Patterns Of Haplotype Diversity Research Articles

Tracing the geographic origins of two forms of Opuntia ficus-indica cultivated in Argentina using haplotype diversity patterns, and cytogenetic and morphological analyses

Tracing the geographic origins of two forms of Opuntia ficus-indica cultivated in Argentina using haplotype diversity patterns, and cytogenetic and morphological analyses

Diversity and distribution of cytochrome oxidase I (COI) haplotypes of the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera, Pentatomidae), along the eastern front of its invasive range in Eurasia

The arrival, establishment and pest status of Halyomorpha halys in Europe and non-native countries in Asia have been well-documented, with thorough characterisation of the genetic diversity and occurrence of cytochrome oxidase I (COI) haplotypes in Switzerland, France, Hungary, Italy and Greece. However, a number of gaps exist in terms of the characterisation of the haplotype diversity and occurrence of H. halys along the invasion front that covers eastern Europe, western and central Asia. To contribute towards filling this gap, the COI haplotype diversity and distribution were investigated for H. halys collected in Serbia, Ukraine, Russia, Georgia and Kazakhstan. A total of 646 specimens were analysed and five haplotypes were found (H1, H3, H8, H33 and H80). Haplotype H1 was present in all five countries investigated and was the only haplotype detected amongst > 500 specimens collected from Ukraine, Russia and Georgia. H1 (82%) was the dominant haplotype found in Kazakhstan, alongside H3 (18%). In contrast to the low or no diversity observed in these four countries, Serbia had higher haplotype diversity and was represented by five haplotypes. Although H3 was dominant (47%) in Serbia, H1 was also prevalent (40%); the remaining haplotypes (H8, H33 and H80) were minor contributors (1–11%) to the haplotype composition. The results are discussed in context with other known populations in neighbouring countries and patterns of haplotype diversity indicate the movement of successful invasive populations in Europe to generate secondary invasions along the eastern front of the invasion in Eurasia. Possible scenarios regarding the spread of particular haplotypes in these regions are discussed, along with suggestions for future research to fill existing gaps.

An approach for estimating haplotype diversity from sequences with unequal lengths

Abstract Genetic diversity is an essential component of biodiversity. Developing robust quantification methods is critically important in depicting the genetic diversity underlying the geographical distributions of species, especially for the sequence data with unequal lengths. Traditional calculation of genetic diversity depends on sequences of equal length. However, many homologous sequences downloaded from online repositories vary in length, posing a significant challenge to quantify the genetic diversity, especially haplotype diversity. We developed a new approach independent of sequence length by applying the same parameters used in calculating nucleotide diversity to estimate haplotype diversity. We compared this novel approach with the calculations by the program DNAsp, and we used simulation data from terrestrial vertebrates (birds, mammals and amphibians) and Homo sapiens to validate the method's performance. We further applied this approach to explore the global latitudinal gradients of haplotype diversity in amphibians, mammals and birds, and compared the results by traditional methods. The haplotype diversity calculated by our novel approach is consistent with the results from DNAsp. The simulations showed that our approach is robust and has a good estimating performance for sequence data with unequal lengths. For the datasets of terrestrial vertebrates and H. sapiens, our approach is capable of estimating haplotype diversity with unequal intraspecific sequence lengths. In contrast to patterns based on traditional methods, we observed different latitudinal patterns of haplotype diversity between the northern and southern hemispheres for terrestrial vertebrates, which is consistent with the updated pattern of nucleotide diversity for mammals. The present work contributes to the development of more precise quantification methods, which may be broadly applied to assessing biogeographical patterns of genetic diversity.

Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests

Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.

