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DNA methylation in clonal Duckweed lineages (Lemna minor L.) reflects current and historical environmental exposures.
<p>The following depository contains raw phenotypic data and intermediate DNA methylation data presented in the article <strong>"DNA methylation in clonal Duckweed lineages (<em>Lemna minor </em>L.) reflects current and historical environmental exposures.</strong>" :</p> <p><strong>1) Raw phenotypic data</strong></p> <p>- Frond_area_Phase1_Phase2 -> Frond area measured at different time points (week 1, 6, 7 and 8) during the experiment.</p> <p>- Frond_number_Phase1_Phase2 -> Frond number measured at different time points (week 1, 6, 7 and 8) during the experiment.</p> <p><strong>2) Intermediate files obtained from running the epiGBS2 pipeline. The following files are available:</strong></p> <p>- consensus_cluster.renamed.fa -> epiGBS <em>de novo </em>loci. This file consists of the <em>de novo </em>epiGBS reference sequence file obtained during the <em>de novo </em>reference creation.</p> <p>- methylation.filtMETH -> The filtered DNA methylation data. This data was obtained after filtering the raw DNA methylation data. Cytosines which had a 10X coverage or higher and which were present in 80% of all samples were kept for further analysis.</p> <p>Demultiplexed and raw data were deposited at NCBI: BioProject: <strong>PRJNA883550</strong></p>
Figure 3 in Checklist of Water mites in Mexico. Historical background and DNA barcoding perspectives
Figure 3 Neighbor joining tree based on all worldwideNeumaniaCOI sequences. The name is followed by the barcode index number (BIN). * Without data collection.
Table 1 in Checklist of Water mites in Mexico. Historical background and DNA barcoding perspectives
<p><b>Table 1</b> Checklist of water mite species in Mexico. * Without data collection.</p><table><tbody><tr><th><b>Species</b></th><th><b>State</b></th><th><b>Habitat</b></th><th><b>Reference</b></th></tr><tr><th><b>Arrenuridae</b></th></tr></tbody><tbody><tr><th><i>Arrenurus (Arrenurus) dentipetiolatus</i></th><td>Oaxaca, Guanajuato</td><td>Pond</td><td>Marshall 1908</td></tr><tr><th><i>Arrenurus (Arrenurus) valencius</i></th><td>Campeche, Tabasco</td><td>Water-filled roadside</td><td>Marshall 1919</td></tr><tr><th><i>Arrenurus (Arrenurus) munovus</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Arrenurus) wucabus</i></th><td>Oaxaca</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Arrenurus) tamauulipensis</i></th><td>Tamaulipas</td><td>Lake</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Arrenurus) xochimilcoensis</i></th><td>Mexico City</td><td>Standing waters</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Megaluracarus) manubriator</i></th><td>Tabasco</td><td>Pond</td><td>Marshall 1903</td></tr><tr><th><i>Arrenurus (Megaluracarus) birgei</i></th><td>Campeche</td><td>Lagoon</td><td>Marshall 1903</td></tr><tr><th><i>Arrenurus (Megaluracarus) marshallae</i></th><td>Campeche</td><td>Water-filled ditch</td><td>Piersig 1904</td></tr><tr><th><i>Arrenurus (Megaluracarus) gricalus</i></th><td>Veracruz</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) hartesus</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) neoexpansus</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) tabascoensis</i></th><td>Campeche</td><td>Water-filled ditch</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) trassamus</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) zitavus</i></th><td>Campeche</td><td>Water filled-ditch</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) campechensis</i></th><td>Campeche</td><td>Water filled-ditch</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) wolardus</i></th><td>Veracruz, Colima</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Megaluracarus) costeroae</i></th><td>Tamaulipas</td><td>Lake</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Megaluracarus) alloexpansus</i></th><td>Colima</td><td>Not specified</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Megaluracarus) apizanus</i></th><td>Tamaulipas</td><td>Lake</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Megaluracarus) catoi</i></th><td>Tamaulipas</td><td>Lake</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Megaluracarus) champayanus</i></th><td>Tamaulipas</td><td>Lake</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Megaluracarus) colitus</i></th><td>Tamaulipas</td><td>Lake</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Megaluracarus) anae</i></th><td>Tamaulipas</td><td>Lake</td><td>Cramer and Cook 1998</td></tr><tr><th><i>Arrenurus (Megaluracarus) anitahoffmannae</i></th><td>Tabasco</td><td>Lake, pond, canal</td><td>Ramirez-Sánchez and Rivas 2013</td></tr><tr><th><i>Arrenurus (Megaluracarus) olmeca</i></th><td>Tabasco</td><td>Lake, pond, canal</td><td>Ramirez-Sánchez and Rivas 2013</td></tr><tr><th><i>Arrenurus (Megaluracarus) maya</i></th><td>Yucatán, Quintana Roo</td><td>Cenote</td><td>Ramirez-Sánchez and Rivas 2013</td></tr><tr><th><i>Arrenurus (Megaluracarus) urbanus</i></th><td>Mexico city</td><td>Canal</td><td>Ramirez-Sánchez and Rivas 2013</td></tr><tr><th><i>Arrenurus (Megaluracarus) eduardoi</i></th><td>Quintana Roo</td><td>Pool (in a stream)</td><td>Montes-Ortiz et al.2022</td></tr><tr><th><i>Arrenurus (Megaluracarus) federicoi</i></th><td>Quintana Roo</td><td>Pool (in a stream)</td><td>Montes-Ortiz et al.2022</td></tr><tr><th><i>Arrenurus (Megaluracarus) ecosur</i></th><td>Quintana Roo</td><td>Cenote, lagoon, wetlands</td><td>Montes-Ortiz et al.2022</td></tr><tr><th><i>Arrenurus (Megaluracarus) beatrizae</i></th><td>Quintana Roo, Tabasco</td><td>Wetland, lagoon</td><td>Montes-Ortiz et al.2022</td></tr><tr><th><i>Arrenurus (Dadayella) zempoala</i></th><td>Mexico state</td><td>Small