Unique mtDNA Haplotypes Research Articles

Mitochondrial DNA diversity and maternal origins of Pakistani donkey.

Domestic donkey plays a key role as a draft animal in rural economy of Pakistan where its population is increasing every year. The complete mtDNA control region of forty randomly sampled donkeys was PCR- amplified and sequenced bi-directionally using specific primers. Distinct mtDNA haplotypes obtained in the current study (KY446001-KY446011) were subjected to haplotype (h) and nucleotide diversity (π) measures using DnaS as well as to phylogenetic, Network, and AMOVA analyses. There were a total 27 polymorphic sites present within 11 unique mtDNA haplotypes from the studied 40 animals from different regions. Neighbor-joining network and median-joining network both illustrated the splitting of all these haplotypes into two well-defined Nubian and Somali lineages, confirming African maternal origin of Pakistani domestic donkey. Diversity parameters h (0.967± 0.037) and π (0.02917± 0.00307) were found to reveal high levels of genetic diversity in Pakistani donkeys. AMOVA demonstrated only 1% of genetic differences between two mtDNA maternal lineages, pointing to lack of population substructure in Pakistani donkeys as is the case with worldwide domestic donkey population. Pakistani donkeys have African maternal origin and high levels of mtDNA diversity. High genetic diversity may be due to non-selective breeding and heteroplasmy. We herein provide the first report on mtDNA diversity of control region in Pakistani domestic donkey.

Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia.

As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.

Genetic diversity of rodent species sold in South African pet shops

AbstractMurid rodents are considered globally important invasive species, yet they are still sold in the pet trade. Little is known about the genetic diversity of traded rodents, and many species are incorrectly identified in the pet trade. We used mitochondrial gene regions to assess the taxonomy and genetic diversity of 149 rodents sold in pet shops across eight South African provinces. We identified a total of 112 specimens as Mus musculus, while 31 were Rattus norvegicus, and six were identified as the southern African endemic, southern multimammate mouse Mastomys coucha. Phylogenetic analyses revealed that the three species were monophyletic. Mus musculus and R. norvegicus showed higher levels of genetic diversity, with 19 unique mtDNA haplotypes recovered for M. musculus and eight haplotypes for R. norvegicus. KwaZulu‐Natal, Western Cape and Gauteng Provinces had the most unique haplotypes than other provinces. Our findings showed that non‐native species are widely distributed in the South African pet trade industry, while M. coucha was not widely traded, although recorded in three provinces. This suggests that most provinces comply with the trade regulations on native species, but the threat of invasive rodents to South Africa's unique biodiversity is highlighted.

Mitochondrial D-loop sequences and haplotypes diversity in Egyptian rabbit breeds

Rabbit breeds in Egypt are local and adapted foreign breeds that have been imported since the middle of the last century. Stressful environmental conditions including climatic changes, exposure to diseases and breeding selection have an influence on how gene flow has shaped the genetic diversity of the breeds. Mitochondrial DNA D-loop is a genetic marker used to trace the geographic distribution of genetic variation for the investigation of expansions, migrations and other gene flow patterns. The study aimed to determine the genetic diversity of the mitochondrial DNA D-loop (mtDNA D-loop) in Black Baladi, Red Baladi, Gabali, APRI line and New Zealand breeds to gather the scientific data required to create a proper conservation and sustainable management plan. Blood samples were taken from animals unrelated to each other. A 332-bp of mtDNA D-loop was successfully amplified and alignment sequences were deposited in the GenBank database. The results detected six haplotypes in the five breeds. Haplotype diversity within individual breeds varied from 0 (Red Baladi) to 0.551±0.114 (Gabali). The nucleotide diversity (π) value was relatively low (0.001-0.006), with greater values in APRI and New Zealand. Pairwise distances between breeds yielded varying values ranging from 0 to 0.254, and the values between the Red Baladi and other breeds were comparatively high, with pairwise distances from 0.172 to 0.254. The phylogenetic analysis involved 74 nucleotide sequences of the Egyptian rabbit and thirty-one sequences retrieved from GenBank of the reference samples of different haplogroups. The results of the phylogenetic analysis correlated to the reference mtDNA GenBank database showed that the five Egyptian rabbit breeds were grouped into haplotypes A, B and K. The results of the genetic diversity using mtDNA shed light on the importance of the local breed’s genetic diversity information and revealed unique mtDNA haplotypes, which is an important finding for breeding strategies designed to conserve genetic variants and provide sustainable management.

