Microsatellite Allele Frequencies Research Articles

Leaf shredding as an alternative strategy for managing apple scab resistance to demethylation inhibitor fungicides

Within integrated apple scab control there is a strong focus on reduction of Venturia inaequalis primary inoculum. The hypothesis that leaf shredding as an orchard sanitation practice would reduce the effective population size of the fungus (resulting in lower genetic variation due to reduction in sexual offspring) was tested. Assuming the allele causing fungicide resistance is already present in the population, it will be widely distributed at the end of the season, since selection occurs when the demethylation inhibitor (DMI) fungicide was applied. For short-term disease management a reduction of inoculum size, (i.e. potential ascospore dose) is most important. In the long-term resistant isolates/genotypes would be less likely to survive the winter and/or to infect in the spring, if that inoculum (i.e. in fallen leaves) has been removed. To sustain the use of highly effective synthetic fungicides, such as the DMIs, fungicide resistance management practices have to be evaluated. Fungicide resistance, which negatively affects pathogen fitness, is hypothetically reversible, if the selection pressure by the fungicide is removed. This study quantified the effect of leaf shredding on changes in the pathogen’s flusilazole sensitivity and population genetic structure using SSR markers. Venturia inaequalis populations in orchard trials, where sanitation practices had been applied, were tested for flusilazole sensitivity in planta and in vitro. Significant shifts towards flusilazole resistance were identified in orchards with a history of DMI application without sanitation treatment, with a mean sensitivity of EC50= 0.208 ug/ml (n=49) compared to an unexposed V. inaequalis population (EC50= 0.104 ug/ml, n=55). However, the isolates from the same sanitation trial orchards, from leaf shredding treatment in combination with a fungicide spray programme, had a mean EC50 of 0.110 ug/ml (n=41), similar to an unexposed V. inaequalis population. Furthermore, V. inaequalis offspring after sanitation treatment, showed shifts in microsatellite allele frequency distribution patterns used as an indicator of sexual reproduction. This study concludes that sanitation treatments, i.e. leaf shredding, impact on fungicide sensitivity and therefore effectively contributes to fungicide resistance management.

Biological Investigation of the Endangered Northern Madtom in the North Channel St. Clair River

AbstractAquatic organisms and the habitats they live in are declining globally, yet managers often lack even basic biological information for individual imperiled species. This makes assessment of the current status, management needs, and recovery targets for these species challenging. One such organism is the Northern Madtom Noturus stigmosus, a small, bottom‐dwelling catfish of the family Ictaluridae. Northern Madtom are listed as endangered in the state of Michigan and the province of Ontario, with only a handful of isolated populations known in each region. To address life history uncertainties and to provide fisheries managers with baseline information to inform decision making, the Michigan Department of Natural Resources annually sampled Northern Madtom in the St. Clair River using minnow traps and amassed the largest known data set for this species. We handled 871 individuals from 2010 to 2022, with yearly catch rates ranging from 0.17 to 1.33 individuals/trap. Age estimates derived from otoliths and dorsal spines of 17 individuals showed no clear pattern of bias, indicating that nonlethally collected dorsal spines provide a suitable age estimation method. We developed an age–length key to assign ages to all individuals in our data set, calculated growth parameters, and determined that annual mortality rates across all ages ranged from 46% to 69%. Diet analysis revealed that caddisfly (order Trichoptera) larvae were the dominant prey item and fecundity averaged 178 eggs/female. We compared microsatellite allele frequencies and mitochondrial DNA haplotypes among samples collected in the St. Clair River and the Detroit River. Significant evidence of genetic structure was present, indicating limited gene flow and suggesting that separate management of these two populations may be warranted. Collectively, these data provide context for managers interested in the development of biological reference points and planning for the conservation and management of this species.

