Recent Population Expansion Research Articles

Move to stay: genetic structure and demographic history of a wolf spider inhabiting coastal sand dunes of southern South America

Dispersal ability can enhance the probability of an organism surviving and reproducing, and affects the geographic structure of its genetic variability. Allocosa senex is a nocturnal sand-dwelling wolf spider strictly associated with oceanic, estuarine and freshwater sandy coast habitats of southern South America, including Uruguay, Brazil, and Argentina. Recent research has revealed the presence of diverse dispersal strategies, both aerial and aquatic. Here we investigated the genetic structure and demographic history of A. senex using sequences of the mitochondrial genome and genomic scanning using amplified fragment length polymorphisms (AFLPs). We hypothesized the presence of a weak population genetic structure in space because of high levels of gene flow. We analysed individuals from 21 localities from Uruguay, Argentina, and Brazil. We obtained 60 sequences for the cox1 (17 haplotypes) and 445 AFLP polymorphic loci of 90 individuals. The results were in agreement with our hypothesis. They revealed an absence of spatially structured genetic diversity, neither among localities nor among basins, suggesting little isolation by distance in the group. The mitochondrial gene tree was dated and age estimates revealed a recent origin of A. senex, which was traced back to the Middle Pleistocene. Both the mitochondrial star-like topology and the departures from neutrality, further supported by the lack of AFLP population structure and isolation by distance, are in agreement with a recent population expansion. Demographic changes could be related to climatic oscillations and geological changes undergone by the study area during the Pleistocene.

Study on population genetics of Sillago aeolus (Perciformes: Sillaginidae) in the Coast of China

Sillago aeolus is a species from Sillaginidae, which is a widely distributed species with important scientific and economic value in the coast of China. Its population genetics have not been studied. This study investigated the population genetics of S. aeolus in the eastern and southern coast of China based on the mitochondrial control region markers obtained from 248 individuals of 9 locations. The population was characterized by a high population diversity with a low nucleotide diversity. There were no branches corresponding to the sampling sites according to the haplotype network and NJ tree. Recent asymmetric gene flow exchanges and significant genetic differences were detected between the Haikou population and the other populations. AMOVA result indicated slight genetic structures with homogeneity suggested. The neutral test and the mismatch distribution revealed a recent population expansion event. Historical geographic events may be the reason for the homogeneity within the population.

Mitochondrial DNA diversity and origin of indigenous pigs in South China and their contribution to western modern pig breeds

Indigenous pigs in South China are valuable genetic resources with many specific and unique characters, which have played an important role in the establishment of some western modern pig breeds. However, the origin and genetic diversity of indigenous pigs in South China have not been fully understood. In the present study, we sequenced 534 novel mitochondrial DNA (mtDNA) D-loop and assembled 54 complete mitogenome sequences for all 17 indigenous pig breeds from Fujian, Guangdong, Guangxi and Hainan in South China. These data were analyzed together with previously published homologous sequences relevant to this study. We found that all 13 coding genes of the mitogenomes were under purifying selection, but ND1 had the most variable sites and CYTB contained the most non-synonymous SNPs. Phylogenetic analysis showed that all indigenous pigs in South China were clustered into the D haplogroup with D1a1, D1b, D1c and D1e sub-haplogroups found to be dominant. Haplotype and nucleotide diversities of D-loop sequences ranged from 0.427 to 0.899 and from 0.00342 to 0.00695, respectively, among which all pigs in Guangdong had the lowest diversity. The estimates of pairwise FST, gene flow (Nm) and genetic distance (Da) indicated that most of these indigenous pig breeds differentiated from each other significantly (P<0.05). Among the western modern breeds, Berkshire and Yorkshire had significant Asian matrilineal footprints from indigenous pigs in South China, especially the Spotted pigs distributed in Guangdong and Guangxi. The neutrality test (Fu's FS) indicated that indigenous pigs from Fujian and Guangxi had gone through recent population expansion events (P<0.05). It is concluded that indigenous pigs in South China were most likely derived from the Mekong region and the middle and downstream regions of Yangtze River through Guangxi and Fujian. Our findings provide a complete and in-depth insight on the origin and distribution pattern of maternal genetic diversity of indigenous pigs in South China.

Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea.

Nonindigenous species pose a major threat for coastal and estuarine ecosystems. Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotyping‐by‐sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F ST .02–.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F ST .36–.39; p < .01). This study demonstrates the utility of GBS to investigate fine‐scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea.OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at: The DNA sequences generated for this study are deposited in the NCBI sequence read archive under SRA accession numbers SRR6950721–SRR6950884, and will be made publically available upon publication of this manuscript.

Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

BackgroundThe black-lip rock oyster (Saccostrea echinata) has considerable potential for aquaculture throughout the tropics. Previous attempts to farm S. echinata failed due to an insufficient supply of wild spat; however, the prospect of hatchery-based aquaculture has stimulated renewed interest, and small-scale farming is underway across northern Australia and in New Caledonia. The absence of knowledge surrounding the population genetic structure of this species has raised concerns about the genetic impacts of this emerging aquaculture industry. This study is the first to examine population genetics of S. echinata and employs both mitochondrial cytochrome c oxidase subunit I gene (COI) and single nucleotide polymorphism (SNP) markers.ResultsThe mitochondrial COI data set included 273 sequences of 594 base pair length, which comprised 74 haplotypes. The SNP data set included 27,887 filtered SNPs for 272 oysters and of these 31 SNPs were identified as candidate adaptive loci. Data from the mitochondrial COI analyses, supports a broad tropical Indo-Pacific distribution of S. echinata, and showed high haplotype and nucleotide diversities (0.887–1.000 and 0.005–0.008, respectively). Mitochondrial COI analyses also revealed a ‘star-like’ haplotype network, and significant and negative neutrality tests (Tajima’s D = − 2.030, Fu’s Fs = − 25.638, P < 0.001) support a recent population expansion after a bottleneck. The SNP analyses showed significant levels of population subdivision and four genetic clusters were identified: (1) the Noumea (New Caledonia) sample location; (2) the Bowen (north Queensland, Australia) sample location, and remaining sample locations in the Northern Territory, Australia (n = 8) were differentiated into two genetic clusters. These occurred at either side of the Wessel Islands and were termed (3) ‘west’ and (4) ‘east’ clusters, and two migrant individuals were detected between them. The SNP data showed a significant positive correlation between genetic and geographic distance (Mantel test, P < 0.001, R2 = 0.798) and supported isolation by distance. Three candidate adaptive SNPs were identified as occurring within known genes and gene ontology was well described for the sex peptide receptor gene.ConclusionsData supports the existence of genetically distinct populations of S. echinata, suggesting that management of wild and farmed stocks should be based upon multiple management units. This research has made information on population genetic structure and connectivity available for a new aquaculture species.

Phylogeography of sand‐burrowing amphipods (Haustoriidae) supports an ancient suture zone in the Gulf of Mexico

AbstractAimTo evaluate the impact of a proposed ancient suture zone in the Gulf of Mexico on the distribution and molecular diversity of dispersal‐limited, sand‐burrowing amphipods of the genera Haustorius and Lepidactylus (Haustoriidae: Amphipoda).LocationGulf of Mexico, USA and Mexico.MethodsPhylogenetic and population genetic analyses were performed using mitochondrial (COI and 16S) and nuclear (18S and 28S) data from 93 amphipod individuals from 16 sites across the Gulf of Mexico. Bayesian and ML phylogenies were constructed for all genes, divergence times were estimated using a molecular clock for COI (0.007–0.013 subs./site per Myr), and four species delimitation methods were used to identify operational taxonomic units (OTUs) within each amphipod species. The mitochondrial COI gene was used to construct haplotype networks and estimate population genetic parameters to evaluate historical changes in effective population sizes.ResultsDeep divergences (most estimated to be &gt;4 Ma) were uncovered between sister clades of both amphipod genera on either side of the Mississippi River as well as within Lepidactylus triarticulatus where each sample site was found to harbour a unique genetic lineage. Two cryptic OTUs of L. triarticulatus were identified living sympatrically at Pass Christian, Mississippi. Two distinct OTUs representing western and eastern Haustorius galvezi clades were identified along the Texas and Mexico coastlines with abutting ranges. Population genetic results show some support for recent population expansions for western Gulf OTUs, while eastern Gulf OTUs may have suffered population bottlenecks in the past.Main conclusionsDivergences between sister species of sand‐burrowing amphipods exceeds the timing of previous vicariant hypotheses. The split appears to be consistent with Miocene sedimentation levels from the Mississippi River acting as an east–west barrier to gene flow in the Gulf of Mexico. Given their strong population structure and cryptic diversity, haustoriid amphipods are ideal model organisms for studying open coast biogeography.