Phylogeographic Structure of Freshwater Tor sp. in River Basins of Sabah, Malaysia

We characterized the genetic diversity, phylogeography, and demography of Tor sp. (Cyprinidae) from Sabah, Malaysian Borneo, by examining nucleotide variation in the D-loop region of the mtDNA. Sequence analysis of 18 populations (N = 173) yielded 35 unique mtDNA haplotypes with mean haplotype and nucleotide diversity of 0.833 and 0.023, respectively. Phylogenetic reconstructions using Bayesian, neighbor-joining, and maximum parsimony methods, as well as haplotype network, revealed four well-defined clades, namely, the eastern, central, northwestern, and southwestern clades, which corresponded to evolutionarily significant units (ESUs). These ESUs were estimated to have become separated since the late Miocene to Pliocene era (between 5 and 1 million years ago), with the central highlands of Sabah Crocker Trusmadi Range (CTR) constituting the main barrier to genetic exchange between clades. Analysis of molecular variance (AMOVA) and pairwise genetic differentiation showed significant population structuring (Φct = 0.575–1.000, p < 0.05). We further identified eight major groups of river systems harboring reproductively isolated Tor subpopulations. Neutrality statistics and Bayesian skyline plots (BSP) suggested constant population size over time for most Tor populations. Tor sp. in Sabah is comprised of four ESUs (eastern, central, northwestern, and southwestern ESUs), and that each ESU can be compartmentalized into 1–4 MUs. Due to isolation by distance, the highest number of MU occurs in the low-elevation drainages of Eastern Sabah, which is the largest in terms of land area. The evidence provided by this study supports the hypothesis that the four ESU represent genetically distinct subpopulations of Tor and highlight the urgent need for the in situ conservation of these subpopulations.

Highly diverse and rapidly spreading: Melanagromyza sojae threatens the soybean belt of South America

The soybean stem fly, Melanagromyza sojae, an Asian native insect, has successfully established in Brazil, Argentina, Paraguay and Bolivia. These countries are among the lead global soybean producing nations, being collectively known as the soybean belt of South America. Infestation levels of M. sojae grow by the year, facilitated by the lack of efficient management strategies. Previous studies have revealed a high number of maternal lineages in M. sojae populations from Southern Brazil and Paraguay, but a comprehensive survey on genetic diversity combining samples from all countries within the South American soybean belt remains absent. We used the mitochondrial DNA cytochrome oxidase I partial gene (mtCOI) to characterize specimens of M. sojae collected in fourteen Brazilian sites and one Argentine site, and then combined our mtCOI data with previously published data from Australia, Bolivia, Paraguay, and other Brazilian sites, to investigate genetic diversity in this invasive agricultural pest species. Based on the molecular characterisation of the mtCOI gene, haplotypes Msoj-COI-01 and Msoj-COI-02 have the highest frequencies in the continent. The high genetic diversity found is evidence of introductions involving multiple female founders into the continent, and the high proportion of unique mtDNA haplotypes identified from Brazil, Paraguay and Bolivia (~ 50%) suggests potential novel introductions have taken place. The findings from our study will contribute to a better understanding of M. sojae genetic diversity in South America, supporting the development of management strategies for this highly invasive pest and assisting with biosecurity preparedness of other emerging Agromyzidae flies of economic importance.