Phylogeographical and cytogeographical history ofArtemisia herba-alba(Asteraceae) in the Iberian Peninsula and North Africa: mirrored intricate patterns on both sides of the Mediterranean Sea

AbstractArtemisia herba-alba is an important component of Mediterranean dry steppe floras, being widely distributed in arid areas of the Iberian Peninsula and North-West Africa. In this study, we use genetic, cytogenetic and niche modelling tools to investigate the natural history of the species, focusing particularly on the role played by polyploidization to explain current diversity patterns throughout the main distribution range of the plant. Our sequencing data indicate a complex phylogeographical structure showing similar haplotype diversity patterns on both sides of the Strait of Gibraltar and no clear signals of genetic refugia. According to our cytogeographical results, we inferred multiple polyploidization events, which probably took place on the Iberian Peninsula and in North Africa independently. Environmental niche modelling suggested stable potential distributions of A. herba-alba on both sides of the Mediterranean Sea under present and past Last Glacial Maximum conditions, which could be related to the intricate spatial genetic and cytogenetic patterns shown by the species. Finally, environmental modelling comparison among cytotypes revealed that the niche of tetraploids is narrower and nested in that of diploids, a result that could indicate environmental specialization and could potentially explain recurrent establishment success of tetraploids.

Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories

Distance decay principles predict that species with larger geographic ranges would have greater intraspecific genetic diversity than more restricted species. However, invasive pest species may not follow this prediction, with confounding implications for tracking phenomena including original ranges, invasion pathways and source populations. We sequenced an 815 base-pair section of the COI gene for 441 specimens of Bactrocera correcta, 214 B. zonata and 372 Zeugodacus cucurbitae; three invasive pest fruit fly species with overlapping hostplants. For each species, we explored how many individuals would need to be included in a study to sample the majority of their haplotype diversity. We also tested for phylogeographic signal and used demographic estimators as a proxy for invasion potency. We find contrasting patterns of haplotype diversity amongst the species, where B. zonata has the highest diversity but most haplotypes were represented by singletons; B. correcta has ~7 dominant haplotypes more evenly distributed; Z. cucurbitae has a single dominant haplotype with closely related singletons in a ‘star-shape’ surrounding it. We discuss how these differing patterns relate to their invasion histories. None of the species showed meaningful phylogeographic patterns, possibly due to gene-flow between areas across their distributions, obscuring or eliminating substructure.

High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds

BackgroundWith the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals.ResultsBased on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included.ConclusionsHere, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes.

The major histocompatibility complex (MHC) contains the most polymorphic genetic system in humans, the human leukocyte antigen (HLA) genes of the adaptive immune system. High allelic diversity in HLA is argued to be maintained by balancing selection, such as negative frequency-dependent selection or heterozygote advantage. Selective pressure against immune escape by pathogens can maintain appreciable frequencies of many different HLA alleles. The selection pressures operating on combinations of HLA alleles across loci, or haplotypes, have not been extensively evaluated since the high HLA polymorphism necessitates very large sample sizes, which have not been available until recently. We aimed to evaluate the effect of selection operating at the HLA haplotype level by analyzing HLA A~C~B~DRB1~DQB1 haplotype frequencies derived from over six million individuals genotyped by the National Marrow Donor Program registry. In contrast with alleles, HLA haplotype diversity patterns suggest purifying selection, as certain HLA allele combinations co-occur in high linkage disequilibrium. Linkage disequilibrium is positive (Dij'>0) among frequent haplotypes and negative (Dij'<0) among rare haplotypes. Fitting the haplotype frequency distribution to several population dynamics models, we found that the best fit was obtained when significant positive frequency-dependent selection (FDS) was incorporated. Finally, the Ewens-Watterson test of homozygosity showed excess homozygosity for 5-locus haplotypes within 23 US populations studied, with an average Fnd of 28.43. Haplotype diversity is most consistent with purifying selection for HLA Class I haplotypes (HLA-A, -B, -C), and was not inferred for HLA Class II haplotypes (-DRB1 and—DQB1). We discuss our empirical results in the context of evolutionary theory, exploring potential mechanisms of selection that maintain high linkage disequilibrium in MHC haplotype blocks.

No obvious genetic erosion, but evident relict status at the westernmost range edge of the Pontic-Pannonian steppe plant Linum flavum L. (Linaceae) in Central Europe.

