Divergence history of the Carpathian and smooth newts modelled in space and time

Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissotriton montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4–6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10^?6 per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.     

Phylogeography of Liquidambar styraciflua (Altingiaceae) in Mesoamerica: survivors of a Neogene widespread temperate forest (or cloud forest) in North America?

We investigate the genetic variation between populations of the American sweetgum (Liquidambar styraciflua), a tree species with a disjunct distribution between northeastern Texas and Mexico, by analyzing sequences of two chloroplast DNA plastid regions in Mesoamerica. Our results revealed phylogeographical structure, with private haplotypes distributed in unique environmental space at either side of the Trans‐Mexican Volcanic Belt, and a split in the absence of gene flow dating back ca. 4.2–1.4 million years ago (MYA). Species distribution modeling results fit a model of refugia along the Gulf and Atlantic coasts but the present ranges of US and Mesoamerican populations persisted disjunct during glacial/interglacial cycles. Divergence between the US and Mesoamerican (ca. 8.4–2.8 MYA) populations of L. styraciflua and asymmetrical gene flow patterns support the hypothesis of a long‐distance dispersal during the Pliocene, with fragmentation since the most recent glacial advance (120,000 years BP) according to coalescent simulations and high effective migration rates from Mesoamerica to the USA and close to zero in the opposite direction. Our findings implicate the Trans‐Mexican Volcanic Belt as a porous barrier driving genetic divergence of L. styraciflua, corresponding with environmental niche differences, during the Pliocene to Quaternary volcanic arc episode 3.6 MYA, and a Mesoamerican origin of populations in the USA.     

A comparative phylogeographic study reveals discordant evolutionary histories of alpine ground beetles (Coleoptera,Carabidae)

Taiwan, an island with three major mountain ranges, provides an ideal topography to study mountain–island effect on organisms that would be diversified in the isolation areas. Glaciations, however, might drive these organisms to lower elevations, causing gene flow among previously isolated populations. Two hypotheses have been proposed to depict the possible refugia for alpine organisms during glaciations. Nunatak hypothesis suggests that alpine species might have stayed in situ in high mountain areas during glaciations. Massif de refuge, on the other hand, proposes that alpine species might have migrated to lower ice‐free areas. By sampling five sympatric carabid species of Nebria and Leistus, and using two mitochondrial genes and two nuclear genes, we evaluated the mountain–island effect on alpine carabids and tested the two proposed hypotheses with comparative phylogeographic method. Results from the phylogenetic relationships, network analysis, lineage calibration, and genetic structure indicate that the deep divergence among populations in all L. smetanai, N. formosana, and N. niitakana was subjected to long‐term isolation, a phenomenon in agreement with the nunatak hypothesis. However, genetic admixture among populations of N. uenoiana and some populations of L. nokoensis complex suggests that gene flow occurred during glaciations, as a massif de refuge depicts. The speciation event in N. niitakana is estimated to have occurred before 1.89 million years ago (Mya), while differentiation among isolated populations in N. niitakana, N. formosana, L. smetanai, and L. nokoensis complex might have taken place during 0.65–1.65 Mya. While each of the alpine carabids arriving in Taiwan during different glaciation events acquired its evolutionary history, all of them had confronted the existing mountain ranges.     

Long‐term panmixia in a cosmopolitan Indo‐Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

Phylogeographical studies have shown that some shallow‐water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long‐term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long‐term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo‐Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two‐fold: first, to test for broad‐scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo‐Pacific and a range‐wide, long‐term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged.     

Understanding the mechanisms of antitropical divergence in the seabird White‐faced Storm‐petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach

Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White‐faced Storm‐petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial Φ_ST = 0.89 (P < 0.01) and global nuclear Φ_ST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long‐term antitropical divergence in isolation. Coalescent‐based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000–1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000–600 000), both probably associated with the profound palaeo‐oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long‐distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.     

