Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach.

BACKGROUND: Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes. METHODS AND RESULTS: In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae. CONCLUSIONS: In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.

GenAPoPop 1.0: A user-friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms.

Autopolyploidy is quite common in most clades of eukaryotes. The emergence of sequence-based genotyping methods with individual and marker tags now enables confident allele dosage, overcoming the main obstacle to the democratization of the population genetic approaches when studying ecology and evolution of autopolyploid populations and species. Reproductive modes, including clonality, selfing and allogamy, have deep consequences on the ecology and evolution of population and species. Analysing genetic diversity and its dynamics over generations is one efficient way to infer the relative importance of clonality, selfing and allogamy in populations. GenAPoPop is a user-friendly solution to compute the specific corpus of population genetic indices, including indices about genotypic diversity, needed to analyse partially clonal, selfed and allogamous polysomic populations genotyped with confident allele dosage. It also easily provides the posterior probabilities of quantitative reproductive modes in autopolyploid populations genotyped at two-time steps and a graphical representation of the minimum spanning trees of the genetic distances between polyploid individuals, facilitating the interpretation of the genetic coancestry between individuals in hierarchically structured populations. GenAPoPop complements the previously existing solutions, including SPAGEDI and POLYGENE, to use genotypings to study the ecology and evolution of autopolyploid populations. It was specially developed with a simple graphical interface and workflow, and comes with a simulator to facilitate practical courses and teaching of population genetics for autopolyploid populations.

Bones and all: a new critically endangered Pantepui species of Stefania (Anura: Hemiphractidae) and a new osteological synapomorphy for the genus.

The hemiphractid frog genus Stefania is one of the many ancient (near-) endemic lineages of vertebrates inhabiting the biodiverse Pantepui biogeographical region in the Guiana Shield Highlands of northern South America-the famous "Lost World" of Arthur Conan Doyle. Previous molecular analyses of the genus Stefania have indicated that species boundaries and phylogenetic relationships are often incongruent with morphological traits in that clade. A substantial number of "taxonomically cryptic" species, often microendemic, remain to be described. This is notably the case for an isolated population from the summit of Wei-Assipu-tepui, a small table-top mountain at the border between Guyana and Brazil. That population was previously known as Stefania sp. 6 and belongs to the S. riveroi clade. The new species is phylogenetically distinct, but phenotypically extremely similar to S. riveroi, a taxon found only on the summit of Yuruaní-tepui in Venezuela and recovered as sister to all the other known species in the S. riveroi clade. The new taxon is described based on morphology and osteology. Data about genetic divergences within the S. riveroi clade are provided. A new synapomorphy for the genus Stefania is proposed: the presence of a distal process on the third metacarpal. Amended definitions are offered for the three other species in the S. riveroi clade (S. ayangannae, S. coxi, S. riveroi). The new species should be listed as Critically Endangered according to IUCN criteria.

Analyzing Autopolyploid Genetic Data Using GenoDive.

Analyzing autopolyploid genetic data still presents numerous challenges due to, e.g., missing dosage information of genotypes and the presence of multiple ploidy levels within species or populations, but also because the choice of software is limited when compared to what is available for diploid data. However, over the last years, the number of software programs that can deal with polyploid data is slowly increasing. The software GENODIVE is one of the most widely used programs for the analysis of polyploid genetic data, presenting a wide array of different methods. In this chapter, I outline several frequently used types of population genetic analyses and explain how these apply to polyploid data, including possible pitfalls and biases. I then explain how GENODIVE approaches these analyses and whether and how it can overcome possible biases. Specifically, I focus on analyses of genetic diversity, Hardy-Weinberg equilibrium, quantifying population differentiation, clustering, and calculation of genetic distances. GENODIVE can be downloaded freely from http://www.patrickmeirmans.com/software .

A new species of Sturisoma Swainson, 1838 (Loricariidae: Loricariinae), from the Madeira River basin, with a discussion of historical biogeography of western Amazonas and Paraguay River basins.