We investigate patterns of genetic variation along an east–west transect of Central European populations of Linum flavum and interpret the Quaternary history of its peripheral populations, especially those at the westernmost isolated range edge, discussing their migrations and possible relict status. We defined our peripheral transect across three study regions from Central Hungary, eastern Austria to southwestern Germany. Using AFLP fingerprinting and cpDNA sequence variation (rpL16 intron, atpI‐H), we analyzed 267 and 95 individuals, respectively, representing each study region by four populations. Hierarchical AMOVA (AFLPs) indicated significant variation among study regions (12% of total variance) and moderate differentiation between populations (10%). Population differentiation was high at the westernmost range edge (11.5%, Germany), but also in the east (13.4%, Hungary), compared to the Austrian study region (8.6%). Correspondingly, AFLP diversity was highest in the center of the study transect in eastern Austria. CpDNA haplotypes support a pattern of regional structuring with the strongest separation of the westernmost range edge, and some haplotype sharing among Austrian and Hungarian individuals. Equilibrating nucleotide versus haplotype diversity patterns, the highly diverse populations at the Pannonian range edge (Austria) indicate long‐term persistence, while Central Pannonian populations are obviously effected by recent bottlenecks. Intermediate nucleotide, but high haplotype diversity within the westernmost exclave (Swabian Alb), is indicative of a founder bottleneck during its pre‐LGM or early postglacial migration history, followed by sufficient time to accumulate cpDNA variation. The not obviously reduced genetic diversity and distinctiveness of L. flavum at the westernmost range edge suggest a long‐term persistence (relict status) of populations in this region, where the species has survived probably even the Würm glaciation in extra‐Mediterranean refugia. This genetic relict variation represents an important part of the overall genetic diversity found in the western periphery of this steppe plant and highlights the high conservation priority of respective gene pools.

A morphological and phylogenetic investigation into divergence among sympatric Australian southern bull kelps (Durvillaea potatorum and D. amatheiae sp. nov.)

Genetic analyses can reveal a wealth of hitherto undiscovered cryptic biodiversity. For co-occurring and morphologically similar species, the combination of molecular, ecological and morphological analyses provides an excellent opportunity for understanding some of the processes that can lead to divergence and speciation.The Australian endemic brown macroalga Durvillaea potatorum (Phaeophyceae) was examined with a combination of genetic and morphological approaches to confirm the presence of two separate species and to infer the processes that led to their divergence. A total of 331 individuals from 11 sites around coastal Tasmania were collected and measured in situ for a range of morphological and ecological characteristics. Tissue samples were also collected for each individual to allow genetic analyses using mitochondrial (COI) and nuclear (28S) markers. Genetic analyses confirmed the presence of two deeply divergent clades. The significant morphological differentiation, despite high levels of intra-lineage variability, further supported their recognition as distinct species.We describe a new species, D. amatheiae sp. nov., which is characterised by a narrower and proportionately shorter stipe, shorter total length, and higher number of stipitate lateral blades and branches than D. potatorum (sensu stricto). The occurrence of both species in sympatry along Tasmania’s eastern and western coasts, as well as their contrasting patterns of haplotype diversity, supports a hypothesis of geographical isolation, allopatric speciation and subsequent secondary contact in response to sea level and ocean current change throughout the Pleistocene glaciation cycles. This research contributes to resolving the phylogenetic relationships, taxonomy and evolution of the ecologically keystone kelp genus Durvillaea.