Population genetic structure of Thryssa kammalensis in the Chinese Seas inferred from control region sequences

Thryssa kammalensis (Bleeker, 1849) is a common pelagic species in the Chinese Seas and plays an important role in marine ecosystems. In the present study, 196 individuals of T. kammalensis were collected from nine localities along the Chinese coastal waters. The partial control region sequences of them were sequenced for analysis. Variable numbers of tandem repeats (VNTRs) were common in the control regions of all individuals, which led to variation in sequence length, ranging from 772 to 924 bp. All the populations exhibited high haplotype diversity (0.946–1.000) and low nucleotide diversity (0.015–0.031). Two distinct lineages were identified based on the neighbor-joining (NJ) tree, Bayesian inference (BI) trees, and minimum spanning tree (MST). However, the relative frequency of individuals occupying the two major lineages did not differ significantly among sampling locations. In addition, both molecular variance analysis (AMOVA) and pairwise FST analysis strongly supported little genetic differentiation among populations, revealing no significant genetic structure for T. kammalensis. Neutrality tests and analysis of mismatch distribution suggested that recent population expansion occurred in the two lineages. The climatic changes during Pleistocene periods and dispersal strategy leading to the continual gene flow might have played an important role in the geographical pattern of T. kammalensis.

Population genetic structure and demographic history of the scallop Argopecten purpuratus from Peru and Northern Chile: implications for management and conservation of natural beds

The scallop Argopecten purpuratus is a heavily exploited resource along the coasts of Peru and north-central Chile, especially after El Nino events, when the species undergoes high increases in abundance. Little is known about its genetic structure or demographic history, two important factors to ensure sustainable exploitation. We sequenced the cytochrome oxidase I and cytochrome b genes of 116 individuals from six localities (between 05°44′S 80°53′W and 23°31′S 70°33′W). We found high levels of genetic diversity in the analyzed populations. No geographical structuring was observed in the haplotype network, which consisted of a few central, widely distributed haplotypes, and many derived population-specific haplotypes separated by few mutations. This pattern suggests a recent population expansion and moderate to low current gene flow among populations. Mismatch analysis, neutrality tests, and a Bayesian skyline analysis confirmed the occurrence of a past event of population expansion approximately 5,000 years ago, which coincides with increasingly stronger and more frequent El Nino events.

Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus)

The objective of the study was to establish and refine a method for the genomic characterization of European hedgehogs in Denmark using the second-generation genotyping technique, genotyping by sequencing (GBS). Single nucleotide polymorphisms (SNPs) were filtered with a read coverage between 20 - 100 and a maximum number of missing data of 25 %. Individuals with &gt; 25 % missing data were removed yielding a total of 2.4 million SNPs, and after filtering for Minor allele frequency (MAF) &gt;1 %, 2902 SNPs remained. Approximately half of the individuals analysed contained less than 75% of the selected SNPs, and were removed, resulting in a sample size of 30. We estimated inbreeding coefficients (F), observed (HO), expected (HE) and unbiased expected (uHE) heterozygosity and the percent of polymorphic loci (P%). We tested for deviations from Hardy-Weinberg equilibrium (HWE) and patterns of isolation by distance (IBD). We assessed the genetic structure of the sampled individuals based on a Bayesian clustering method, and tested for recent population expansion or decline. We found a P% = 94.5%, a uHE and HE of mean ± SE; 0.31 ± 0.04 and 0.30 ± 0.02, respectively and an HO of 0.290 ± 0.03. The heterozygosity deficiency was reflected in a positive F-value; 0.1 ± 0.01 and a significant deviation for HWE (p &lt; 0.05). The Mantel test for association between the genetical and geographical distances of populations was not significant (b = 0.007, R = 0.145, p &gt; 0.05). The significant and positive F-value found, was explained by inbreeding, genetic substructure and low effective population size (Ne) which are all consequences of habitat fragmentation. We failed to detect recent signs of a population bottleneck or expansion. Further studies on a larger scale are needed to obtain a general view of the conservation status of the Danish hedgehog population.