A new loricariin species of Sturisoma is described from the Cautário, Guaporé, Mamoré, Machado and Soteiro rivers, Madeira River basin, in Bolivia and Brazil. The new species is distinguished from its congeners by the presence of a middorsal longitudinal, thin dark brown stripe on the caudal peduncle, extending from two or three plates posterior to the dorsal-fin base, reaching the origin of the caudal fin, or one or two plates anterior to the origin of the caudal fin; small squarish anteriormost abdominal plates; and a middorsal longitudinal dark-brown stripe from first predorsal plate to near the dorsal-fin origin. Furthermore, the new species is diagnosed from congeners by plate morphology, counts on the median series, coalescent plates and ventrolateral thoracic plates, in addition to measurements related to body and head structures. An analysis of genetic distances using cytochrome C oxidase subunit 1 gene marker of the mitochondrial genome between the new species and several congeners is presented, in addition to a likelihood analysis to illustrate the position of the new taxon within Sturisoma. An identification key for species of the genus currently recorded at the upper Amazonas River basin is provided.

Genetic diversity in 10 populations of domestic Turkeys by using microsatellites markers.

The domestic turkey is a native breed in danger of extinction due to the introduction of new breeds specializing in meat production and yield. Turkeys have lost some prominence in urban areas, and only certain breeds of turkeys are preserved in rural areas. Wild and domestic turkeys are different; rural or indigenous turkeys, with black plumage, were domesticated from Mexican turkeys and have been reproduced throughout Latin America. Some of them were taken to Europe in the 16th century and later arrived in North America, where they crossed with another wild species, from which the bronze turkey emerged: the ancestor of all commercial turkeys. The objective of the present work was to evaluate the genetic diversity in 10 populations of domestic turkeys worldwide by using breeds from Europe: Spain and Italy; America: Mexico, United States and Brazil; and the Near East: Iran and Egypt. A total of 522 blood samples of both sexes were collected from domestic turkey populations. Thirty-four microsatellites were used to obtain genetic parameters, and genetic diversity was evaluated. All microsatellites used were polymorphic, and a total of 427 alleles were detected across the 34 markers investigated. In this study, a mean number of 13.44 alleles was found. The four most diverse breeds were from the Andalusia, Mexico, United States, and wild populations, which had the highest mean heterozygosity expected (0.619, 0.612, 0.650, and 0.773) and heterozygosity observed (0.422, 0.521, 0.429, and 0.627), respectively. The MNT348 marker deviated from the HWE in all populations. Our study has shown that the populations close to the species origin are more diverse than those resulting from posterior expansions. Mexican birds were the most diverse, followed by the Spanish populations because Spain imported a large number of turkeys coming from America. Such information can be complementary to other genotypic data required to validate the evolutionary relationships among turkey populations.

DNA Barcode Gap Analysis for Multiple Marker Genes for Phytoplankton Species Biodiversity in Mediterranean Aquatic Ecosystems.

The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered by the substantial lack of reference sequences. The main objective of this study was to analyze the current coverage of DNA barcode reference libraries for phytoplankton species of the aquatic Mediterranean ecoregion in the southeast of Italy (Apulia Region) in order to assess the applicability of DNA metabarcoding and eDNA in this area. To do so, we investigated three main DNA barcode reference libraries, BOLD Systems, GenBank and SILVA, for the availability of DNA barcodes of the examined phytoplankton species. The gap analysis was conducted for three molecular gene markers, 18S, 16S and COI. The results showed a considerable lack of barcodes for all three markers. However, among the three markers, 18S had a greater coverage in the reference libraries. For the 18S gene marker, the barcode coverage gap across the three types of ecosystems examined was 32.21-39.68%, 60.12-65.19% for the 16S marker gene, and 72.44-80.61 for the COI marker gene. Afterwards, the interspecific genetic distance examined on the most represented molecular marker, 18S, was able to distinguish 80% of the species mined for lakes and 70% for both marine and transitional waters. Conclusively, this work highlights the importance of filling the gaps in the reference libraries, and constitutes the basis towards the advancement of DNA metabarcoding and eDNA application for biodiversity assessment and biomonitoring.

Comparative Genetic Analysis of Durum Wheat Landraces and Cultivars Widespread in Tunisia.