Range Expansion or Range Shift? Population Genetics and Historic Range Data Analyses of the Predatory Benthic Sea Slug Phidiana hiltoni (Mollusca, Gastropoda, Nudibranchia)

Phidiana hiltoni is a conspicuous nudibranch sea slug native to the northeastern Pacific Ocean. Over the past thirty years the range of P. hiltoni has expanded about 200 km northward, but the mechanism that facilitated this expansion is poorly understood. In this study, we use mtDNA and microsatellite data to investigate the population structure of P. hiltoni in its historical range as well as in recently colonized localities. Microsatellite analyses reveal little to no genetic structure and thus high gene flow throughout the range of P. hiltoni. This is consistent with mtDNA analysis results, which revealed shared haplotypes between Southern, Central and Northern populations. However, AMOVA of mtDNA data did recover some genetic structure among geographic regions. This, along with same group memberships in the microsatellite data of individuals from sites like Cave Landing, suggest a certain degree of local recruitment and reduced vagility. Recently established populations in Northern California contain two unique mtDNA haplotypes that are not present elsewhere, but microsatellite data do not differentiate these from other populations. The mismatch between mtDNA and microsatellite data could be explained by the mating system of this aggressive, hermaphroditic species as well as the sporadic nature of the northward dispersal. Analyses of historical abundance data of P. hiltoni suggest a population decline in Southern California. Together, these results suggest a northward population shift, rather than a range expansion, possibly related to ongoing changes in nearshore oceanographic conditions in the region.

Distribution, fine-scale subdivision, and population size of San Joaquin kit foxes in the Ciervo-Panoche Natural Area, California

The endangered San Joaquin kit fox (SJKF; Vulpes macrotis mutica) is strongly linked ecologically to xeric areas with high abundance of kangaroo rats. Endemic to the San Joaquin Desert of central California, the elusive nature of SJKF, coupled with steady habitat loss and lack of comprehensive surveys, has precluded efforts to quantify the species’ population size and distribution, especially in the central and northern parts of its range. Because the Ciervo-Panoche Natural Area contains the largest area of high-quality habitat in this central/northern region, we conducted systematic transect surveys for SJKF scats with professionally trained dog-handler teams throughout the area during 2009–2011. We collected almost 600 scats over 473 km of transects, documenting the freshness and location of each scat. Using molecular methods, we identified 93 SJKF individuals (56 males and 37 females) from 332 samples. Half of the individuals carried a mtDNA haplotype with a 16 bp deletion that had not been previously detected in other areas surveyed. Four individuals were recaptured in 2010 and five in 2011, including one female that was captured every year. We documented a unique mtDNA haplotype and more individuals across a wider area of the Ciervo-Panoche Natural Area than expected. Population analyses revealed two distinct subpopulations, with low connectivity between foxes in the Panoche Valley that are separated by hills with unsuitable habitat from those on the adjacent valley floor next to a major Interstate highway (I-5). While individuals detected within 6 km of each other were closely related, overall relatedness within each subpopulation approached zero. Genetic population models indicated a conservative population estimate of 90 kit foxes in total, with 60–90 individuals in the Panoche Valley and 17–27 individuals in the I-5 area. These results will help to inform management of the SJKF and identify areas that may be important to maintaining connectivity between populations.

Genetic differentiation in the mountainous star coral Orbicella faveolata around Cuba

Caribbean coral reefs are biodiversity-rich habitats which provide numerous ecosystem services with both ecological and economical values, but nowadays they are severely degraded. In particular, populations of the major framework-building coral Orbicella faveolata have declined sharply, and therefore, understanding how these threatened coral populations are interconnected and how demographic changes have impacted their genetic diversity is essential for their management and conservation. Previous population genetic surveys showed that gene flow in this species is sometimes locally restricted in the Caribbean; however, little genetic data are available for Cuban populations. Here, we analyzed the variation at the mitochondrial DNA control region and six microsatellite loci from O. faveolata colonies from five distant localities representing most of the main coral reefs around Cuba. Both genetic markers showed evidence of genetic differentiation between the northwestern area (Colorados Archipelago) and the other reefs. Colonies from the Colorados Archipelago harbored the largest number of unique mtDNA haplotypes and microsatellite alleles, which suggests long-term large population size or gene flow from other areas of the Caribbean. These results indicate that the Colorados Archipelago area is particularly important for O. faveolata populations and it is well suited for reef management and restoration efforts.