Comparative phylogeography and demographic history of two marsupials of the Atlantic Forest in eastern Brazil

The Atlantic Forest biodiversity hotspot in eastern South America has been the focus of several phylogeographic studies concerning relationships between populations and areas and how taxa respond to environmental changes. We infer and compare the demographic and biogeographic histories of two didelphid marsupial species, Gracilinanus microtarsus and Marmosops incanus, from the Atlantic Forest of eastern Brazil to determine how these species responded to environmental changes over time, using mitochondrial and nuclear DNA sequences. We found great intraspecific genetic divergence in both species and a strong geographic structure related to similar and spatially cohesive groups within each species. These groups are consistent with the same topographical barriers, such as mountains and river valleys. Intraspecific clades are very old, dating back to a period of tectonic activities in the Neogene (5.39–8.57 Mya). Changes in the environment over the last 7 million years lead to fairly concordant demographic changes in both marsupial species, including population expansion during the last glacial maximum (ca. 21,000 years ago) or last interglacial (ca. 120,000 years ago) or both. These results do not fit the Pleistocene refuge hypothesis as an explanation of the historical biogeography and diversification of both species in the Atlantic Forest, but are compatible with the Atlantis Forest hypothesis.     

Recent colonization by a coastal plant of inland habitats at an ancient freshwater lake,Lake Biwa: multilocus sequencing and a demographic history of Lathyrus japonicus (Fabaceae)

Ancient lakes have been recognized as “long‐term isolated islands” in terrestrial ecosystems. Lake Biwa, one of the few ancient lakes that formed around 4 million years ago, harbors many coastal species that commonly inhabit seashores. The beach pea, Lathyrus japonicus, is a typical coastal species of this freshwater lake, where morphological, physiological, and genetic differentiations have been reported between Biwa and coastal populations. Whether Biwa populations were isolated for long periods throughout Pleistocene climatic oscillations and subsequent range shifts is unclear. We assessed population genetic structure and demography of beach pea in this ancient freshwater lake using the sequences of eight nuclear loci. The results of STRUCTURE analyses showed evidence of admixture between Biwa and coastal populations, reflecting recent gene flow. The estimated demographic parameters implemented by the isolation with migration model (IM model) revealed a recent divergence (postglacial period) of Biwa populations, with some gene flow from Biwa to coastal populations. In addition, Biwa populations were significantly smaller in size than the ancestral or coastal populations. Our study suggests that a Holocene thermal maximum, when transgression could allow seeds from coastal plants to access Lake Biwa, was involved in the origin of the Biwa populations and their genetic divergence. Thus, coastal populations might have migrated to Lake Biwa relatively recently. Our study concluded that ancestral migrants in Lake Biwa were derived from small founding populations and accelerated genetic isolation of Biwa populations during short‐term isolation.     

Resequencing and comparison of whole mitochondrial genome to gain insight into the evolutionary status of the Shennongjia golden snub‐nosed monkey (SNJ R. roxellana)

Shennongjia Rhinopithecus roxellana (SNJ R. roxellana) is the smallest geographical population of R. roxellana. The phylogenetic relationships among its genera and species and the biogeographic processes leading to their current distribution are largely unclear. To address these issues, we resequenced and obtained a new, complete mitochondrial genome of SNJ R. roxellana by next‐generation sequencing and standard Sanger sequencing. We analyzed the gene composition, constructed a phylogenetic tree, inferred the divergence ages based on complete mitochondrial genome sequences, and analyzed the genetic divergence of 13 functional mtDNA genes. The phylogenetic tree and divergence ages showed that R. avunculus (the Tonkin snub‐nosed monkey) was the first to diverge from the Rhinopithecus genus ca. 2.47 million years ago (Ma). Rhinopithecus bieti and Rhinopithecus strykeri formed sister groups, and the second divergence from the Rhinopithecus genus occurred ca. 1.90 Ma. R. roxellana and R. brelichi diverged from the Rhinopithecus genus third, ca. 1.57 Ma. SNJ R. roxellana was the last to diverge within R. roxellana species in 0.08 Ma, and the most recent common ancestor of R. roxellana is 0.10 Ma. The analyses on gene composition showed SNJ R. roxellana was the newest geographic population of R. roxellana. The work will help to develop a more accurate protection policy for SNJ R. roxellana and facilitate further research on selection and adaptation of R. roxellana.     