Phylogeny and phylogeography of the roaches, genus Rutilus (Cyprinidae), at the Eastern part of its range as inferred from mtDNA analysis

The genus Rutilus is a widely distributed lineage of cyprinids and ranges from West Europe to East Siberia. Although matrilineal phylogeny and phylogeography of western species were already studied, roaches from remaining part of the range were not examined. Phylogenetic analysis based on cytochrome b sequences detected the following three major phylogenetic clades: (i) R. frisii, (ii) R. rutilus s. str., and (iii) group of six Ponto–Caspian taxa: R. caspicus, R. heckelii, R. rutilus aralensis, R. rutilus lacustris, R. schelkovnikovi, and R. stoumboudae. Our results suggest that these “species” within Ponto–Caspian clade could be a single species (R. lacustris by priority of description). The Ponto–Caspian clade is most widely distributed among others and covers the freshwaters from the Aegean Sea basin to Laptev Sea tributaries. Both R. rutilus s. str. and Ponto–Caspian clades sympatrically occur in Black Sea and Caspian Sea basins, Azov Sea itself, and even in drainage of White Sea. The vastest zone of contact (approximately 1700 km) was detected in the Volga basin. The spatial pattern of haplotype diversity and the shape of haplotype network argued for multiple refugia in Ponto–Caspian region as well as a rapid post-glacial colonization of Volga River and Siberia.

A phylogenetic perspective on diversity of Galatheoidea (Munida, Munidopsis) from cold-water coral and cold seep communities in the western North Atlantic Ocean

Squat lobsters (Galatheoidea and Chirostyloidea), a diverse group of decapod crustaceans, are ubiquitous members of the deep-sea fauna. Within Galatheoidea, the genera Munida and Munidopsis are the most diverse, but accurate estimates of biodiversity are difficult due to morphological complexity and cryptic diversity. Four species of Munida and nine species of Munidopsis from cold-water coral (CWC) and cold seep communities in the northwestern Atlantic Ocean (NWA) and the Gulf of Mexico (GOM) were collected over eleven years and fifteen research cruises in order to assess faunal associations and estimate squat lobster biodiversity. Identification of the majority of specimens was determined morphologically. Mitochondrial COI sequence data, obtained from material collected during these research cruises, was supplemented with published sequences of congeners from other regions. The phylogenetic analysis of Munida supports three of the four NWA and GOM species (M. microphthalma, M. sanctipauli, and M. valida) as closely related taxa. The fourth species, Munida iris, is basal to most other species of Munida, and is closely related to M. rutllanti, a species found in the northeastern Atlantic Ocean (NEA). The majority of the nine species of Munidopsis included in our analyses were collected from chemosynthetic cold seep sites from the GOM. While seep taxa were scattered throughout the phylogenetic tree, four of these species (Munidopsis livida, M. similis, M. bermudezi, and M. species A) from the NWA and the GOM were part of a large eighteen-species clade that included species collected from Pacific Ocean chemosynthetic habitats, such as hydrothermal vents and whale falls. Shinkaia crosnieri was the sister taxon to the chemosynthetic clade, and M. livida was the most basal member of this clade. Munidopsis sp. B, an undescribed species with representative individuals collected from two GOM chemosynthetic sites, exhibited the largest genetic distance from other northern Atlantic species. Generally, intraspecific diversity was lower and patterns of haplotype diversity more simple in species of Munidopsis relative to Munida. This study puts two genera of NWA and GOM squat lobsters into a population genetic and phylogenetic context with regard to biogeography and habitat to enhance understanding of the history and evolutionary trajectories of these morphologically and ecologically diverse groups.

Sea, wind, or bird: Origin of &lt;i&gt;Fagus multinervis&lt;/i&gt; (Fagaceae) inferred from chloroplast DNA sequences