The combined use of organochlorine contaminant profiles and molecular genetics for stock discrimination of white whales (Delphinapterus leucas) hunted in three communities on southeast Baffin Island

Putative stock differences in white whales (Delphinapterus leucas) landed by hunters between 1992 and 1996 from the southeast Baffin Island communities of Kimmirut (KI), Iqaluit (IQ) and Pangnirtung (PA) were examined using organochlorine contaminant (OC) profiles of 124 whales, the molecular genetics of 270 whales and both types of data from 97 whales. OC concentrations were generally lower in whales hunted in PA than those hunted in KI and IQ, and many OCs were lower in KI than IQ. In canonical discriminant function (CDA) using 13 OC predictor variables (10 OC groups, mirex, octachlorostyrene and endosulfan), the first canonical function accounted for 77% of the variance and separated whales from PA with those from IQ and KI; the second canonical function separated whales from KI with those from IQ. A previous study of the molecular genetics of white whales showed that whales hunted in the three communities were significantly differentiated on the basis of haplotype and/or microsatellite allele frequencies (de March et al., 2002). When the results of two studies were combined, many whales were slightly more strongly associated with a particular source hunting community than they were in the component studies. Using a posteriori crossvalidation probabilities in an analysis with variables from both studies, 72% of white whales were correctly crossvalidated to their source hunting community; 82.5% from PA; 56.5% from IQ; and 58.8% from KI. The highest misclassification rates were KI to IQ (23.5%), IQ to KI and IQ to PA (21.7% in both cases) and the lowest rates were PA to KI (3.5%), PA to IQ (14.0%) and KI to PA (17.6%). This pattern of assignments was not significantly different from those in the genetics or contaminants studies alone. However, the crossvalidation probabilities to the most likely source communities were approximately 20% larger in the combined analysis than in the component studies. Canonical scores in the combined analysis were more strongly correlated with variables from the OC Study than with variables from the genetics study. Whales placed to PA and IQ could be identified primarily by their OC signatures, however many whales from PA also had a strong PA genetics signature. Whales from IQ were identifiable only by their OC signatures. Both a strong KI genetics and OC signature described approximately half of whales from KI. We believe that at least three stocks were sampled from the three communities. Some whales in PA were very distinct, confirming previous beliefs that a separate stock occurs in Cumberland Sound. Whales hunted in IQ and KI differed to a lesser degree, and may be from stocks subject to a gradient or from a mixture of stocks. Some whales from PA are more likely to have genotypes and OC signatures that are also found in IQ and KI than the reverse. It is possible that summering areas of the stocks that were identified in KI and IQ are not consistent from year to year or across generations. The main problems in combining results for individuals used in several studies, particularly when there are many measurements for relatively few individuals, is to find a limited number of relevant predictor variables that can be used in the combined analysis, while avoiding both overparameterisation and results blurred by meaningless variables.

Hierarchical Clustering on Principal Components of Microsatellite Frequency Allele Data from Indonesian Buffaloes

Buffalo is a livestock that is used for meat, milk, draught animals, and religious ceremonies in Indonesia. Buffalo genetic information has not been obtained optimally for the development of buffalo breeding programs. Allele frequency is essential information to determine the genetic diversity of a population. This study investigates the use of one of the multivariate analyzes, hierarchical clustering on principal component (HCPC). The data used were microsatellite allele frequency data of 199 swamp buffaloes and 12 river buffaloes in 8 population (7 populations swamp buffalo and 1 population of river buffalo). Furthermore, the data is processed using factoextra and FactoMineR package in R 4.0.0. The results found that the ILSTS61 and ILSTS17 loci could be used as genetic markers to determine the genetic relationship of Indonesian buffalo. From the study, it is concluded that the HCPC method with allele frequency data can be used to analyze genetic relationships in Indonesian buffalo. The PC (Principle Component) value can describe which loci determines the genetic relationship.
 HIGHLIGHTS
 
 Allele frequency data can be used to determine genetic relationships among population
 Principle component value can determine which the loci is influential in determining a genetic relationship
 Hierarchical Clustering on Principal Components can be used to analyze genetic relationships
 
 GRAPHICAL ABSTRACT

Genetic Analysis of Formosan Subterranean Termite (Blattodea: Rhinotermitidae) Populations in California.

