment length polymorphisms, relative genome size estimation combined with chromosome counting, as well as multivariate morphometrics inferred a weak genetic differentiation that only partly corresponds to the morphological differentiation. Whereas all southern populations have hairy capsules characteristic for E. japygica, only those in south-eastern Italy (Puglia and Basilicata) are genetically divergent. There are, however, additional morphological characters that differentiate them from other populations. Our data are thus in favour of recognizing a single species, E. japygica, which includes E. adriatica that should be treated as a subspecies, named E. japygica subsp. prostrata. We provide a revised taxonomic treatment for E. japygica, including the typification. Our study shows the necessity of further in-depth investigations of diversification of Italian biota.

Diverse Effects of Cryopreservation-Induced Mitochondrial Dysregulation on Cord Blood Cells

Umbilical cord blood transplantation (UCBT) has been performed broadly in clinic by the specific biological and immunological characteristics of umbilical cord blood cells (UCB). UCB-based cell therapy and immune therapy also presents great application potential. UCB was usually cryopreserved for several years before using. Whether and how cryopreservation affects the function of divergent cell populations in UCB still remain to be illuminated. Here, we firstly constructed a single-cell transcriptomic profile of Lineage - CD34 + hematopoietic stem and progenitor cells (HSPCs) and mononuclear cells (MNCs) collected from fresh and cryopreserved UCB with 1, 5, 10 and 19 years. Subpopulations characterized by higher mitochondrial gene expression (Mito high) were identified in all cell populations and found to be increased during cryopreservation. Compared with the fresh group, HSC/MPP cells after cryopreservation showed more active cell cycle and lower expression of HSC/MPP signature genes, especially in the Mito high HSC/MPP cells. Consistently, colony-forming ability as well as long-term hematopoietic reconstitution of HSPCs derived from cryopreserved UCB gradually decreased within 5 years but remained stable thereafter. More importantly, we observed decreased megakaryocyte differentiation ability from cryopreserved HSPCs, which could be partially rescued by antioxidants treatment after cryopreservation. Mechanically, we revealed that the metabolic dysregulation of mitochondria including elevated mitochondrial reactive oxygen species (ROS), reduced adenosine triphosphate (ATP) synthesis and impaired mitochondrial membrane potential of cryopreserved HSPCs led to attenuated hematopoietic reconstitution. Although there was a mild increase of Mito high subpopulations after cryopreservation, the cytokine production levels of T cells and NK cells were comparable to those of fresh samples. Additionally, NK cells exhibited almost same cytotoxic function with the fresh compartments. Taken together, we elucidated the impact of cryopreservation on UCB HSPCs and provided the strategy for rescuing itsfunctional impairment. The unaffected T and NK cells after cryopreservation also paved the way for UCB-based cell therapy and immune therapy. Our study provides important implements for the quality control of applicable UCB both in hematology and immunotherapy.

Within- and between-population comparisons suggest independently acting selection maintaining parallel clines in Scots pine (Pinus sylvestris).

Parallel clines in traits related to adaptation in a species can be due to independent selection on a pair of traits, or due to selection in one trait resulting in a parallel cline in a correlated trait. To distinguish between the mechanisms giving rise to parallel adaptive population divergence of multiple traits along an environmental gradient we need to study variation, correlations, and selective forces within individual populations along the gradient. In many tree species, budset timing (BST) forms a latitudinal cline, and parallel clinal variation is also found in other seedling traits, such as first-year height (FYH) and fall frost injury (FFI). In this study, we set up a common garden experiment with open pollinated progeny from natural populations of Scots pine (Pinus sylvestris), with one large sample from single population (500 families) and smaller samples from across a latitudinal gradient. BST, FYH and induced FFI were first measured in a greenhouse. The seedlings were then planted in the field, where survival and height were measured at the age of 9 years as fitness proxies. We compared between- and within-population variation and genetic correlations of these three seedling traits, and estimated selection gradients at the family level in our main population, taking into account the potential effects of seed weight. Between-population genetic correlations between seedling traits were high (0.76-0.95). Within-population genetic correlations in the main population were lower (0.14-0.35), as in other populations (0.10-0.39). Within population, extensive adaptive variation persists in the seedling traits, in line with rather weak selection gradients, yet maintaining the clines. Although our sampling does not cover the whole cline equally, the results suggest that the individual clines in these traits are maintained by largely independently acting selection, which results in fewer constraints in adaptation under changing climate.

Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced

Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300–400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.

Genomic evidence for climatic adaptation in Fejervarya multistriata

AbstractAimGenetic diversity driven by natural selection contributes to population divergence in amphibians, thus facilitating local adaptation to climate change. Understanding the mechanisms of genetic adaptation is one of the important issues in evolutionary biology. This study set out to reveal drivers responsible for intraspecific divergence in Fejervarya multistriata and further investigate the potential involvement of selected genes in responding to climate challenges.LocationChina.MethodTo identify adaptive traits associated with climate change, we conducted genome RAD‐seq of 300 F. multistriata individuals from 15 locations across a bio‐geographical range with gradual climatic variation in China.ResultsThe results indicate a substantial genetic diversity among populations of F. multistriata and highlight specific genes and pathways that likely contribute to intraspecific divergence. The demographic history of F. multistriata can be traced back to the last interglacial period, during which elevated temperatures may have led to a significant decline in effective population size. The analysis of genome‐climate association identified five candidate genes (BMP2K, NRAP, ZW10, MYH1 and PLB1) potentially involved in local climate adaptation.Main ConclusionsOur findings have shed light on the genetic mechanisms of local adaptation to climate change in F. multistriata, thereby aiding in determining the possible fate of populations under future climate change.

Diversity and Phylogeny of Gyrodactylus spp. (Monogenea: Gyrodactylidae) across the Strait of Gibraltar: Parasite Speciation and Historical Biogeography of West Mediterranean Cyprinid Hosts

Knowledge on the diversity of parasitic flatworms of Western Mediterranean cyprinids is extremely scarce. In the present study, we parasitologically investigated 12 cyprinid species across the Strait of Gibraltar inhabiting watersheds in northwest Africa (Morocco) and Iberia (Portugal and Spain). Taxonomically relevant features of the attachment organ and sequences of the 18S rDNA and ITS regions were used for species delineation and to investigate their phylogenetic relatedness. Among the Gyrodactylus collected from Morocco and Spain, we identified specimens with an unusual T-shaped dorsal bar observed herein for the first time. In contrast, the membranous patch-like structure surrounding the twisted inner roots of hamuli and the median ridge of the ventral bar have been generally observed in Eurasian relatives. Our analyses suggest vicariant speciation of Gyrodactylus across the Strait of Gibraltar. We describe herein G. gibraltarensis sp. nov. from Iberian Luciobarbus graellsii; G. moroccensis sp. nov. from northwest African cyprinids, i.e., L. maghrebensis, L. rabatensis, L. rifensis, L. yahyaouii, and L. zayanensis; and finally, G. pseudomoroccensis sp. nov. from Moroccan L. ksibi, all possessing a new haptoral configuration. The genetic divergence and conservative morphologies in populations of G. moroccensis sp. nov. from five cyprinid species support its ongoing speciation in Northwest Africa. The West Mediterranean lineage was revealed to be monophyletic, with Eurasian species forming a sister group. Morphologically, West Mediterranean Gyrodactylus also appeared to be of Middle Eastern origin. Gyrodactylus spp. possessing an unusual T-shaped dorsal bar have most likely speciated, allowing for the appearance of a haptoral morphology that is restricted to the region across the Strait of Gibraltar. To conclude, viviparous Gyrodactylus reflect parasite speciation across the Strait of Gibraltar and the historical biogeography of cyprinids in the West Mediterranean.

Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea).

Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.

Noise and light pollution elicit endocrine responses in urban but not forest frogs

Urban areas are characterised by the presence of sensory pollutants, such as anthropogenic noise and artificial light at night (ALAN). Animals can quickly adapt to novel environmental conditions by adjusting their behaviour, which is proximately regulated by endocrine systems. While endocrine responses to sensory pollution have been widely reported, this has not often been linked to changes in behaviour, hampering the understanding of adaptiveness of endocrine responses. Our aim was, therefore, to investigate the effects of urbanisation, specifically urban noise and light pollution, on hormone levels in male urban and forest túngara frogs (Engystomops pustulosus), a species with reported population divergence in behaviour in response to urbanisation. We quantified testosterone and corticosterone release rates in the field and in the lab before and after exposure to urban noise and/or light. We show that urban and forest frogs differ in their endocrine phenotypes under field as well as lab conditions. Moreover, in urban frogs exposure to urban noise and light led, respectively, to an increase in testosterone and decrease in corticosterone, whereas in forest frogs sensory pollutants did not elicit any endocrine response. Our results show that urbanisation, specifically noise and light pollution, can modulate hormone levels in urban and forest populations differentially. The observed endocrine responses are consistent with the observed behavioural changes in urban frogs, providing a proximate explanation for the presumably adaptive behavioural changes in response to urbanisation.