울릉도의 낙엽활엽수림에 ìš°ì í•˜ê³ ìžˆëŠ” 너도밤나무를 대상으로 엽록체 반수체형(haplotype)의 다양성과 ê³µê°„ì  분포를 íŒŒì• í•˜ê¸° 위해 울릉도 ì „ì—­ì—ì„œ 채집한 총 144개체로부터 psbA-trnH 구간의 염기서열을 ê²°ì •í•˜ì˜€ë‹¤. 너도밤나무의 ê·¼ì—°ì¢ ì„ 포함하여 계통분석을 수행한 ê²°ê³¼, 너도밤나무의 엽록체 반수체형은 일본산 F. japonica와 중국산 F. engleriana 분계조와 자매관계를 이루는 것으로 나타났다. 또한, 분석한 ëª¨ë“ ë„ˆë„ë°¤ë‚˜ë¬´ì˜ 개체들은 동일한 염기서열을 ê°–ê³ ìžˆëŠ” 것으로 나타나, 엽록체 반수체형의 다양성은 매우 낮은 것으로 íŒëª ë˜ì—ˆë‹¤. 이러한 결과는 동위효소 분석에 근거한 ìœ ì „ìž 다양성이 매우 높다는 기존 연구 결과와 대비되는 것으로서, 너도밤나무는 핵 ìœ ì „ìžì˜ 다양성은 높으나 엽록체 ìœ ì „ìžì˜ 다양성은 낮은 것으로 판단되며, 이것은 두 가지 가설로 ì„¤ëª í• ìˆ˜ 있다. 하나는 너도밤나무의 조상이 울릉도로 이주하여 ì •ì°©í• ì´ˆê¸° 단계에서 엽록체 반수체형이 ì§€ì—­ì ì¸ 구조를 갖는 조상 모집단으로부터 ì¢ ìžê°€ ì§€ì†ì ìœ¼ë¡œ ìœ ìž ëœ 결과로 í•´ì„í• ìˆ˜ 있다. 다른 하나는 육지의 조상 모집단으로부터 새 또는 태풍에 의해 소수의 ì¢ ìžê°€ ìœ ìž ë˜ì–´ ì •ì°©í•œ 후, 바람에 의해 조상 모집단의 화분이 ì§€ì†ì ìœ¼ë¡œ ìœ ìž ëœ 결과인 것으로 ì¶”ë¡ í• ìˆ˜ 있다. 울릉도 내의 다양한 ê³ ìœ ìžìƒì‹ë¬¼ì˜ 기원을 ê·œëª í•˜ëŠ” 데 있어서 ëª¨ê³„ìœ ì „ì„ 함으로 인해 ì¢ ìžì˜ 이동을 ì¶”ì í• ìˆ˜ 있는 엽록체 DNA에 근거한 ë¹„êµê³„í†µì§€ë¦¬í•™ì  연구가 필요한 것으로 사료된다. 주요어: 너도밤나무, 엽록체 DNA, 반수체형, 울릉도

Occurrence and genetic diversity of new populations of Halyomorpha halys in Europe

Originating in East Asia, the brown marmorated stink bug, Halyomorpha halys, has established in North America and Europe where it has become an urban and agricultural pest. Although initial populations in Europe were only reported in Switzerland, H. halys has expanded its range to include areas in France, Greece, Hungary, and Italy. Analysis of a portion of the mitochondrial COI gene was used to evaluate the genetic diversity of these populations and to investigate the movement and spread of different COI haplotypes of this pest in Europe. A total of 9 haplotypes are now confirmed in Europe. Four of these haplotypes have not been previously reported elsewhere, and one of these haplotypes has not been previously reported in Europe but is known from Korea. The H. halys population in Greece was the most diverse, with 7 of the 9 haplotypes occurring in the area of collection. Haplotype H1, which is known from North America, Italy, and China, was also present in samples collected in France, Greece, Hungary, and Switzerland. In fact, the H1 haplotype was the dominant haplotype detected in Budapest, Hungary and also occurred frequently in the samples from Athens, Greece. Patterns of haplotype diversity indicate the movement of successful invasive populations to generate secondary invasions within Europe (‘bridgehead effect’), as well as the occurrence of multiple invasions from Asia. Scenarios regarding the movement and spread of particular haplotypes in Europe are discussed.

Comparative phylogeography of eight herbs and lianas (Marantaceae) in central African rainforests.