Maternal inheritance of deltamethrin resistance in the salmon louse Lepeophtheirus salmonis (Krøyer) is associated with unique mtDNA haplotypes.

Parasitic infections by the salmon louse, Lepeophtheirus salmonis (Krøyer), cause huge economic damage in salmon farming in the northern hemisphere, with combined treatment costs and production losses in 2014 having been estimated at US$ 350 million for Norway (annual production 1.25 million tonnes). The control of L. salmonis relies significantly on medicinal treatments, supplemented by non-pharmacological approaches. However, efficacy losses have been reported for several delousing agents, including the pyrethroid deltamethrin. The aim of the present study was to analyse the genetic basis of deltamethrin resistance in L. salmonis. Deltamethrin median effective concentrations (EC50) were 0.28 μg L-1 in the drug susceptible L. salmonis strain IoA-00 and 40.1 μg L-1 in the pyrethroid resistant strain IoA-02. IoA-00 and IoA-02 were crossed to produce families spanning one parental and three filial generations (P0, F1-F3). In three families derived from P0 crosses between an IoA-00 sire and an IoA-02 dam, 98.8% of F2 parasites (n = 173) were resistant, i.e. remained unaffected after exposure to 2.0 μg L-1 deltamethrin. F3 parasites from these crosses showed a deltamethrin EC50 of 9.66 μg L-1. In two families of the inverse orientation at P0 (IoA-02 sire x IoA-00 dam), 16.7% of F2 parasites were resistant (n = 84), while the deltamethrin EC50 in F3 animals was 0.26 μg L-1. The results revealed a predominantly maternal inheritance of deltamethrin resistance. The 15,947-nt mitochondrial genome was sequenced and compared among six unrelated L. salmonis strains and parasites sampled from wild salmon in 2010. IoA-02 and three further deltamethrin resistant strains, established from isolates originating from different regions of Scotland, showed almost identical mitochondrial haplotypes. In contrast, the mitochondrial genome was variable among susceptible strains and L. salmonis from wild hosts. Deltamethrin caused toxicity and depletion of whole body ATP levels in IoA-00 but not IoA-02 parasites. The maternal inheritance of deltamethrin resistance and its association with mitochondrial haplotypes suggests that pyrethroid toxicity in L. salmonis may involve molecular targets encoded by mitochondrial genes.

Combining phylogenetic and demographic inferences to assess the origin of the genetic diversity in an isolated wolf population.

The survival of isolated small populations is threatened by both demographic and genetic factors. Large carnivores declined for centuries in most of Europe due to habitat changes, overhunting of their natural prey and direct persecution. However, the current rewilding trends are driving many carnivore populations to expand again, possibly reverting the erosion of their genetic diversity. In this study we reassessed the extent and origin of the genetic variation of the Italian wolf population, which is expanding after centuries of decline and isolation. We genotyped wolves from Italy and other nine populations at four mtDNA regions (control-region, ATP6, COIII and ND4) and 39 autosomal microsatellites. Results of phylogenetic analyses and assignment procedures confirmed in the Italian wolves a second private mtDNA haplotype, which belongs to a haplogroup distributed mostly in southern Europe. Coalescent analyses showed that the unique mtDNA haplotypes in the Italian wolves likely originated during the late Pleistocene. ABC simulations concordantly showed that the extant wolf populations in Italy and in south-western Europe started to be isolated and declined right after the last glacial maximum. Thus, the standing genetic variation in the Italian wolves principally results from the historical isolation south of the Alps.