A new infestation of the Formosan subterranean termite, Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae), was discovered in Canyon Lake, Riverside County, California. We used three mitochondrial DNA (COI, COII, and 16S) and seven polymorphic microsatellite markers to characterize the genetic relationship of the colony with two other colonies that were collected in 1992 and 2018 in La Mesa, San Diego County. Maximum likelihood phylogeny of C. formosanus based on concatenated COI and COII sequences revealed that the two La Mesa populations (CA01 and CA02) and the Canyon Lake population (CA03) were from different maternal lineages. Based on the 14 COII haplotypes of C. formosanus found world-wide, CA01 and CA02 belonged to a haplotype widely distributed across the United States, while CA03 was grouped under a haplotype predominantly found in Asia. Microsatellite allele frequencies across all loci for both La Mesa populations were relatively similar, but significant genetic differences were found between CA02 and CA03 colonies (FST = 0.24; Dest = 0.30; G″ ST = 0.55; P < 0.01).

Multivariate analysis of five chicken breed in Indonesia based on microsatellite allele frequency

&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Objective: &lt;/strong&gt;This study tries to examine several multivariate methods in classifying genetic diversity using microsatellite allele frequency data.&lt;/p&gt;&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Methods: &lt;/strong&gt;This study used microsatellite allele frequency data from White Leghorn (n = 48), Kampung (n = 48), Pelung (n = 24), Sentul (n = 24), and Black Kedu (n = 25) from Indonesian Research Institute for Animal Production. Allele frequency data were analyzed by the Neighbor-Joining (NJ) method using the POPTREE2 program. The data was also analyzed by the Principal Component Analysis (PCA), Correspondence Analysis (CA), and Hierarchical Clustering on Principal Components (HCPC) methods using the factoextra and FactoMineR packages in the R 4.0.0 program.&lt;strong&gt;&lt;/strong&gt;&lt;/p&gt;&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Results: &lt;/strong&gt;Correspondence Analysis (CA) found Sentul is more closer to Black Kedu. However, based on NJ, PCA, and HCPC showed Sentul is closer to Kampung. Based on the value of Dimension 1, Correspondence Analysis (80.7%) can explain greater variation than PCA (58.9%). However, CA method generated different results compared to NJ, PCA, and HCPC. NJ, PCA, and HCPC found four chicken clusters, namely cluster 1 (White Leghorn), cluster 2 (Pelung), cluster 3 (Black Kedu), and cluster 4 (Kampung and Sentul).&lt;strong&gt;&lt;/strong&gt;&lt;/p&gt;&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;In conclusion, HCPC is a better multivariate method for analyzing allele frequency data than PCA and CA. HCPC can be used to analyze allele frequency data better than PCA, because HCPC is a combination of methods from hierarchical clustering and principal components.&lt;/p&gt;

Expanding population edge craniometrics and genetics provide insights into dispersal of commensal rats through Nusa Tenggara, Indonesia

The Nusa Tenggara island chain consists of an archipelago that runs roughly east-west in eastern Indonesia. As part of Wallacea, it has never been connected to any continental landmass, and has been subject to a variety of biological invasions that have populated the islands. Here, we examine the craniometric and molecular genetic records of several species of Rattus sensu lato in the island chain. We use the predictions of expanding population edge phenotypic selection in an effort to understand the movement of Rattus rattus and Rattus exulans through the archipelago. We also examine the mitochondrial haplotype networks of R. argentiventer, R. exulans, and the R. rattus Complex (RrC) and microsatellite allele frequency clustering patterns for the RrC, to examine relationships within and between Nusa Tenggara populations, and those of Asia and the Pacific where relevant for each taxon. In the RrC LIV and RrC LII haplotype networks, 20 haplotypes with seven from Nusa Tenggara were observed for RrC LIV, and 100 haplotypes with seven from Nusa Tenggara observed for RrC LII. The top performing RrC craniometric model had a negative association between size and distance from the easternmost point of the samples from Nusa Tenggara, consistent with increasing size moving west to east. The cytochrome b network for the R. exulans sequences comprised 14 haplotypes, with three observed from mainland Southeast Asia, one shared with Nusa Tenggara and regions further east, and another haplotype observed in Nusa Tenggara and in the Pacific. The R. exulans craniometric model selection produced four equally well performing models, with no migration scenario preferred. Finally, the haplotype network of R. argentiventer comprised 10 haplotypes, with six observed in Nusa Tenggara, including a relatively early cluster from the east of the archipelago. Our results are compatible with a polyphasic and polydirectional invasion of Nusa Tenggara by Rattus, likely beginning with RrC from the west to the east, an expansion of R. exulans from Flores, seemingly in no preferred overall direction, and finally the invasion of R. argentiventer from the east to the west. We find some support for the Dong Son drum maritime exchange network contributing to the distribution of the latter species.