The durum wheat (Triticum turgidum L. ssp. durum Desf.) landraces constitute a useful natural germplasm to increase the genetic diversity in the modern durum cultivars. The Tunisian durum germplasm constitutes 28 accessions conserved in Genebank of Tunisia, which are still unexplored. In this study, a comparative genetic analysis was performed to investigate the relationships between the Tunisian durum lines and the modern cultivars and detect divergent loci involved in breeding history. The genetic diversity analyses carried out using nine morphological descriptors and the 25K single-nucleotide polymorphism (SNP) array allowed us to distinguish two groups of Tunisian landraces and one of durum cultivars. The analysis of molecular variance and diversity indices confirmed the genetic variability among the groups. A total of 529 SNP loci were divergent between Tunisian durum landraces and modern cultivars. Candidate genes related to plant and spike architecture, including FLOWERING LOCUS T (FT-B1), zinc finger CONSTANS, and AP2/EREBPs transcription factors, were identified. In addition, divergent genes involved in grain composition and biotic stress nucleotide-binding site and leucine-reach repeats proteins and disease resistance proteins (NBS-LRR and RPM) were found, suggesting that the Tunisian durum germplasm may represent an important source of favorable alleles to be used in future durum breeding programs for developing well-adapted and resilient cultivars.

Biochemical characterization for determination of genetic distances among different indigenous chickpea (Cicer arietinum L. ) varieties of North-West Pakistan / Caracterização bioquímica para determinação de distâncias genéticas entre diferentes variedades indígenas de grão-de-bico (Cicer arietinum L. ) do noroeste do Paquistão

Abstract Genetic distances among different chickpea varieties and evaluation of their free amino acid profiles were determined on the basis of Sodium dodecyle sulphate polyacrylamide gels electrophoresis (SDS-PAGE). Total soluble proteins were resolved on 10% SDS Polyacrylamide gel. Low variability in tested varieties was observed. Dendogram based on electrophoretic data clustered the genotypes into 2 groups. The results showed that the average protein content of all the varieties was 26.01% within the range 22.8% for Thal-2006 to 34.06% Sheenghar-2000 of dry seed weight. On the basis of total protein content Bittal-98, Dasht and Sheen Ghar-2000, Karak-3 and CM-98, Paidar -91 and Fakhr-e-Thal, C-44, Balaksar and KK-1showed similar concentrations for protein contents among each other but showed variation from the rest of the varieties. Different proteins were separated on the basis of changes in their molecular weights by means of Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE). Dasht, CM-98, and Sheen Ghar showed 100% similarity. Balaksar and Fakhr-e- Thal, KK-2 and Chattan and KC-98, KK-1 and Lawaghar were 100% similar among each other but showed variation from the rest of the accessions. The overall dendrogram showed high and low level of variation among the accessions. The concentration of free amino acids varied among the 16 chickpea varieties. A significant difference of both essential and non-essential amino acids was found among the chickpea cultivars. The total concentration of essential amino acid was recorded 40.81 g/100 g protein while non-essential was recorded 59.18343 g/100 g protein in the given cultivars. The highest concentration of essential amino acids was found in C-44 followed by KK-2, KK-1 and Fakhr E Tal while the lowest concentration was recorded in Cm-98, Paidar-91 and Sheen Ghar-2000 respectively. Cultivars TAL-2006, Chattan and Karak-3 showed maximum concentration of both essential and endogenous amino acids. In conclusion; for broadening the genetic pools in breeding programs or to search for exotic characters, for instance new disease resistance alleles, accession with low similarity coefficients (Lawaghar and Battal-98) may be utilized. Furthermore the information acquired from this study could be used to device a proficient breeding approach intended at improving nutritional as well as broadening the genetic base of this essential food crop of Pakistan.