A new mitochondrial haplotype confirms the distinctiveness of the Italian wolf (Canis lupus) population

In the past century the Italian wolf has been repeatedly indicated as a distinct subspecies, Canis lupus italicus, due to its unique morphology and its distinctive mtDNA control region (CR) monomorphism. However, recent studies on wolf x dog hybridization in Italy documented the presence of a second mtDNA CR haplotype (W16), previously found only in wolves from Eastern Europe, casting doubts on the genetic uniqueness of the Italian wolves. To test whether this second haplotype belongs to the Italian wolf population, we genotyped 92 wolf DNA samples from Italy, Slovenia, Greece and Bulgaria at four mtDNA regions (control-region, ATP6, COIII and ND4 genes) and at 39 autosomal microsatellites. Results confirm the presence of two mtDNA multi-fragment haplotypes (WH14 and WH19) in the Italian wolves, distinct from all the other European wolves. Network analyses of the multi-fragment mtDNA haplotypes identified two strongly differentiated clades, with the Italian wolf WH14 and WH19 multi-fragment haplotypes rooted together. Finally, Bayesian clustering clearly assigned all the wolves sampled in Italy to the Italian population, regardless of the two different multi-fragment haplotypes. These results demonstrate that the W16 CR haplotype is part of the genetic pool of the Italian wolf population, reconfirming its distinctiveness from other European wolves. Overall, considering the presence of unique mtDNA and Y-linked haplotypes, the sharply different frequencies of genome-wide autosomal alleles and the distinct morphological features of Italian wolves, we believe that this population should be considered a distinct subspecies.

Novel Concordance Between Geographic, Environmental, and Genetic Structure in the Ecological Generalist Prickly Sculpin (Cottus asper) in California.

Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California. We then incorporated genetic and GIS data into ecological niche models to assess ecological conditions within identified groups. Though not reciprocally monophyletic, unique mtDNA haplotypes, microsatellite clustering, and measures of isolation by distance (Coastal: r = 0.960, P < 0.001; Inland: r = 0.277, P = 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained to Great Central Valley). Divergence estimates of 41-191 kya combined with the regional biogeographic history suggest geographic barriers are absent between groups since divergence, but ecological niche modeling revealed significant environmental differences (t = 10.84, P < 0.001). Introgressed individuals were also discovered between groups in an ecologically and geographically intermediate region. Population structure was limited, predominately found in tributaries of the San Joaquin basin in the Inland group. Overall, C. asper exhibited substantial genetic diversity, despite its ecological generality, reflecting California's historically unique and complex hydrology. More broadly, this study illustrates variable environments within the range of a generalist species may mask genetic divergences and should not be overlooked in biodiversity assessments.

Mitochondrial DNA Variation in Southeastern Pre-Columbian Canids.

The taxonomic status of the red wolf (Canis rufus) is heavily debated, but could be clarified by examining historic specimens from the southeastern United States. We analyzed mitochondrial DNA (mtDNA) from 3 ancient (350-1900 year olds) putative wolf samples excavated from middens and sinkholes within the historic red wolf range. We detected 3 unique mtDNA haplotypes, which grouped with the coyote mtDNA clade, suggesting that the canids inhabiting southeastern North America prior to human colonization from Europe were either coyotes, which would vastly expand historic coyote distributions, an ancient coyote-wolf hybrid, or a North American evolved red wolf lineage related to coyotes. Should the red wolf prove to be a distinct species, our results support the idea of either an ancient hybrid origin for red wolves or a shared common ancestor between coyotes and red wolves.

Pluvial Drainage Patterns and Holocene Desiccation Influenced the Genetic Architecture of Relict Dace, Relictus solitarius (Teleostei: Cyprinidae).