Effects of urbanization on population genetic structure of western gray squirrels

Habitat loss and fragmentation due to urbanization are key contributors to the decline of biodiversity. The consequence of these factors is small, isolated populations that are more susceptible to deterministic and stochastic threats of extinction. There is an increasing trend in population reductions of the western gray squirrel (Sciurus griseus) in urban areas of Southern California, USA. Griffith Park (GP) contains one of the last urban populations of western gray squirrels (WGS) present in Los Angeles. We used hairtubes to collect hair of WGS at 3 sites within GP and at 5 sites outside of GP. Twelve microsatellite loci and a 550 bp segment of the mitochondrial control region were used to examine the genetic diversity within GP and among all sample sites, and to determine gene flow within GP. Results revealed subpopulations within GP have low levels of allelic richness at microsatellite loci (AR = 2.28–2.53) and low mitochondrial haplotype diversity (HD = 0.000–0.271). We found significant genetic differentiation (FST = 0.109–0.156, p < 0.001), high levels of relatedness within each GP subpopulation (0.399–0.633), and a lack of private alleles (AP = 0.09–0.27) at microsatellite loci. Mode shifts in microsatellite allele frequencies and positive M-ratio tests provide evidence of bottlenecks within a GP subpopulation. The effective population size for GP (Ne = 9.1) highlights the effects of genetic drift on this isolated population. We suggest conservation efforts that could maintain these last extant populations of a native species in urban Los Angeles.

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species.

Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe×niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

Diversity of Kabardian horses and their genetic relationships with selected breeds in the Russian Federation based on 17 microsatellite loci

17 standard microsatellite loci, used for horse identification and origin control, were deployed for studying the genetic structure of Kabardian breed. The observed (Ho) and expected (He) heterozygosity, level of polymorphism (Na), polymorphism information content (PIC), and fixation index (Fis) were calculated. The results of microsatellite analysis were used for description of the Kabardian breed at the population level. The distribution and frequency of microsatellite alleles was compared with Russian populations of Arab and Thoroughbred horses.

Understanding genetic diversity, structure and population differentiation in selected wild species and cultivated Indian and exotic rose varieties based on microsatellite allele frequencies

Roses are the most important commercial ornamental plants grown for flowers, perfumery and nutraceutical compounds. Commercially cultivated roses (Rosa × hybrida L.) are complex interspecific hybrids probably derived from 8-10 wild species among the large diversity of 130-200 species in genus Rosa. Wild germplasm is a primary source of variability and plays a major role in improving existing varieties by broadening their genetic base. In the present investigation, we have utilized the previously identified SSR primers for studying the diversity among 148 selected rose genotypes, including wild species and cultivated varieties of Indian and exotic origin. A total of 88 alleles was scored using 30 polymorphic loci; they produced average 2.9±1 alleles per locus. Polymorphism information content (PIC) values for different SSR loci ranged from 0.08 to 0.8 with a mean value of 0.5±0.2. The neighbor-joining tree generated based on Nei’s (1978) genetic distance values grouped the population into three major clusters. Cluster-I and II consists of all modern rose cultivars (Rosa × hybrida L.) originated from India and cluster-III consists of all exotic cultivars, wild species and a few cultivars from India. STRUCTURE analysis based on microsatellite allelic data, partitioned the total rose genotypes into four different sub-populations with some individual genotypes having genomic admixture. Population subdivision estimates, FST between different subpopulations ranged from 0.01-0.15 indicates low to moderate level of divergence existing among the rose cultivars and germplasm. Population differentiation in rose cultivars and wild species corresponds to their geographical origin and lineages. Analysis of molecular variance (AMOVA) results revealed that 83.12 % of the variance was accounted for by within sub-groups followed by significant levels of variation among the populations (10.42%) and least variance (6.46%) was noticed among individuals within groups.