Patterns of reproductive isolation within and between two Lygaeus species characterized by sexual conflicts over mating

Theory suggests that, under some circumstances, sexual conflict over mating can lead to divergent sexually antagonistic coevolution among populations for traits associated with mating, and that this can promote reproductive isolation and hence speciation. However, sexual conflict over mating may also select for traits (e.g. male willingness to mate) that enhance gene flow between populations, limiting population divergence. In the present study, we compare pre‐ and post‐mating isolation within and between two species characterized by male–female conflict over mating rate. We quantify sexual isolation among five populations of the seed bug Lygaeus equestris collected from Italy and Sweden, and two replicates of a population of the sister‐species Lygaeus simulans, also collected from Italy. We find no evidence of reproductive isolation amongst populations of L. equestris, suggesting that sexual conflict over mating has not led to population divergence in relevant mating traits in L. equestris. However, there was strong asymmetric pre‐mating isolation between L. equestris and L. simulans: male L. simulans were able to mate successfully with female L. equestris, whereas male L. equestris were largely unable to mate with female L. simulans. We found little evidence for strong post‐mating isolation between the two species, however, with hybrid F₂ offspring being produced. Our results suggest that sexual conflict over mating has not led to population divergence, and indeed perhaps supports the contrary theoretical prediction that male willingness to mate may retard speciation by promoting gene flow.     

Comparative rangewide phylogeography of four endemic Taiwanese bat species

Phylogeographic reconstructions of codistributed taxa can help reveal the interplay between abiotic factors, such as altitude and climate, and species‐specific attributes, in shaping patterns of population genetic structure. Recent studies also demonstrate the value of both rangewide sampling and species distribution modelling (SDM) in comparative phylogeography. Here, we combine these approaches to study the population histories of four phylogenetically related forest‐dependent bat species. All are endemic to the mountainous island of Taiwan but show differences in their tolerance to altitude, with Murina gracilis considered to be a high‐altitude specialist, M. recondita and Kerivoula sp. low‐altitude specialists, and M. puta an altitudinal generalist. We tested the prediction that contrasting habitat preferences would impact on patterns of past and contemporary gene flow and found broad concordance between the results of population genetic analyses and species distribution models based on the Model for Interdisciplinary Research on Climate. Both lowland species showed evidence of genetic divergence between the east and west of the island, consistent with SDMs that indicated the Central Mountain Range (CMR) has presented a long‐term and continuous barrier to gene flow since before the Last Glacial Maximum. In contrast, Murina gracilis and M. puta showed lower degrees of historical isolation and genetic differentiation associated with the CMR, reflecting greater gene flow, possibly coupled with past population growth in M. puta. Together our results highlight the usefulness of combining distribution models with phylogeographic analyses to understand the drivers of genetic structure.     

Glacial cycles drive rapid divergence of cryptic field vole species

Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single‐nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis). The SNPs demonstrate high genomic divergence (pairwise F_ST values of 0.45–0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status.     

Inferring the history of speciation in house mice from autosomal,X‐linked,Y‐linked and mitochondrial genes

Patterns of genetic differentiation among taxa at early stages of divergence provide an opportunity to make inferences about the history of speciation. Here, we conduct a survey of DNA‐sequence polymorphism and divergence at loci on the autosomes, X chromosome, Y chromosome and mitochondrial DNA in samples of Mus domesticus, M. musculus and M. castaneus. We analyzed our data under a divergence with gene flow model and estimate that the effective population size of M. castaneus is 200 000–400 000, of M. domesticus is 100 000–200 000 and of M. musculus is 60 000–120 000. These data also suggest that these species started to diverge approximately 500 000 years ago. Consistent with this recent divergence, we observed considerable variation in the genealogical patterns among loci. For some loci, all alleles within each species formed a monophyletic group, while at other loci, species were intermingled on the phylogeny of alleles. This intermingling probably reflects both incomplete lineage sorting and gene flow after divergence. Likelihood ratio tests rejected a strict allopatric model with no gene flow in comparisons between each pair of species. Gene flow was asymmetric: no gene flow was detected into M. domesticus, while significant gene flow was detected into both M. castaneus and M. musculus. Finally, most of the gene flow occurred at autosomal loci, resulting in a significantly higher ratio of fixed differences to polymorphisms at the X and Y chromosomes relative to autosomes in some comparisons, or just the X chromosome in others, emphasizing the important role of the sex chromosomes in general and the X chromosome in particular in speciation.     