Changing drainage patterns have played a significant role in the evolution of western North American aquatic taxa. Relict dace, Relictus solitarius, is a Great Basin endemic cyprinid with a native range that is restricted to four valleys in eastern Nevada. Relictus solitarius now occupies spring systems that are the remnants of Pleistocene-era pluvial lakes, although it may have occurred in the area for much longer. Here we use mitochondrial DNA sequence data to assess range-wide genetic diversity of R. solitarius, and to estimate divergence times to determine whether pluvial drainages played an important role in shaping intraspecific genetic diversity. Genetic diversification within R. solitarius began during the early to mid-Pleistocene, separating populations within two sets of valleys (Butte/Ruby and Goshute/Steptoe). Additional diversification in each of the two sets of valleys occurred more recently, in the mid- to late-Pleistocene. Holocene desiccation has further isolated populations, and each population sampled contains unique mtDNA haplotypes. Pluvial drainage patterns did contribute to the genetic structure observed within R. solitarius, but most of the intraspecific diversification does not appear to be associated with the Last Glacial Maximum. Holocene desiccation has also contributed to the observed genetic structure. The relict dace populations we sampled are all unique, and we recommend that future management efforts should strive to preserve as much of the genetic diversity as possible.

Admixture of Eastern and Western European Red Deer Lineages as a Result of Postglacial Recolonization of the Czech Republic (Central Europe).

Due to a restriction of the distributional range of European red deer (Cervus elaphus L.) during the Quaternary and subsequent recolonization of Europe from different refugia, a clear phylogeographical pattern in genetic structure has been revealed using mitochondrial DNA markers. In Central Europe, 2 distinct, eastern and western, lineages of European red deer are present; however, admixture between them has not yet been studied in detail. We used mitochondrial DNA (control region and cytochrome b gene) sequences and 22 microsatellite loci from 522 individuals to investigate the genetic diversity of red deer in what might be expected to be an intermediate zone. We discovered a high number of unique mtDNA haplotypes belonging to each lineage and high levels of genetic diversity (cyt b H = 0.867, D-loop H = 0.914). The same structuring of red deer populations was also revealed by microsatellite analysis, with results from both analyses thus suggesting a suture zone between the 2 lineages. Despite the fact that postglacial recolonization of Central Europe by red deer occurred more than 10000 years ago, the degree of admixture between the 2 lineages is relatively small, with only 10.8% admixed individuals detected. Direct translocations of animals by humans have slightly blurred the pattern in this region; however, this blurring was more apparent when using maternally inherited markers than nuclear markers.

Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts

The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of host distribution and ecology on the evolutionary history of the parasite. High haplotype (h=0.986) and nucleotide diversity (π=0.013) were seen, with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with most of the variation (78%) arising from variability within hookworms from individual colonies. This is supported by the low genetic differentiation co-efficient (GST=0.007) and a high gene flow (Nm=35.25) indicating a high migration rate between the populations of hookworms. The haplotype network demonstrated no clear distribution and delineation of haplotypes according to geographical location. Our data rejects the vicariance hypothesis; that female host natal site fidelity and the transmammary route of infection restrict hookworm gene flow between N. cinerea populations and highlights the value of studies of parasite diversity and dispersal to challenge our understanding of parasite and host ecology.

Locals, resettlers, and pilgrims: a genetic portrait of three pre-Columbian Andean populations.

The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for 25 individuals and autosomal microsatellite profiles for 20 individuals from Acchaymarca and Puca sites. These were compared with previously published genetic data for Tompullo 2 and other pre-Columbian populations. We found differences among the genetic portraits of the three populations, congruent with the archaeologically described functions and characteristics of the sites. The Acchaymarca population had the highest genetic diversity and possessed the lowest number of unique mtDNA haplotypes. The Tompullo 2 population exhibited the lowest level of genetic diversity. The Puca population was distinct from the other two populations owing to a high frequency of haplogroup A haplotypes, what potentially explains the non-local character of the burial architecture. Our analyses of microsatellite data suggest that gene flow between sites was mostly mediated by females, which is consistent with ethnohistorical knowledge of the social organization of the pre-Columbian communities.