Vegetation history in tropical Africa is still to date hardly known and the drivers of population differentiation and speciation processes are little documented. It has often been postulated that population fragmentations following climate changes have played a key role in shaping the geographic distribution patterns of genetic diversity and in driving speciation. Here we analyzed phylogeographic patterns (chloroplast-DNA sequences) within and between eight (sister) species of widespread rainforest herbs and lianas from four genera of Marantaceae (Halopegia, Haumania, Marantochloa, Megaphrynium), searching for concordant patterns across species and concordance with the Pleistocene refuge hypothesis. Using 1146 plastid DNA sequences sampled across African tropical lowland rainforest, particularly in the Lower Guinean (LG) phytogeographic region, we analyzed intra- and interspecific patterns of genetic diversity, endemism and distinctiveness. Intraspecific patterns of haplotype diversity were concordant among most species as well as with the species-level diversity pattern of Marantaceae. Highest values were found in the hilly areas of Cameroon and Gabon. However, the spatial distribution of endemic haplotypes, an indicator for refuge areas in general, was not congruent across species. Each proposed refuge exhibited high values of endemism for one or a few species indicating their potential role as area of retraction for the respective species only. Thus, evolutionary histories seem to be diverse across species. In fact, areas of high diversity might have been both refuge and/or crossing zone of recolonization routes i.e., secondary contact zone. We hypothesize that retraction of species into one or the other refuge happened by chance depending on the species' distribution range at the time of climate deterioration. The idiosyncratic patterns found in Marantaceae species are similar to those found among tropical tree species, especially in southern LG.

Intraspecific genetic variation in selected mosses of Scandinavian interglacial refugia suggests contrasting distribution history patterns

Three pleurocarpous mosses were studied to explore the haplotype diversity patterns in a Scandinavian system of interglacial refugia in which low-competitive species of calcareous or base-rich habitats occur. Hypnum bambergeri and H. vaucheri displayed little variation across Scandinavia. For the third species, Drepanocladus turgescens, an analysis of molecular variance showed that two S Scandinavian lowland regional populations were significantly different from each other and differed or almost differed (Gotland vs. Jamtland, according to pair-wise ΦPT) from the populations of the Scandinavian mountain range and Svalbard. Haplotype diversity displayed little variation among regional populations, and did not reflect the higher frequency of sexual reproduction in southern than in mountain populations. A coalescent-based analysis (LAMARC) indicated immigration into the population now found in the lowlands from that represented in the mountains. This is contrary to that found in Rhytidium rugosum in an earlier study and, together with the fact that sporophytes are produced almost exclusively in the lowlands, speaks against this direction of post-glacial migration. Therefore, if the LAMARC results reflect migration patterns, these most probably reflect events that occurred earlier. Taken together with the results on R. rugosum, this study emphasizes the fact that moss species having similar distribution patterns reached these distributions in partly different ways. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 295–310.

Southern Scandinavian lowland populations of Rhytidium rugosum (Hedw.) Kindb. (Bryophyta, Rhytidiaceae) differ significantly from those in the mountains

Haplotype diversity patterns based on internal transcribed spacer (ITS) and gpd (glyceraldehyde 3-phosphate dehydrogenase) in Scandinavian Rhytidium rugosum were compared between four populations from the mountain range and two in the southern lowlands. The mountain populations differ from the southern lowland ones in haplotype composition and the lowland ones differ from each other, suggesting different histories. A coalescent-based analysis (LAMARC) indicated immigration into the population now found in the mountains from that represented in the lowlands. Because several factors argue against such a dispersal scenario within the relatively short postglacial period, it is proposed that these migration patterns are older than the postglacial period. It is suggested that the mountain range populations immigrated from a source population either in the north-east or within Scandinavia, whereas the lowland populations are likely to represent remains of the glacial population of lowland Europe. The highest haplotype diversity in Scandinavia was found in the Gudbrandsdalen area in southern Norway. This is probably explained by the fact that this is the only region in Europe where R. rugosum regularly reproduces sexually. The lowest diversity was found on the Great Alvar on the island of Öland off the Baltic coast of southern Sweden, and is most likely a result of gradual loss of haplotypes over time.