Small marsupial, big dispersal? Broad- and fine-scale genetic structure of an endangered marsupial from the Australian arid zone

The irregular nature of rainfall in the Australian arid and semiarid zones results in a heterogeneous distribution of resources in both time and space. The mammal species that reside in these regions are uniquely adapted to these climatic conditions, often occurring in naturally low densities and increasing significantly in numbers following major rainfall events. We investigated how these adaptations may influence genetic diversity and gene flow across the landscape in an endangered semiarid/arid-zone marsupial, the sandhill dunnart (Sminthopsis psammophila), from three known populations in southern Australia. Analyses of mitochondrial control region (CR) sequences and microsatellite loci revealed that S. psammophila had maintained similar levels of genetic diversity to other sympatric Sminthopsis species despite its endangered status. There was no evidence for significant phylogeographic structure within the species, but each population was genetically differentiated, based on the frequency of microsatellite alleles and CR haplotypes, suggesting that they should be considered as distinct Management Units for conservation. At a fine spatial scale, no significant genetic structure or sex-biased dispersal was detected within a study site of 240km2. These findings suggest that both sexes are highly mobile, which allows individuals to locate localised resource patches when they become available. We detected evidence of a genetic bottleneck within the population, possibly caused by a recent drought. Our study highlights the importance of maintaining connectivity across the landscape for semiarid- and arid-zone species to enable them to track resource pulses and maintain genetic diversity.

Investigating the genetic structure of trout from the Garden of Ninfa (central Italy): Suggestions for conservation and management

AbstractMediterranean populations of brown trout (Salmo trutta L. complex) have lost a large part of their genetic distinctiveness, mostly due to massive restocking, and the waters of the Gardens of Ninfa (province of Latina, central Italy, Site of Community Importance since 2013) are regarded as one of a few potential reservoirs of autochthonous trout lineages in the Tyrrhenian drainage of the Italian peninsula. In this study, nuclear and mitochondrial markers were used on brown trout samples from Ninfa to estimate non‐Mediterranean influence in the population gene pool, potential changes of genetic structure over time and genetic relationships with other sites known (or suspected) to host native trout gene pools. Striking changes in both microsatellite and mtDNA allele frequencies over a 9‐year time span were found and provided evidence of unrecorded stocking from the nearby Lake Fibreno. Results are analysed in the light of potential ecological consequences of such events on a longer time scale and provide a scientific background for fisheries management and conservation programmes in the area.

Spatial genetic structure and recruitment dynamics of burbot (Lota lota) in Eastern Lake Michigan and Michigan tributaries

Abstract Burbot (Lota lota) are the only freshwater member of the Cod like (Lotidae) family that have a circumpolar distribution and occupy the widest geographic distribution of all Laurentian Great Lakes fish species. Information regarding burbot spatial genetic structure and recruitment dynamics is critical for the development of effective management strategies. Although burbot are a species of conservation concern throughout their range, little demographic or behavioral information exists. We estimated levels of genetic diversity within, and the degree of spatial population structure between samples collected from Lake Michigan and tributaries of the Manistee River, MI. Measures of genetic diversity across 10 microsatellite loci were moderately high. Disparities between adult groups sampled in Lake Michigan and the Manistee River were notable for observed heterozygosity (0.662 vs 0.488) and allelic richness (11.7 vs 6.6). Significant levels of inter-population variance in microsatellite allele frequencies (FST 0.154 to 0.208) were detected between Lake Michigan and the Manistee River samples. Results indicate reproductive isolation between what plausibly may be riverine and lacustrine spawning life history types. Pedigree analyses for three cohorts sampled in the Manistee River revealed that a sizeable number of adults contributed reproductively to multiple cohorts, indicating spawning philopatry. While data were collected from restricted areas in lacustrine and river habitats, analyses revealing microgeographic genetic structuring, potentially attributed to life history polymorphisms, have significant implications for burbot management in the Great Lakes.