Maternal Genetic Heritage of Southeastern Europe Reveals a New Croatian Isolate and a Novel, Local Sub-Branching in the X2 Haplogroup

High mtDNA variation in Southeastern Europe (SEE) is a reflection of the turbulent and complex demographic history of this area, influenced by gene flow from various parts of Eurasia and a long history of intermixing. Our results of 1035 samples (488 from Croatia, 239 from Bosnia and 130 from Herzegovina, reported earlier, and 97 Slovenians and 81 individuals from Žumberak, reported here for the first time) show that the SEE maternal genetic diversity fits within a broader European maternal genetic landscape. The study also shows that the population of Žumberak, located in the continental part of Croatia, developed some unique mtDNA haplotypes and elevated haplogroup frequencies due to distinctive demographic history and can be considered a moderate genetic isolate. We also report seven samples from the Bosnian population and one Herzegovinian sample designated as X2* individuals that could not be assigned to any of its sublineages (X2a'o) according to the existing X2 phylogeny. In an attempt to clarify the phylogeny of our X2 samples, their mitochondrial DNA has been completely sequenced. We suppose that these lineages are signs of local microdifferentiation processes that occurred in the recent demographic past in this area and could possibly be marked as SEE-specific X2 sublineages.

Can genetic diversity be maintained in long term mass selected populations without pedigree information? — A case study using banana shrimp Fenneropenaeus merguiensis

Abstract This study assesses the changes in genetic diversity using two different methods in eight captive bred lines of banana shrimp (Fenneropenaeus merguiensis) that had been mass selected for length for up to 14 generations. Specifically, mitochondrial D-loop DNA sequencing and genotyping using five DNA microsatellite loci were used to document changes in haplotype diversity and allelic diversity numbers at several time points during and up to 14 generations of captive bred lines, typically maintained without intercrossing among lines. Data from eight of the lines were compared with each other and to a reference sample of wild caught animals. As each wild animal had a unique mtDNA haplotype, we estimate that there were 20 different mtDNA haplotypes in each of the two different founding stocks. The average number of haplotypes was 1.8 after 11 or more generations of captive breeding. Similarly, whereas the wild reference stock had an average number of more than 13 microsatellite alleles per locus, the descendent lines had an average of 5.6 per locus after 11 or more generations. These declines were evident despite strategies that had been put in place to maintain genetic variation, including the use of up to 1000 brood stock per generation. The loss of genetic variation was unequivocal being evident for both DNA methods and in all the different lines. Effective population size (Ne), as derived from linkage disequilibrium, was estimated to average about nine after 11–13 generations in the captively bred lines, compared with 263 estimated in the wild samples. This corresponds to a rate of inbreeding of about 4% per generation for the captively bred lines. Additive genetic variance of the captively bred lines, estimated under the assumption of neutrality, ranged from about 75% to 25% that in the wild samples. We therefore conclude that mass selection, even when using a relatively large number of broodstock, still results in substantial loss of allelic diversity within lines over generations, and a reduction of effective population size and genetic variance, to the degree that productivity could have been compromised compared with similarly selected but outbred stocks. Loss occurred relatively consistently among the different lines. It was common for different microsatellite alleles or mtDNA haplotypes to have persisted in the different lines, such that the total number of haplotypes and allele types among all lines was much greater than that within given single lines, and the number of alleles among lines approximated that found in the wild. This observation, evident because many different lines were monitored, suggests that under certain circumstances (fixation and selection), more net genetic variability can be maintained over many generations of selection by keeping multiple different and independent lines rather than one large single line. Accordingly, if multiple lines are maintained, there could be some practical options to reconstitute allelic and haplotype variation without new introductions of genetically unimproved stock from the wild.