117 Combining Large Broiler Populations into a Single Genomic Evaluation: Dealing with Genetic Divergence

Abstract Combining populations that diverged at some point is a common practice, especially in poultry, where generation intervals are short and genetic evaluations should be available often. This study assessed whether combining large, divergent broiler populations into one genomic evaluation is feasible and the best strategy for doing that in single-step GBLUP. The pedigree for populations 1 and 2 included 397,954 and 411,780 animals, of which 154,911 and 168,429 were genotyped. Phenotypes for body weight (g), carcass yield (%), mortality (0-1), and feet health (0-6) were available for 397,954 animals in population 1 and 411,780 in population 2. A four-trait model was used in the analyses, and the genetic differences between the two populations were modeled in different ways: M1) included an extra fixed effect that accounted for population origin; M2) added origin-specific fixed effects, where the animal origin was concatenated with all fixed effects in the model. The two models were compared against a conventional model without accounting for the animal origin as a fixed effect (M0). Unknown parent groups (UPG) were fit to account for the genetic differences in M0, M1, and M2; therefore, they were set based origin population of the animal and sex. The models were evaluated based on accuracy, bias, and dispersion from the linear regression (LR) method and predictive ability (PA), where GEBV in the reduced data was compared against phenotypes adjusted for fixed effects. Validations were done separately in single and multi-populations to better assess the benefits of combining the two populations. Overall, the accuracy obtained by PA was less than by LR. No apparent accuracy, PA, bias, and dispersion differences were observed among the multi-population models across all traits. This was also true when comparing validation parameters in a multi-population against the ones from a single population. However, we observed that animals from one population were always superior to the other. A multi-trait model was applied, treating the same trait in each population differently. Genetic correlations between the same trait in different populations were moderate to low, suggesting that the two lines should possibly be evaluated separately. Defining whether populations should be combined in a single evaluation may go beyond validation parameters. Identifying if traits are the same across populations is crucial for the feasibility of combined evaluations.

Genomic divergence and introgression between cryptic species of a widespread North American songbird.

Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulate evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least three species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum.

Population genetics of the endangered Clanwilliam sandfish Labeo seeberi: considerations for conservation management

The Cape Fold Ecoregion (CFE) is one of southern Africa’s unique aquatic ecoregions and its freshwater fish fauna is characterized by high levels of endemism. As with many other Mediterranean-type ecosystems, the region is also a hotspot for threatened and range-restricted freshwater fish. Many of the CFE’s endemic species are at risk for extinction, with declines in population sizes and distribution ranges. The Clanwilliam sandfish Labeo seeberi is an example of such a species and is considered one of South Africa’s most endangered large migratory cyprinids. This species is endemic to the Olifants/Doring river system in the CFE and has been subject to a major population decline, mainly as a result of invasive alien fish and adverse climate events. Little is known of the genetics of the Clanwilliam sandfish, thus this study aimed to provide basic population genetic parameters to inform future conservation interventions. Both microsatellite and mitochondrial DNA (mtDNA) markers were used to assess populations from three sites within the Olifants/Doring river system. Genetic diversity was moderate to low and did not reflect the drastic decline expected on the basis of previous relative abundance data. This is likely due to a lag effect between ecological/life history demographics (due to juvenile recruitment failures) and population genetic composition. Furthermore, there was limited genetic differentiation between the sampling locations, suggesting a single breeding population, but mtDNA haplotype distribution and slight divergence of the smaller populations does suggest that the population might have become recently fragmented. The results show that the effective population size of the current breeding population might still be sufficient to maintain evolutionary potential in the short term, which could act as a buffer until conservation strategies focusing on protecting breeding animals and maximizing juvenile survival can restore population numbers.

Non-additive effects between genotypes: Implications for competitive fitness assays.

Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged Drosophila simulans populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: (1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. (2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype × environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.