Genomic replacement of native Cobitis lutheri with introduced C. tetralineata through a hybrid swarm following the artificial connection of river systems

River connections via artificial canals will bring about secondary contacts between previously isolated fish species. Here, we present a genetic consequence of such a secondary contact between Cobitis fish species, C. lutheri in the Dongjin River, and C. tetralineata in the Seomjin River in Korea. The construction of water canals about 80 years ago has unidirectionally introduced C. tetralineata into the native habitat of C. lutheri, and then these species have hybridized in the main stream section of the Dongjin River. According to the divergence population genetic analyses of DNA sequence data, the two species diverged about 3.3 million years ago, which is interestingly coincident with the unprecedented paleoceanographic change that caused isolations of the paleo‐river systems in northeast Asia due to sea‐level changes around the late Pliocene. Multilocus genotypic data of nine microsatellites and three nuclear loci revealed an extensively admixed structure in the hybrid zone with a high proportion of various post‐F1 hybrids. Surprisingly, pure native C. lutheri was absent in the hybrid zone in contrast to the 7% of pure C. tetralineata. Such a biased proportion must have resulted from the dominant influence of continually introducing C. tetralineata on the native C. lutheri which has no supply of natives from other tributaries to the hybrid zone due to numerous low‐head dams. In addition, mating experiments indicated that there is no discernible reproductive isolation between them. All the results suggest that the gene pool of native C. lutheri is being rapidly replaced by that of continually introducing C. tetralineata through a hybrid swarm for the last 80 years, which will ultimately lead to the genomic extinction of natives in this hybrid zone.     

Gene flow and Andean uplift shape the diversification of Gasteracantha cancriformis (Araneae: Araneidae) in Northern South America

The Andean uplift has played a major role in shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here, we examined the phylogeography of the widespread color polymorphic spider Gasteracantha cancriformis to evaluate the effect of the northern Andean uplift on its divergence and assess whether its diversification occurred in the presence of gene flow. We inferred phylogenetic relationships and divergence times in G. cancriformis using mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence, and population structure were quantified. We also compared multiple demographic scenarios for this species using a model‐based approach (Phrapl ) to determine divergence with or without gene flow. At last, we evaluated the association between genetic variation and color polymorphism. Both nuclear and mitochondrial data supported two well‐differentiated clades, which correspond to populations occurring on opposite sides of the Eastern cordillera of the Colombian Andes. The final uplift of this cordillera was identified as the most likely force that shaped the diversification of G. cancriformis in northern South America, resulting in a cis‐ and trans‐Andean phylogeographic structure for the species. We also found shared genetic variation between the cis‐ and trans‐Andean clades, which is better explained by a scenario of historical divergence in the face of gene flow. This has been likely facilitated by the presence of low‐elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example in which the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.     

Narrow water barriers prevent multiple colonizations and limit gene flow among California Channel Island wild buckwheats (Eriogonum: Polygonaceae)

The relative roles of chance colonization and subsequent gene flow in the development of insular endemic biotas have been extensively studied in remote oceanic archipelagos, but are less well characterized on nearshore island systems. The current study investigated patterns of colonization and divergence between and within two wild buckwheat species (Polygonaceae), Eriogonum arborescens and E. giganteum, endemic to the California Channel Islands to determine whether geographical isolation is driving diversification. Using plastid and nuclear sequence data and microsatellite allele frequencies, we determined that gene flow in these Eriogonum spp. is restricted by isolation. The data suggest that successful colonization of and gene flow among the islands are infrequent. Colonization appears to have followed a stepping‐stone model that is consistent with a north‐to‐south pattern across the islands. This colonization pattern coupled with relatively little post‐colonization inter‐island gene flow, particularly among southern islands, has generated a pattern of more divergent lineages on the isolated southern islands. These results run counter to the general expectation that all islands close to a continental source should receive a high level of gene flow. Finally, management recommendations focused on protecting the lineages from loss of private alleles and the erosion of the remaining genetic diversity are offered.     

