The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species

Abstract Background The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species. Results Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N=1), Oriental (N=4), and the Eastern Palearctic (N=4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes.Conclusions Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.

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The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species

10.21203/rs.2.19982/v2 ◽

2020 ◽

Author(s):

Gunilla Ståhls ◽

Rudolf Meier ◽

Christoph Sandrock ◽

Martin Hauser ◽

Ljiljana Šašić Zorić ◽

...

Keyword(s):

Genetic Diversity ◽

Haplotype Diversity ◽

28S Rdna ◽

Coi Gene ◽

Invasion History ◽

Black Soldier Fly ◽

Hermetia Illucens ◽

Mitochondrial Coi ◽

Western Palearctic ◽

Biogeographic Regions

Abstract Background The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens ) is renowned for bioconversion ability of organic waste, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens . We here use genetic data of 424 rearing culture and wild caught fly samples from 38 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA). Results Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial COI gene (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear ITS2 and 28S rDNA markers are invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (54 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely explained by many independent acquisitions of cultures via sharing and/or establishing new colonies from wild-caught flies. However, explaining the observed high diversity in most biogeographic regions is difficult. The origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. But distinct, private haplotypes are also known from the Australasian (N=2), Oriental (N=4), and the Palearctic (N=5) populations. We review museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and the Afrotropical regions which lack distinct, private haplotypes. Conclusions Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and to share this data in research publications and when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.

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The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species

10.21203/rs.2.19982/v1 ◽

2020 ◽

Author(s):

Gunilla Ståhls ◽

Rudolf Meier ◽

Christoph Sandrock ◽

Martin Hauser ◽

Ljiljana Šašić Zorić ◽

...

Keyword(s):

Genetic Diversity ◽

Haplotype Diversity ◽

28S Rdna ◽

Coi Gene ◽

Invasion History ◽

Black Soldier Fly ◽

Hermetia Illucens ◽

Mitochondrial Coi ◽

Western Palearctic ◽

Biogeographic Regions

Abstract Background The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for bioconversion ability of organic waste, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here use genetic data of 424 rearing culture and wild caught fly samples from 38 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA). Results Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial COI gene (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear ITS2 and 28S rDNA markers are invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (54 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely explained by many independent acquisitions of cultures via sharing and/or establishing new colonies from wild-caught flies. However, explaining the observed high diversity in most biogeographic regions is difficult. The origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. But distinct, private haplotypes are also known from the Australasian (N=2), Oriental (N=4), and the Palearctic (N=5) populations. We review museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and the Afrotropical regions which lack distinct, private haplotypes. Conclusions Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and to share this data in research publications and when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.

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Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽

10.3390/d13020040 ◽

2021 ◽

Vol 13 (2) ◽

pp. 40

Author(s):

Evgeny Genelt-Yanovskiy ◽

Yixuan Li ◽

Ekaterina Stratanenko ◽

Natalia Zhuravleva ◽

Natalia Strelkova ◽

...

Keyword(s):

Genetic Diversity ◽

Barents Sea ◽

Haplotype Diversity ◽

Brittle Star ◽

The Arctic ◽

Coi Gene ◽

High Genetic Diversity ◽

Svalbard Archipelago ◽

Mitochondrial Coi ◽

The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

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Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

BMC Zoology ◽

10.1186/s40850-021-00080-y ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Gabriela Padilla-Jacobo ◽

Tiberio C. Monterrubio-Rico ◽

Horacio Cano-Camacho ◽

María Guadalupe Zavala-Páramo

Keyword(s):

Genetic Diversity ◽

Dna Sequences ◽

Haplotype Diversity ◽

Coastal Region ◽

Central American ◽

Illegal Trade ◽

Wild Populations ◽

High Genetic Diversity ◽

Genealogical Relationship ◽

Genetic Pool

Abstract Background The Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets. Results Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico. Conclusions Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

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Indo-Pacific Phylogeography of the Lemon Sponge Leucetta chagosensis

Diversity ◽

10.3390/d12120466 ◽

2020 ◽

Vol 12 (12) ◽

pp. 466

Author(s):

Olivier Pasnin ◽

Oliver Voigt ◽

Gert Wörheide ◽

Andrea P. Murillo Rincón ◽

Sophie von der Heyden

Keyword(s):

Genetic Diversity ◽

Spatial Variation ◽

Haplotype Diversity ◽

Wide Distribution ◽

Evolutionary Patterns ◽

High Haplotype Diversity ◽

Sponge Diversity ◽

The Indian Ocean ◽

Biogeographic Regions ◽

First Time

The sponge Leucetta chagosensis Dendy (1913) has a wide distribution throughout the Indo-Pacific (IP) region, with previous studies focussing primarily on the western Pacific Ocean. To increase our knowledge of the spatial variation of genetic diversity throughout the IP, we constructed a phylogeny for L. chagosensis for the IP to assess the evolutionary patterns for this species. We generated 188 sequences of L. chagosensis and constructed maximum likelihood and Bayesian inference trees, using concatenated mitochondrial cytochrome oxidase subunit 3 gene (cox3) and nuclear ribosomal RNA gene (28S) markers for the first time. The spatial variation of genetic diversity of L. chagosensis was assessed using a phylogeographic approach. Leucetta chagosensis is composed of five cryptic lineages confined to different biogeographic regions with the specimens found in the Indian Ocean differing significantly from those found in the rest of the IP region. Genetic divergence was particularly high for the cox3 marker, with a low nucleotide diversity but high haplotype diversity for most lineages. This study highlights the need for a sustained effort in studying sponge diversity, boosted by the ongoing discovery of hidden biodiversity among this ecologically important taxon.

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High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Forests ◽

10.3390/f11040469 ◽

2020 ◽

Vol 11 (4) ◽

pp. 469 ◽

Cited By ~ 1

Author(s):

Yanwen Deng ◽

Tingting Liu ◽

Yuqing Xie ◽

Yaqing Wei ◽

Zicai Xie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Human Disturbance ◽

Haplotype Diversity ◽

Conservation Strategy ◽

Ex Situ ◽

Conservation Strategies ◽

High Genetic Diversity ◽

Cpdna Markers

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

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Molecular investigations on the Rajanpuri strain of Beetal goat breed of Pakistan by complete mtDNA displacement region and microsatellite markers

Veterinarska stanica ◽

10.46419/vs.52.5.8 ◽

2021 ◽

Vol 52 (5) ◽

Author(s):

Abdul Wajid ◽

Tanveer Hussain ◽

Faiz M. M. T. Marikar ◽

Muneeb M. Musthafa ◽

Kamran Abbas ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Sequences ◽

Haplotype Diversity ◽

Allelic Diversity ◽

Local Strain ◽

Goat Breed ◽

High Genetic Diversity ◽

Mode Shift ◽

Bottleneck Analysis ◽

Beetal Goat

The mitochondrial DNA sequences of DNA-D loops (mtDNA) from 105 individuals (11 Beetal goat Rajanpuri strains and 94 sequences extracted from GenBank) from 19 geographically and phenotypically defined domestic goat breeds in Pakistan were analysed in this experiment. In this study, we examined variability and molecular phylogeny of breeds. A total of 81 haplotypes were observed in 105 individuals, with a haplotype diversity of 0.984±0.006 and nucleotide diversity of 0.03953±0.00843. Phylogenetic analysis based on the mtDNA hyper variable segment (HVI) of the control region (481 bp), showed four mtDNA haplogroups (A, B1, C, and D) identified in Pakistani domestic goats, in which haplogroup A (84.11%) was dominant and widely distributed among all investigated breeds. The study revealed that all Rajanpuri strain haplotypes belonged to haplogroup A. The Rajanpuri is a rare local strain of Beetal goat breed located in western Punjab province of Pakistan. The results of genetic diversity based on 11 microsatellite loci revealed allelic diversity (3.6363) and high genetic diversity (0.8342) in the examined Rajanpuri goat breeds. The analysis for signature bottleneck events, using three models, revealed significant deviation of Rajanpuri goats from mutation drift equilibrium. The qualitative test of mode shift analysis also supported the results obtained under three models, indicating the presence of a recent genetic bottleneck in the Rajanpuri strain. This study provides the first information on the mtDNA architecture, genetic diversity and bottleneck analysis, which will be useful in the conservation and management of the highly valued Rajanpuri goat.

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Ancient divergence, a crisis of salt and another of ice shaped the evolution of the west Mediterranean butterfly Euchloe tagis

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa129 ◽

2020 ◽

Vol 131 (3) ◽

pp. 487-504

Author(s):

Eduardo Marabuto ◽

Francisco Pina-Martins ◽

Maria Teresa Rebelo ◽

Octávio S Paulo

Keyword(s):

Genetic Diversity ◽

Mediterranean Region ◽

Evolutionary History ◽

Climate Changes ◽

Genetic Composition ◽

The West ◽

Nuclear Markers ◽

High Genetic Diversity ◽

Mitochondrial And Nuclear Markers ◽

General Perspective

Abstract The Mediterranean region is an extremely complex hotspot where, since the Miocene, extensive geological, habitat and climate changes have taken place, alternating between warm and cold periods. These phenomena have taken a toll on the genetic composition of species, and surviving lineages have often adapted locally and diverged to the point of (complete) speciation. To study these phenomena, in this study we used one of the most enigmatic butterflies, the Portuguese dappled white, Euchloe tagis, a west Mediterranean endemic with fragmented, morphologically differentiated populations whose status have long been disputed. Even its affiliations with other Anthocharidini are largely unresolved. We used mitochondrial and nuclear markers under a phylogenetic and phylogeographical framework to evaluate its placement among relatives and population differentiation, reconstructing its evolutionary history. We found that this species had a Miocene origin ~15 Mya and was nearest to Euchloe s.s. and Elphinstonia. Its populations showed high genetic diversity but all coalesced to 5.3 Mya, when European and all but one African population diverged. Our multiple findings concerning the evolution of E. tagis through a changing, narrow habitable area might provide a more general perspective on how species survive within this hotspot of paramount importance.

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High Genetic Diversity among Breeding Red-Backed Shrikes Lanius collurio in the Western Palearctic

Diversity ◽

10.3390/d11030031 ◽

2019 ◽

Vol 11 (3) ◽

pp. 31 ◽

Cited By ~ 2

Author(s):

Liviu Pârâu ◽

Roberto Frias-Soler ◽

Michael Wink

Keyword(s):

Genetic Diversity ◽

Direct Consequence ◽

Migration Routes ◽

Genetic Population ◽

High Genetic Diversity ◽

Lanius Collurio ◽

Breeding Populations ◽

Western Palearctic ◽

Western Asia ◽

Mitochondrial Cytochrome B

Revealing the genetic population structure in abundant avian species is crucial for understanding speciation, conservation, and evolutionary history. The Red-backed Shrike Lanius collurio, an iconic songbird renowned for impaling its prey, is widely distributed as a breeder across much of Europe, Asia Minor and western Asia. However, in recent decades, many populations have declined significantly, as a result of habitat loss, hunting along migration routes, decrease of arthropod food, and climate change e.g., severe droughts in Africa. Within this context, gene flow among different breeding populations becomes critical to ensure the survival of the species, but we still lack an overview on the genetic diversity of the species. In this paper, we analyzed the mitochondrial cytochrome b gene (mtDNA) and the cytochrome c oxidase subunit 1 gene (mtDNA) of 132 breeding Red-backed Shrikes from across the entire breeding range to address this knowledge gap. Our results revealed consistent genetic diversity and 76 haplotypes among the Eurasian populations. Birds are clustered in two major groups, with no clear geographical separation, as a direct consequence of Pleistocene glaciations and apparent lineage mixing in refugia. This has led to genetic panmixia.

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Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

10.22541/au.161478201.16689055/v1 ◽

2021 ◽

Author(s):

Athumani Nguluma

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Haplotype Diversity ◽

Capra Hircus ◽

Maternal Origin ◽

High Genetic Diversity ◽

Ecological Zones ◽

Goat Population ◽

D Loop ◽

Indigenous Goats

The Small East African (SEA) goat (Capra hircus) breeds are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.

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