Dispersal at a Snail’s Pace: Historical Processes Affect Contemporary Genetic Structure in the Exploited Wavy Top Snail (Megastraea undosa)

We used population genetics to assess historical and modern demography of the exploited wavy top snail, Megastraea undosa, which has a 5-10 day pelagic larval duration. Foot tissue was sampled from an average of 51 individuals at 17 sites across the range of M. undosa. Genetic structure at the mtDNA locus is strikingly high (ΦST of 0.19 across 1000 km), and a major cline occurs in northern Baja California (ΦCT of 0.29 between northern and southern populations). Genetic data indicate that the northern region is highly connected through larval dispersal, whereas the southern region exhibits low genetic structure. However, additional analyses based on patterns of haplotype diversity and relationships among haplotypes indicate that M. undosa has likely recently expanded into the Southern California Bight or expanded from a small refugial population, and analysis using isolation by distance to calculate dispersal distance indicates surprisingly short estimates of dispersal from 30 m to 3 km. This scenario of a northward expansion and limited larval dispersal is supported by coalescent-based simulations of genetic data. The different patterns of genetic variation between northern and southern populations are likely artifacts of evolutionary history rather than differences in larval dispersal and this may have applications to management of this species. Specifically, these data can help to inform the scale at which this species should be managed, and given the potentially very small dispersal distances, this species should be managed at local scales. Consideration of the evolutionary history of target species allows for a more accurate interpretation of genetic data for management.

Identification of quantitative trait loci influencing skeletal architecture in mice: emergence of Cdh11 as a primary candidate gene regulating femoral morphology.

Bone strength is influenced by many properties intrinsic to bone, including its mass, geometry, and mineralization. To further advance our understanding of the genetic basis of bone-strength-related traits, we used a large (n = 815), moderately (G(4) ) advanced intercross line (AIL) of mice derived from a high-runner selection line (HR) and the C57BL/6J inbred strain. In total, 16 quantitative trait loci (QTLs) were identified that affected areal bone mineral density (aBMD) and femoral length and width. Four significant (p < .05) and one suggestive (p < .10) QTLs were identified for three aBMD measurements: total body, vertebral, and femoral. A QTL on chromosome (Chr.) 3 influenced all three aBMD measures, whereas the other four QTLs were unique to a single measure. A total of 10 significant and one suggestive QTLs were identified for femoral length (FL) and two measures of femoral width, anteroposterior (AP) and mediolateral (ML). FL QTLs were distinct from loci affecting AP and ML width, and of the 7 AP QTLs, only three affected ML. A QTL on Chr. 8 that explained 7.1% and 4.0% of the variance in AP and ML, respectively, was mapped to a 6-Mb region harboring 12 protein-coding genes. The pattern of haplotype diversity across the QTL region and expression profiles of QTL genes suggested that of the 12, cadherin 11 (Cdh11) was most likely the causal gene. These findings, when combined with existing data from gene knockouts, identify Cdh11 as a strong candidate gene within which genetic variation may affect bone morphology.

Gateways to Hawai‘i: Genetic Population Structure of the Tropical Sea CucumberHolothuria atra

Holothuria atrais one of the most common and widest ranging tropical, coral reef sea cucumbers in the world, and here we examine population genetic structure based on mitochondrial COI to aid in determining the appropriate scale for coral reef management. Based on SAMOVA, AMOVA and BARRIER analyses, we show that despite its large range,H. atrahas hierarchical, fine-scale population structure driven primarily by between-archipelago barriers, but with significant differences between sites within an archipelago as well. Migrate analyses along with haplotype networks and patterns of haplotype diversity suggest that Hawai‘i and Kingman reef are important centers of the genetic diversity in the region rather than an evolutionary dead-end for migrants from the Indo-Pacific. Finally we show that forH. atraKingman Reef is the most likely stepping stone between Hawai‘i and the rest of the Pacific, not Japan or Johnston Atoll as previously presumed. Based on our data, Johnston Atoll can instead be seen as an outpost of the Northwestern Hawaiian Islands rather than a gateway to the Hawaiian Archipelago.