Lack of introgressive hybridization by North African catfish (Clarias gariepinus) in native Vietnamese bighead catfish (Clarias macrocephalus) populations as revealed by novel nuclear and mitochondrial markers

The widespread farming of catfish (genus Clarias) hybrids between bighead catfish (C. macrocephalus, Cm) and the introduced North African Catfish (C. gariepinus, Cg) in the Mekong Delta, where flooding is common, has raised concerns of introgression of Cg into the native catfish due to backcrossing by escaped hybrids with wild Cm. This study employed novel PCR-RFLP analyses of a mitochondrial (Cytochrome c oxidase subunit I, COI) and two nuclear (Rhodopsin and Tropomyosin) markers and six microsatellite loci to differentiate hybrid individuals from their parental species, and evaluate whether introgression has occurred in wild and cultured Cm populations in the region. Results of marker screening showed that sizes and frequencies of microsatellite alleles differed between the two parental species. Four loci exhibited fixed species-specific differences in allele frequency (monomorphic in Cg and highly polymorphic in Cm). Levels of sequence variation varied at the three genes examined, ranging from 3 to 8% (sequence length 652bp for COI, 802bp for Rhodopsin and 925bp for Tropomyosin). Based on variable sites identified that were not shared between the two species, 3 restriction enzymes (SpeI, XcmI and PflMI) were selected to digest PCR products at species-specific sites within the COI, Rhodopsin and Tropomyosin genes, respectively. Results of PCR-RFLP analyses confirmed that Cm is the maternal lineage of cultured hybrids, while nuclear genes (Rhodopsin and Tropomyosin) and microsatellite loci revealed that hybrids possessed admixed multi-locus genotypes relative to the two parental species. Analyses of six microsatellite loci and PCR-RFLP of two nuclear genes in 473 individuals collected from 11 wild and three cultured populations revealed one F1 hybrid in the wild but no evidence of widespread introgression into native bighead catfish. These results differ from findings in Thailand where intensive catfish culture and deliberate species hybridization is practiced.

Local recruitment of humpback whales in Glacier Bay and Icy Strait, Alaska, over 30 years

We provide new information on the scale at which fidelity and recruitment underlie observed increases in humpback whale Megaptera novaeangliae populations. We used photo- identification records and DNA profiles from whales in Glacier Bay and Icy Strait (GBIS), south- eastern Alaska (SEAK) to investigate 3 sources of population increase over 33 yr (1973�2005): local GBIS recruitment, recruitment from elsewhere in SEAK, and immigration from outside SEAK. We defined 2 temporal strata for these longitudinal records: 'founder' individuals identified from 1973 to 1985 (n = 74; n = 46 with DNA profiles) and 'contemporary' individuals identified from 2004 to 2005 (n = 171; n = 118 with DNA profiles). To distinguish between local recruitment and recruitment from elsewhere in SEAK, we estimated the proportion of the contemporary stra- tum that was either a returning founder or descended from a founder female. After excluding 42 contemporary whales without a known mother or genotype to infer maternity, 73.6% of the con- temporary stratum was confirmed or inferred through parentage analysis to be either a returning founder or a descendant of a founder mother. Of the 25 females with genotypes in the founder stratum, 24 (96%) were either represented in the contemporary stratum, had at least 1 descendant in the contemporary stratum, or both. We found no significant differences in microsatellite allele or mtDNA frequencies between the strata, suggesting little or no immigration from other feeding grounds. Our results highlight the importance of local habitat protection for a recovering species with culturally inherited migratory destinations.

Postglacial recolonizations, watershed crossings and human translocations shape the distribution of chub lineages around the Swiss Alps.