YY males of the dioecious plant Mercurialis annua are fully viable but produce largely infertile pollen.

Summary The suppression of recombination during sex‐chromosome evolution is thought to be favoured by linkage between the sex‐determining locus and sexually antagonistic loci, and leads to the degeneration of the chromosome restricted to the heterogametic sex. Despite substantial evidence for genetic degeneration at the sequence level, the phenotypic effects of the earliest stages of sex‐chromosome evolution are poorly known.Here, we compare the morphology, viability and fertility between XY and YY individuals produced by crossing seed‐producing males in the dioecious plant Mercurialis annua, which has young sex chromosomes with limited X−Y sequence divergence.We found no significant difference in viability or vegetative morphology between XY and YY males. However, electron microscopy revealed clear differences in pollen anatomy, and YY males were significantly poorer sires in competition with their XY counterparts. Our study suggests either that the X chromosome is required for full male fertility in M. annua, or that male fertility is sensitive to the dosage of relevant Y‐linked genes.We discuss the possibility that the maintenance of male‐fertility genes on the X chromosome might have been favoured in recent population expansions that selected for the ability of females to produce pollen in the absence of males.

Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments.

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

The presence of a cryptic barrier in the West Pacific Ocean suggests the effect of glacial climate changes on a widespread sea-dispersed plant, Vigna marina (Fabaceae).

Ocean currents are an important driver of evolution for sea‐dispersed plants, enabling them to maintain reciprocal gene flow via sea‐dispersed diaspores and obtain wide distribution ranges. Although geographic barriers are known to be the primary factors shaping present genetic structure of sea‐dispersed plants, cryptic barriers which form clear genetic structure within oceanic regions are poorly understood. To test the presence of a cryptic barrier, we conducted a phylogeographic study together with past demographic inference for a widespread sea‐dispersed plant, Vigna marina, using 308 individuals collected from the entire Indo‐West Pacific (IWP) region. Chloroplast DNA variation showed strong genetic structure that separated populations into three groups: North Pacific (NP), South Pacific (SP) and Indian Ocean (IN) (F′CT among groups = 0.954–1.000). According to the Approximate Bayesian computation inference, splitting time between NP and SP was approximately 20,200 years (95%HPD, 4,530–95,400) before present. Moreover, a signal of recent population expansion was detected in the NP group. This study clearly showed the presence of a cryptic barrier in the West Pacific region of the distributional range of V. marina. The locations of the cryptic barrier observed in V. marina corresponded to the genetic breaks found in other plants, suggesting the presence of a common cryptic barrier for sea‐dispersed plants. Demographic inference suggested that genetic structure related to this cryptic barrier has been present since the last glacial maximum and may reflect patterns of past population expansion from refugia.

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

BackgroundGenomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species.ResultsUsing whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30–180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms.ConclusionsOur results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.

Diversity of two Theileria parva CD8+ antigens in cattle and buffalo-derived parasites in Tanzania