Resumo As distâncias genéticas entre as diferentes variedades de grão-de-bico e a avaliação de seus perfis de aminoácidos livres foram determinadas com base na eletroforese em gel de poliacrilamida com dodecil sulfato de sódio (SDS-PAGE). As proteínas solúveis totais foram resolvidas em SDS-PAGE a 10%. Foi observada baixa variabilidade nas variedades testadas. O dendrograma fundamentado em dados eletroforéticos agrupou os genótipos em dois grupos. Os resultados mostraram que o teor médio de proteínas de todas as variedades foi de 26,01%, na faixa de 22,8% para Thal-2006 a 34,06% para Sheenghar-2000 do peso de sementes secas. Com base no conteúdo total de proteínas, Bittal-98, Dasht, Sheen Ghar-2000, Karak-3, CM-98, Paidar-91, Fakhr-e-Thal, C-44, Balaksar e KK-1 apresentaram concentrações semelhantes para o conteúdo de proteínas entre si, mas tiveram variação quanto ao restante das variedades. Diferentes proteínas foram separadas com base nas alterações de seus pesos moleculares por meio de eletroforese em gel de poliacrilamida com dodecil sulfato de sódio (SDS-PAGE). Dasht, CM-98 e Sheen Ghar mostraram 100% de similaridade. Balaksar, Fakhr-e-Thal, KK-2, Chattan e KC-98, KK-1 e Lawaghar foram 100% semelhantes entre si, mas apresentaram variação em relação ao restante dos acessos. O dendrograma geral mostrou alto e baixo nível de variação entre os acessos. A concentração de aminoácidos livres variou entre as 16 variedades de grão-de-bico. Foi encontrada uma diferença significativa entre os aminoácidos essenciais e não essenciais nas cultivares de grão-de-bico. A concentração total de aminoácidos essenciais foi registrada em 40,81 g / 100 g de proteína, enquanto a não essencial foi registrada em 59,18343 g / 100 g de proteína nas cultivares. A maior concentração de aminoácidos essenciais foi encontrada em C-44, seguida de KK-2, KK-1 e Fakhr-e-Thal, enquanto a menor concentração foi registrada em CM-98, Paidar-91 e Sheen Ghar-2000. As cultivares TAL-2006, Chattan e Karak-3 apresentaram concentração máxima de aminoácidos essenciais e endógenos. Em conclusão, para ampliar os pools genéticos em programas de melhoramento ou procurar caracteres exóticos, por exemplo, novos alelos de resistência a doenças, pode ser utilizada a adesão com baixos coeficientes de similaridade (Lawaghar e Battal-98). Além disso, as informações adquiridas neste estudo poderiam ser usadas para criar uma abordagem de criação eficiente, com o objetivo de melhorar a nutrição e ampliar a base genética dessa cultura alimentar essencial do Paquistão.

Comparative Analysis of Eight Mitogenomes of Bark Beetles and Their Phylogenetic Implications.

Many bark beetles of the subfamily Scolytinae are the most economically important insect pests of coniferous forests worldwide. In this study, we sequenced the mitochondrial genomes of eight bark beetle species, including Dendroctonus micans, Orthotomicus erosus, Polygraphus poligraphus, Dryocoetes hectographus, Ips nitidus, Ips typographus, Ips subelongatus, and Ips hauseri, to examine their structural characteristics and determine their phylogenetic relationships. We also used previously published mitochondrial genome sequence data from other Scolytinae species to identify and localize the eight species studied within the bark beetle phylogeny. Their gene arrangement matched the presumed ancestral pattern of these bark beetles. Start and stop codon usage, amino acid abundance, and the relative codon usage frequencies were conserved among bark beetles. Genetic distances between species ranged from 0.037 to 0.418, and evolutionary rates of protein-coding genes ranged from 0.07 for COI to 0.69 for ND2. Our results shed light on the phylogenetic relationships and taxonomic status of several bark beetles in the subfamily Scolytinae and highlight the need for further sequencing analyses and taxonomic revisions in additional bark beetle species.

Proposed Update to the Taxonomy of Pestiviruses: Eight Additional Species within the Genus Pestivirus, Family Flaviviridae.