The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate ‘genomic island of speciation’

Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a ‘genomic island of divergence’ spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X‐island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X‐island despite a lack of autosomal divergence; (ii) individuals with multiple‐recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination‐driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.     

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co‐occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next‐generation sequencing, and combined these with microsatellite data for coalescent‐based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation‐with‐migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.     

Population genetic structure,differentiation, and diversity in Tetrix subulata pygmy grasshoppers: roles of population size and immigration

Genetic diversity within and among populations and species is influenced by complex demographic and evolutionary processes. Despite extensive research, there is no consensus regarding how landscape structure, spatial distribution, gene flow, and population dynamics impact genetic composition of natural populations. Here, we used amplified fragment length polymorphisms (AFLPs) to investigate effects of population size, geographic isolation, immigration, and gene flow on genetic structure, divergence, and diversity in populations of Tetrix subulata pygmy grasshoppers (Orthoptera: Tetrigidae) from 20 sampling locations in southern Sweden. Analyses of 1564 AFLP markers revealed low to moderate levels of genetic diversity (PPL = 59.5–90.1; Hj = 0.23–0.32) within and significant divergence among sampling localities. This suggests that evolution of functional traits in response to divergent selection is possible and that gene flow is restricted. Genetic diversity increased with population size and with increasing proportion of long‐winged phenotypes (a proxy of recent immigration) across populations on the island of Öland, but not on the mainland. Our data further suggested that the open water separating Öland from the mainland acts as a dispersal barrier that restricts migration and leads to genetic divergence among regions. Isolation by distance was evident for short interpopulation distances on the mainland, but gradually disappeared as populations separated by longer distances were included. Results illustrate that integrating ecological and molecular data is key to identifying drivers of population genetic structure in natural populations. Our findings also underscore the importance of landscape structure and spatial sampling scheme for conclusions regarding the role of gene flow and isolation by distance.     

The shape of things to come in the study of the origin of species?

Perhaps Darwin would agree that speciation is no longer the mystery of mysteries that it used to be. It is now generally accepted that evolution by natural selection can contribute to ecological adaptation, resulting in the evolution of reproductive barriers and, hence, to the evolution of new species (Schluter & Conte 2009 ; Meyer 2011 ; Nosil 2012 ). From genes that encode silencing proteins that cause infertility in hybrid mice (Mihola et al. 2009 ), to segregation distorters linked to speciation in fruit flies (Phadnis & Orr 2009 ), or pollinator‐mediated selection on flower colour alleles driving reinforcement in Texan wildflowers (Hopkins & Rausher 2012 ), characterization of the genes that drive speciation is providing clues to the origin of species (Nosil & Schluter 2011 ). It is becoming apparent that, while recent work continues to overturn historical ideas about sympatric speciation (e.g. Barluenga et al. 2006 ), ecological circumstances strongly influence patterns of genomic divergence, and ultimately the establishment of reproductive isolation when gene flow is present (Elmer & Meyer 2011 ). Less clear, however, are the genetic mechanisms that cause speciation, particularly when ongoing gene flow is occurring. Now, in this issue, Franchini et al. ( 2014 ) employ a classic genetic mapping approach augmented with new genomic tools to elucidate the genomic architecture of ecologically divergent body shapes in a pair of sympatric crater lake cichlid fishes. From over 450 segregating SNPs in an F2 cross, 72 SNPs were linked to 11 QTL associated with external morphology measured by means of traditional and geometric morphometrics. Annotation of two highly supported QTL further pointed to genes that might contribute to ecological divergence in body shape in Midas cichlids, overall supporting the hypothesis that genomic regions of large phenotypic effect may be contributing to early‐stage divergence in Midas cichlids.