Theileria parva is a tick-transmitted protozoan parasite that causes a disease called East Coast fever (ECF) in cattle. This important tick borne-disease (TBD) causes significant economic losses in cattle in many sub-Saharan countries, including Tanzania. Cattle immunization using Muguga cocktail has been recommended as an effective method for controlling ECF in pastoral farming systems in Tanzania. However, immunity provided through immunization is partially strain-specific. Therefore, the control of ECF in Tanzania is still a challenge due to inadequate epidemiological information. This study was conducted to assess genetic diversity of Tp1 and Tp2 genes from T. parva isolates that are recognized by CD8 + T-cells in cattle and buffalo. The Tp1 and Tp2 genes are currently under evaluation as candidates for inclusion in a subunit vaccine. A total of 130 blood samples collected from cattle which do not interact with buffalo (98), cattle co-grazing with buffalo (19) and buffalo (13) in Mara, Mbeya, Morogoro, Tanga, and Coast regions in Tanzania were used in this study. Genomic DNA was extracted from the blood samples, Tp1 and Tp2 genes were amplified using nested PCR and the PCR products were purified and sequenced. The partial sequencing of the Tp1 and Tp2 genes from T. parva isolates exhibited polymorphisms in both loci, including the epitope-containing regions. Results for sequence analysis showed that the overall nucleotide polymorphism (π) was 0.7% and 13.5% for Tp1 and Tp2, respectively. The Tajima’s D and Fu’s Fs test showed a negative value for both Tp1 and Tp2 genes, indicating deviations from neutrality due to a recent population expansion. The study further revealed a low to high level of genetic differentiations between populations and high genetic variability within populations. The study also revealed that most samples from the seven populations possessed several epitopes in antigens that were identical to those in the T. parva Muguga reference stock, which is the main component of the widely used live vaccine cocktail. Therefore, different strategic planning and cost-effective control measures should be implemented in order to reduce losses caused by ECF in the study areas.

Phylogeography and population genetics of Acanthophyllum squarrosum complex (Caryophyllaceae) in the Irano-Turanian region

Acanthophyllum squarrosum and two closely related species, A. heratense and A. laxiusculum (Caryophyllaceae), form a complex that covers parts of subalpine steppes of the Irano-Turanian (IT) region. In this study, we explored the genetic structure and phylogeography of this complex based on partial sequences of two chloroplasts (psbA–trnH and rpl32–trnL (UAG)) and two nuclear (EST24 and nrITS) DNA regions. We analysed 80 individuals from eight populations and detected 12 chloroplast haplotypes, 16 and eight nuclear alleles in EST24 and nrITS sequences, respectively. Phylogenetic trees and haplotype networks did not show distinct genetic groups in the complex and this could be explained by incomplete lineage sorting or introgression between species. Divergence time analysis revealed a Quaternary origin for A. squarrosum complex at approximately 1.8 million years ago (Mya) and the neutrality test results indicated that this complex experienced a recent population expansion. AMOVA analysis of the chloroplast regions showed a significant genetic differentiation among populations and low genetic differentiation within populations, but opposite results were found with nuclear markers, implying introgression between A. squarrosum complex populations.

Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans

Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.

Pleistocene climatic instability drove the historical distribution of forest islands in the northeastern Brazilian Atlantic Forest

To investigate the past spatial dynamics of Atlantic Forest (AF) ‘island-like’ enclaves in northeastern Brazil, we employed ecological niche modeling (ENM) using a set of georeferenced records of 13 woody plant species. ENMs were constructed using the Ensemble forecasting approach and were projected into past climatic conditions for the last interglacial period (LIG, 120 kyr), last glacial maximum (LGM, 21 kyr), and the Middle Holocene (MH, 6 kyr). Our results suggest an expansion of wetter forests during the LGM into areas currently covered by the Caatinga seasonally dry woodlands, with recent retraction to the current distribution. Central AF islands located south of the São Francisco River underwent a different history compared to Northern AF islands north of this river: the former were mostly connected to coastal AF since the LIG (with a very recent separation), whereas the latter presented a more dynamic historical distribution. Results reveal contrasting spatiotemporal histories of forest instability and isolation across the various enclaves, supporting three main biogeographic hypotheses: i) moderate connectivity with coastal AF and a recent population bottleneck in the Araripe and Pernambuco/Paraíba enclaves, ii) low connectivity to, and long-term isolation from, other enclaves, as well as recent population bottleneck, in the northernmost North Ceará enclaves; and iii) high connectivity with coastal AF and recent population expansion in the southernmost Chapada Diamantina enclaves. Future comparative phylogeography studies will largely aid in assessing the herein proposed biogeographic scenarios during the highly dynamic recent history of the AF enclaves.