Pestiviruses are plus-stranded RNA viruses belonging to the family Flaviviridae. They comprise several important pathogens like classical swine fever virus and bovine viral diarrhea virus that induce economically important animal diseases. In 2017, the last update of pestivirus taxonomy resulted in demarcation of 11 species designated Pestivirus A through Pestivirus K. Since then, multiple new pestiviruses have been reported including pathogens associated with disease in pigs or small ruminants. In addition, pestivirus sequences have been found during metagenomics analysis of different non-ungulate hosts (bats, rodents, whale, and pangolin), but the consequences of this pestivirus diversity for animal health still need to be established. To provide a systematic classification of the newly discovered viruses, we analyzed the genetic relationship based on complete coding sequences (cds) and deduced polyprotein sequences and calculated pairwise distances that allow species demarcation. In addition, phylogenetic analysis was performed based on a highly conserved region within the non-structural protein NS5B. Taking into account the genetic relationships observed together with available information about antigenic properties, host origin, and characteristics of disease, we propose to expand the number of pestivirus species to 19 by adding eight additional species designated Pestivirus L through Pestivirus S.

New species of the genus Inversidens Haas, 1911 (Unionoida, Unionidae, Gonideinae) from Jiangxi Province, China.

We diagnose and describe a new freshwater mussel species of the genus Inversidens, I.rentianensis sp. nov. from Jiangxi Province, China based on morphological characters and molecular data. This paper includes a morphological description and photograph of the holotype, and partial sequences of mitochondrial COI as DNA barcode data.

Analysis of Geographical Genetic Differences of Arkshell Populations in Korea.

A PCR-founded genetic analysis aim and principle was used to foster a hierarchical polar dendrogram of the Euclidean genetic distances (GDs) for two arkshell populations, Scapharca broughtonii (YEOSU, Yeosu population and JINHAE, Jinhae population). Five oligonucleotides primers were make use of to craft 354 and 390 scorable bands in the Yeosu and Jinhae populations, respectively, outspreading in DNA fragment size from 100 bp to 1,600 bp. The bandsharing (BS) results disclosed that the Jinhae population had a higher average BS value (0.700) than that for the Yeosu population (0.692). The GD between individuals supported an adjacent association in grouping II (JINHAE 12 - JINHAE 22). The observation of a noteworthy GD between the two Scapharca populations verified that this PCR-generated technique could be a profitable attempt for within- and between-population-grounded biological DNA scrutiny. The potential of PCR inquiry will be favorable in the selection of individuals and/or populations for several reproductive- and/or quarantine-connected characters in aquafarming manufacture.

Genetic Distances between Tailfin Anchovy (Coilia nasus) Populations Analyzed by PCR.

The author established a PCR-based genetic platform to examine the hierarchical polar dendrogram of Euclidean genetic distances of one tailfin anchovy population, especially for Coilia nasus, which was further associated with other fish population, by connecting with specifically designed oligonucleotide primer sets. Five oligonucleotide primers were used to generate a total of 260 and 211 scorable fragments in Coilia populations I and II, respectively. The DNA fragments ranged from greater than (approximately) 100 to more than 2,000 bp. The average bandsharing values (BS) of individuals from the anchovy population I (0.693) displayed higher values than individuals from population II (0.675). The genetic distance between individuals established the existence of a close relationship in group II. Comparatively, individuals of one anchovy population were fairly related to other fish populations, as shown in the polar hierarchical dendrogram of Euclidean genetic distances. The noteworthy genetic distance determined between two Coilia nasus populations demonstrates that this PCR technique can be applied as one of the several devices for individuals and/or population biological DNA researches undertaken for safeguarding species and for production of anchovies in the littoral area of Korea.

Morphological and Molecular Data Reveal Two New Species of Viannaia (Nematoda: Viannaiidae), Parasitizing Opossums (Mammalia: Didelphidae) in Mexico.

Two new species of Viannaia from the intestine of the North American opossums, Didelphis virginiana (Virginia opossum), and Philander opossum (gray four-eyed opossum), are described based on morphological and molecular data, through an integrative taxonomic approach. Maximum likelihood and Bayesian inference analyses for each dataset and the concatenated dataset were performed using a mitochondrial cytochrome c oxidase subunit 1 (COI) gene, and the nuclear ribosomal internal transcribed spacer region (ITS1-5.8S-ITS2). The phylogenetic analyses revealed 2 new species that occur in Mexico, one from the western state of Colima and another from the southern state of Chiapas. Our phylogenetic trees for both molecular markers and concatenated datasets yielded similar topologies with high bootstrap values and posterior probabilities. Viannaia is recovered as a monophyletic group, but the family Viannaiidae appears as non-monophyletic, due to the position of Travassostrongylus scheibelorum, similar to previous studies. Finally, the morphology of Viannaia and Hoineffia is discussed.