BackgroundDistributions of European fish species were shaped by glaciations and the geological history of river networks until human activities partially abrogated the restrictions of biogeographical regions. The nearby origins of the Rhine, Rhone, Danube and Po rivers in the Swiss Alps allow the examination of historical and human-influenced patterns in fish genetic structure over a small geographic scale. We investigated these patterns in the widespread European chub (Squalius cephalus) from the Rhone, Rhine and Danube catchments and its proposed southern sister species Italian chub (Squalius squalus) from the Po catchment.ResultsA phylogenetic tree constructed from mitochondrial Cytochrome b and COI sequences was consistent with earlier work in that it showed a separation of European chub and Italian chub, which was also reflected in microsatellite allele frequencies, morphological traits and shape differences quantified by geometric morphometrics. A new finding was that the predominant mitochondrial haplotype of European chub from the Rhine and Rhone catchments was also discovered in some individuals from Swiss populations of the Italian chub, presumably as a result of human translocation. Consistent with postglacial recolonizations from multiple refugia along the major rivers, the nuclear genetic structure of the European chub largely reflected drainage structure, but it was modified by watershed crossings between Rhine and Rhone near Lake Geneva as well as between Danube and Rhine near Lake Constance.ConclusionOur study adds new insights into the cyprinid colonization history of central Europe by showing that multiple processes shaped the distribution of different chub lineages around the Swiss Alps. Interestingly, we find evidence that cross-catchment migration has been mediated by unusual geological events such as drainage captures or watershed crossings facilitated by retreating glaciers, as well as evidence that human transport has interfered with the historical distribution of these fish (European chub haplotypes present in the Italian chub). The desirable preservation of evolutionarily distinct lineages will thus require the prevention of further translocations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0750-9) contains supplementary material, which is available to authorized users.

Phylogeography of the freshwater mussel species Lasmigona costata: testing post-glacial colonization hypotheses

Understanding genetic diversity across large spatial scales helps to reveal patterns of population structure. Mitochondrial DNA sequences and microsatellite loci were used to analyze the phylogeography of a common unionid species (Lasmigona costata) from the Laurentian Great Lakes and historically connected river drainages. Phylogeographic patterns were assessed to determine colonization routes into the Great Lakes following glacial recession. A suite of seven microsatellite loci were genotyped and a fragment of the mitochondrial gene COI was sequenced. Multiple analyses using microsatellite allele frequencies suggest at least two distinct genetic populations for L. costata. A total of seven hypothesized post-glacial dispersal scenarios were compared using isolation by distance to test the various dispersal models. Evidence was strongest for two post-glacial dispersal routes into the Great Lakes: one utilizing a connection between the Wabash and Maumee River watersheds, and one utilizing a connection between the Wisconsin River and Green Bay watersheds. A highly differentiated and monophyletic population of L. costata was identified in the Ozark Highlands, which may constitute a unique taxonomic entity.

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.

Cultural traditions across a migratory network shape the genetic structure of southern right whales around Australia and New Zealand.

Fidelity to migratory destinations is an important driver of connectivity in marine and avian species. Here we assess the role of maternally directed learning of migratory habitats, or migratory culture, on the population structure of the endangered Australian and New Zealand southern right whale. Using DNA profiles, comprising mitochondrial DNA (mtDNA) haplotypes (500 bp), microsatellite genotypes (17 loci) and sex from 128 individually-identified whales, we find significant differentiation among winter calving grounds based on both mtDNA haplotype (FST = 0.048, ΦST = 0.109, p < 0.01) and microsatellite allele frequencies (FST = 0.008, p < 0.01), consistent with long-term fidelity to calving areas. However, most genetic comparisons of calving grounds and migratory corridors were not significant, supporting the idea that whales from different calving grounds mix in migratory corridors. Furthermore, we find a significant relationship between δ13C stable isotope profiles of 66 Australian southern right whales, a proxy for feeding ground location, and both mtDNA haplotypes and kinship inferred from microsatellite-based estimators of relatedness. This indicates migratory culture may influence genetic structure on feeding grounds. This fidelity to migratory destinations is likely to influence population recovery, as long-term estimates of historical abundance derived from estimates of genetic diversity indicate the South Pacific calving grounds remain at <10% of pre-whaling abundance.