The first large-scale assessment of three-spined stickleback (Gasterosteus aculeatus) biomass and spatial distribution in the Baltic Sea

Abstract Declines in predatory fish in combination with the impact of climate change and eutrophication have caused planktivores, including three-spined stickleback (Gasterosteus aculeatus), to increase dramatically in parts of the Baltic Sea. Resulting impacts of stickleback on coastal and offshore foodwebs have been observed, highlighting the need for increased knowledge on its population characteristics. In this article, we quantify abundance, biomass, size structure, and spatial distribution of stickleback using data from the Swedish and Finnish parts of the Baltic International Acoustic Survey (BIAS) during 2001–2014. Two alternative methods for biomass estimation suggest an increase in biomass of stickleback in the Baltic Proper, stable or increasing mean size over time, and larger individuals toward the north. The highest abundance was found in the central parts of the Baltic Proper and Bothnian Sea. The proportion of stickleback biomass in the total planktivore biomass increased from 4 to 10% in the Baltic Proper and averaged 6% of the total planktivore biomass in the Bothnian Sea. In some years, however, stickleback biomass has ranged from half to almost twice that of sprat (Sprattus sprattus) in both basins. Given the recent population expansion of stickleback and its potential role in the ecosystem, we recommend that stickleback should be considered in future monitoring programmes and in fisheries and environmental management of the Baltic Sea.

Population genetic divergence as consequence of past range expansion of the smooth hammerhead shark Sphyrna zygaena

The Smooth Hammerhead Shark Sphyrna zygaena is a species with anti-tropical distribution in the eastern Pacific from California USA, to southern Chile with a remarkably gap in abundance in equatorial areas between southern Mexico and Central America. For temperate species, warm waters can represent oceanographic barriers limiting the gene flow between adjacent populations. The mtDNA control region was used to infer the phylogeography and historical demography of the Smooth Hammerhead in the eastern Pacific. An AMOVA comparing locations grouped into northern and southern eastern Pacific equatorial areas indicated significant genetic differentiation. Each population had a common haplotype separated by two mutational differences suggesting that divergence occurred very recently. The pattern of genetic differences matches with the anti-tropical distribution of S. zygaena in the eastern Pacific. Gene diversity was lower in the northern population when compared to the southern area, a pattern indicative of a recent founder event. Broadly, this pattern suggests a recent population expansion occurring 25,000–10,000 years. bp, during the last glacial cycle, when the drop of surface sea temperatures created favorable conditions at equatorial latitudes to cross the thermal barrier imposed by warm waters at equatorial latitudes. These genetically distinct population groups might lead to delineate a management plan that considers two separated stocks in the eastern Pacific.

Evidence for frequency-dependent selection maintaining polymorphism in the Batesian mimic Papilio polytes in multiple islands in the Ryukyus, Japan.

Batesian mimicry is a well‐studied adaptation for predation avoidance, in which a mimetic species resembles an unpalatable model species. Batesian mimicry can be under positive selection because of the protection gained against predators, due to resemblance to unpalatable model species. However, in some mimetic species, nonmimetic individuals are present in populations, despite the benefits of mimicry. The mechanism for evolution of such mimetic polymorphism remains an open question. Here, we address the hypothesis that the abundance of mimics is limited by that of the models, leading to mimetic polymorphism. In addition, other forces such as the effects of common ancestry and/or isolation by distance may explain this phenomenon. To investigate this question, we focused on the butterfly, Papilio polytes, that exhibits mimetic polymorphism on multiple islands of the Ryukyus, Japan, and performed field surveys and genetic analysis. We found that the mimic ratio of P. polytes was strongly correlated with the model abundance observed on each of the five islands, suggesting negative frequency‐dependent selection is driving the evolution of polymorphism in P. polytes populations. Molecular phylogenetic analysis indicated that the southern island populations are the major source of genetic diversity, and the middle and northern island populations arose by relatively recent migration. This view was also supported by mismatch distribution and Tajima's D analyses, suggesting a recent population expansion on the middle and northern islands, and stable population persistence on the southern islands. The frequency of the mimetic forms within P. polytes populations is thus explained by variations in the model abundance rather than by population structure. Thus, we propose that predation pressure, rather than neutral forces, have shaped the Batesian mimicry polymorphism in P. polytes observed in the Ryukyus.