stream</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Dadayella) adrianae</i></th><td>Colima, Michoacan</td><td>Wetland, lagoon</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Dadayella) veracruzensis</i></th><td>Veracruz</td><td>Pond</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Dadayella) aztecus</i></th><td>Veracruz</td><td>Wetland, lagoon</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Dadayella) colimensis</i></th><td>Colima</td><td>Wetland, lagoon</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (Dadayella) cristinae</i></th><td>Quintana Roo</td><td>Wetland</td><td>Montes-Ortiz et al.2022</td></tr><tr><th><i>Arrenurus (Truncaturus) plevamus</i></th><td>Guerrero</td><td>Small stream</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Truncaturus) zukovus</i></th><td>Chiapas</td><td>Gravel-bottom stream</td><td>Cook 1980</td></tr><tr><th><i>Arrenurus (Truncaturus)teoceloensis</i></th><td>Veracruz</td><td>Stream</td><td>Rivas and Cramer 1992</td></tr><tr><th><i>Arrenurus (?Arrhenuropsis) mexicanus</i></th><td>Tamaulipas, Colima</td><td>Lagoon</td><td>Cramer and Cook 1992</td></tr><tr><th><i>Arrenurus (?) nayaritensis</i></th><td>Nayarit</td><td>Small stream</td><td>Cook 1980</td></tr><tr><th><b>Hydrachnidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Hydrachna miliaria</i></th><td>Oaxaca</td><td>Pond</td><td>Berlese 1888 in Cook 1980</td></tr><tr><th><i>Hydrachna leovazquezae</i></th><td>Mexico state</td><td>Temporal pond</td><td>Cramer and Costero 1986</td></tr><tr><th><i>Hydrachna guanajuatensis</i></th><td>Guanajuato</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Hydrachna mexicana</i></th><td>Veracruz</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Hydrachna rotunda</i></th><td>Oaxaca, Nayarit, Guanajuato.</td><td>Pond</td><td>Marshall 1930 in Cook 1980</td></tr><tr><th><b>Limnocharidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Rhyncholimnochares (Rhyncholimnochares)</i></th><td>Chiapas</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Rhyncholimnochares (Paralimnochares)</i></th><td>Chiapas</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Eylaidae</i></th><td></td><td></td><td></td></tr><tr><th><i>Eylais guanajuatensis</i></th><td>Guanajuato</td><td>*</td><td>Dugés 1873</td></tr><tr><th><i>Eylais mexicana</i></th><td>Mexico state</td><td>Helocrene spring</td><td>Cook 1980</td></tr><tr><th><i>Hydriyphantidae</i></th></tr><tr><th><i>Hydryphantes (Hydryphantes) ramosus ramosus</i> Oaxaca</th><td>Pond</td><td>Daday 1905 in Cook 1980</td></tr><tr><th><i>Thyopsella obscura</i></th><td>Mexico state.</td><td>Helocrene spring</td><td>Cook 1980</td></tr><tr><th><i>Protzia</i></th><td>Querétaro</td><td>Stream</td><td>Goldschmidt et al. 2015</td></tr><tr><th><b>Hydrodromidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Hydrodroma peregrina perigrina</i></th><td>Campeche, Guanajuato</td><td>Pond</td><td>Lundblad 1941 in Cook 1980</td></tr><tr><th><i>Hydrodroma (Clavipes) despisciens</i></th><td>Oaxaca, Chiapas, Veraruz, San Luis Potosí.</td><td>Stream, river.</td><td>Lundblad 1953 in Cook 1980</td></tr><tr><th><b>Rhynchohydracaridae</b></th></tr><tr><th><i>Clathrosperchon punctatus</i></th><td>Oaxaca, Chiapas, Veracruz.</td><td>Matted roots, bottom of stream</td><td>Cook 1980</td></tr><tr><th><b>Sperchontidae</b></th></tr><tr><th><i>Sperchon mexicanus</i></th><td>Mexico state</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Sperchon neotropicus</i></th><td>Oaxaca, Coahuila, Veracruz.</td><td>Algae on rocks, stream</td><td>Cook 1980</td></tr><tr><th><i>Sperchon (Hispidopershon) gledhilli</i></th><td>Oaxaca, Veracruz, Guerrero.</td><td>Stream</td><td>Viets 1977</td></tr><tr><th><i>Sperchon (Acadiosperchon) pontifex</i></th><td>Oaxaca</td><td>Submerged vegetation</td><td>Otero-Colina 1987a</td></tr><tr><th><i>Sperchon (Mixosperchon) oaxacensis</i></th><td>Oaxaca</td><td>Submerged vegetation</td><td>Otero-Colina 1987a</td></tr><tr><th><b>Anisitsiellidae</b></th></tr><tr><th><i>Bandakia hoffmannae</i></th><td>Mexico state.</td><td>Spring</td><td>Cramer and Smith 1991</td></tr><tr><th><i>Bandakia mexicana</i></th><td>Mexico state.</td><td>Spring</td><td>Cramer and Smith 1991</td></tr><tr><th><i>Mamersella mesoamericana</i></th><td>Tabasco</td><td>Lagoon</td><td>Otero-Colina 1987a</td></tr><tr><th><i>Mamersellides costenius</i></th><td>Veracruz, Colima, Estados Unidos (Florida)</td><td>Ponds, Marshes, backwater pools of streams.</td><td>Cramer and Smith 1993</td></tr><tr><th><b>Lebertiidae</b></th></tr><tr><th><i>Lebertia (Pseudolebertia) azteca</i></th><td>Mexico state</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><b>Oxidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Oxus dugesi</i></th><td>Veracruz, Costa Rica</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Oxus stolli</i></th><td>Guerrero</td><td>Tributary river</td><td>Cook 1980</td></tr><tr><th><b>Torrenticolidae</b></th></tr><tr><th><i>Torrenticola (Monoatractides) lembada</i></th><td>Chiapas, Costa Rica</td><td>Stream, river.</td><td>Cook 1980</td></tr><tr><th><i>Torrenticola (Monoatractides) gorda</i></th><td>Nayarit, Guerrero, Oaxaca</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Torrenticola (Monoatractides) veracruzensis</i></th><td>Veracruz, Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Torrenticola (Torrenticola) rala</i></th><td>Guerrero</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Torrenticola (Torrenticola) keesdavidsi</i></th><td>Mexico state.</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Torrenticola (Torrenticola) carlbaderi</i></th><td>Mexico state.</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Torrenticola (Torrenticola) esbelta</i></th><td>Mexico state.</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Torrenticola (Torrenticola) kurtvietsi</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Neotorrenticola (Neotorrenticola) davecooki</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1987</td></tr><tr><th><i>Pseudotorrenticola (Pseudotorrenticola)</i></th><td>Veracruz</td><td>Stream</td><td>Cramer and Cook 2000</td></tr><tr><th><i>Pseudotorrenticola (Psedotorrenticola) boettgeri</i></th><td>Veracruz</td><td>Stream</td><td>Viets 1977 in Cramer and Cook 2000</td></tr><tr><th><b>Limnesiidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Neomamersa (Neomamersa) mexicana</i></th><td>Oaxaca, Guerrero</td><td>Bottom deposits of stream</td><td>Cook 1980</td></tr><tr><th><i>Neomamersa (Neomamersa) triacebulata</i></th><td>Chiapas</td><td>Gravels deposits of stream</td><td>Cook 1980</td></tr><tr><th><i>Neomamersa (Neomamersa) temazcala</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1987</td></tr><tr><th><i>Meramecia (Meramecia)mexicana</i></th><td>Chiapas, Oaxaca, Puebla</td><td>Gravel deposits of stream</td><td>Cook 1980</td></tr><tr><th><i>Kawamuracarus (Kawamuracarus) expansipes</i></th><td>Oaxaca, Chiapas</td><td>Gravel deposits of stream</td><td>Cook 1980</td></tr><tr><th><i>Kawamuracarus (Kawamuracarus) novus</i></th><td>Puebla</td><td>Gravel deposits of stream</td><td>Cook 1980</td></tr><tr><th><i>Kawamuracarus (Kawamuracarus) iansmithi</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1987</td></tr><tr><th><i>Tyrrelia viuda</i></th><td>Puebla</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Tyrrelia ovalis</i></th><td>Puebla, Mexico state</td><td>Stream</td><td>Marshall 1940 in Cook 1980</td></tr><tr><th><i>Centrolimnesia (Centrolimnesia)motasi</i></th><td>Chiapas</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Centrolimnesia (Centrolimnesia) bondi</i></th><td>Veracruz, Campeche</td><td>Swam, Pond</td><td>Lundblad 1935 in Cook 1980</td></tr><tr><th><i>Limnesia alzatei</i></th><td>Guanajuato</td><td>*</td><td>Dugés 1884</td></tr><tr><th><i>Limnesia laeta</i></th><td>Oaxaca, Tabasco</td><td>Pond</td><td>Stoll 1887 in Cook 1980</td></tr><tr><th><i>Limnesia puteorum</i></th><td>Guanajuato</td><td>*</td><td>Stoll 1987 in Wolcott 1903</td></tr><tr><th><i>Limnesia (Limnesia) abenda</i></th><td>Mexico state</td><td>Helocrene spring</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) banola</i></th><td>Nayarit, Veracruz</td><td>Spring</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) canvada</i></th><td>Nayarit</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) dimorpha</i></th><td>Nayarit</td><td>Spring</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) dornera</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) mesoamericana</i></th><td>Guerrero, Oaxaca, Chiapas, Morelos, Nayarit</td><td>River, stream</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) neodentipalpis</i></th><td>Veracruz</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) setacoxalis</i></th><td>Veracruz, Chiapas, Guerrero</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) trehona</i></th><td>Guerrero</td><td>Spring</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesia) zomplina</i></th><td>Nayarit, Veracruz</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Limnesia (Limnesiella) mexicana</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Limnesia parafalsificata</i></th><td>Tabasco, Chiapas</td><td>Pond</td><td>Otero-Colina 1987a</td></tr><tr><th><i>Psammolimnesia (Psammolimnesia) mexicana</i></th><td>Chiapas</td><td></td><td>Cook 1974</td></tr><tr><th><b>Omartacaridae</b></th></tr><tr><th><i>Omartacarus elongatus</i></th><td>Puebla</td><td>Interstitial waters</td><td>Cook 1963 in Cook 1980</td></tr><tr><th><i>Omartacarus brevipalpis</i></th><td>Chiapas</td><td>Interstitial waters</td><td>Cook 1974</td></tr><tr><th><i>Omartacarus motasi</i></th><td>Chiapas</td><td>Sand and gravel of stream</td><td>Cook 1980</td></tr><tr><th><b>Hygrobatidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Corticacarus novum</i></th><td>Veracruz</td><td>Stream</td><td>Cramer and Cook 1998</td></tr><tr><th><i>Corticacarus (Paracorticacarus) mexicanus</i></th><td>Guerrero, Oaxaca, Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Corticacarus (Polycorticacarellus) similis</i></th><td>Guerrero</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Corticacarus (Polycorticacarellus) mebosus</i></th><td>Chiapas, Veracruz</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Neoatractides curvispinatus</i></th><td>Tabasco</td><td>Gravel in a stream</td><td>Otero-Colina 1987a</td></tr><tr><th><i>Neotractides mexicana</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Neoatractides nayaritensis</i></th><td>Nayarit</td><td>Stream</td><td>Cramer and Cook 2000</td></tr><tr><th><i>Neoatractides abueloi</i></th><td>Veracruz</td><td>Stream</td><td>Cramer and Cook 2000</td></tr><tr><th><i>Neoatractides celiae</i></th><td>Veracruz</td><td>Stream</td><td>Cramer and Cook 2000</td></tr><tr><th><i>Hygrobates (Hygrobates) boettgeri</i></th><td>Oaxaca, Chiapas, Guerrero, Morelos, Nayarit</td><td>Stream</td><td>Viets 1975 in Cook 1980</td></tr><tr><th><i>Hygrobates (Hygrobates) plebejus</i></th><td>Oaxaca, Chiapas, Veracruz, Morelos, Nayarit.</td><td>River</td><td>Lundblad 1930 in Cook 1930</td></tr><tr><th><i>Hygrobates (Hygrobates) amplipalpis</i></th><td>Oaxaca, Veracruz</td><td>Stream</td><td>Viets 1936 in Cook 1980</td></tr><tr><th><i>Hygrobates (Hygrobates) ampliatus</i></th><td>Veracruz, San Luis Potosí, Morelos</td><td>Stream</td><td>Viets 1936 in Cook 1980</td></tr><tr><th><i>Hygrobates (Hygrobates) procursus</i></th><td>Guerrero</td><td>Stream</td><td>Viets 1936 in Cook 1980</td></tr><tr><th><i>Hygrobates (Hygrobates) blatolus</i></th><td>Oaxaca</td><td>Tributary river</td><td>Cook 1980</td></tr><tr><th><i>Hygrobates (Hygrobates) mexicanus</i></th><td>Nayarit</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) crassitarsis</i></th><td>Guerrero</td><td>Stream</td><td>Lundblad 1942 in Cook 1980</td></tr><tr><th><i>Atractides (Atractides) imitatus</i></th><td>Oaxaca</td><td>River</td><td>Viets 1978 in Cook 1980</td></tr><tr><th><i>Atractides (Atractides) guatemaltecus</i></th><td>Oaxaca, Chiapas, Guerrero.</td><td>Tributary river, stream</td><td>Viets 1978 in Cook 1980</td></tr><tr><th><i>Atractides (Atractides) blazonus</i></th><td>Oaxaca</td><td>Tributary river</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) mexicanus</i></th><td>Oaxaca</td><td>Tributary river</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) neolongitarsus</i></th><td>Coahuila</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) prasadi</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) tanutus</i></th><td>Mexico state</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) tembolus</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) tolas</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) toldomus</i></th><td>Coahuila</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) travanus</i></th><td>Chiapas, Oaxaca, Guerrero</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) wevamus</i></th><td>Nayarit</td><td>River bottom deposits</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) zempoalus</i></th><td>Mexico state</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Atractides (Atractides) bassolsae</i></th><td>Oaxaca</td><td>Stream</td><td>Otero-Colina 1987a</td></tr><tr><th><i>Atractides (Octomegapus) peltatus</i></th><td>Chiapas</td><td>River</td><td>Viets 1977 in Cook 1980</td></tr><tr><th><i>Atractidella obtusidens</i></th><td>Oaxaca, Chiapas, Veracruz</td><td>River, stream</td><td>Lundblad 1953 in Cook 1980</td></tr><tr><th><i>Atractidella mesoamericana</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Paraschizobates scutatus</i></th><td>Nayarit, Chiapas, Oaxaca</td><td>River, stream</td><td>Cook 1980</td></tr><tr><th><i>Diamphidaxona mexicana</i></th><td>Chiapas</td><td>Gravel deposits in stream</td><td>Cook 1980</td></tr><tr><th><i>Diamphidaxona anitae</i></th><td>Mexico state</td><td>Stream</td><td>Cramer and Letechipía 1996</td></tr><tr><th><b>Unionicolidae</b></th></tr><tr><th><i>Unionicola gracilipalpis tenuis</i></th><td>Oaxaca, Campeche</td><td>Pond, water filled roadside</td><td>Lundblad 1935 in Cook 1980</td></tr><tr><th><i>Unionicola (Unionicola) mexicana</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Unionicola (Pentatax) conjuncta</i></th><td>Chiapas</td><td>Stream</td><td>Viets 1954 in Cook 1980</td></tr><tr><th><i>Unionicola (Pentatax) furculopsis</i></th><td>Oaxaca</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Unionicola (Pentatax) aculeata</i></th><td>Tamaulipas, northern and central Mexico</td><td>Freshwater mussel <i>Anodonta sp., Cyrtonaias tampicoensis, Disconaias sp., Friersonia sp.</i></td><td>Koenike 1914 in Vidrine 1996</td></tr><tr><th><i>Unionicola (Atacella) neoperforata</i></th><td>Tamaulipas, San Luis Potosí.</td><td>Freshwater mussel <i>A. trapesialis glaucus</i></td><td>Vidrine 1985b</td></tr><tr><th><i>Unionicola (Atacella) petita</i></th><td>Veracruz</td><td>Freshwater mussel <i>A. trapesialis glaucus</i></td><td>Vidrine 1985b</td></tr><tr><th><i>Unionicola (Atacella) entrerrianensis</i></th><td>Tamaulipas, San Luis Potosí, Veracruz.</td><td>Freshwater mussel <i>A. trapesialis glaucus</i></td><td>Rosso de Ferradás 1976</td></tr><tr><th><i>Unionicola (Atacella) fissipes</i></th><td>Western Mexico</td><td>Freshwater mussel <i>Anodontites</i></td><td>Koenike, 1891</td></tr><tr><th><i>Unionicola (Berezatax) berezai</i></th><td>Veracruz, San Luis Potosí</td><td>Freshwater mussel <i>Nephronaias sp.</i></td><td>Vidrine 1985a</td></tr><tr><th><i>Unionicola (Berezatax) acylindrotarsa</i></th><td>Tamaulipas, San Luis Potosí</td><td>Freshwater mussel <i>Popenaias, Nephronaias</i></td><td>Vidrine 1985a</td></tr><tr><th><i>Unionicola (Causeyatax) hensleyi</i></th><td>San Luis Potosí, Tamaulipas</td><td>Freshwater mussel <i>Friersonia iridella</i></td><td>Vidrine 1985c</td></tr><tr><th><i>Unionicola (Clarkatax) serrata</i></th><td>San Luis Potosí, Tamaulipas, Veracruz (Panuco river system)</td><td>Friersonia iridella, F. moctezumensis</td><td>Wolcott 1898 in Vidrine 1996</td></tr><tr><th><i>Unionicola (Hexatax) laurentiana</i></th><td>San Luis Potosí, Tamaulipas, Veracruz (Panuco river system)</td><td>Freshwater mussel <i>Disconaias fimbriata, Nephronaias sp., Popenaias sp.</i></td><td>Crowell and Davids 1979 in</td></tr><tr><th><i>Unionicola (Unionicolides) burchi</i></th><td>Guanajuato</td><td>Freshwater mussel <i>Anodonta sp.</i></td><td>Vidrine 1996</td></tr><tr><th><i>Unionicola (Unionicolides) calnani</i></th><td>Tamaulipas, Veracruz</td><td>Freshwater mussel <i>Cyrtonaias tampicoensis, Disconaias discus.</i></td><td>Vidrine 1986</td></tr><tr><th><i>Unionicola (Unionicolides) hoesei</i></th><td>San Luis Potosí, Tamaulipas, Veracruz (Panuco river system)</td><td>Freshwater mussel</td><td>Vidrine 1986</td></tr><tr><th><i>Unionicola (Neoatax) abnormipes</i></th><td>Tamaulipas</td><td>Freshwater mussel <i>Cyrtonaias tampicoensis</i></td><td>Vidrine 1986</td></tr><tr><th><i>Neumania (Neumania) conroyi</i></th><td>Mexico state</td><td>Reocrene spring</td><td>Cook 1980</td></tr><tr><th><i>Neumania (Neumania) diversipalpa</i></th><td>Chiapas</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Neumania (Neumania) alticola</i></th><td>Chiapas, Campeche, Oaxaca, Tabasco, Veracruz.</td><td>Pond, stream.</td><td>Stoll 1886 in Cook 1980</td></tr><tr><th><i>Neumania (Tetraneumania) nondanda</i></th><td>Chiapas, Tabasco, Campeche</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Neumania (Tetraneumania) cesateca</i></th><td>Tabasco, Chiapas</td><td>River, Pond</td><td>Otero-Colina 1987b</td></tr><tr><th><i>Recifella (Recifella) bella</i></th><td>Veracruz, Chiapas</td><td>River, stream</td><td>Cook 1980</td></tr><tr><th><i>Recifella (Eorecifella?) azteca</i></th><td>Oaxaca</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Recifella (Eorecifella) cemoba</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Recifella (Eorecifella) laversi</i></th><td>Chiapas</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Recifella (Eorecifella) alpa</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Recifella (Eorecifella) indistincta</i></th><td>Yucatán</td><td>Cenote (Sinkhole)</td><td>Marshall 1936 in Cook 1980</td></tr><tr><th><i>Recifella (Recifellopsis) mexicana</i></th><td>Chiapas, Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Recifella (Vietsella)veracruzana</i></th><td>Veracruz</td><td>Pond</td><td>Cramer and Cook 1998</td></tr><tr><th><i>Koenikea (Koenikea) canerma</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Koenikea) clazona</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Koenikea) gracilipes</i></th><td>Nayarit, Chiapas, Guerrero</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Koenikea) tobarana</i></th><td>Nayarit</td><td>River, stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Koenikea) trocala</i></th><td>Guerrero</td><td>Spring</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Koenikea) yenona</i></th><td>Nayarit</td><td>Tributary river</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Koenikea) zedima</i></th><td>Chiapas, Tabasco</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Koenikea) zolada</i></th><td>Veracruz</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Koenikea mesoamericana</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (?Diplokoenikea) bispina</i></th><td>Veracruz</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (?Diplokoenikea) blepta</i></th><td>Guerrero</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (?Diplokoenikea) beltista</i></th><td>Chiapas, Veracruz, Puebla.</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Diplokoenikea) neopectinifera</i></th><td>Campeche, Tabasco</td><td>Waterfilled ditch, pond</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Diplokoenikea) clavigera</i></th><td>Chiapas, Oaxaca</td><td>Pond</td><td>Lundblad 1943 in Cook 1980</td></tr><tr><th><i>Koenikea (Notomideopsis) paragrossa</i></th><td>Oaxaca</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Notomideopsis) sexmaculata</i></th><td>Oaxaca, Veracruz</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Notomideopsis) toloma</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Notomideopsis) veracruzensis</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Notomideopsis) nayaritensis</i></th><td>Nayarit</td><td>Spring</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Notomideopsis) taninulensis</i></th><td>San Luis Potosí</td><td>Sulphurous stream</td><td>Cramer 1983</td></tr><tr><th><i>Koenikea (Sespekoenikea) chiapasana</i></th><td>Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Sespekoenikea) piotiformis</i></th><td>Nayarit, Guerrero</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Tanaognathus) kurtvietsi</i></th><td>Guerrero</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Koenikea (Parakoenikea) curvipalpis</i></th><td>Oaxaca</td><td>River</td><td>Lundblad 1936 in Cook 1980</td></tr><tr><th><b>Pionidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Piona bromada</i></th><td>Tabasco, Campeche, Veracruz, Oaxaca.</td><td>Pond, waterfilled ditch</td><td>Cook 1980</td></tr><tr><th><i>Piona mexicana</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Piona neoacutidens</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Piona (Piona) triangularis</i></th><td>*</td><td>*</td><td>Wolcott1902 in Marín-Hernández and Cramer-Hemkes 2009</td></tr><tr><th><i>Piona (Tetrapiona) rotunda sudamericana</i></th><td>*</td><td>*</td><td>Viets 1910 in Marín-Hernández and Cramer-Hemkes 2009</td></tr><tr><th><i>Piona alzatei</i></th><td>*</td><td>*</td><td>Dugés 1884</td></tr><tr><th><i>Piona pearsei</i></th><td>*</td><td>*</td><td>Marshall 1936</td></tr><tr><th><i>Piona amimitli</i></th><td>Mexico city</td><td>Stream</td><td>Marín-Hernández 2009</td></tr><tr><th><b>Aturidae</b></th></tr><tr><th><i>Aturus matlatzinca</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1991</td></tr><tr><th><i>Aturus catoantoni</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1991</td></tr><tr><th><i>Aturus guillecrameri</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Aturus celiahemkesae</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Aturus oxtotilpanensis</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1992</td></tr><tr><th><i>Aturus primitivus</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 1991</td></tr><tr><th><i>Neoaturus kurtvietsi</i></th><td>Oaxaca, Chiapas, Veracruz, Guerrero</td><td>River, stream</td><td>Cook 1980</td></tr><tr><th><i>Neoaturus projectus</i></th><td>Veracruz</td><td>River</td><td>Lundblad 1936 in Cook 1980</td></tr><tr><th><i>Adelaxonopsella pallida</i></th><td>Veracruz</td><td>Interstitial water stream</td><td>Cook 1974</td></tr><tr><th><i>Albia (Anchistalbia) iantha</i></th><td>Nayarit</td><td>Spring</td><td>Cook 1980</td></tr><tr><th><i>Albia (Anchistalbia) ianthopsis</i></th><td>Quintana Roo</td><td>Lagoon</td><td>Otero-Colina 1987b</td></tr><tr><th><i>Axonopsella (?) mesoamericana</i></th><td>Guerrero, Morelos, Nayarit</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Axonopsella (Neoaxonopsella) nayaritensis</i></th><td>Nayarit</td><td>Cataracts</td><td>Cook 1980</td></tr><tr><th><i>Axonopsella (Neoaxonopsella) vicina</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Axonopsis (Brachypodopsis) columbicola</i></th><td>Chiapas, Oaxaca, Puebla. Nayarit</td><td>River, stream</td><td>Lundblad 1953 in Cook 1980</td></tr><tr><th><i>Axonopsis (Brachypodopsis) cemoba</i></th><td>Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Axonopsis (Brachypodopsis) cerucha</i></th><td>Veracruz, San Luis Potosí</td><td>River, Stream</td><td>Cook 1980</td></tr><tr><th><i>Axonopsis (Brachypodopsis) mesoamericana</i></th><td>Veracruz, Chiapas</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Axonopsis (Brachypodopsis) trocala</i></th><td>Chiapas</td><td>Chiapas</td><td>Cook 1980</td></tr><tr><th><i>Polyaxonopsella mexicana</i></th><td>Oaxaca</td><td>Stream</td><td>Otero-Colina 1987b</td></tr><tr><th><i>Frontipodopsis mesoamericana</i></th><td>Chiapas</td><td>Bottom deposits of stream</td><td>Cook 1980</td></tr><tr><th><i>Kongsbergia antoniocatoi</i></th><td>Mexico state</td><td>Gravel deposits of stream</td><td>Cramer 2000</td></tr><tr><th><i>Kongsbergia cosita</i></th><td>Mexico state</td><td>Gravel deposits of stream</td><td>Cramer 2000</td></tr><tr><th><i>Kongsbergia tigrina</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 2000</td></tr><tr><th><i>Kongsbergia eterna</i></th><td>Mexico state</td><td>Stream</td><td>Cramer 2000</td></tr><tr><th><i>Kongsbergia (Kongsbergia) mexicana</i></th><td>Oaxaca</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Kongsbergia glopipalpis</i></th><td>Chiapas and Veracruz</td><td>Stream</td><td>Lundblad 1953 in Cook 1980</td></tr><tr><th><i>Kongsbergia materna</i></th><td>Chiapas, Mexico state, Oaxaca, Veracruz.</td><td>Tributary river</td><td>Thor 1899 in Cramer 2000</td></tr><tr><th><i>Submiraxona (Submiraxona) bella</i></th><td>Nayarit</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Submiraxona (Submiraxona) lundbladi</i></th><td>Guerrero, Chiapas</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Submiraxona (Submiraxona) stolli</i></th><td>Guerrero</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Miraxona (Miraxona) expansipes</i></th><td>Guerrero</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Miraxona (Miraxona) mexicana</i></th><td>Guerrero</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Miraxonides (Miraxonidella) similis</i></th><td>Nayarit, Veracruz</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Miraxona (Miraxonides) geronimoi</i></th><td>Nayarit</td><td>Stream</td><td>Cramer and Cook 1991</td></tr><tr><th><i>Stygalbiella mexicana</i></th><td>Mexico state</td><td>Spring</td><td>Cramer 1992</td></tr><tr><th><i>Neoaxona (?Lamellaxona) mexicana</i></th><td>Nayarit</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Woolastookia gretae</i></th><td>Nayarit</td><td>River, stream</td><td>Viets 1978 in Cook 1980</td></tr><tr><th><i>Forelia mesoamericana</i></th><td>Chiapas</td><td>Lagoon</td><td>Otero-Colina 1987b</td></tr><tr><th><b>Feltriidae</b></th></tr><tr><th><i>Feltria (Tropifeltria) neotropica</i></th><td>Chiapas</td><td>Waterfalls</td><td>Otero-Colina 1987b</td></tr><tr><th><i>Feltria (Feltriella) anahoffmannae</i></th><td>Mexico state</td><td>Mountain spring</td><td>Cramer 1986</td></tr><tr><th><b>Mideopsidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Mideopsis (Mideopsis) cartesa</i></th><td>Nayarit, Veracruz</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Mideopsis (Mideopsides) beta</i></th><td>Chiapas</td><td>Gravel deposits of stream</td><td>Cook 1980</td></tr><tr><th><i>Mideopsis (Mideopsis) magna</i></th><td>Veracruz, Morelos</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Mideopsis (Neoxystonotus) nobilis</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Mideopsis orbicularis</i></th><td>Yucatán</td><td>Cenote</td><td>Müller 1776</td></tr><tr><th><i>Mideopsis (Neoxystonotus) mexicana</i></th><td>Mexico state</td><td>Helocrene spring</td><td>Cook 1980</td></tr><tr><th><i>Mideopsis (Neoxystonotus) gennada</i></th><td>Chiapas</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Mideopsis (Neoxystonotus) canzolla</i></th><td>Guerrero</td><td>Tributary river</td><td>Cook 1980</td></tr><tr><th><b>Krendowskiidae</b></th><td></td><td></td><td></td></tr><tr><th><i>Krendowskia (Krendowskiella) azteca</i></th><td>Guerrero</td><td>Tributary river</td><td>Cook 1980</td></tr><tr><th><i>Krendowskia (Krendowskiella) moyara</i></th><td>Chiapas</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Krendowskia (Krendowskiella) trodroma</i></th><td>Veracruz, Nayarit</td><td>Stream</td><td>Cook 1980</td></tr><tr><th><i>Krendowskia (Krendowskiella) vicina</i></th><td>Tabasco</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><i>Geayia (Geayia) amacuzaca</i></th><td>Morelos</td><td>River</td><td>Cook 1980</td></tr><tr><th><i>Geayia (Geayia) mitchelli</i></th><td>Tabasco, Chiapas</td><td>Pond</td><td>Cook 1980</td></tr><tr><th><b>Arenohydracaridae</b></th><td></td><td></td><td></td></tr><tr><th><i>Arenohydracarus eremitus</i></th><td>*</td><td>*</td><td>Cook 1974</td></tr><tr><th><i>Arenohydracarus minimus</i></th><td>Oaxaca, Guerrero</td><td>Intertitial waters</td><td>Cook 1974</td></tr><tr><th><b>Chappuisididae</b></th></tr><tr><th><i>Chappuisides notialis</i></th><td>Mexico state</td><td>Spring</td><td>Cramer and Smith 1991</td></tr><tr><th><b>Hungarohydracaridae</b></th></tr><tr><th><i>Stygarrenurus armoniensis</i></th><td>Mexico state</td><td>Interstitial deposits of spring.</td><td>Cramer and Cook 1996</td></tr><tr><th><b>Neoacaridae</b></th></tr><tr><th><i>Neoacarus adocetus</i></th><td>Mexico state</td><td>Spring</td><td>Cramer and Smith 1991</td></tr></tbody></table>
Data from: Hare pseudo-reference genome from: the genomic impact of historical hybridization with massive mitochondrial DNA introgression
<p><b>Background:</b> The extent to which selection determines interspecific patterns of genetic exchanges enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, <i>Lepus granatensis</i>, displays in its northern range extensive mitochondrial DNA introgression from <i>L. timidus</i>, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.</p> <p><b>Results:</b> Although the average nuclear and mtDNA introgression patterns are strongly contrasted, they fit a single neutral model of post-glacial invasive replacement of <i>timidus</i> by <i>granatensis</i>. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X-chromosome and in low recombining regions.</p> <p><b>Conclusion:</b> General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.</p>
Figure 2 in Checklist of Water mites in Mexico. Historical background and DNA barcoding perspectives
Figure 2 Number of species recorded by state in Mexico.
Figure 1 in Checklist of Water mites in Mexico. Historical background and DNA barcoding perspectives
Figure 1 Species richness by family in Mexico.
Table 2 Unidentified species with a in Checklist of Water mites in Mexico. Historical background and DNA barcoding perspectives
<p><b>Table 2</b> Unidentified species with a DNA barcode in BOLD database. BINs indicate putative species. * Unique BINs this database.</p><table><tbody><tr><th><i>Taxa</i></th><th>BIN</th><th><i>Taxa</i></th><th>BIN</th><th><i>Taxa</i></th><th>BIN</th></tr></tbody><tbody><tr><th>Arrenuridae</th><td></td><td>Limnesiidae</td><td></td><td><b>Pionidae</b></td><td></td></tr><tr><th>Arrenuridae</th><td>AEA 4828*</td><td><i>Limnesiidae</i></td><td>AEA 4382*</td><td><i>Pionidae</i></td><td>AEA 4809*</td></tr><tr><th><i>Arrenurus cristinae</i></th><td>AEA 7842*</td><td><i>Centrolimnesia</i></td><td>AEA 3914*</td><td><i>Piona</i></td><td>AEA 5358*</td></tr><tr><th><i>Arrenurus eduardoi</i></th><td>AEA 7844*</td><td><i>Limnesia</i></td><td>AEA 6471*</td><td><i>Piona</i></td><td>AEE 5501*</td></tr><tr><th><i>Arrenurus federicoi</i></th><td>AEB 7095*</td><td><i>Limnesia</i></td><td>ACX 7759</td><td><i>Piona</i></td><td>AEN 6046*</td></tr><tr><th><i>Arrenurus ecosur</i></th><td>ACX 8463</td><td><i>Limnesia</i></td><td>ACY 7380</td><td><i>Piona</i></td><td>AEO 7290*</td></tr><tr><th><i>Arrenurus marshallae</i></th><td>ACL2521</td><td><i>Limnesia</i></td><td>AEA 5595</td><td><i>Piona</i></td><td>AER1599 *</td></tr><tr><th><i>Arrenurus</i></th><td>ACX 8462*</td><td><b>Hygrobatidae</b></td><td></td><td><i>Piona</i></td><td>AER1600 *</td></tr><tr><th><i>Arrenurus</i></th><td>ACX 8788*</td><td>Hygrobatidae</td><td>AEA 5236*</td><td><i>Piona</i></td><td>AER1601 *</td></tr><tr><th><i>Arrenurus</i></th><td>ACX 8789*</td><td>Hygrobatidae</td><td>AEA 4089*</td><td><b>Mideopsidae</b></td><td></td></tr><tr><th><i>Arrenurus</i></th><td>ACY 6809*</td><td><i>Atractides</i></td><td>ACX 7786*</td><td>Mideopsidae</td><td>AEB 4633*</td></tr><tr><th><i>Arrenurus</i></th><td>ADI 3752*</td><td><i>Hygrobates</i></td><td>AEA 3689*</td><td><i>Mideopsis</i></td><td>ACY 7169*</td></tr><tr><th><i>Arrenurus</i></th><td>ADI 4458*</td><td><i>Hygrobates</i></td><td>AEA 3690*</td><td><i>Mideopsis</i></td><td>AEA 6512*</td></tr><tr><th><i>Arrenurus</i></th><td>AEA 3972*</td><td><i>Hygrobates</i></td><td>AEA 3924*</td><td><i>Mideopsis</i></td><td>ACX 8679</td></tr><tr><th><i>Arrenurus</i></th><td>AEA 7182*</td><td><i>Hygrobates</i></td><td>ACX 7887</td><td><b>Krendowskiidae</b></td><td></td></tr><tr><th><i>Arrenurus</i></th><td>AEA 7843*</td><td><i>Hygrobates</i></td><td>ADO 7098</td><td><i>Krendowskia</i></td><td>ACX 8435*</td></tr><tr><th><i>Arrenurus</i></th><td>AEA 8234*</td><td><b>Unionicolidae</b></td><td></td><td><i>Geayia</i></td><td>ACT 6195</td></tr><tr><th><i>Arrenurus</i></th><td>AEF1989 *</td><td>Unionicolidae</td><td>AEA 6658*</td><td><b>Hydrachnidia</b></td><td>AEA3823*</td></tr><tr><th><i>Arrenurus</i></th><td>AEF 8444*</td><td>Unionicolidae</td><td>ACY 7381</td><td></td><td>AEA4343*</td></tr><tr><th><i>Arrenurus</i></th><td>ACL2418</td><td>Unionicolidae</td><td>AEB1594 *</td><td></td><td>AEF3494*</td></tr><tr><th><i>Arrenurus</i></th><td>ACX 8464</td><td>Unionicolidae</td><td>AEA 7951*</td><td></td><td>AEF8255*</td></tr><tr><th><b>Limnocharidae</b></th><td></td><td>Unionicolidae</td><td>AEA 6062*</td><td></td><td>AEF0324*</td></tr><tr><th>Limnocharidae</th><td>AEA 4515*</td><td>Unionicolidae</td><td>AEA 4829*</td><td></td><td>AEI2293*</td></tr><tr><th><i>Limnochares</i></th><td>ACY 6840*</td><td>Unionicolidae</td><td>AEA 3726*</td><td></td><td>AEI2954*</td></tr><tr><th><i>Limnochares</i></th><td>ADI 4862*</td><td>Unionicolidae</td><td>AEA 4514*</td><td></td><td>AEI4296*</td></tr><tr><th><i>Eylaidae</i></th><td></td><td><i>Unionicola</i></td><td>ACX 8035*</td><td></td><td>AEI4327*</td></tr><tr><th><i>Eylaidae</i></th><td>AEA 4696*</td><td><i>Unionicola</i></td><td>ADM 7936*</td><td></td><td>AEI4328*</td></tr><tr><th><i>Eylaidae</i></th><td>AEA 5669*</td><td><i>Unionicola</i></td><td>AEB 4634*</td><td></td><td>AEI4329*</td></tr><tr><th><i>Eylais</i></th><td>ADD 9174*</td><td><i>Unionicola</i></td><td>AEE 0841*</td><td></td><td>AEI8266*</td></tr><tr><th><b>Hydryphantidae</b></th><td></td><td><i>Unionicola</i></td><td>ACX 9008</td><td></td><td>AEI8707*</td></tr><tr><th><i>Hydryphantes</i></th><td>AEA 5005*</td><td><i>Unionicola</i></td><td>AEF2345</td><td></td><td>AEI 9124*</td></tr><tr><th><b>Hydrodromidae</b></th><td></td><td><i>Unionicola</i></td><td>ACX 8034</td><td></td><td>AEJ2119*</td></tr><tr><th><i>Hydrodroma</i></th><td>ADF 3732</td><td><i>Neumania</i></td><td>AEA 8101*</td><td></td><td>AEN6047*</td></tr><tr><th><b>Anisitsiellidae</b></th><td></td><td><i>Neumania</i></td><td>ACY 6829</td><td></td><td>AEN8226*</td></tr><tr><th><i>Mamersellides</i></th><td>AEA 6955*</td><td><i>Koenikea</i></td><td>ACY 7384*</td><td></td><td>AEN8227*</td></tr><tr><th><i>Mamersellides</i></th><td>AEA 6956*</td><td><i>Koenikea</i></td><td>ACB 9299</td><td></td><td>AEO5260*</td></tr><tr><th><i>Torrenticolidae</i></th><td></td><td><i>Koenikea</i></td><td>ADI2928</td><td></td><td>AER2566 *</td></tr><tr><th><i>Torrenticolidae</i></th><td>AEA 4395*</td><td><i>Koenikea</i></td><td>ADI 3114</td><td></td><td>AEB1898</td></tr><tr><th><i>Torrenticola</i></th><td>AEA 7372*</td><td></td><td></td><td></td><td></td></tr></tbody></table>
Historical DNA reveals climate adaptation in an endangered songbird
<p>To cope with climate change, species may shift their distributions or adapt <em>in situ</em> to changing environmental conditions. However, clear examples of genetic changes via adaptation are limited. We explore evolutionary responses to climate change in the endangered southwestern willow flycatcher (<em>Empidonax</em> <em>trailli</em> <em>extimus</em>) through whole-genome comparisons between historical specimens, collected from 1888–1909 near San Diego, CA, and contemporary individuals from across the breeding range. Genomic analyses revealed that introgression into San Diego increased adaptive potential over time and shifted genome-wide population structure towards that of neighboring populations. In contrast, loci linked to climate (dew point temperature and precipitation) shifted away from neighboring populations and in a direction consistent with adaptation to climate change in southern CA. This research highlights the role of admixture in facilitating adaptive shifts through its impact on genome-wide genetic variation and represents one of the few studies to document climate adaptation in a wild population.</p>
Historical DNA reveals climate adaptation in an endangered songbird
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Data from: The genomic impact of historical hybridization with massive mitochondrial DNA introgression
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Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).
Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographic distance among localities, the environment, and the position of localities in relation to main rivers were tested by Redundancy Analysis (RDA). Results: We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE, or historical factors. Main conclusions: Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that non-linear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.
Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)
Recent research has shown that the helmeted terrapin (Pelomedusa subrufa), a species that occurs throughout sub-Saharan Africa, in Madagascar and the southwestern Arabian Peninsula, consists of several deeply divergent genetic lineages. Here we examine all nominal taxa currently synonymized with Pelomedusa subrufa (Bonnaterre, 1789) and provide mitochondrial DNA sequences of type specimens or topotypic material for most taxa. Lectotypes are designated for Testudo galeata Schoepff, 1792, Pentonyx capensis Duméril & Bibron, 1835, Pelomedusa nigra Gray, 1863, Pelomedusa galeata var. disjuncta Vaillant & Grandidier, 1910, and Pelomedusa galeata damarensis Hewitt, 1935. For Pelomedusa gasconi Rochebrune, 1884, a taxon without preserved type material, a neotype is designated. Type material of Pentonix americana Cornalia, 1849, a nominal species without credible type locality, is lost and its identity remains questionable. Also the holotype of Pelomedusa galeata orangensis Hewitt, 1935 is lost, but its allocation to the only genetic lineage occurring in South Africa is unambiguous. Phylogenetic analyses of type sequences or topotypic material reveal that the remaining nominal taxa represent three of the nine previously identified lineages of Pelomedusa. Among these three lineages is the South African one. Type specimens of Pentonyx gehafie Rüppell, 1835 correspond to an additional distinct lineage. The present study provides a sound basis for a subsequent integrative taxonomic revision of the Pelomedusa complex.
Data from: Matrix correspondence tests on the DNA phylogeny of the Tenerife lacertid elucidate both historical causes and morphological adaptation
Previous studies using partial regression Mantel tests of matrix correspondence on within-island geographic variation in the color pattern of the Tenerife (Canary Islands) lacertid lizard (Gallotia galloti) support natural selection for different north--south climatically determined biotopes but do not support any historical cause. However, tests on the DNA phylogeny based primarily on population data from 57 localities on Tenerife support the hypothesis that there were populations on two putative precursor islands that have come into secondary contact and introgressed after these islands were joined to form Tenerife by the eruption of the Canadas edifice. Subsequent partial Mantel tests continue to support the hypothesis that color pattern is adapted to the climatic biotopes even when this phylogenetic information is taken into account by (1) testing for color pattern adaptation separately within each lineage and (2) testing for color pattern adaptation across the entire island while considering the molecular phylogenetic relationships as representing an alternative explanation. Selection has largely expunged any trace of the geological history from current morphological variation, and the introgression of these island populations after an estimated 0.7 million years of separation gives an insight into the relationships between allopatric divergence and reproductive isolation.
Data from: Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
Data from: Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA, and implications for restoration
Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analyzed for genetic variability at 12 microsatellite loci, and compared to 17 present-day O. nerka populations—exhibiting either anadromous (sockeye salmon) or non-anadromous (kokanee) life histories—from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee rivers (pairwise FST = 0.004 and 0.002, respectively) and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise FST = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration-timing suggesting that this group represented a putative historical ESU originating in headwater lakes in British Columbia that was likely extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.
Data from: Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding
Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in "oceans" of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km2 of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years, and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528±75 cal yr BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes likely being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.
Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar
Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM) approach to faunal identification, where DNA from non-diagnostic bone fragments is extracted and sequenced in parallel. However, a large proportion of fishing communities (both past and present) live in tropical regions that have sub-optimal conditions for long-term aDNA preservation. To date, the BBM method has never been applied to fish bones before, or to fossils excavated from an exposed context within a tropical climate. Here, we demonstrate that morphologically indistinct bulk fish bone from the tropics can be identified by sequencing aDNA extracted from 100 to 300 ya archaeological midden material in southwest Madagascar. Despite the biases of the approach, we rapidly obtained family, genus, and species-level assemblage information, and used this to describe a subset of the ichthyofauna exploited by an 18th century fishing community. We identified 23 families of fish, including benthic, pelagic, and coral-dwelling fishes, suggesting a reliance on a variety of marine and brackish habitats. When possible, BBM should be used alongside osteological approaches to address the limitations of both; however, this study highlights how genetic methods can nevertheless be a valuable tool for helping resolve faunal assemblages when morphological identification is hindered by taphonomic processes, lack of adequate comparative collections, and time constraints, and can provide a temporal perspective on fish biodiversity in the context of accelerated exploitation of the marine environment.
Figure 10 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 10. Mantidactylus (Mantidactylus) radaka sp. nov. being prepared for human consumption. (a) Frogs and crabs are collected from broad streams. Then (b) the frogs are gutted and skinned, and the head, hands and feet removed. The frog is then rinsed in the stream, leaving (c) cleaned animals for cooking in a stew. Note the ovaries full with hundreds of eggs.
Figure 9 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 9. Preserved type specimens of the four nomina in the Mantidactylus subgenus Mantidactylus and one of the paralectotypes of Rana guttulata.
Figure 7 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 7. Photographs of living specimens of Mantidactylus (Mantidactylus) guttulatus, M. (M.) grandidieri, and of three candidate species. (a, b) M. (M.) guttulatus, female ZSM 1013/2003 (FGMV 2002.438) from Ranomafana. (c) Unidentified specimen from Ranomafana, assigned tentatively to M. (M.) guttulatus (no genetic evidence). (d, e) M. (M.) guttulatus, specimen KU 340853 (CRH729) from Ranomafana. (f) M. (M.) grandidieri, specimen ZSM 5077/2005 (ZCMV 2159) from Nosy Mangabe. (g) M. (M.) grandidieri, specimen ZSM 276/2005 (FGZC 2682) from Vohidrazana. (h) M. (M.) grandidieri, unidentified specimen (probably subadult) from Andranofotsy. (i, j) M. (M.) grandidieri, specimen KU
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