Notes on the genus Zaranga Moore with description of a new species in the Zaranga pannosa species group (Lepidoptera: Notodontidae).

The Zaranga pannosa species group of the genus Zaranga Moore, 1884 is reviewed and a new species, Zaranga koreana sp. nov. from Korea, is described based on morphology and genetic data. An updated checklist, key, and ecological and distributional notes to the species are provided. Diagnoses and description are given for the described species. A new locality to Zaranga tukuringra Streltzov et Yakovlev, 2007, is given and this species is considered as narrow local endemic of north-west Amur basin, distributed on the huge distance from other Zapanga species.

Two New Species of the Genus Eucorydia (Blattodea: Corydiidae) from the Nansei Islands in Southwest Japan.

Two new species of the cockroach genus Eucorydia Hebard, 1929 from the Nansei Islands in Southwest Japan were compared to two closely related congeners, Eucorydia yasumatsui Asahina, 1971 and Eucorydia dasytoides (Walker, 1868). Eucorydia donanensis Yanagisawa, Sakamaki, and Shimano sp. nov. from Yonaguni-jima Island was characterized by an overall length of 12.5-14.5 mm in males. The dorsal side of the male abdomen was entirely dark purple and there was an obscure orange band running down the middle of the tegmen. Eucorydia tokaraensis Yanagisawa, Sakamaki, and Shimano sp. nov. was characterized by an overall length of 12.0-13.0 mm in males and a distinct orange band running down the middle of the tegmen. Eucorydia yasumatsui, E. donanensis, E. tokaraensis and the zonata population of E. dasytoides were divided into four lineages in a maximum-likelihood tree generated from a dataset concatenated from five (two nuclear, 28S rRNA, histone H3, and three mitochondrial, COII, 12S rRNA, 16S rRNA) genes. We recognized the three Japanese lineages E. yasumatsui, E. donanensis, and E. tokaraensis as distinct species, which were also supported by the pairwise genetic distances (5.4-7.8%, K2P) of the COI sequences. Morphometric analysis was performed on the genitalia. A principal component analysis plot revealed that the sizes of the genitalia in the three Japanese species were similar to each other and smaller than that of the zonata population of E. dasytoides. The analysis also revealed that the three Japanese species were distinguished from each other by combinations of the sizes of L3 and L7 sclerites and the shape of R2 sclerite, with some overlapping exceptions.

Convergent Evolution of Himalayan Marmot with Some High-Altitude Animals through ND3 Protein.

The Himalayan marmot (Marmota himalayana) mainly lives on the Qinghai-Tibet Plateau and it adopts multiple strategies to adapt to high-altitude environments. According to the principle of convergent evolution as expressed in genes and traits, the Himalayan marmot might display similar changes to other local species at the molecular level. In this study, we obtained high-quality sequences of the CYTB gene, CYTB protein, ND3 gene, and ND3 protein of representative species (n = 20) from NCBI, and divided them into the marmot group (n = 11), the plateau group (n = 8), and the Himalayan marmot (n = 1). To explore whether plateau species have convergent evolution on the microscale level, we built a phylogenetic tree, calculated genetic distance, and analyzed the conservation and space structure of Himalayan marmot ND3 protein. The marmot group and Himalayan marmots were in the same branch of the phylogenetic tree for the CYTB gene and CYTB protein, and mean genetic distance was 0.106 and 0.055, respectively, which was significantly lower than the plateau group. However, the plateau group and the Himalayan marmot were in the same branch of the phylogenetic tree, and the genetic distance was only 10% of the marmot group for the ND3 protein, except Marmota flaviventris. In addition, some sites of the ND3 amino acid sequence of Himalayan marmots were conserved from the plateau group, but not the marmot group. This could lead to different structures and functional diversifications. These findings indicate that Himalayan marmots have adapted to the plateau environment partly through convergent evolution of the ND3 protein with other plateau animals, however, this protein is not the only strategy to adapt to high altitudes, as there may have other methods to adapt to this environment.

Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses.

Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei's distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright's fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders' gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively).