The Holocaust in Lithuania is the most extensive in all affected countries, reducing pre-War Jewish population from 210,000 to only 15,000. The figure likely a bit higher as the Soviet Union has deported 7,000 Jews after the occupation of Lithuania and Chiune Sugihara - God bless his soul - helped 6,000 to leave the country by issuing them visas.
The total destruction of Lithuanian Jewry is the direct result of an extensive Lithuanian collaboration. The first pogroms started even before Germans entered the country. One publication called Nazis not instigators, but enablers to Lithuanians. This is, of course, an exaggeration, but barely.
Edit: The various sources put the percentage of Jews killed in Lithuania into a range of 90-96%, which is the highest among the countries, but not that higher than in Poland or Bohemia. In Ukraine and Belorussia, more than third survived. My grand-grandmother was one of them. The main distinction is the speed of extermination as according to the Stahler's report to Himmler for the period of October 16, 1941, to January 31, 1942, seven months into the invasion, 136 thousand were killed (the overall death toll was even larger). In contrast, a neighbouring Belorussia being a home to a bit larger number of Jews had suffered "only" 42 thousand losses by this point.
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So to start off I want to point to recent research concerning the Soviet deportations you mentioned: Atina Grossmann in a lot of her recent work points to the fact that the majority of Eastern European Jews who survived the Second World War did so because of Soviet deportations and evacuations into the central Asian republics of the USSR. I write more about this in this answer but to directly cite Grossmann:
This forced migration away from the Soviet territories first attacked by the Germans therefore provided—and I keep repeating this fact because it still seems alien to the dominant narrative—the main chance for eastern European Jewry’s survival. The so-called Asiatics who survived the extreme hardships of the Soviet “refuge” constituted the numerical, if not the most visible or articulate, core of the She’erit Hapleta (the core of Eastern European survivors of the Holocaust) Yet we know remarkably little about these Jews’ everyday life, about the political decisions and wartime contingencies that determined their fate, about their numbers, about the relations between Jewish and non-Jewish Polish refugees, about relations with Soviet citizens, Jewish and not. It is astonishing.
Anyways, on to Lithuania.
Scholarship on the issue has identified several factors that played a major role in Lithuania having its Jewish community so thoroughly annihilated and becoming the first European territory to be declared "Jew-free". One of these factors was that it served in the words of historian Konrad Kwiet a "rehearsal stage" and Nazi case study for how the Holocaust in the Soviet Union and more specifically the Einsatzgruppen operated. Secondly, and in contrast to other territories of the Soviet Union and Poland, the Jewish community in Lithuania was highly concentrated in the urban centers and at the same time, easy to identify and isolated from the majority population (I will get to that); and thirdly, a history of organized political anti-Semitism dating back to the inter-war period, that the Germans were able to activate and use for their purposes in order to make use of a relatively small portion of Lithuanian society serving as very active collaborators.
As Michael MacQueen writes in his article The Context of Mass Destruction: Agents and Prerequisites of the Holocaust in Lithuania:
[T]hree themes are central to our understanding of how the Lithuanian Holocaust happened: (1) the nature of Lithuanian nationalism and its setting; (2) the political context of the late interwar and early war years (i.e. spring 1938-June 1941); and (3) the notion of the complete disruption, perhaps more accurately atomization, of Lithuanian society in the period in question. Although this atomization requires additional research, it appears to have provided a prime element of the setting for mass murder. Antisemitism in Lithuania, especially the violent forms it took during the Holocaust, derived impetus from all three of these elements.
Concerning Lithuanian nationalism, there are several developments that kicked off in the 19th century that are fairly typical for the development of nationalism overall. Once a nation has been "invented", so to speak, it will in the minds and arguments of its nationalists, have already existed for a long time. History is always a prime method of legitimizing nationalist positions and aspirations and in Lithuania the history that was rather obvious to serve as this backdrop was that of the Lithuanian Grand Duchy and the subsequent Lithuanian-Polish commonwealth. However, in terms of Lithuanian nationalist policies of the 19th century the Commonwealth was viewed rather negatively. MacQueen cites a Lithuanian historian who describes it as "disastrous to the Lithuanian people and state: the union opened wide the doors for the influence of western Polish culture and the anarchy that accompanied it". The end of the Commonwealth with the partition of Poland spelled – to them – a disastrous end to Lithuanian identity and politics that needed to be re-asserted in opposition to Polish and other foreign culture. They blamed the decline of Lithuania from the greatness of the Grand Duchy to an alleged illiterate peasant people on the Poles. Alleged "polonization" and the link of Lithuania's fate to the Polish pursuit of revolutionary goals had ended,in their interpretations, in the near eradication of Lithuania during the repressions and Russification that followed the abortive nineteenth-century Polish-led uprisings. Lithuanian nationalists came to regard the smothering power of Polish culture in its historical perspective as the engine which had denationalized the local elite and caused it to identify with a nation other than that from which it had originated. This became especially pertinent in the aftermath of WWI when the newly created Polish Republic seized Vilnius in 1920, which the Lithuanians claimed as the capital of their state.
Enter the Jewish community of Lithuania – or rather, Russian imperial policies regarding the Jewish community. The very short version of the background here is that after attempts to either convert Jews or drive them out of the country, Tsarist Russia in 1791 created the so-called "Pale of Settlement", a territory in the West of Russia which was the only territory Jews were allowed to reside in. The Pale did include parts of Lithuania and in the 100+ years it existed fostered a particular Eastern European Jewish culture that differed from Western Europe in as far as assimilation of Jews into the majority society was something that started comparatively late and was more difficult due to several cultural and political obstacles.
The most notable of the obstacles in the Lithuanian case was language. To speak Lithuanian became – as was the case in other developments of nationalism – the prime signifier of allegiance to the Lithuanian nation and people. Jews on the other hand, who had been forced to live in shtetls (almost exclusively Jewish villages) or ghettos in the major imperial cities, did not speak Lithuanian en large. Their primary language was Yiddish and their secondary languages Polish and Russian. Lithuanian had until the Independence of Lithuania not been the language of power and administration nor the lingua franca of the territory. This is an important detail in as far as to both nationalist Lithuanians and political active Jews in Lithuania, the fact that the Jews did not speak Lithuanian made a mutual understanding as Lithuanians not really possible.
This perceived lack of identity between the Jewish and Lithuanian national interests created tensions that were compounded by traditional and newly formed forms of Antisemitism in the inter-war period. Next to "traditional" forms of Antisemitism such as clerical (Christ killers) and economic (money lenders), the spread of the idea of Jewish-Bolshevism was a most important element. The idea of the Jewish international conspiracy was one that was highly popular in Tsarist Russia (see f.ex. the Protocolls of the Elders of Zion) and that with the Russian Civil War of 1917-1922 morphed into the idea of Bolshevism being a forced controlled by said Jewish conspiracy. Many national movements, including that in Lithuania, saw Jews as "anti-national" and agents and executioners of the Bolshevik policies.
These issues were further compounded by the development of political culture in inter-war Lithuania, starting with Antanas Smetona's 1926 coup d'etat. Smetona had already served as the first president of Lithuania after independence and was a highly prominent figure in Lithuanian nationalism. Enveloped in anti-Polish irredentism and revanchism, he and Augustinas Voldemaras – another prominent Lithuanian nationalist – supported a military coup against a more left leaning government and installed themselves as president and prime minister respectively. Over subsequent years of Smetona's rule Lithuanian political culture took a noticeable turn to the right, including becoming very hostile towards Jewish and Polish minorities and prevalence of organized political violence, especially in from of the Voldemarist Iron Wolf movement, which was founded after Voldemaras was removed from power in 1929.
Already enveloped in these trends, the political crisis of 1938-1941 further worsened the atomization of Lithuanian society. In 1938 Poland forced Lithuania under threat of war to recognize their sovereignty over Vilnius. In 1939 Germany forced the retrocession of Memel/Klajpeda, adding to the profound sense of national demoralization. In the same year, the Soviets offered to station troops in Lithuania to "protect" it from further incursions; a pretext that lead to the occupation and annexation of Lithuania by the USSR in 1940.
Just for clarification, what were the numbers like for other countries? My understanding was that Jewish populations in Poland, Hungary, and the Ukraine were pretty thoroughly wiped out, too, in no small part due to collaborators. Is there a major discrepancy in Lithuania, or is the difference just incremental?
I should note that I like Tim and his work a lot and think it is incredibly valuable. A panel with him would be fun!